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Deputy Director of Department
Deputy Director of National Reference Center
Deputy Head of Facility
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Department: Genomes and Genetics

All Publications

Lou T, Sugrue JA, Patin E, , Quintana-Murci L, Duffy D, O'Farrelly C, Altered DNA methylation of the ABO gene is associated with differential plasma levels of von willebrand factor and E-selectin., Transfusion 2025 Sep; 65(9): 1693-1706.

Pfeifer E, d'Humières C, Lamy-Besnier Q, Oñate FP, Denisé R, Dion S, Condamine B, Touchon M, Ma L, Burdet C, Mentré F, Denamur E, Rocha EPC, Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages., Cell Rep 2025 Aug; 44(8): 116020.

Chapard C, Bastié N, Cournac A, Chaptal L, Mboumba H, Queille S, Thierry A, Gadal O, Lengronne A, Koszul R, Beckouët F, RNA Pol II-based regulations of chromosome folding., Cell Genom 2025 Aug; (): 100970.

Mazzamurro F, Touchon M, Charpentier X, Rocha EPC, Impact of Natural Transformation on the Acquisition of Novel Genes in Bacteria., Mol Biol Evol 2025 Jul; 42(8): .

Delphine Bonhomme, Hugo Vaysset, Eirene Marie Q. Ednacot, Vasco Rodrigues, Yazan Salloum, Jean Cury, Anny Wang, Axel Benchetrit, Pierre Affaticati, Veronica Hernandez Trejo, Paul Vittot, Charlie Bories, Alexis Cornec, Jean-Pierre Levraud, Pedro Hernández, Philippe Benaroch, Benjamin Morehouse, Aude Bernheim, Enzo Poirier, A human homolog of SIR2 antiphage proteins mediates immunity via the Toll-like receptor pathway, Science, 2025, 389 (6758), pp.eadr8536. ⟨10.1126/science.adr8536⟩.

Coleon A, Larrous F, Kergoat L, Tichit M, Hardy D, Obadia T, Kornobis E, Bourhy H, de Melo GD, Hamsters with long COVID present distinct transcriptomic profiles associated with neurodegenerative processes in brainstem, Nat Commun 2025 Jul; 16(1): 6714.

Flavio Alvarez, Guilherme Dias de Melo, Florence Larrous, Lauriane Kergoat, Batiste Boëda, Vincent Michel, Danielle Seilhean, Magali Tichit, David Hing, David Hardy, Etienne Kornobis, Hervé Bourhy, Nicolas Wolff, Célia Caillet-Saguy, The SARS-CoV-2 envelope PDZ binding motif acts as a virulence factor disrupting host’s epithelial cell–cell junctions [brief report], Cellular and Molecular Biology Letters, 2025, 30 (1), pp.80. ⟨10.1186/s11658-025-00758-y⟩.

Isabelle Bouyssou, Lemu Golassa, Inès Vigan-Womas, Matthieu Schoenhals, Arsène Ratsimbasoa, Ali Ould Mohamed Salem Boukhary, Maria de Fátima Ferreira-Da-Cruz, Sandrine Houzé, Laurence Ma, Feng Lu, Chetan Chitnis, Pascal Campagne, Didier Ménard, Genomic analysis of Plasmodium vivax field isolates circulating in sub-Saharan Africa, Communications Biology, 2025, 8 (1), pp.1012. ⟨10.1038/s42003-025-08276-5⟩.

Vesin B, Fert I, Noirat A, Authié P, Ciret S, Blanc C, Vitrenko Y, Charneau P, Majlessi L, Anna F, Optimized lentiviral backbone induces robust and diverse T cell immunity against neoantigens to counteract tumor heterogeneity., NPJ Vaccines 2025 Jul; 10(1): 143.

Miguel Gomez-Raya-Vilanova, Jérôme Teulière, Sofia Medvedeva, Yuping Dai, Eduardo Corel, Philippe Lopez, François-Joseph Lapointe, Debashish Bhattacharya, Louis-Patrick Haraoui, Elodie Turc, Marc Monot, Virginija Cvirkaite-Krupovic, Eric Bapteste, Mart Krupovic, Transcriptional landscape of the cell cycle in a model thermoacidophilic archaeon reveals similarities to eukaryotes, Nature Communications, 2025, 16 (1), pp.5697. ⟨10.1038/s41467-025-60613-8⟩.

Parul Singh, Justine Couble, Jacques Serizay, Maureen D Cabahug, Catarina Rosa, Patty Chen, Artur Scherf, Romain Koszul, Sebastian Baumgarten, Jessica M Bryant, High-resolution map of the Plasmodium falciparum genome reveals MORC/ ApiAP2-mediated links between distant, functionally related genes, Nature Microbiology, 2025, 10 (7), pp.1665-1683. ⟨10.1038/s41564-025-02038-z⟩.

Ravneet Kaur Sidhu, Guillem Mas Fiol, Pierre Lê-Bury, Christian E Demeure, Emelyne Bougit, Rémi Beau, Charlotte Balière, Aurelia Kwasiborski, Valérie Caro, Jennifer Klunk, Daniel J Salkeld, Ann Carmichael, Nükhet Varlık, Debi Poinar, David J D Earn, Benjamin M Bolker, Jonathan Dushoff, G Brian Golding, Nicolas Rascovan, Olivier Dussurget, Edward C Holmes, Javier Pizarro-Cerdá, Hendrik N Poinar, Attenuation of virulence in Yersinia pestis across three plague pandemics, Science, 2025, 388 (6750), pp.eadt3880. ⟨10.1126/science.adt3880⟩.

Pereda J, Espinosa R, García-Solís B, Guerra-Galán T, Van-Den-Rym A, Kars ME, Mena R, Galán V, de Andrés-Martín A, Rodríguez-Gallego C, López-Lera A, Corvillo F, Pérez-Martínez A, López-Collazo E, Sánchez-Ramón S, Martínez-Barricarte R, Quintana-Murci L, Lorenzo-Salazar JM, Itan Y, Flores C, Pérez-de-Diego R, IEIVariantFilter: a bioinformatics tool to speed up genetic diagnosis of inborn errors of immunity patients., NAR Genom Bioinform 2025 Jun; 7(2): lqaf069.

Lopopolo M, Avanzi C, Duchene S, Luisi P, de Flamingh A, Ponce-Soto GY, Tressieres G, Neumeyer S, Lemoine F, Nelson EA, Iraeta-Orbegozo M, Cybulski JS, Mitchell J, Marks VT, Adams LB, Lindo J, DeGiorgio M, Ortiz N, Wiens C, Hiebert J, Bonifaz A, Montes de Oca G, Paredes-Solis V, Franco-Paredes C, Vera-Cabrera L, Pereira Brunelli JG, Jackson M, Spencer JS, Salgado CG, Han XY, Pearce CM, Warren AK, Rosa PS, de Finardi AJ, Belone AFF, Ferreira C, Suffys PN, Fontes ANB, Vasconcellos SEG, Schaub R, Couppié P, Drak Alsibai K, Hernández-Castro R, Silva Miranda M, Estrada-Garcia I, Jurado-Santacruz F, Orlando L, Schroeder H, Quintana-Murci L, Del Papa M, Lahiri R, Malhi RS, Rasmussen S, Rascovan N, Pre-European contact leprosy in the Americas and its current persistence., Science 2025 May; (): eadu7144.

, Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems, Science, 388, 6747, (2025)..

Darracq B, Littner E, Brunie M, Bos J, Kaminski PA, Depardieu F, Slesak W, Debatisse K, Touchon M, Bernheim A, Bikard D, Le Roux F, Mazel D, Rocha EPC, Loot C, Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems., Science, 2025 May; 388(6747): eads0768.

Mazzuoli MV, van Raaphorst R, Martin LS, Bock FP, Thierry A, Marbouty M, Waclawiková B, Stinenbosch J, Koszul R, Veening JW, HU promotes higher order chromosome organization and influences DNA replication rates in Streptococcus pneumoniae., Nucleic Acids Res 2025 Apr; 53(8): .

Augias A, Ponce-Soto GY, Chimènes A, Charlier P, Rascovan N, An ancient Epstein-Barr virus genome recovered from a museum penis gourd from Papua., J Infect Dis 2025 Apr; (): .

Charles Bernard, Yannick Labreuche, Carine Diarra, Pauline Daszkowski, Karine Cahier, David Goudenège, Martin G Lamarche, Gregory B Whitfield, Manon Lang, Jeffrey Valencia, Justine Groseille, Damien Piel, Yan-Jiun Lee, Peter Weigele, Yves V Brun, Eduardo P. C. Rocha, Frédérique Le Roux, Adaptive genomic plasticity in large-genome, broad-host-range vibrio phages, The International Society of Microbiologial Ecology Journal, In press, pp.wraf063. ⟨10.1093/ismejo/wraf063⟩.

Léa Deltourbe, Jamie Sugrue, Elizabeth Maloney, Florian Dubois, Anthony Jaquaniello, Jacob Bergstedt, Etienne Patin, Lluis Quintana-Murci, Molly Ingersoll, Darragh Duffy, Steroid hormone levels vary with sex, aging, lifestyle, and genetics, Science Advances , 2025, 11 (13), pp.eadu6094. ⟨10.1126/sciadv.adu6094⟩.

Coluzzi C, Rocha EPC, The Spread of Antibiotic Resistance Is Driven by Plasmids Among the Fastest Evolving and of Broadest Host Range., Mol Biol Evol 2025 Mar; 42(3): .

Vendrell-Fernández S, Beamud B, Abou Haydar Y, Am de Sousa J, Burlaud-Gaillard J, Kornobis E, Raynal B, Vinh J, Bikard D, Ghigo JM, Incomplete lytic cycle of a widespread Bacteroides bacteriophage leads to the formation of defective viral particles., PLoS Biol 2025 Mar; 23(3): e3002787.

Girard F, Even A, Thierry A, Ruault M, Meneu L, Larrous P, Garnier M, Adiba S, Taddei A, Koszul R, Cournac A, Parasitic plasmids are anchored to inactive regions of eukaryotic chromosomes through a nucleosome signal., EMBO J 2025 Feb; (): .

Léa Meneu, Christophe Chapard, Jacques Serizay, Alex Westbrook, Etienne Routhier, Myriam Ruault, Manon Perrot, Alexandros Minakakis, Fabien Girard, Amaury Bignaud, Antoine Even, Géraldine Gourgues, Domenico Libri, Carole Lartigue, Aurèle Piazza, Agnès Thierry, Angela Taddei, Frédéric Beckouët, Julien Mozziconacci, Romain Koszul, Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus, Science, 2025, 387 (6734), pp.eadm9466. ⟨10.1126/science.adm9466⟩.

Mesquita Peixoto M, Soares-da-Silva F, Bonnet V, Zhou Y, Ronteix G, Santos RF, Mailhe MP, Nogueira G, Feng X, Pereira JP, Azzoni E, Anselmi G, de Bruijn MFTR, Perkins A, Baroud CN, Pinto-do-Ó P, Cumano A, Spatiotemporal dynamics of fetal liver hematopoietic niches., J Exp Med 2025 Feb; 222(2): .

Michella Khoury Damaa, Jacques Serizay, Rémi Balagué, Amélie-Rose Boudjema, Marion Faucourt, Nathalie Delgehyr, Kim Jee Goh, Hao Lu, Ee Kim Tan, Cameron T James, Catherine Faucon, Rana Mitri, Diana Carolin Bracht, Colin D Bingle, Norris Ray Dunn, Sebastian J Arnold, Laure-Emmanuelle Zaragosi, Pascal Barbry, Romain Koszul, Heymut Omran, Gabriel Gil-Gómez, Estelle Escudier, Marie Legendre, Sudipto Roy, Nathalie Spassky, Alice Meunier, Cyclin O controls entry into the cell-cycle variant required for multiciliated cell differentiation, Cell Reports, 2025, 44 (1), pp.115117. ⟨10.1016/j.celrep.2024.115117⟩.

Niault T, Talavera A, Le Cam E, Baconnais S, Skovgaard O, Fournes F, Wagner L, Tamman H, Thompson A, Echemendia-Blanco D, Guzzi N, Garcia-Pino A, Mazel D, Val ME, Dynamic transitions of initiator binding coordinate the replication of the two chromosomes in Vibrio cholerae., Nat Commun 2025 Jan; 16(1): 485.

Fruchard L, Babosan A, Carvalho A, Lang M, Li B, Duchateau M, Giai Gianetto Q, Matondo M, Bonhomme F, Hatin I, Arbes H, Fabret C, Corler E, Sanchez G, Marchand V, Motorin Y, Namy O, de Crécy-Lagard V, Mazel D, Baharoglu Z, Aminoglycoside tolerance in Vibrio cholerae engages translational reprogramming associated with queuosine tRNA modification., Elife 2025 Jan; 13(): .

Vaysset H, Meers C, Cury J, Bernheim A, Sternberg SH, Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons., Nat Microbiol 2025 Jan; (): .

Bénédicte Condamine, Thibaut Morel-Journel, Florian Tesson, Guilhem Royer, Mélanie Magnan, Aude Bernheim, Erick Denamur, François Blanquart, Olivier Clermont, Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series, The International Society of Microbiologial Ecology Journal, 2025, 19 (1), ⟨10.1093/ismejo/wrae245⟩.

Serizay J, Khoury Damaa M, Boudjema AR, Balagué R, Faucourt M, Delgehyr N, Noûs C, Zaragosi LE, Barbry P, Spassky N, Koszul R, Meunier A, Cyclin switch tailors a cell cycle variant to orchestrate multiciliogenesis., Cell Rep 2024 Dec; (): 115103.

Patin E, Quintana-Murci L, Tracing the Evolution of Human Immunity Through Ancient DNA., Annu Rev Immunol 2024 Dec; (): .

Vorobevskaia E, Loot C, Mazel D, Schlierf M, The recombination efficiency of the bacterial integron depends on the mechanical stability of the synaptic complex., Sci Adv 2024 Dec; 10(50): eadp8756.

Arribas YA, Baudon B, Rotival M, Suárez G, Bonté PE, Casas V, Roubert A, Klein P, Bonnin E, Mchich B, Legoix P, Baulande S, Sadacca B, Diharce J, Waterfall JJ, Etchebest C, Carrascal M, Goudot C, Quintana-Murci L, Burbage M, Merlotti A, Amigorena S, Transposable element exonization generates a reservoir of evolving and functional protein isoforms., Cell 2024 Dec; (): .

Tesson F, Huiting E, Wei L, Ren J, Johnson M, Planel R, Cury J, Feng Y, Bondy-Denomy J, Bernheim A, Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements., Nucleic Acids Res 2024 Dec; (): .

Hafner L, Gadin E, Huang L, Frouin A, Laporte F, Gaultier C, Vieira A, Maudet C, Varet H, Moura A, Bracq-Dieye H, Tessaud-Rita N, Maury M, Dazas M, Legendre R, Gastineau P, Tsai YH, Coppée JY, Charlier C, Patin E, Chikhi R, Rocha EPC, Leclercq A, Disson O, Aschard H, Lecuit M, Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes., Nat Microbiol 2024 Dec; 9(12): 3345-3361.

von Stemann JH, Dubois F, Saint-André V, Bondet V, Posseme C, Charbit B, Quintana-Murci L, Hansen MB, Ostrowski SR, Duffy D, Cytokine Autoantibodies Alter Gene Expression Profiles of Healthy Donors., Eur J Immunol 2025 Jan; 55(1): e202451211.

Espinosa E, Challita J, Desfontaines JM, Possoz C, Val ME, Mazel D, Marbouty M, Koszul R, Galli E, Barre FX, MatP local enrichment delays segregation independently of tetramer formation and septal anchoring in Vibrio cholerae., Nat Commun 2024 Nov; 15(1): 9893.

Dorison L, Béchon N, Martin-Gallausiaux C, Chamorro-Rodriguez S, Vitrenko Y, Ouazahrou R, Villa R, Deschamps J, Briandet R, Gribaldo S, Ghigo J-M, Beloin C, Identification of Veillonella parvula and Streptococcus gordonii adhesins mediating co-aggregation and its impact on physiology and mixed biofilm structure., mBio 2024 Nov; (): e0217124.

Blanco P, Trigo da Roza F, Toribio-Celestino L, García-Pastor L, Caselli N, Morón Á, Ojeda F, Darracq B, Vergara E, Amaro F, San Millán Á, Skovgaard O, Mazel D, Loot C, Escudero JA, Chromosomal integrons are genetically and functionally isolated units of genomes., Nucleic Acids Res 2024 Nov; 52(20): 12565-12581.

Manuel Ares-Arroyo, Amandine Nucci, Eduardo Rocha, Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids, Nature Microbiology, In press, ⟨10.1038/s41564-024-01844-1⟩.

Gaborieau B, Vaysset H, Tesson F, Charachon I, Dib N, Bernier J, Dequidt T, Georjon H, Clermont O, Hersen P, Debarbieux L, Ricard JD, Denamur E, Bernheim A, Prediction of strain level phage-host interactions across the Escherichia genus using only genomic information., Nat Microbiol 2024 Nov; 9(11): 2847-2861.

Ciccarella M, Laurent R, Szpiech ZA, Patin E, Dessarps-Freichey F, Utgé J, Lémée L, Semo A, Rocha J, Verdu P, Nested admixture during and after the Trans-Atlantic Slave Trade on the island of São Tomé., bioRxiv 2024 Oct; (): .

Marta Ciccarella, Romain Laurent, Zachary Szpiech, Etienne Patin, Françoise Dessarps-Freichey, José Utgé, Laure Lémée, Armando Semo, Jorge Rocha, Paul Verdu, Nested admixture during and after the Trans-Atlantic Slave Trade on the island of São Tomé, 2025.

Debatisse K, Niault T, Peeters S, Maire A, Toktas B, Darracq B, Baharoglu Z, Bikard D, Mazel D, Loot C, Fine-tuning of a CRISPRi screen in the seventh pandemic Vibrio cholerae., BMC Genomics 2024 Oct; 25(1): 985.

Louis Dorison L, Béchon N, Martin-Gallausiaux C, Chamorro Rodriguez S, Vitrenko dI Ouazahrou RI Villa R, Deschamps J, Briandet R, Gribaldo SI S, Ghigo JM, Beloin C, Identification of V. parvula and S. gordonii adhesins mediating co-agregation and its impact on physiology and mixedbiofilm structure., mBio. 2024, in press.

Maroofian R, Pagnamenta AT, Navabazam A, Schwessinger R, Roberts HE, Lopopolo M, Dehghani M, Vahidi Mehrjardi MY, Haerian A, Soltanianzadeh M, Noori Kooshki MH, Knight SJL, Miller KA, McGowan SJ, Chatron N, Timberlake AT, Melo US, Mundlos S, Buck D, Twigg SRF, Taylor JC, Wilkie AOM, Calpena E, Familial severe skeletal Class II malocclusion with gingival hyperplasia caused by a complex structural rearrangement at the KCNJ2-KCNJ16 locus., HGG Adv 2024 Oct; 5(4): 100352.

Mazzamurro F, Chirakadavil JB, Durieux I, Poiré L, Plantade J, Ginevra C, Jarraud S, Wilharm G, Charpentier X, P C Rocha E, Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species., PLoS Biol 2024 Oct; 22(10): e3002814.

Anjou C, Royer M, Bertrand É, Bredon M, Le Bris J, Salgueiro IA, Caulat LC, Dupuy B, Barbut F, Morvan C, Rolhion N, Martin-Verstraete I, Adaptation mechanisms of Clostridioides difficile to auranofin and its impact on human gut microbiota., NPJ Biofilms Microbiomes 2024 Sep; 10(1): 86.

Dumont A, Mendiboure N, Savocco J, Anani L, Moreau P, Thierry A, Modolo L, Jost D, Piazza A, Mechanism of homology search expansion during recombinational DNA break repair in Saccharomyces cerevisiae., Mol Cell 2024 Sep; 84(17): 3237-3253.e6.

Zeitler L, Goldar A, Denby Wilkes C, Soutourina J, The next-generation sequencing-chess problem., NAR Genom Bioinform 2024 Sep; 6(4): lqae144.

Laval G, Patin E, Quintana-Murci L, Kerner G, Deep estimation of the intensity and timing of natural selection from ancient genomes., Mol Ecol Resour 2024 Aug; (): e14015.

Meeks GL, Scelza B, Asnake HM, Prall S, Patin E, Froment A, Fagny M, Quintana-Murci L, Henn BM, Gopalan S, Common DNA sequence variation influences epigenetic aging in African populations., bioRxiv 2024 Aug; (): .

Jean Cury, Matthieu Haudiquet, Veronica Hernandez Trejo, Ernest Mordret, Anael Hanouna, Maxime Rotival, Florian Tesson, Delphine Bonhomme, Gal Ofir, Lluis Quintana-Murci, Philippe Benaroch, Enzo Z Poirier, Aude Bernheim, Conservation of antiviral systems across domains of life reveals immune genes in humans, Cell Host & Microbe, 2024, 32 (9), pp.1594-1607.e5. ⟨10.1016/j.chom.2024.08.002⟩.

Nathaniel Burman, Svetlana Belukhina, Florence Depardieu, Royce Wilkinson, Mikhail Skutel, Andrew Santiago-Frangos, Ava Graham, Alexei Livenskyi, Anna Chechenina, Natalia Morozova, Trevor Zahl, William Henriques, Murat Buyukyoruk, Christophe Rouillon, Baptiste Saudemont, Lena Shyrokova, Tatsuaki Kurata, Vasili Hauryliuk, Konstantin Severinov, Justine Groseille, Agnès Thierry, Romain Koszul, Florian Tesson, Aude Bernheim, David Bikard, Blake Wiedenheft, Artem Isaev, A virally encoded tRNA neutralizes the PARIS antiviral defence system, Nature, 2024, 634 (8033), pp.424-431. ⟨10.1038/s41586-024-07874-3⟩.

Schiffer PH, Natsidis P, Leite DJ, Robertson HE, Lapraz F, Marlétaz F, Fromm B, Baudry L, Simpson F, Høye E, Zakrzewski AC, Kapli P, Hoff KJ, Müller S, Marbouty M, Marlow H, Copley RR, Koszul R, Sarkies P, Telford MJ, Insights into early animal evolution from the genome of the xenacoelomorph worm Xenoturbella bocki., Elife 2024 Aug; 13(): .

Serizay J, Koszul R, Epigenomics coverage data extraction and aggregation in R with tidyCoverage., Bioinformatics 2024 Aug; 40(8): .

Bertrand A, Sugrue J, Lou T, Bourke NM, Quintana-Murci L, Saint-André V, O'Farrelly C, Duffy D, Impact of socioeconomic status on healthy immune responses in humans., Immunol Cell Biol 2024 Aug; 102(7): 618-629.

Lena Le Quellec , Andrey Aristov , Salomé Gutiérrez Ramos, Gabriel Amselem, Julia Bos, Zeynep Baharoglu, Didier Mazel, Charles N. Baroud, Measuring single-cell susceptibility to antibiotics within monoclonal bacterial populations, https://doi.org/10.1371/journal.pone.0303630.

Planchais C, Fernández I, Chalopin B, Bruel T, Rosenbaum P, Beretta M, Dimitrov JD, Conquet L, Donati F, Prot M, Porrot F, Planas D, Staropoli I, Guivel-Benhassine F, Baquero E, van der Werf S, Haouz A, Simon-Lorière E, Montagutelli X, Maillère B, Rey FA, Guardado-Calvo P, Nozach H, Schwartz O, Mouquet H, Broad sarbecovirus neutralization by combined memory B cell antibodies to ancestral SARS-CoV-2., iScience 2024 Jul; 27(7): 110354.

Marchal A, Cirulli ET, Neveux I, Bellos E, Thwaites RS, Schiabor Barrett KM, Zhang Y, Nemes-Bokun I, Kalinova M, Catchpole A, Tangye SG, Spaan AN, Lack JB, Ghosn J, Burdet C, Gorochov G, Tubach F, Hausfater P, , , , , , , , , , Dalgard CL, Zhang SY, Zhang Q, Chiu C, Fellay J, Grzymski JJ, Sancho-Shimizu V, Abel L, Casanova JL, Cobat A, Bolze A, Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection., HGG Adv 2024 Jul; 5(3): 100300.

Helena Shomar, Héloïse Georjon, Yanlei Feng, Bismarck Olympio, Marie Guillaume, Florian Tesson, Jean Cury, Fabai Wu, Aude Bernheim, Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold, Nature Ecology & Evolution, 2024, 8 (9), pp.667-1679. ⟨10.1038/s41559-024-02463-z⟩.

Bernheim A, Cury J, Poirier EZ, The immune modules conserved across the tree of life: Towards a definition of ancestral immunity., PLoS Biol 2024 Jul; 22(7): e3002717.

Fert I, Douguet L, Vesin B, Moncoq F, Noirat A, Authié P, Ciret S, Le Chevalier F, Blanc C, Vitrenko Y, Charneau P, Majlessi L, Anna F, T-cell immunity induced and reshaped by an anti-HPV immuno-oncotherapeutic lentiviral vector., NPJ Vaccines 2024 Jun; 9(1): 102.

Fruchard Louna, Babosan Anamaria, Carvalho Andre, Lang Manon, Li Blaise, Duchateau Magalie, Giai-Gianetto Quentin, Matondo Mariette, Bonhomme Frédéric, Hatin Isabelle, Arbes Hugo, Fabret Céline, Sanchez Guillaume, Marchand Virginie, Motorin Yuri, Namy Olivier, de Crécy-Lagard Valérie, Mazel Didier, Baharoglu Zeynep, Aminoglycoside tolerance in Vibrio cholerae engages translational reprogramming associated to queuosine tRNA modification, Elife.

Rémi Planel, Victoire Baillet, Rachel Torchet, Vincent Guillemot, Pascal Campagne, Jean Jaubert, Marion Rincel, Christian A. J. Vosshenrich, Xavier Montagutelli, Caroline Manet, ccqtl-db, 2024, ⟨swh:1:dir:b3362746041f9acd17180af8a77dc963f9ec5443;origin=https://gitlab.pasteur.fr/cc-qtl/cc-qtl-db;visit=swh:1:snp:ee61a4e0ae9068c1d9dd665bd485ffc6a5287dfd;anchor=swh:1:rev:d796db76a93e9c192563777fa07656da3db747a8⟩.

Boetto C, Frouin A, Henches L, Auvergne A, Suzuki Y, Patin E, Bredon M, Chiu A, Consortium MI, Sankararaman S, Zaitlen N, Kennedy SP, Quintana-Murci L, Duffy D, Sokol H, Aschard H, MANOCCA: a robust and computationally efficient test of covariance in high-dimension multivariate omics data., Brief Bioinform 2024 May; 25(4): .

Mistretta M, Cimino M, Campagne P, Volant S, Kornobis E, Hebert O, Rochais C, Dallemagne P, Lecoutey C, Tisnerat C, Lepailleur A, Ayotte Y, LaPlante SR, Gangneux N, Záhorszká M, Korduláková J, Vichier-Guerre S, Bonhomme F, Pokorny L, Albert M, Tinevez JY, Manina G, Dynamic microfluidic single-cell screening identifies pheno-tuning compounds to potentiate tuberculosis therapy., Nat Commun 2024 May; 15(1): 4175.

Benz F, Camara-Wilpert S, Russel J, Wandera KG, Čepaitė R, Ares-Arroyo M, Gomes-Filho JV, Englert F, Kuehn JA, Gloor S, Mestre MR, Cuénod A, Aguilà-Sans M, Maccario L, Egli A, Randau L, Pausch P, Rocha EPC, Beisel CL, Madsen JS, Bikard D, Hall AR, Sørensen SJ, Pinilla-Redondo R, Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans., Cell Host Microbe 2024 May; (): .

Bignaud A, Koszul R, [Transcription: The backbone of bacterial chromosome architecture]., Med Sci (Paris) 2024 May; 40(5): 412-413.

Gnaien M, Maufrais C, Rebai Y, Kallel A, Ma L, Hamouda S, Khalsi F, Meftah K, Smaoui H, Khemiri M, Hadj Fredj S, Bachellier-Bassi S, Najjar I, Messaoud T, Boussetta K, Kallel K, Mardassi H, d'Enfert C, Bougnoux ME, Znaidi S, A gain-of-function mutation in zinc cluster transcription factor Rob1 Drives Candida albicans adaptive growth in the cystic fibrosis lung environment., PLoS Pathog 2024 Apr; 20(4): e1012154.

Brunet J, Choucha Z, Gransagne M, Tabbal H, Ku M-W, Buchrieser J, Fernandes P, Batalie D, Lopez J, Ma L, Dufour E, Simon E, Hardy D, Petres S, Guinet F, Strick-Marchand H, Monot M, Charneau P, Majlessi L, Duprex WP, Gerke C, Martin A, Escriou N, A measles-vectored vaccine candidate expressing prefusion-stabilized SARS-CoV-2 spike protein brought to phase I/II clinical trials: candidate selection in a preclinical murine model., J Virol 2024 Apr; (): e0169323.

Richard E, Darracq B, Littner E, Millot GA, Conte V, Cokelaer T, Engelstädter J, Rocha EPC, Mazel D, Loot C, Belt and braces: Two escape ways to maintain the cassette reservoir of large chromosomal integrons., PLoS Genet 2024 Apr; 20(4): e1011231.

Forest T, Achaz G, Marbouty M, Bignaud A, Thierry A, Koszul R, Milhes M, Lledo J, Pons JM, Fuchs J, Chromosome-level genome assembly of the European green woodpecker Picus viridis., G3 (Bethesda) 2024 Mar; (): .

Lopes A-A, Vendrell-Fernández S, Deschamps J, Georgeault S, Cokelaer T, Briandet R, Ghigo J-M, Bile-induced biofilm formation in Bacteroides thetaiotaomicron requires magnesium efflux by an RND pump., mBio 2024 May 8;15(5): e0348823.

Bastié N, Chapard C, Cournac A, Nejmi S, Mboumba H, Gadal O, Thierry A, Beckouët F, Koszul R, Sister chromatid cohesion halts DNA loop expansion., Mol Cell 2024 Mar; 84(6): 1139-1148.e5.

Legrand S, Saifudeen A, Bordelet H, Vernerey J, Guille A, Bignaud A, Thierry A, Acquaviva L, Gaudin M, Sanchez A, Johnson D, Friedrich A, Schacherer J, Neale MJ, Borde V, Koszul R, Llorente B, Absence of chromosome axis protein recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri., Proc Natl Acad Sci U S A 2024 Mar; 121(12): e2312820121.

d'Humières C, Delavy M, Alla L, Ichou F, Gauliard E, Ghozlane A, Levenez F, Galleron N, Quinquis B, Pons N, Mullaert J, Bridier-Nahmias A, Condamine B, Touchon M, Rainteau D, Lamazière A, Lesnik P, Ponnaiah M, Lhomme M, Sertour N, Devente S, Docquier JD, Bougnoux ME, Tenaillon O, Magnan M, Ruppé E, Grall N, Duval X, Ehrlich D, Mentré F, Denamur E, Rocha EPC, Le Chatelier E, Burdet C, Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases., Microbiome 2024 Mar; 12(1): 50.

Matthieu Haudiquet, Julie Le Bris, Amandine Nucci, Rémy A Bonnin, Pilar Domingo-Calap, Eduardo P C Rocha, Olaya Rendueles, Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency, Nature Communications, 2024, 15 (1), pp.2032. ⟨10.1038/s41467-024-46147-5⟩.

Jain S, Belkadi H, Michaut A, Sart S, Gros J, Genet M, Baroud CN, Using a micro-device with a deformable ceiling to probe stiffness heterogeneities within 3D cell aggregates., Biofabrication 2024 Mar; (): .

Valentin Bonnet, Erik Maikranz, Marianne Madec, Nadia Vertti-Quintero, Céline Cuche, Marta Mastrogiovanni, Andrés Alcover, Vincenzo Di Bartolo, Charles N Baroud, Cancer-on-a-chip model shows that the adenomatous polyposis coli mutation impairs T cell engagement and killing of cancer spheroids, Proceedings of the National Academy of Sciences of the United States of America, 2024, 121 (11), pp.e2316500121. ⟨10.1073/pnas.2316500121⟩.

Pfeifer E, Rocha EPC, Phage-plasmids promote recombination and emergence of phages and plasmids., Nat Commun 2024 Feb; 15(1): 1545.

Brulport A, Bourdon M, Vaiman D, Drouet C, Pocate-Cheriet K, Bouzid K, Marcellin L, Santulli P, Abo C, Jeljeli M, Chouzenoux S, Chapron C, Batteux F, Berthelot C, Doridot L, An integrated multi-tissue approach for endometriosis candidate biomarkers: a systematic review., Reprod Biol Endocrinol 2024 Feb; 22(1): 21.

Bastard P, Gervais A, Taniguchi M, Saare L, Särekannu K, Le Voyer T, Philippot Q, Rosain J, Bizien L, Asano T, Garcia-Prat M, Parra-Martínez A, Migaud M, Tsumura M, Conti F, Belot A, Rivière JG, Morio T, Tanaka J, Javouhey E, Haerynck F, Duvlis S, Ozcelik T, Keles S, Tandjaoui-Lambiotte Y, Escoda S, Husain M, Pan-Hammarström Q, Hammarström L, Ahlijah G, Abi Haidar A, Soudee C, Arseguel V, Abolhassani H, Sahanic S, Tancevski I, Nukui Y, Hayakawa S, Chrousos GP, Michos A, Tatsi EB, Filippatos F, Rodriguez-Palmero A, Troya J, Tipu I, Meyts I, Roussel L, Ostrowski SR, Schidlowski L, Prando C, Condino-Neto A, Cheikh N, Bousfiha AA, El Bakkouri J, , , , Peterson P, Pujol A, Lévy R, Quartier P, Vinh DC, Boisson B, Béziat V, Zhang SY, Borghesi A, Pession A, Andreakos E, Marr N, Mentis AA, Mogensen TH, Rodríguez-Gallego C, Soler-Palacin P, Colobran R, Tillmann V, Neven B, Trouillet-Assant S, Brodin P, Abel L, Jouanguy E, Zhang Q, Martinón-Torres F, Salas A, Gómez-Carballa A, Gonzalez-Granado LI, Kisand K, Okada S, Puel A, Cobat A, Casanova JL, Higher COVID-19 pneumonia risk associated with anti-IFN-α than with anti-IFN-ω auto-Abs in children., J Exp Med 2024 Feb; 221(2): .

Serizay J, Matthey-Doret C, Bignaud A, Baudry L, Koszul R, Orchestrating chromosome conformation capture analysis with Bioconductor., Nat Commun 2024 Feb; 15(1): 1072.

Saint-André V, Charbit B, Biton A, Rouilly V, Possémé C, Bertrand A, Rotival M, Bergstedt J, Patin E, Albert ML, Quintana-Murci L, Duffy D, Smoking changes adaptive immunity with persistent effects., Nature 2024 Feb; 626(8000): 827-835.

F. Tesson, R. Planel, A. Egorov, H. Georjon, H. Vaysset, B. Brancotte, B. Néron, E. Mordret, G. Atkinson, A Bernheim, J. Cury, A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases, 2024.

Barcia-Cruz R, Goudenège D, Moura de Sousa JA, Piel D, Marbouty M, Rocha EPC, Le Roux F, Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages., Nat Commun 2024 Jan; 15(1): 664.

Egill Richard, Baptiste Darracq, Eloi Littner, Claire Vit, Clémence Whiteway, Julia Bos, Florian Fournes, Geneviève Garriss, Valentin Conte, Delphine Lapaillerie, Vincent Parissi, François Rousset, Ole Skovgaard, David Bikard, Eduardo P. C. Rocha, Didier Mazel, Céline Loot, Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems., Science Advances , 2024, 10 (2), pp.eadj3498. ⟨10.1126/sciadv.adj3498⟩.

Bignaud A, Cockram C, Borde C, Groseille J, Allemand E, Thierry A, Marbouty M, Mozziconacci J, Espéli O, Koszul R, Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes., Nat Struct Mol Biol 2024 Jan; (): .

Loot C, Millot GA, Richard E, Littner E, Vit C, Lemoine F, Néron B, Cury J, Darracq B, Niault T, Lapaillerie D, Parissi V, Rocha EPC, Mazel D, Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites., Nat Microbiol 2024 Jan; 9(1): 228-240.

Del Papa M, De Los Reyes M, Poiré DG, Rascovan N, Jofré G, Delgado M, Anthropic cut marks in extinct megafauna bones from the Pampean region (Argentina) at the last glacial maximum., PLoS One 2024 ; 19(7): e0304956.

Rotival M, Quintana-Murci L, Environmental variation and genetic diversity contribute to population differences in immune responses to SARS-CoV-2 and COVID-19 risk., Genes Immun 2023 Dec; (): .

Patitucci C, Hernández-Camacho JD, Vimont E, Yde S, Cokelaer T, Chaze T, Giai Gianetto Q, Matondo M, Gazi A, Nemazanyy I, Stroud DA, Hock DH, Donnarumma E, Wai T, Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis., Nat Commun 2023 Dec; 14(1): 8474.

Li L, Ma X, Cui Y, Rotival M, Chen W, Zou X, Ding R, Qin Y, Wang Q, Quintana-Murci L, Li W, Immune-response 3’UTR alternative polyadenylation quantitative trait loci contribute to variation in human complex traits and diseases., Nat Commun 2023 Dec; 14(1): 8347.

Bhargava A, Szachnowski U, Chazal M, Foretek D, Caval V, Aicher SM, Pipoli da Fonseca J, Jeannin P, Beauclair G, Monot M, Morillon A, Jouvenet N, Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2., iScience 2023 Dec; 26(12): 108449.

Niault T, Czarnecki J, Lambérioux M, Mazel D, Val M-E, Cell cycle-coordinated maintenance of the Vibrio bipartite genome., EcoSal Plus 2023 Dec; 11(1): eesp00082022.

Delavy M, Sertour N, Patin E, Le Chatelier E, Cole N, Dubois F, Xie Z, Saint-André V, Manichanh C, Walker AW, Quintana-Murci L, Duffy D, d'Enfert C, Bougnoux ME, Consortium MI, Unveiling Candida albicans intestinal carriage in healthy volunteers: the role of micro- and mycobiota, diet, host genetics and immune response., Gut Microbes 2023 Dec; 15(2): 2287618.

Ludivine Amable, Luis Antonio Ferreira Martins, Remi Pierre, Marcio Do Cruseiro, Ghita Chabab, Arnauld Sergé, Camille Kergaravat, Marc Delord, Christophe Viret, Jean Jaubert, Chaohong Liu, Saoussen Karray, Julien C Marie, Magali Irla, Hristo Georgiev, Emmanuel Clave, Antoine Toubert, Bruno Lucas, Jihene Klibi, Kamel Benlagha, Intrinsic factors and CD1d1 but not CD1d2 expression levels control invariant natural killer T cell subset differentiation, Nature Communications, 2023, 14 (1), pp.7922. ⟨10.1038/s41467-023-43424-7⟩.

de Castro RJA, Marina CL, Sturny-Leclère A, Hoffmann C, Bürgel PH, Wong SSW, Aimanianda V, Varet H, Agrawal R, Bocca AL, Alanio A, Kicking sleepers out of bed: Macrophages promote reactivation of dormant Cryptococcus neoformans by extracellular vesicle release and non-lytic exocytosis., PLoS Pathog 2023 Nov; 19(11): e1011841.

Schindler D, Walker RSK, Jiang S, Brooks AN, Wang Y, Müller CA, Cockram C, Luo Y, García A, Schraivogel D, Mozziconacci J, Pena N, Assari M, Sánchez Olmos MDC, Zhao Y, Ballerini A, Blount BA, Cai J, Ogunlana L, Liu W, Jönsson K, Abramczyk D, Garcia-Ruiz E, Turowski TW, Swidah R, Ellis T, Pan T, Antequera F, Shen Y, Nieduszynski CA, Koszul R, Dai J, Steinmetz LM, Boeke JD, Cai Y, Design, construction, and functional characterization of a tRNA neochromosome in yeast., Cell 2023 Nov; 186(24): 5237-5253.e22.

Luo J, Vale-Silva LA, Raghavan AR, Mercy G, Heldrich J, Sun X, Li MK, Zhang W, Agmon N, Yang K, Cai J, Stracquadanio G, Thierry A, Zhao Y, Coelho C, McCulloch LH, Lauer S, , Kaback DB, Bader JS, Mitchell LA, Mozziconacci J, Koszul R, Hochwagen A, Boeke JD, Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function., Cell Genom 2023 Nov; 3(11): 100439.

Bernheim S, Borgel A, Le Garrec JF, Perthame E, Desgrange A, Michel C, Guillemot L, Sart S, Baroud CN, Krezel W, Raimondi F, Bonnet D, Zaffran S, Houyel L, Meilhac SM, Identification of Greb1l as a genetic determinant of crisscross heart in mice showing torsion of the heart tube by shortage of progenitor cells., Dev Cell 2023 Nov; 58(21): 2217-2234.e8.

Camila Duitama González, Riccardo Vicedomini, Téo Lemane, Nicolas Rascovan, Hugues Richard, Rayan Chikhi, decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods, Microbiome, 2023, 11 (1), pp.1-12. ⟨10.1186/s40168-023-01670-3⟩.

Le Voyer T, Parent AV, Liu X, Cederholm A, Gervais A, Rosain J, Nguyen T, Perez Lorenzo M, Rackaityte E, Rinchai D, Zhang P, Bizien L, Hancioglu G, Ghillani-Dalbin P, Charuel JL, Philippot Q, Gueye MS, Maglorius Renkilaraj MRL, Ogishi M, Soudée C, Migaud M, Rozenberg F, Momenilandi M, Riller Q, Imberti L, Delmonte OM, Müller G, Keller B, Orrego J, Franco Gallego WA, Rubin T, Emiroglu M, Parvaneh N, Eriksson D, Aranda-Guillen M, Berrios DI, Vong L, Katelaris CH, Mustillo P, Raedler J, Bohlen J, Bengi Celik J, Astudillo C, Winter S, , , McLean C, Guffroy A, DeRisi JL, Yu D, Miller C, Feng Y, Guichard A, Béziat V, Bustamante J, Pan-Hammarström Q, Zhang Y, Rosen LB, Holland SM, Bosticardo M, Kenney H, Castagnoli R, Slade CA, Boztuğ K, Mahlaoui N, Latour S, Abraham RS, Lougaris V, Hauck F, Sediva A, Atschekzei F, Sogkas G, Poli MC, Slatter MA, Palterer B, Keller MD, Pinzon-Charry A, Sullivan A, Droney L, Suan D, Wong M, Kane A, Hu H, Ma C, Grombiříková H, Ciznar P, Dalal I, Aladjidi N, Hie M, Lazaro E, Franco J, Keles S, Malphettes M, Pasquet M, Maccari ME, Meinhardt A, Ikinciogullari A, Shahrooei M, Celmeli F, Frosk P, Goodnow CC, Gray PE, Belot A, Kuehn HS, Rosenzweig SD, Miyara M, Licciardi F, Servettaz A, Barlogis V, Le Guenno G, Herrmann VM, Kuijpers T, Ducoux G, Sarrot-Reynauld F, Schuetz C, Cunningham-Rundles C, Rieux-Laucat F, Tangye SG, Sobacchi C, Doffinger R, Warnatz K, Grimbacher B, Fieschi C, Berteloot L, Bryant VL, Trouillet Assant S, Su H, Neven B, Abel L, Zhang Q, Boisson B, Cobat A, Jouanguy E, Kampe O, Bastard P, Roifman CM, Landegren N, Notarangelo LD, Anderson MS, Casanova JL, Puel A, Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency., Nature 2023 Nov; 623(7988): 803-813.

Aël Hardy, Helena Shomar, Aude Bernheim, Immunité bactérienne : à la découverte d’un nouveau monde [Bacterial immunity: Uncovering a new world], Médecine/Sciences, 2023, 39 (11), pp.862-868. ⟨10.1051/medsci/2023163⟩.

Gracias S, Chazal M, Decombe A, Unterfinger Y, Sogues A, Pruvost L, Robert V, Lacour SA, Lemasson M, Sourisseau M, Li Z, Richardson J, Pellegrini S, Decroly E, Caval V, Jouvenet N, Tick-borne flavivirus NS5 antagonizes interferon signaling by inhibiting the catalytic activity of TYK2., EMBO Rep 2023 Dec; 24(12): e57424.

Rémi Planel, Victoire Baillet, Jean Jaubert, Christian A. J. Vosshenrich, Rachel Torchet, Marion Rincel, Pascal Campagne, Xavier Montagutelli, CCQTL: facilitating QTL mapping in the Collaborative Cross, 20th Annual Meeting of the Complex Trait Community | Rat Genome & Models, University of Tennessee Health Science Center [Memphis, Tennessee], Oct 2023, Memphis, TN, United States.

Coluzzi C, Guillemet M, Mazzamurro F, Touchon M, Godfroid M, Achaz G, Glaser P, Rocha EPC, Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes., Mol Biol Evol 2023 Oct; 40(10): .

Georjon H, Bernheim A, The highly diverse antiphage defence systems of bacteria., Nat Rev Microbiol 2023 Oct; 21(10): 686-700.

Yáñez-Cuna FO, Koszul R, Insights in bacterial genome folding., Curr Opin Struct Biol 2023 Oct; 82(): 102679.

Quiroz-Morales SE, Muriel-Millán LF, Ponce-Soto GY, González-Valdez A, Castillo-Juárez I, Servín-González L, Soberón-Chávez G, Pseudomonas aeruginosa strains belonging to phylogroup 3 frequently exhibit an atypical quorum sensing response: the case of MAZ105, a tomato rhizosphere isolate., Microbiology (Reading) 2023 Oct; 169(10): .

Selam Mihreteab, Lucien Platon, Araia Berhane, Barbara Stokes, Marian Warsame, Pascal Campagne, Alexis Criscuolo, Laurence Ma, Nathalie Petiot, Cécile Doderer-Lang, Eric Legrand, Kurt Ward, Assefash Zehaie Kassahun, Pascal Ringwald, David Fidock, Didier Ménard, Increasing Prevalence of Artemisinin-Resistant HRP2-Negative Malaria in Eritrea, New England Journal of Medicine, 2023, 389 (13), pp.1191-1202. ⟨10.1056/NEJMoa2210956⟩.

Dott T, Culina S, Chemali R, Mansour CA, Dubois F, Jagla B, Doisne JM, Rogge L, Huetz F, Jönsson F, Commere PH, Di Santo J, Terrier B, Quintana-Murci L, Duffy D, Hasan M, Standardized high-dimensional spectral cytometry protocol and panels for whole blood immune phenotyping in clinical and translational studies., Cytometry A 2024 Feb; 105(2): 124-138.

Bourdon M, Manet C, Conquet L, Ramaugé Parra C, Kornobis E, Bonnefoy E, Montagutelli X, Susceptibility to Zika virus in a Collaborative Cross mouse strain is induced by Irf3 deficiency in vitro but requires other variants in vivo., PLoS Pathog 2023 Sep; 19(9): e1011446.

Laure Mancini, Boris Guirao, Sara Ortica, Miriam Labusch, Felix Cheysson, Valentin Bonnet, Minh Son Phan, Sébastien Herbert, Pierre Mahou, Emilie Menant, Sébastien Bedu, Jean-Yves Tinevez, Charles Baroud, Emmanuel Beaurepaire, Yohanns Bellaiche, Laure Bally-Cuif, Nicolas Dray, Apical size and deltaA expression predict adult neural stem cell decisions along lineage progression, Science Advances , 2023, 9 (35), pp.eadg7519. ⟨10.1126/sciadv.adg7519⟩.

, A second update on mapping the human genetic architecture of COVID-19., Nature 2023 Sep; 621(7977): E7-E26.

Parey E, Fernandez-Aroca D, Frost S, Uribarren A, Park TJ, Zöttl M, St John Smith E, Berthelot C, Villar D, Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits., Genome Res 2023 Sep; 33(9): 1513-1526.

Yann Aquino, Aurélie Bisiaux, Zhi Li, Mary O'Neill, Javier Mendoza-Revilla, Sarah Hélène Merkling, Gaspard Kerner, Milena Hasan, Valentina Libri, Vincent Bondet, Nikaïa Smith, Camille de Cevins, Mickaël Ménager, Francesca Luca, Roger Pique-Regi, Giovanna Barba-Spaeth, Stefano Pietropaoli, Olivier Schwartz, Geert Leroux-Roels, Cheuk-Kwong Lee, Kathy Leung, Joseph Wu, Malik Peiris, Roberto Bruzzone, Laurent Abel, Jean-Laurent Casanova, Sophie Valkenburg, Darragh Duffy, Etienne Patin, Maxime Rotival, Lluis Quintana-Murci, Dissecting human population variation in single-cell responses to SARS-CoV-2, Nature, 2023, 53 (8), pp.e2250307. ⟨10.1038/s41586-023-06422-9⟩.

George Butler, Julia Bos, Robert H. Austin, Sarah R. Amend and Kenneth J. Pienta, Escherichia coli survival in response to ciprofloxacin antibiotic stress correlates with increased nucleoid length and effective misfolded protein management, Butler George, Bos Julia, Austin Robert H., Amend Sarah R. and Pienta Kenneth J. 2023Escherichia coli survival in response to ciprofloxacin antibiotic stress correlates with increased nucleoid length and effective misfolded protein managementR. Soc. open sci.10230338230338.

Amandine Nucci, Eduardo P C Rocha, Olaya Rendueles, Latent evolution of biofilm formation depends on life-history and genetic background, npj Biofilms and Microbiomes, 2023, 9 (1), pp.53. ⟨10.1038/s41522-023-00422-3⟩.

Razanajatovo IM, Andrianomiadana L, Habib A, Randrianarisoa MM, Razafimanjato H, Rakotondrainipiana M, Andriantsalama P, Randriamparany R, Andriamandimby SF, Vonaesch P, Sansonetti PJ, Lacoste V, Randremanana RV, Collard JM, Heraud JM, On Behalf Of The Afribiota Investigators, Factors Associated with Carriage of Enteropathogenic and Non-Enteropathogenic Viruses: A Reanalysis of Matched Case-Control Data from the AFRIBIOTA Site in Antananarivo, Madagascar., Pathogens 2023 Aug; 12(8): .

Maxime Borry, Adrian Forsythe, Aida Andrades Valtueña, Alexander Hübner, Anan Ibrahim, Andrea Quagliariello, Anna E White, Arthur Kocher, Bjørn Peare Bartholdy, Diāna Spurīte, Gabriel Yaxal Ponce-Soto, Gunnar Neumann, I-Ting Huang, Ian Light, Irina M Velsko, Iseult Jackson, Jasmin Frangenberg, Javier G Serrano, Julien Fumey, Kadir T Özdoğan, Kelly E Blevins, Kevin G Daly, Maria Lopopolo, Markella Moraitou, Megan Michel, Meriam van Os, Miriam J Bravo-Lopez, Mohamed S Sarhan, Nihan D Dagtas, Nikolay Oskolkov, Olivia S Smith, Ophélie Lebrasseur, Piotr Rozwalak, Raphael Eisenhofer, Sally Wasef, Shreya L Ramachandran, Valentina Vanghi, Christina Warinner, James A Fellows Yates, Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT, F1000Research, 2023, 12, pp.926. ⟨10.12688/f1000research.134798.1⟩.

Villain E, Chanson A, Mainka M, Kampschulte N, Le Faouder P, Bertrand-Michel J, Brandolini-Bulon M, Charbit B, Musvosvi M, Bilek N, Scriba TJ, Quintana-Murci L, Schebb NH, Duffy D, Gladine C, Integrated analysis of whole blood oxylipin and cytokine responses after bacterial, viral, and T cell stimulation reveals new immune networks., iScience 2023 Aug; 26(8): 107422.

Georjon H, Tesson F, Shomar H, Bernheim A, Genomic characterization of the antiviral arsenal of Actinobacteria., Microbiology (Reading) 2023 Aug; 169(8): .

O'Donnell S, Yue JX, Saada OA, Agier N, Caradec C, Cokelaer T, De Chiara M, Delmas S, Dutreux F, Fournier T, Friedrich A, Kornobis E, Li J, Miao Z, Tattini L, Schacherer J, Liti G, Fischer G, Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae., Nat Genet 2023 Aug; 55(8): 1390-1399.

Pierlé SA, Lang M, López-Igual R, Krin E, Fourmy D, Kennedy SP, Val ME, Baharoglu Z, Mazel D, Identification of the active mechanism of aminoglycoside entry in V. cholerae through characterization of sRNA ctrR, regulating carbohydrate utilization and transport., bioRxiv 2023 Jul; (): .

Legendre L, Rode J, Germon I, Pavie M, Quiviger C, Policarpo M, Leclercq J, Père S, Fumey J, Hyacinthe C, Ornelas-García P, Espinasa L, Rétaux S, Casane D, Genetic identification and reiterated captures suggest that the Astyanax mexicanus El Pachón cavefish population is closed and declining., Zool Res 2023 Jul; 44(4): 701-711.

Angelidakis E, Chen S, Zhang S, Wan Z, Kamm RD, Shelton SE, Impact of Fibrinogen, Fibrin Thrombi, and Thrombin on Cancer Cell Extravasation Using In Vitro Microvascular Networks., Adv Healthc Mater 2023 Jul; 12(19): e2202984.

Cokelaer T, Cohen-Boulakia S, Lemoine F, Reprohackathons: promoting reproducibility in bioinformatics through training., Bioinformatics 2023 Jun; 39(39 Suppl 1): i11-i20.

Fevre R, Mary G, Vertti-Quintero N, Durand A, Tomasi RF, Del Nery E, Baroud CN, Combinatorial drug screening on 3D Ewing sarcoma spheroids using droplet-based microfluidics., iScience 2023 May; 26(5): 106651.

Lamy-Besnier Q, Bignaud A, Garneau JR, Titecat M, Conti DE, Von Strempel A, Monot M, Stecher B, Koszul R, Debarbieux L, Marbouty M, Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria., Microbiome 2023 May; 11(1): 111.

Auria E, Hunault L, England P, Monot M, Pipoli Da Fonseca J, Matondo M, Duchateau M, Tremblay YDN, Dupuy B, , The cell wall lipoprotein CD1687 acts as a DNA binding protein during deoxycholate-induced biofilm formation in Clostridioides difficile., NPJ Biofilms Microbiomes 2023 May; 9(1): 24.

García-García A, Pérez de Diego R, Flores C, Rinchai D, Solé-Violán J, Deyà-Martínez À, García-Solis B, Lorenzo-Salazar JM, Hernández-Brito E, Lanz AL, Moens L, Bucciol G, Almuqamam M, Domachowske JB, Colino E, Santos-Perez JL, Marco FM, Pignata C, Bousfiha A, Turvey SE, Bauer S, Haerynck F, Ocejo-Vinyals JG, Lendinez F, Prader S, Naumann-Bartsch N, Pachlopnik Schmid J, Biggs CM, Hildebrand K, Dreesman A, Cárdenes MÁ, Ailal F, Benhsaien I, Giardino G, Molina-Fuentes A, Fortuny C, Madhavarapu S, Conway DH, Prando C, Schidlowski L, Martínez de Saavedra Álvarez MT, Alfaro R, Rodríguez de Castro F, , , Meyts I, Hauck F, Puel A, Bastard P, Boisson B, Jouanguy E, Abel L, Cobat A, Zhang Q, Casanova JL, Alsina L, Rodríguez-Gallego C, Humans with inherited MyD88 and IRAK-4 deficiencies are predisposed to hypoxemic COVID-19 pneumonia., J Exp Med 2023 May; 220(5): .

Larotonda L, Mornico D, Khanna V, Bernal-Bayard J, Ghigo JM, Val ME, Comerci D, Mazel D, Soler-Bistué A, Chromosomal Position of Ribosomal Protein Genes Affects Long-Term Evolution of Vibrio cholerae., mBio 2023 Apr; 14(2): e0343222.

Jack-Christophe Cossec* , Tatiana Traboulsi* , Sébastien Sart* , Yann Loe-Mie , Manuel Guthmann , Ivo A Hendriks , Ilan Theurillat , Michael L Nielsen , Maria-Elena Torres-Padilla , Charles N Baroud , Anne Dejean , Transient suppression of SUMOylation in embryonic stem cells generates embryo-like structures, Cell Rep . 2023 Apr 15;42(4):112380. doi: 10.1016/j.celrep.2023.112380.

Chekli Y, Stevick RJ, Kornobis E, Briolat V, Ghigo JM, Beloin C, Escherichia coli Aggregates Mediated by Native or Synthetic Adhesins Exhibit Both Core and Adhesin-Specific Transcriptional Responses., Microbiol Spectr 2023 Apr; (): e0069023.

Matuozzo D, Talouarn E, Marchal A, Zhang P, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Abou Tayoun A, Aiuti A, Alavi Darazam I, Allende LM, Alonso-Arias R, Arias AA, Aytekin G, Bergman P, Bondesan S, Bryceson YT, Bustos IG, Cabrera-Marante O, Carcel S, Carrera P, Casari G, Chaïbi K, Colobran R, Condino-Neto A, Covill LE, Delmonte OM, El Zein L, Flores C, Gregersen PK, Gut M, Haerynck F, Halwani R, Hancerli S, Hammarström L, Hatipoğlu N, Karbuz A, Keles S, Kyheng C, Leon-Lopez R, Franco JL, Mansouri D, Martinez-Picado J, Metin Akcan O, Migeotte I, Morange PE, Morelle G, Martin-Nalda A, Novelli G, Novelli A, Ozcelik T, Palabiyik F, Pan-Hammarström Q, de Diego RP, Planas-Serra L, Pleguezuelo DE, Prando C, Pujol A, Reyes LF, Rivière JG, Rodriguez-Gallego C, Rojas J, Rovere-Querini P, Schlüter A, Shahrooei M, Sobh A, Soler-Palacin P, Tandjaoui-Lambiotte Y, Tipu I, Tresoldi C, Troya J, van de Beek D, Zatz M, Zawadzki P, Al-Muhsen SZ, Alosaimi MF, Alsohime FM, Baris-Feldman H, Butte MJ, Constantinescu SN, Cooper MA, Dalgard CL, Fellay J, Heath JR, Lau YL, Lifton RP, Maniatis T, Mogensen TH, von Bernuth H, Lermine A, Vidaud M, Boland A, Deleuze JF, Nussbaum R, Kahn-Kirby A, Mentre F, Tubiana S, Gorochov G, Tubach F, Hausfater P, , , , , , , , , , Meyts I, Zhang SY, Puel A, Notarangelo LD, Boisson-Dupuis S, Su HC, Boisson B, Jouanguy E, Casanova JL, Zhang Q, Abel L, Cobat A, Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19., Genome Med 2023 Apr; 15(1): 22.

Bucciol G, , Meyts I, Inherited and acquired errors of type I interferon immunity govern susceptibility to COVID-19 and multisystem inflammatory syndrome in children., J Allergy Clin Immunol 2023 Apr; 151(4): 832-840.

Rendueles O, de Sousa JAM, Rocha EPC, Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies., Elife 2023 Mar; 12(): .

Arcangioli B, Gangloff S, , The Fission Yeast Mating-Type Switching Motto: “One-for-Two” and “Two-for-One”., Microbiol Mol Biol Rev 2023 Mar; 87(1): e0000821.

Kerner G, Choin J, Quintana-Murci L, , Ancient DNA as a tool for medical research., Nat Med 2023 Mar; (): .

D'Angelo F, Rocha EPC, Rendueles O, , The Capsule Increases Susceptibility to Last-Resort Polymyxins, but Not to Other Antibiotics, in Klebsiella pneumoniae., Antimicrob Agents Chemother 2023 Mar; (): e0012723.

Temmam S, Montagutelli X, Herate C, Donati F, Regnault B, Attia M, Baquero Salazar E, Chretien D, Conquet L, Jouvion G, Pipoli Da Fonseca J, Cokelaer T, Amara F, Relouzat F, Naninck T, Lemaitre J, Derreudre-Bosquet N, Pascal Q, Bonomi M, Bigot T, Munier S, Rey FA, Le Grand R, van der Werf S, Eloit M, SARS-CoV-2-related bat virus behavior in human-relevant models sheds light on the origin of COVID-19., EMBO Rep 2023 Apr; 24(4): e56055.

de Sousa JAM, Fillol-Salom A, Penadés JR, Rocha EPC, Identification and characterization of thousands of bacteriophage satellites across bacteria., Nucleic Acids Res 2023 Mar; (): .

Muffato M, Louis A, Nguyen NTT, Lucas J, Berthelot C, Roest Crollius H, Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom., Nat Ecol Evol 2023 Mar; 7(3): 355-366.

Parey E, Louis A, Montfort J, Bouchez O, Roques C, Iampietro C, Lluch J, Castinel A, Donnadieu C, Desvignes T, Floi Bucao C, Jouanno E, Wen M, Mejri S, Dirks R, Jansen H, Henkel C, Chen WJ, Zahm M, Cabau C, Klopp C, Thompson A, Robinson-Rechavi M, Braasch I, Lecointre G, Bobe J, Postlethwait JH, Berthelot C, Crollius HR, Guiguen Y, , Genome structures resolve the early diversification of teleost fishes., Science 2023 Feb; 379(6632): 572-575.

Moore CP, Husson J, Boudaoud A, Amselem G, Baroud CN, Clogging of a Rectangular Slit by a Spherical Soft Particle., Phys Rev Lett 2023 Feb; 130(6): 064001.

Kerner G, Neehus AL, Philippot Q, Bohlen J, Rinchai D, Kerrouche N, Puel A, Zhang SY, Boisson-Dupuis S, Abel L, Casanova JL, Patin E, Laval G, Quintana-Murci L, , Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe., Cell Genom 2023 Feb; 3(2): 100248.

Chen KY, Karuppusamy J, O'Neill MB, Opuu V, Bahin M, Foulon S, Ibanez P, Quintana-Murci L, Ozawa T, van der Werf S, Nghe P, Naffakh N, Griffiths A, Isel C , High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing., Proc Natl Acad Sci U S A 2023 Feb; 120(6): e2211098120.

Tesson F, Bernheim A, Synergy and regulation of antiphage systems: toward the existence of a bacterial immune system?, Curr Opin Microbiol 2023 Feb; 71(): 102238.

López-Igual R, Dorado-Morales P, Mazel D, , Increasing the Scalability of Toxin-Intein Orthogonal Combinations., ACS Synth Biol 2023 Jan; (): .

Nucci A, Janaszkiewicz J, Rocha EPC, Rendueles O, Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola., Microlife 2023 ; 4(): uqad038.

Kerner G, Quintana-Murci L, [Paleogenomics and the evolution of the human immune system over the last ten millennia]., Med Sci (Paris) 2023 ; 39(6-7): 496-499.

Vonaesch P, Billy V, Mann AE, Morien E, Habib A, Collard JM, Dédé M, Kapel N, Sansonetti PJ, Parfrey LW, The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status., Microlife 2023 ; 4(): uqad033.

Roca Suarez AA, Planel S, Grand X, Couturier C, Tran T, Porcheray F, Becker J, Reynier F, Delgado A, Cascales E, Peyrot L, Tamellini A, Saliou A, Elie C, Baum C, Vuong BQ, Testoni B, Roques P, Zoulim F, Hasan U, Chemin I, Interspecies comparison of the early transcriptomic changes associated with hepatitis B virus exposure in human and macaque immune cell populations., Front Cell Infect Microbiol 2023 ; 13(): 1248782.

Teiti I, Aubry M, Fernandes-Pellerin S, Patin E, Madec Y, Boucheron P, Vanhomwegen J, Torterat J, Lastère S, Olivier S, Jaquaniello A, Roux M, Mendiboure V, Harmant C, Bisiaux A, Rijo de León G, Liu D, Bossin H, Mathieu-Daudé F, Gatti C, Suhas E, Chung K, Condat B, Ayotte P, Conte E, Jolly N, Manuguerra JC, Sakuntabhai A, Fontanet A, Quintana-Murci L, Cao-Lormeau VM, Unravelling the determinants of human health in French Polynesia: the MATAEA project., Front Epidemiol 2023 ; 3(): 1201038.

Borry M, Forsythe A, Andrades Valtueña A, Hübner A, Ibrahim A, Quagliariello A, White AE, Kocher A, Vågene ÅJ, Bartholdy BP, Spurīte D, Ponce-Soto GY, Neumann G, Huang IT, Light I, Velsko IM, Jackson I, Frangenberg J, Serrano JG, Fumey J, Özdoğan KT, Blevins KE, Daly KG, Lopopolo M, Moraitou M, Michel M, van Os M, Bravo-Lopez MJ, Sarhan MS, Dagtas ND, Oskolkov N, Smith OS, Lebrasseur O, Rozwalak P, Eisenhofer R, Wasef S, Ramachandran SL, Vanghi V, Warinner C, Fellows Yates JA, Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT., F1000Res 2023 ; 12(): 926.

Laure Mancini, Boris Guirao, Sara Ortica, Miriam Labusch, Felix Cheysson, Valentin Bonnet, Minh Son Phan, Sébastien Herbert, Pierre Mahou, Emilie Menant, Sébastien Bedu, Jean-Yves Tinevez, Charles Baroud, Emmanuel Beaurepaire, Yohanns Bellaiche, Laure Bally-Cuif, Nicolas Dray, Apical size and deltaA expression predict adult neural stem cell decisions along lineage progression, 2023.

Lee D, Le Pen J, Yatim A, Dong B, Aquino Y, Ogishi M, Pescarmona R, Talouarn E, Rinchai D, Zhang P, Perret M, Liu Z, Jordan I, Elmas Bozdemir S, Bayhan GI, Beaufils C, Bizien L, Bisiaux A, Lei W, Hasan M, Chen J, Gaughan C, Asthana A, Libri V, Luna JM, Jaffré F, Hoffmann HH, Michailidis E, Moreews M, Seeleuthner Y, Bilguvar K, Mane S, Flores C, Zhang Y, Arias AA, Bailey R, Schlüter A, Milisavljevic B, Bigio B, Le Voyer T, Materna M, Gervais A, Moncada-Velez M, Pala F, Lazarov T, Levy R, Neehus AL, Rosain J, Peel J, Chan YH, Morin MP, Pino-Ramirez RM, Belkaya S, Lorenzo L, Anton J, Delafontaine S, Toubiana J, Bajolle F, Fumadó V, DeDiego ML, Fidouh N, Rozenberg F, Pérez-Tur J, Chen S, Evans T, Geissmann F, Lebon P, Weiss SR, Bonnet D, Duval X, , Covid HGE, Pan-Hammarström Q, Planas AM, Meyts I, Haerynck F, Pujol A, Sancho-Shimizu V, Dalgard C, Bustamante J, Puel A, Boisson-Dupuis S, Boisson B, Maniatis T, Zhang Q, Bastard P, Notarangelo L, Béziat V, Perez de Diego R, Rodriguez-Gallego C, Su HC, Lifton RP, Jouanguy E, Cobat A, Alsina L, Keles S, Haddad E, Abel L, Belot A, Quintana-Murci L, Rice CM, Silverman RH, Zhang SY, Casanova JL, , Inborn errors of OAS-RNase L in SARS-CoV-2-related multisystem inflammatory syndrome in children., Science 2022 Dec; (): eabo3627.

Manet C, Mansuroglu Z, Conquet L, Bortolin V, Comptdaer T, Segrt H, Bourdon M, Menidjel R, Stadler N, Tian G, Herit F, Niedergang F, Souès S, Buée L, Galas MC, Montagutelli X, Bonnefoy E, , Zika virus infection of mature neurons from immunocompetent mice generates a disease-associated microglia and a tauopathy-like phenotype in link with a delayed interferon beta response., J Neuroinflammation 2022 Dec; 19(1): 307.

Rostain W, Zaplana T, Boutard M, Baum C, Tabuteau S, Sanitha M, Ramya M, Guss A, Ettwiller L, Tolonen AC, Tuning of Gene Expression in Clostridium phytofermentans Using Synthetic Promoters and CRISPRi., ACS Synth Biol 2022 Dec; 11(12): 4077-4088.

Vertti-Quintero N., Levien E., Poggi L., Amir A., Richard G.-F. and Baroud C. N. , Time-resolved microfluidics unravels individual cellular fates during double-strand break repair., BMC Biol 20, 269 (2022).

Vertti-Quintero N, Levien E, Poggi L, Amir A, Richard GF, Baroud CN, , Time-resolved microfluidics unravels individual cellular fates during double-strand break repair., BMC Biol 2022 Dec; 20(1): 269.

Ares-Arroyo M, Coluzzi C, P C Rocha E, , Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation., Nucleic Acids Res 2022 Nov; (): .

Ares-Arroyo M, Fernández-García M, Wedel E, Montero N, Barbas C, Rey-Stolle MF, Garcia A, González-Zorn B, , Genomics, Transcriptomics, and Metabolomics Reveal That Minimal Modifications in the Host Are Crucial for the Compensatory Evolution of ColE1-Like Plasmids., mSphere 2022 Nov; (): e0018422.

Miatello J, Lukaszewicz AC, Carter MJ, Faivre V, Hua S, Martinet KZ, Bourgeois C, Quintana-Murci L, Payen D, Boniotto M, Tissières P, , CIITA promoter polymorphism impairs monocytes HLA-DR expression in patients with septic shock., iScience 2022 Nov; 25(11): 105291.

Foresto E, Revale S, Primo E, Nievas F, Carezzano E, Puente M, Alzari P, Martínez M, Ben-Assaya M, Mornico D, Santoro M, Martínez-Abarca F, Giordano W, Bogino P, , Complete Genome Sequence of Mesorhizobium ciceri Strain R30, a Rhizobium Used as a Commercial Inoculant for Chickpea in Argentina., Microbiol Resour Announc 2022 Nov; 11(11): e0077922.

Millman A, Melamed S, Leavitt A, Doron S, Bernheim A, Hör J, Garb J, Bechon N, Brandis A, Lopatina A, Ofir G, Hochhauser D, Stokar-Avihail A, Tal N, Sharir S, Voichek M, Erez Z, Ferrer JLM, Dar D, Kacen A, Amitai G, Sorek R, An expanded arsenal of immune systems that protect bacteria from phages., Cell Host Microbe 2022 Nov; 30(11): 1556-1569.e5.

Lacote S, Tamietti C, Chabert M, Confort MP, Conquet L, Pulido C, Aurine N, Baquerre C, Thiesson A, Pain B, De Las Heras M, Flamand M, Montagutelli X, Marianneau P, Ratinier M, Arnaud F, Intranasal Exposure to Rift Valley Fever Virus Live-Attenuated Strains Leads to High Mortality Rate in Immunocompetent Mice., Viruses 2022 Nov; 14(11): .

Krin E, Baharoglu Z, Sismeiro O, Varet H, Coppée JY, Mazel D, , Systematic transcriptome analysis allows the identification of new type I and type II Toxin/Antitoxin systems located in the superintegron of Vibrio cholerae., Res Microbiol 2023 ; 174(1-2): 103997.

Donnarumma E, Kohlhaas M, Vimont E, Kornobis E, Chaze T, Gianetto QG, Matondo M, Moya-Nilges M, Maack C, Wai T, , Mitochondrial Fission Process 1 controls inner membrane integrity and protects against heart failure., Nat Commun 2022 Nov; 13(1): 6634.

Bourdon M, Montagutelli X, stuart: an R package for the curation of SNP genotypes from experimental crosses., G3 (Bethesda) 2022 Nov; 12(11): .

Boutet I, Alves Monteiro HJ, Baudry L, Takeuchi T, Bonnivard E, Billoud B, Farhat S, Gonzales-Araya R, Salaun B, Andersen AC, Toullec JY, Lallier FH, Flot JF, Guiglielmoni N, Guo X, Li C, Allam B, Pales-Espinosa E, Hemmer-Hansen J, Moreau P, Marbouty M, Koszul R, Tanguy A, Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic resource for aquaculture., Evol Appl 2022 Nov; 15(11): 1730-1748.

Garb J, Lopatina A, Bernheim A, Zaremba M, Siksnys V, Melamed S, Leavitt A, Millman A, Amitai G, Sorek R, , Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion., Nat Microbiol 2022 Nov; 7(11): 1849-1856.

Liu H, Chansoria P, Delrot P, Angelidakis E, Rizzo R, Rütsche D, Applegate LA, Loterie D, Zenobi-Wong M, Filamented Light (FLight) Biofabrication of Highly Aligned Tissue-Engineered Constructs., Adv Mater 2022 Nov; 34(45): e2204301.

Kumar S, Schmitt C, Gorgette O, Marbouty M, Duchateau M, Giai Gianetto Q, Matondo M, Guigner JM, De Reuse H, , Bacterial Membrane Vesicles as a Novel Strategy for Extrusion of Antimicrobial Bismuth Drug in Helicobacter pylori., mBio 2022 Oct; 13(5): e0163322.

Felipe-Ruiz A, Marina A, Rocha EPC, , Structural and Genomic Evolution of RRNPPA Systems and Their Pheromone Signaling., mBio 2022 Oct; (): e0251422.

Xavier Montagutelli, Bérénice Decaudin, Maxime Beretta, Hugo Mouquet, Etienne Simon-Lorière, SARS-CoV-2 infection in domestic rats after transmission from their infected owner, 2023.

Bergstedt J, Azzou SAK, Tsuo K, Jaquaniello A, Urrutia A, Rotival M, Lin DTS, MacIsaac JL, Kobor MS, Albert ML, Duffy D, Patin E, Quintana-Murci L, The immune factors driving DNA methylation variation in human blood., Nat Commun 2022 Oct; 13(1): 5895.

Garcia-Luis J, Bordelet H, Thierry A, Koszul R, Aragon L, , Depletion or cleavage of cohesin during anaphase differentially affects chromatin structure and segregation., Elife 2022 Oct; 11(): .

Bolze A, Mogensen TH, Zhang SY, Abel L, Andreakos E, Arkin LM, Borghesi A, Brodin P, Hagin D, Novelli G, Okada S, Peter J, Renia L, Severe K, Tiberghien P, Vinh DC, , Cirulli ET, Casanova JL, Hsieh EWY, , Decoding the Human Genetic and Immunological Basis of COVID-19 mRNA Vaccine-Induced Myocarditis., J Clin Immunol 2022 Oct; 42(7): 1354-1359.

Flaugnatti N, Isaac S, Lemos Rocha LF, Stutzmann S, Rendueles O, Stoudmann C, Vesel N, Garcia-Garcera M, Buffet A, Sana TG, Rocha EPC, Blokesch M, , Human commensal gut Proteobacteria withstand type VI secretion attacks through immunity protein-independent mechanisms., Nat Commun 2021 Oct; 12(1): 5751.

Pfeifer E, Bonnin RA, Rocha EPC, , Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion., mBio 2022 Sep; (): e0185122.

Matthieu Haudiquet, How capsules protect the cell, shape genetic exchanges and drive bacterial evolution Comment la capsule protège la cellule, façonne les échanges génétiques et influence l’évolution bactérienne, Life Sciences [q-bio]. Universite Paris Cité, 2022. English. ⟨NNT : ⟩.

Matthey-Doret C, Colp MJ, Escoll P, Thierry A, Moreau P, Curtis B, Sahr T, Sarrasin M, Gray MW, Lang BF, Archibald JM, Buchrieser C, Koszul R, , Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin reorganization., Genome Res 2022 Sep; (): .

Anamaria Babosan, Louna Fruchard, Evelyne Krin, André Carvalho, Didier Mazel, Zeynep Baharoglu, Nonessential tRNA and rRNA modifications impact the bacterial response to sub-MIC antibiotic stress, microLife, Volume 3, 2022, uqac019.

Arauna LR, Bergstedt J, Choin J, Mendoza-Revilla J, Harmant C, Roux M, Mas-Sandoval A, Lémée L, Colleran H, François A, Valentin F, Cassar O, Gessain A, Quintana-Murci L, Patin E, , The genomic landscape of contemporary western Remote Oceanians., Curr Biol 2022 Sep; (): .

Lazarini F, Lannuzel A, Cabié A, Michel V, Madec Y, Chaumont H, Calmont I, Favrat M, Montagutelli X, Roze E, Lledo PM, Olfactory outcomes in Zika virus-associated Guillain-Barré syndrome., Eur J Neurol 2022 Sep; 29(9): 2823-2831.

Nievas F, Revale S, Foresto E, Cossovich S, Puente M, Alzari P, Martínez M, Ben-Assaya M, Mornico D, Santoro M, Martínez-Abarca F, Giordano W, Bogino P, , Complete Genome Sequence of Bradyrhizobium sp. Strain C-145, a Nitrogen-Fixing Rhizobacterium Used as a Peanut Inoculant in Argentina., Microbiol Resour Announc 2022 Aug; 11(8): e0050522.

Parey E, Louis A, Montfort J, Guiguen Y, Roest Crollius H, Berthelot C, , An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication., Genome Res 2022 Aug; (): .

Vonaesch P, Winkel M, Kapel N, Nestoret A, Barbot-Trystram L, Pontoizeau C, Barouki R, Rakotondrainipiana M, Kandou K, Andriamanantena Z, Andrianonimiadana L, Habib A, Rodriguez-Pozo A, Hasan M, Vigan-Womas I, Collard JM, Gody JC, Djorie S, Sansonetti PJ, Randremanana RV, On Behalf Of The Afribiota Investigators, Putative Biomarkers of Environmental Enteric Disease Fail to Correlate in a Cross-Sectional Study in Two Study Sites in Sub-Saharan Africa., Nutrients 2022 Aug; 14(16): .

Ronteix G, Aristov A, Bonnet V, Sart S, Sobel J, Esposito E, Baroud CN, , Griottes: a generalist tool for network generation from segmented tissue images., BMC Biol 2022 08; 20(1): 178.

Lazar-Stefanita L, Luo J, Montagne R, Thierry A, Sun X, Mercy G, Mozziconacci J, Koszul R, Boeke JD, , Karyotype engineering reveals spatio-temporal control of replication firing and gene contacts., Cell Genom 2022 Aug; 2(8): None.

Zhang Q, Matuozzo D, Le Pen J, Lee D, Moens L, Asano T, Bohlen J, Liu Z, Moncada-Velez M, Kendir-Demirkol Y, Jing H, Bizien L, Marchal A, Abolhassani H, Delafontaine S, Bucciol G, , Bayhan GI, Keles S, Kiykim A, Hancerli S, Haerynck F, Florkin B, Hatipoglu N, Ozcelik T, Morelle G, Zatz M, Ng LFP, Lye DC, Young BE, Leo YS, Dalgard CL, Lifton RP, Renia L, Meyts I, Jouanguy E, Hammarström L, Pan-Hammarström Q, Boisson B, Bastard P, Su HC, Boisson-Dupuis S, Abel L, Rice CM, Zhang SY, Cobat A, Casanova JL, , Recessive inborn errors of type I IFN immunity in children with COVID-19 pneumonia., J Exp Med 2022 Aug; 219(8): .

Vabret N, Najburg V, Solovyov A, Gopal R, McClain C, Šulc P, Balan S, Rahou Y, Beauclair G, Chazal M, Varet H, Legendre R, Sismeiro O, Sanchez David RY, Chauveau L, Jouvenet N, Markowitz M, van der Werf S, Schwartz O, Tangy F, Bhardwaj N, Greenbaum BD, Komarova AV, Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1., iScience 2022 Jul; 25(7): 104599.

Randrianarisoa MM, Rakotondrainipiana M, Randriamparany R, Andriantsalama PV, Randrianarijaona A, Habib A, Robinson A, Raharimalala L, Hunald FA, Etienne A, Collard JM, Randrianirina F, Barouki R, Pontoizeau C, Nestoret A, Kapel N, Sansonetti P, Vonaesch P, Randremanana RV, Factors associated with anaemia among preschool- age children in underprivileged neighbourhoods in Antananarivo, Madagascar., BMC Public Health 2022 Jul; 22(1): 1320.

Campbell TM, Liu Z, Zhang Q, Moncada-Velez M, Covill LE, Zhang P, Alavi Darazam I, Bastard P, Bizien L, Bucciol G, Lind Enoksson S, Jouanguy E, Karabela ŞN, Khan T, Kendir-Demirkol Y, Arias AA, Mansouri D, Marits P, Marr N, Migeotte I, Moens L, Ozcelik T, Pellier I, Sendel A, Shahrooei M, Smith CIE, Vandernoot I, Willekens K, , Bergman P, Abel L, Cobat A, Casanova JL, Meyts I, Bryceson YT, , Respiratory viral infections in otherwise healthy humans with inherited IRF7 deficiency., J Exp Med 2022 Jul; 219(7): .

Planchais C, Fernández I, Bruel T, de Melo GD, Prot M, Beretta M, Guardado-Calvo P, Dufloo J, Molinos-Albert LM, Backovic M, Chiaravalli J, Giraud E, Vesin B, Conquet L, Grzelak L, Planas D, Staropoli I, Guivel-Benhassine F, Hieu T, Boullé M, Cervantes-Gonzalez M, Ungeheuer MN, Charneau P, van der Werf S, Agou F, , , Dimitrov JD, Simon-Lorière E, Bourhy H, Montagutelli X, Rey FA, Schwartz O, Mouquet H, Potent human broadly SARS-CoV-2-neutralizing IgA and IgG antibodies effective against Omicron BA.1 and BA.2., J Exp Med 2022 Jul; 219(7): .

Hajheidari M, Gerlach N, Dorau K, Omidbakhshfard MA, Pesch L, Hofmann J, Hallab A, Ponce-Soto GY, Kuhalskaya A, Medeiros DB, Bourceret A, , Usadel B, Mayer J, Fernie A, Mansfeldt T, Sonnewald U, Bucher M, Crop genetic diversity uncovers metabolites, elements, and gene networks predicted to be associated with high plant biomass yields in maize., PNAS Nexus 2022 Jul; 1(3): pgac068.

Kerner G, Quintana-Murci L, , The genetic and evolutionary determinants of COVID-19 susceptibility., Eur J Hum Genet 2022 Jun; (): .

Vincendeau E, Wei W, Zhang X, Planchais C, Yu W, Lenden-Hasse H, Cokelaer T, Pipoli da Fonseca J, Mouquet H, Adams DJ, Alt FW, Jackson SP, Balmus G, Lescale C, Deriano L, , SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination., Nat Commun 2022 Jun; 13(1): 3707.

Posseme C, Llibre A, Charbit B, Bondet V, Rouilly V, Saint-André V, Boussier J, Bergstedt J, Smith N, Townsend L, Sugrue JA, Ní Cheallaigh C, Conlon N, Rotival M, Kobor MS, Mottez E, Pol S, Patin E, Albert ML, Quintana-Murci L, Duffy D, Early IFNβ secretion determines variable downstream IL-12p70 responses upon TLR4 activation., Cell Rep 2022 Jun; 39(13): 110989.

Trutschel D, Bost P, Mariette X, Bondet V, Llibre A, Posseme C, Charbit B, Thorball CW, Jonsson R, Lessard CJ, Felten R, Ng WF, Chatenoud L, Dumortier H, Sibilia J, Fellay J, Brokstad KA, Appel S, Tarn JR, Quintana-Murci L, Mingueneau M, Meyer N, Duffy D, Schwikowski B, Gottenberg JE, Variability of Primary Sjögren’s Syndrome Is Driven by Interferon-α and Interferon-α Blood Levels Are Associated With the Class II HLA-DQ Locus., Arthritis Rheumatol 2022 Dec; 74(12): 1991-2002.

Dos Reis R, Kornobis E, Pereira A, Tores F, Carrasco J, Gautier C, Jahannault-Talignani C, Nitschké P, Muchardt C, Schlosser A, Maric HM, Ango F, Allemand E, , Complex regulation of Gephyrin splicing is a determinant of inhibitory postsynaptic diversity., Nat Commun 2022 Jun; 13(1): 3507.

Choin J, Quintana-Murci L, , Paleogenomics: The demographic past of prehistoric Europeans., Curr Biol 2022 Jun; 32(11): R535-R538.

Bastard P, Hsiao KC, Zhang Q, Choin J, Best E, Chen J, Gervais A, Bizien L, Materna M, Harmant C, Roux M, Hawley NL, Weeks DE, McGarvey ST, Sandoval K, Barberena-Jonas C, Quinto-Cortés CD, Hagelberg E, Mentzer AJ, Robson K, Coulibaly B, Seeleuthner Y, Bigio B, Li Z, Uzé G, Pellegrini S, Lorenzo L, Sbihi Z, Latour S, Besnard M, Adam de Beaumais T, Jacqz Aigrain E, Béziat V, Deka R, Esera Tulifau L, Viali S, Reupena MS, Naseri T, McNaughton P, Sarkozy V, Peake J, Blincoe A, Primhak S, Stables S, Gibson K, Woon ST, Drake KM, Hill AVS, Chan CY, King R, Ameratunga R, Teiti I, Aubry M, Cao-Lormeau VM, Tangye SG, Zhang SY, Jouanguy E, Gray P, Abel L, Moreno-Estrada A, Minster RL, Quintana-Murci L, Wood AC, Casanova JL, , A loss-of-function IFNAR1 allele in Polynesia underlies severe viral diseases in homozygotes., J Exp Med 2022 Jun; 219(6): .

Ronteix G, Jain S, Angely C, Cazaux M, Khazen R, Bousso P, Baroud CN, , High resolution microfluidic assay and probabilistic modeling reveal cooperation between T cells in tumor killing., Nat Commun 2022 Jun; 13(1): 3111.

Coluzzi C, Garcillán-Barcia MP, de la Cruz F, Rocha EPC, , Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids., Mol Biol Evol 2022 Jun; 39(6): .

Bastié N, Chapard C, Dauban L, Gadal O, Beckouët F, Koszul R, , Smc3 acetylation, Pds5 and Scc2 control the translocase activity that establishes cohesin-dependent chromatin loops., Nat Struct Mol Biol 2022 Jun; 29(6): 575-585.

Cury J, Bernheim A, CRISPR-Cas and restriction-modification team up to achieve long-term immunity., Trends Microbiol 2022 Jun; 30(6): 513-514.

François Rousset, Florence Depardieu, Solange Miele, Julien Dowding, Anne-Laure Laval, Erica Lieberman, Daniel Garry, Eduardo P. C. Rocha, Aude Bernheim, David Bikard, Phages and their satellites encode hotspots of antiviral systems, Cell Host & Microbe, 2022, 30 (5), pp.740 - 753.e5. ⟨10.1016/j.chom.2022.02.018⟩.

Tesson F, Hervé A, Mordret E, Touchon M, d'Humières C, Cury J, Bernheim A, Systematic and quantitative view of the antiviral arsenal of prokaryotes., Nat Commun 2022 May; 13(1): 2561.

Jacob JM, Di Carlo SE, Stzepourginski I, Lepelletier A, Ndiaye PD, Varet H, Legendre R, Kornobis E, Benabid A, Nigro G, Peduto L, , PDGFRα-induced stromal maturation is required to restrain postnatal intestinal epithelial stemness and promote defense mechanisms., Cell Stem Cell 2022 May; 29(5): 856-868.e5.

Mongelli V, Lequime S, Kousathanas A, Gausson V, Blanc H, Nigg J, Quintana-Murci L, Elena SF, Saleh MC, , Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster., Nat Ecol Evol 2022 05; 6(5): 565-578.

Collard JM, Andrianonimiadana L, Habib A, Rakotondrainipiana M, Andriantsalama P, Randriamparany R, Rabenandrasana MAN, Weill FX, Sauvonnet N, Randremanana RV, Guillemot V, Vonaesch P, Sansonetti PJ, High prevalence of small intestine bacteria overgrowth and asymptomatic carriage of enteric pathogens in stunted children in Antananarivo, Madagascar., PLoS Negl Trop Dis 2022 May; 16(5): e0009849.

Czarnecki J, Chapkauskaitse E, Bos J, Sentkowska D, Wawrzyniak P, Wyszyńska A, Szuplewska M, Bartosik D, , Differential Localization and Functional Specialization of parS Centromere-Like Sites in repABC Replicons of Alphaproteobacteria., Appl Environ Microbiol 2022 04; 88(8): e0020722.

Patin E, , Human evolution: The unsealed fates of foragers and farmers., Curr Biol 2022 04; 32(8): R362-R365.

Sugrue JA, Smith M, Posseme C, Charbit B, , Bourke NM, Duffy D, O'Farrelly C, Rhesus negative males have an enhanced IFNγ-mediated immune response to influenza A virus., Genes Immun 2022 Apr; 23(2): 93-98.

Sart S, Ronteix G, Jain S, Amselem G, Baroud CN, , Cell Culture in Microfluidic Droplets., Chem Rev 2022 Apr; 122(7): 7061-7096.

Brodin P, Casari G, Townsend L, O'Farrelly C, Tancevski I, Löffler-Ragg J, Mogensen TH, Casanova JL, , , Studying severe long COVID to understand post-infectious disorders beyond COVID-19., Nat Med 2022 Apr; (): .

Etienne Simon-Loriere, Xavier Montagutelli, Frederic Lemoine, Flora Donati, Franck Touret, Jerome Bourret, Matthieu Prot, Sandie Munier, Mikael Attia, Laurine Conquet, Scott Nguyen, Faustine Amara, Anna Maisa, Lucie Fournier, Angela Brisbarre, Oceane Dehan, Laurine Levillayer, Vithiagaran Gunalan, Jannik Fonager, Morten Rasmussen, Stephan Kemeny, Abdelali Zrhidri, Thomas Duret, Sylvie Behillil, Vincent Enouf, Christophe Rodriguez, Slim Fourati, Jean-Michel Pawlotsky, Nicolas Capron, Hugues Leroy, Elodie Alessandri-Gradt, Florian Juszczak, Laetitia Gheysen, Véronique Brodard, Hélène Moret, Martine Bos, Matthijs Welkers, Claus Scholz, Sofia Paraskevopoulou, Laurence Josset, Claire Cervi, Brigitte Couzon, Stéphanie Marque-Juillet, Deborah Delaune, Slim El Khiari, Julien Fumey, Marie-Charlotte Hallouin-Bernard, Félix Rey, Yazdan Yazdanpanah, Bruno Coignard, Xavier de Lamballerie, Sylvie van Der Werf, Axelle Paquin, Rapid characterization of a Delta-Omicron SARS-CoV-2 recombinant detected in Europe, 2022.

Moyon L, Berthelot C, Louis A, Nguyen NTT, Roest Crollius H, , Classification of non-coding variants with high pathogenic impact., PLoS Genet 2022 Apr; 18(4): e1010191.

Zaworski J, Dagva O, Brandt J, Baum C, Ettwiller L, Fomenkov A, Raleigh EA, Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains., PLoS Genet 2022 Apr; 18(4): e1009943.

Néron B, Littner E, Haudiquet M, Perrin A, Cury J, Rocha EPC, , IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella., Microorganisms 2022 Mar; 10(4): .

Conin B, Billault-Chaumartin I, El Sayyed H, Quenech'Du N, Cockram C, Koszul R, Espéli O, , Extended sister-chromosome catenation leads to massive reorganization of the E. coli genome., Nucleic Acids Res 2022 03; 50(5): 2635-2650.

Caron B, Patin E, Rotival M, Charbit B, Albert ML, Quintana-Murci L, Duffy D, Rausell A, Integrative genetic and immune cell analysis of plasma proteins in healthy donors identifies novel associations involving primary immune deficiency genes., Genome Med 2022 Mar; 14(1): 28.

Richard E, Darracq B, Loot C, Mazel D, Unbridled Integrons: A Matter of Host Factors., Cells 2022 Mar; 11(6): .

Montagutelli X, van der Werf S, Rey FA, Simon-Loriere E, SARS-CoV-2 Omicron emergence urges for reinforced One-Health surveillance., EMBO Mol Med 2022 Mar; 14(3): e15558.

Guillaume Achaz, Serge Gangloff, and Benoit Arcangioli, The quiescent X, the replicative Y and the Autosomes, Peer Community Journal, 2: e18.

, A blood atlas of COVID-19 defines hallmarks of disease severity and specificity., Cell 2022 Mar; 185(5): 916-938.e58.

Giraud É, Varet H, Legendre R, Sismeiro O, Aubry F, Dabo S, Dickson LB, Valiente Moro C, Lambrechts L, Mosquito-bacteria interactions during larval development trigger metabolic changes with carry-over effects on adult fitness., Mol Ecol 2022 Mar; 31(5): 1444-1460.

Cuadros-Espinoza S, Laval G, Quintana-Murci L, Patin E, , The genomic signatures of natural selection in admixed human populations., Am J Hum Genet 2022 Mar; (): .

Piel L, Rajan KS, Bussotti G, Varet H, Legendre R, Proux C, Douché T, Giai-Gianetto Q, Chaze T, Cokelaer T, Vojtkova B, Gordon-Bar N, Doniger T, Cohen-Chalamish S, Rengaraj P, Besse C, Boland A, Sadlova J, Deleuze JF, Matondo M, Unger R, Volf P, Michaeli S, Pescher P, Späth GF, Experimental evolution links post-transcriptional regulation to Leishmania fitness gain., PLoS Pathog 2022 Mar; 18(3): e1010375.

Serafini N, Jarade A, Surace L, Goncalves P, Sismeiro O, Varet H, Legendre R, Coppee JY, Disson O, Durum SK, Frankel G, Di Santo JP, , Trained ILC3 responses promote intestinal defense., Science 2022 Feb; 375(6583): 859-863.

Dias JD, Sarica N, Cournac A, Koszul R, Neuveut C, , Crosstalk between Hepatitis B Virus and the 3D Genome Structure., Viruses 2022 02; 14(2): .

Béchon N, Mihajlovic J, Lopes AA, Vendrell-Fernández S, Deschamps J, Briandet R, Sismeiro O, Martin-Verstraete I, Dupuy B, Ghigo JM, , Bacteroides thetaiotaomicron uses a widespread extracellular DNase to promote bile-dependent biofilm formation., Proc Natl Acad Sci U S A 2022 02; 119(7):e2111228119. doi: 10.1073/pnas.2111228119. .

Klompe SE, Jaber N, Beh LY, Mohabir JT, Bernheim A, Sternberg SH, Evolutionary and mechanistic diversity of Type I-F CRISPR-associated transposons., Mol Cell 2022 Feb; 82(3): 616-628.e5.

Planas D, Saunders N, Maes P, Guivel-Benhassine F, Planchais C, Buchrieser J, Bolland WH, Porrot F, Staropoli I, Lemoine F, Péré H, Veyer D, Puech J, Rodary J, Baele G, Dellicour S, Raymenants J, Gorissen S, Geenen C, Vanmechelen B, Wawina-Bokalanga T, Martí-Carreras J, Cuypers L, Sève A, Hocqueloux L, Prazuck T, Rey FA, Simon-Loriere E, Bruel T, Mouquet H, André E, Schwartz O, Considerable escape of SARS-CoV-2 Omicron to antibody neutralization., Nature 2022 Feb; 602(7898): 671-675.

Zhang Q, Bastard P, , Cobat A, Casanova JL, , Human genetic and immunological determinants of critical COVID-19 pneumonia., Nature 2022 Jan; (): .

Claireaux M, Robinot R, Kervevan J, Patgaonkar M, Staropoli I, Brelot A, Nouël A, Gellenoncourt S, Tang X, Héry M, Volant S, Perthame E, Avettand-Fenoël V, Buchrieser J, Cokelaer T, Bouchier C, Ma L, Boufassa F, Hendou S, Libri V, Hasan M, Zucman D, de Truchis P, Schwartz O, Lambotte O, Chakrabarti LA, , Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry., Nat Commun 2022 Jan; 13(1): 521.

Moura de Sousa JA, Rocha EPC, , To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites., Philos Trans R Soc Lond B Biol Sci 2022 Jan; 377(1842): 20200475.

Babosan A, Skurnik D, Muggeo A, Pier GB, Baharoglu Z, Jové T, Ploy MC, Griveau S, Bedioui F, Vergnolle S, Moussalih S, de Champs C, Mazel D, Guillard T, , A qnr-plasmid allows aminoglycosides to induce SOS in Escherichia coli., Elife 2022 Jan; 11(): .

Manry J, Bastard P, Gervais A, Voyer TL, Rosain J, Philippot Q, Michailidis E, Hoffmann HH, Eto S, Garcia-Prat M, Bizien L, Parra-Martínez A, Yang R, Haljasmägi L, Migaud M, Särekannu K, Maslovskaja J, de Prost N, Tandjaoui-Lambiotte Y, Luyt CE, Amador-Borrero B, Gaudet A, Poissy J, Morel P, Richard P, Cognasse F, Troya J, Trouillet-Assant S, Belot A, Saker K, Garçon P, Rivière JG, Lagier JC, Gentile S, Rosen L, Shaw E, Morio T, Tanaka J, Dalmau D, Tharaux PL, Sene D, Stepanian A, Mégarbane B, Triantafyllia V, Fekkar A, Heath J, Franco J, Anaya JM, Solé-Violán J, Imberti L, Biondi A, Bonfanti P, Castagnoli R, Delmonte O, Zhang Y, Snow A, Holland S, Biggs C, Moncada-Vélez M, Arias A, Lorenzo L, Boucherit S, Anglicheau D, Planas A, Haerynck F, Duvlis S, Nussbaum R, Ozcelik T, Keles S, Bousfiha A, Bakkouri JE, Ramirez-Santana C, Paul S, Pan-Hammarstrom Q, Hammarstrom L, Dupont A, Kurolap A, Metz C, Aiuti A, Casari G, Lampasona V, Ciceri F, Barreiros L, Dominguez-Garrido E, Vidigal M, Zatz M, van de Beek D, Sahanic S, Tancevski I, Stepanovskyy Y, Boyarchuk O, Nukui Y, Tsumura M, Vidaur L, Tangye S, Burrel S, Duffy D, Quintana-Murci L, Klocperk A, Kann N, Shcherbina A, Lau YL, Leung D, Coulongeat M, Marlet J, Koning R, Reyes L, Chauvineau-Grenier A, Venet F, Monneret G, Nussenzweig M, Arrestier R, Boudhabhay I, Baris-Feldman H, Hagin D, Wauters J, Meyts I, Dyer A, Kennelly S, Bourke N, Halwani R, Sharif-Askari F, Dorgham K, Sallette J, Mehlal-Sedkaoui S, AlKhater S, Rigo-Bonnin R, Morandeira F, Roussel L, Vinh D, Erikstrup C, Condino-Neto A, Prando C, Bondarenko A, Spaan A, Gilardin L, Fellay J, Lyonnet S, Bilguvar K, Lifton R, Mane S, Anderson M, Boisson B, Béziat V, Zhang SY, Andreakos E, Hermine O, Pujol A, Peterson P, Mogensen TH, Rowen L, Mond J, Debette S, deLamballerie X, Burdet C, Bouadma L, Zins M, Soler-Palacin P, Colobran R, Gorochov G, Solanich X, Susen S, Martinez-Picado J, Raoult D, Vasse M, Gregersen P, Rodríguez-Gallego C, Piemonti L, Notarangelo L, Su H, Kisand K, Okada S, Puel A, Jouanguy E, Rice C, Tiberghien P, Zhang Q, Casanova JL, Abel L, Cobat A, , The risk of COVID-19 death is much greater and age-dependent with type I IFN autoantibodies., Res Sq 2022 Jan; (): .

Anne-Sophie L'Honneur, Juliana Pipoli Da Fonseca, Thomas Cokelaer, Flore Rozenberg, JC Polyomavirus whole genome sequencing at the single molecule level reveals emerging neurotropic populations in Progressive Multifocal Leucoencephalopathy, J. Infect. Dis..

Marbouty M, Koszul R, , Metagenomes Binning Using Proximity-Ligation Data., Methods Mol Biol 2022 ; 2301(): 163-181.

Matthey-Doret C, Baudry L, Mortaza S, Moreau P, Koszul R, Cournac A, , Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization., Methods Mol Biol 2022 ; 2301(): 1-15.

Florian Tesson, Alexandre Hervé, Ernest Mordret, Marie Touchon, Camille D’humières, Jean Cury, Aude Bernheim, Systematic and quantitative view of the antiviral arsenal of prokaryotes, Nature Communications, 2022, 13 (1), pp.2561. ⟨10.1038/s41467-022-30269-9⟩.

Brandys P, Montagutelli X, Merenkova I, Barut GT, Thiel V, Schork NJ, Trüeb B, Conquet L, Deng A, Antanasijevic A, Lee HK, Valière M, Sindhu A, Singh G, Herold J, A mRNA Vaccine Encoding for a RBD 60-mer Nanoparticle Elicits Neutralizing Antibodies and Protective Immunity Against the SARS-CoV-2 Delta Variant in Transgenic K18-hACE2 Mice., Front Immunol 2022 ; 13(): 912898.

Kim S, Larrous F, Varet H, Legendre R, Feige L, Dumas G, Matsas R, Kouroupi G, Grailhe R, Bourhy H, , Early Transcriptional Changes in Rabies Virus-Infected Neurons and Their Impact on Neuronal Functions., Front Microbiol 2021 ; 12(): 730892.

Phoka T, Fule L, Da Fonseca JP, Cokelaer T, Picardeau M, Patarakul K., Investigating the role of the carbon storage regulator A (CsrA) Leptospira spp., PLoS One . 2021 Dec 13;16(12):e0260981.

Laval G, Patin E, Boutillier P, Quintana-Murci L, , Sporadic occurrence of recent selective sweeps from standing variation in humans as revealed by an approximate Bayesian computation approach., Genetics 2021 Dec; 219(4): .

Zavala-Alvarado C, G Huete S, Vincent AT, Sismeiro O, Legendre R, Varet H, Bussotti G, Lorioux C, Lechat P, Coppée JY, Veyrier FJ, Picardeau M, Benaroudj N, The oxidative stress response of pathogenic Leptospira is controlled by two peroxide stress regulators which putatively cooperate in controlling virulence., PLoS Pathog 2021 Dec; 17(12): e1009087.

Frantz PN, Barinov A, Ruffié C, Combredet C, Najburg V, de Melo GD, Larrous F, Kergoat L, Teeravechyan S, Jongkaewwattana A, Billon-Denis E, Tournier JN, Prot M, Levillayer L, Conquet L, Montagutelli X, Tichit M, Hardy D, Fernandes P, Strick-Marchand H, Di Santo J, Simon-Lorière E, Bourhy H, Tangy F, A live measles-vectored COVID-19 vaccine induces strong immunity and protection from SARS-CoV-2 challenge in mice and hamsters., Nat Commun 2021 Nov; 12(1): 6277.

Andreakos E, Abel L, Vinh DC, Kaja E, Drolet BA, Zhang Q, O'Farrelly C, Novelli G, Rodríguez-Gallego C, Haerynck F, Prando C, Pujol A, , Su HC, Casanova JL, Spaan AN, , Author Correction: A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection., Nat Immunol 2021 Nov; (): .

Carvalho A, Krin E, Korlowski C, Mazel D, Baharoglu Z, , Interplay between Sublethal Aminoglycosides and Quorum Sensing: Consequences on Survival in V. cholerae., Cells 2021 11; 10(11): .

Liascukiene I, Amselem G, Landoulsi J, Gunes DZ, Baroud CN, , Intermittent dynamics of bubble dissolution due to interfacial growth of fat crystals., Soft Matter 2021 Nov; 17(44): 10042-10052.

Pelleau S, Woudenberg T, Rosado J, Donnadieu F, Garcia L, Obadia T, Gardais S, Elgharbawy Y, Velay A, Gonzalez M, Nizou JY, Khelil N, Zannis K, Cockram C, Merkling SH, Meola A, Kerneis S, Terrier B, de Seze J, Planas D, Schwartz O, Dejardin F, Petres S, von Platen C, Pellerin SF, Arowas L, de Facci LP, Duffy D, Cheallaigh CN, Dunne J, Conlon N, Townsend L, Duong V, Auerswald H, Pinaud L, Tondeur L, Backovic M, Hoen B, Fontanet A, Mueller I, Fafi-Kremer S, Bruel T, White M, Kinetics of the Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Response and Serological Estimation of Time Since Infection., J Infect Dis 2021 Nov; 224(9): 1489-1499.

Fournes F, Niault T, Czarnecki J, Tissier-Visconti A, Mazel D, Val ME, The coordinated replication of Vibrio cholerae’s two chromosomes required the acquisition of a unique domain by the RctB initiator., Nucleic Acids Res 2021 Nov; 49(19): 11119-11133.

Baum C, Lin YC, Fomenkov A, Anton BP, Chen L, Yan B, Evans TC, Roberts RJ, Tolonen AC, Ettwiller L, Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes., Nucleic Acids Res 2021 Nov; 49(19): e113.

Elie Hammam, Ameya Sinha, Sebastian Baumgarten, Flore Nardella, Jiaqi Liang, Samia Miled, Frédéric Bonhomme, Diane Erdmann, Benoit Arcangioli, Paola B. Arimondo, Peter Dedon, Peter Preiser, Artur Scherf, Malaria Parasite Stress Tolerance Is Regulated by DNMT2-Mediated tRNA Cytosine Methylation, mBio. 2021 Nov-Dec; 12(6): e02558-21.

Piazza A, Bordelet H, Dumont A, Thierry A, Savocco J, Girard F, Koszul R, , Cohesin regulates homology search during recombinational DNA repair., Nat Cell Biol 2021 Nov; 23(11): 1176-1186.

Ares-Arroyo M, Rocha EPC, Gonzalez-Zorn B, , Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance., PLoS Genet 2021 Nov; 17(11): e1009919.

Jansen K, Shikama-Dorn N, Attar M, Maio S, Lopopolo M, Buck D, Holländer GA, Sansom SN, RBFOX splicing factors contribute to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus., Genome Res 2021 Nov; 31(11): 2022-2034.

Lang M, Krin E, Korlowski C, Sismeiro O, Varet H, Coppée JY, Mazel D, Baharoglu Z, , Sleeping ribosomes: Bacterial signaling triggers RaiA mediated persistence to aminoglycosides., iScience 2021 Oct; 24(10): 103128.

Rascle P, Jacquelin B, Petitdemange C, Contreras V, Planchais C, Lazzerini M, Dereuddre-Bosquet N, Le Grand R, Mouquet H, Huot N, Müller-Trutwin M, , NK-B cell cross talk induces CXCR5 expression on natural killer cells., iScience 2021 Oct; 24(10): 103109.

Andreakos E, Abel L, Vinh DC, Kaja E, Drolet BA, Zhang Q, O'Farrelly C, Novelli G, Rodríguez-Gallego C, Haerynck F, Prando C, Pujol A, , Su HC, Casanova JL, Spaan AN, , A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection., Nat Immunol 2021 Oct; (): .

Fule L, Halifa R, Fontana C, Sismeiro O, Legendre R, Varet H, Coppée JY, Murray GL, Adler B, Hendrixson DR, Buschiazzo A, Guo S, Liu J, Picardeau M, , Role of the major determinant of polar flagellation FlhG in the endoflagella-containing spirochete Leptospira., Mol Microbiol 2021 Oct; (): .

Huang YN, Peng K, Popejoy AB, Hu J, Nowicki TS, Gold SM, Quintana-Murci L, Fuentes-Guajardo M, Shugay M, Greiff V, Burkhardt AM, Alachkar H, Mangul S, , Ancestral diversity is limited in published T cell receptor sequencing studies., Immunity 2021 Oct; 54(10): 2177-2179.

Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Gaudray FR, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL, Labadie K, Limasset A, Llirós M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ, Hallet B, Koszul R, Lenormand T, Flot JF, Van Doninck K, , Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga., Sci Adv 2021 Oct; 7(41): eabg4216.

Sart S, F-X Tomasi R, Barizien A, Amselem G, Cumano A, Baroud CN, , Structural and Functional Mapping of Mesenchymal Bodies., Bio Protoc 2021 Oct; 11(19): e4177.

Gaspard Kerner, Etienne Patin, Lluis Quintana-Murci, New insights into human immunity from ancient genomics, Current Opinion in Immunology, 2021, 72, pp.116-125. ⟨10.1016/j.coi.2021.04.006⟩.

Carvalho A, Mazel D, Baharoglu Z, , Deficiency in cytosine DNA methylation leads to high chaperonin expression and tolerance to aminoglycosides in Vibrio cholerae., PLoS Genet 2021 10; 17(10): e1009748.

Rotival M, Quintana-Murci L, , Towards a functional understanding of adaptive phenotypes in humans., J Anthropol Sci 2021 Sep; 99(): .

Julian R. Garneau, Véronique Legrand, Martial Marbouty, Maximilian O. Press, Dean R. Vik, Louis-Charles Fortier, Matthew B. Sullivan, David Bikard , Marc Monot, High‑throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome, Sci Rep 11, 18319 (2021)..

Mazzuoli MV, Daunesse M, Varet H, Rosinski-Chupin I, Legendre R, Sismeiro O, Gominet M, Kaminski PA, Glaser P, Chica C, Trieu-Cuot P, Firon A, , The CovR regulatory network drives the evolution of Group B Streptococcus virulence., PLoS Genet 2021 Sep; 17(9): e1009761.

Thompson AW, Hawkins MB, Parey E, Wcisel DJ, Ota T, Kawasaki K, Funk E, Losilla M, Fitch OE, Pan Q, Feron R, Louis A, Montfort J, Milhes M, Racicot BL, Childs KL, Fontenot Q, Ferrara A, David SR, McCune AR, Dornburg A, Yoder JA, Guiguen Y, Roest Crollius H, Berthelot C, Harris MP, Braasch I, , The bowfin genome illuminates the developmental evolution of ray-finned fishes., Nat Genet 2021 09; 53(9): 1373-1384.

Bastard P, Gervais A, Le Voyer T, Rosain J, Philippot Q, Manry J, Michailidis E, Hoffmann HH, Eto S, Garcia-Prat M, Bizien L, Parra-Martínez A, Yang R, Haljasmägi L, Migaud M, Särekannu K, Maslovskaja J, de Prost N, Tandjaoui-Lambiotte Y, Luyt CE, Amador-Borrero B, Gaudet A, Poissy J, Morel P, Richard P, Cognasse F, Troya J, Trouillet-Assant S, Belot A, Saker K, Garçon P, Rivière JG, Lagier JC, Gentile S, Rosen LB, Shaw E, Morio T, Tanaka J, Dalmau D, Tharaux PL, Sene D, Stepanian A, Megarbane B, Triantafyllia V, Fekkar A, Heath JR, Franco JL, Anaya JM, Solé-Violán J, Imberti L, Biondi A, Bonfanti P, Castagnoli R, Delmonte OM, Zhang Y, Snow AL, Holland SM, Biggs C, Moncada-Vélez M, Arias AA, Lorenzo L, Boucherit S, Coulibaly B, Anglicheau D, Planas AM, Haerynck F, Duvlis S, Nussbaum RL, Ozcelik T, Keles S, Bousfiha AA, El Bakkouri J, Ramirez-Santana C, Paul S, Pan-Hammarström Q, Hammarström L, Dupont A, Kurolap A, Metz CN, Aiuti A, Casari G, Lampasona V, Ciceri F, Barreiros LA, Dominguez-Garrido E, Vidigal M, Zatz M, van de Beek D, Sahanic S, Tancevski I, Stepanovskyy Y, Boyarchuk O, Nukui Y, Tsumura M, Vidaur L, Tangye SG, Burrel S, Duffy D, Quintana-Murci L, Klocperk A, Kann NY, Shcherbina A, Lau YL, Leung D, Coulongeat M, Marlet J, Koning R, Reyes LF, Chauvineau-Grenier A, Venet F, Monneret G, Nussenzweig MC, Arrestier R, Boudhabhay I, Baris-Feldman H, Hagin D, Wauters J, Meyts I, Dyer AH, Kennelly SP, Bourke NM, Halwani R, Sharif-Askari NS, Dorgham K, Sallette J, Sedkaoui SM, AlKhater S, Rigo-Bonnin R, Morandeira F, Roussel L, Vinh DC, Ostrowski SR, Condino-Neto A, Prando C, Bonradenko A, Spaan AN, Gilardin L, Fellay J, Lyonnet S, Bilguvar K, Lifton RP, Mane S, , , , , , , , , , , , , , , , , , , , , Anderson MS, Boisson B, Béziat V, Zhang SY, Vandreakos E, Hermine O, Pujol A, Peterson P, Mogensen TH, Rowen L, Mond J, Debette S, de Lamballerie X, Duval X, Mentré F, Zins M, Soler-Palacin P, Colobran R, Gorochov G, Solanich X, Susen S, Martinez-Picado J, Raoult D, Vasse M, Gregersen PK, Piemonti L, Rodríguez-Gallego C, Notarangelo LD, Su HC, Kisand K, Okada S, Puel A, Jouanguy E, Rice CM, Tiberghien P, Zhang Q, Cobat A, Abel L, Casanova JL, Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths., Sci Immunol 2021 Aug; 6(62): .

Asano T, Boisson B, Onodi F, Matuozzo D, Moncada-Velez M, Maglorius Renkilaraj MRL, Zhang P, Meertens L, Bolze A, Materna M, Korniotis S, Gervais A, Talouarn E, Bigio B, Seeleuthner Y, Bilguvar K, Zhang Y, Neehus AL, Ogishi M, Pelham SJ, Le Voyer T, Rosain J, Philippot Q, Soler-Palacín P, Colobran R, Martin-Nalda A, Rivière JG, Tandjaoui-Lambiotte Y, Chaïbi K, Shahrooei M, Darazam IA, Olyaei NA, Mansouri D, Hatipoğlu N, Palabiyik F, Ozcelik T, Novelli G, Novelli A, Casari G, Aiuti A, Carrera P, Bondesan S, Barzaghi F, Rovere-Querini P, Tresoldi C, Franco JL, Rojas J, Reyes LF, Bustos IG, Arias AA, Morelle G, Christèle K, Troya J, Planas-Serra L, Schlüter A, Gut M, Pujol A, Allende LM, Rodriguez-Gallego C, Flores C, Cabrera-Marante O, Pleguezuelo DE, de Diego RP, Keles S, Aytekin G, Akcan OM, Bryceson YT, Bergman P, Brodin P, Smole D, Smith CIE, Norlin AC, Campbell TM, Covill LE, Hammarström L, Pan-Hammarström Q, Abolhassani H, Mane S, Marr N, Ata M, Al Ali F, Khan T, Spaan AN, Dalgard CL, Bonfanti P, Biondi A, Tubiana S, Burdet C, Nussbaum R, Kahn-Kirby A, Snow AL, , , , , , , , , , Bustamante J, Puel A, Boisson-Dupuis S, Zhang SY, Béziat V, Lifton RP, Bastard P, Notarangelo LD, Abel L, Su HC, Jouanguy E, Amara A, Soumelis V, Cobat A, Zhang Q, Casanova JL, , X-linked recessive TLR7 deficiency in ~1% of men under 60 years old with life-threatening COVID-19., Sci Immunol 2021 08; 6(62): .

de Melo GD, Lazarini F, Larrous F, Feige L, Kornobis E, Levallois S, Marchio A, Kergoat L, Hardy D, Cokelaer T, Pineau P, Lecuit M, Lledo PM, Changeux JP, Bourhy H, , Attenuation of clinical and immunological outcomes during SARS-CoV-2 infection by ivermectin., EMBO Mol Med 2021 Aug; 13(8): e14122.

Czernecki D., Bonhomme F., Kaminski PA. and Delarue M., Characterization of a triad of genes in cyanophage S-2Lsufficient to replace adenine by 2-aminoadenine in bacterial DNA, NATURE.

Gauthier J, Boulain H, van Vugt JJFA, Baudry L, Persyn E, Aury JM, Noel B, Bretaudeau A, Legeai F, Warris S, Chebbi MA, Dubreuil G, Duvic B, Kremer N, Gayral P, Musset K, Josse T, Bigot D, Bressac C, Moreau S, Periquet G, Harry M, Montagné N, Boulogne I, Sabeti-Azad M, Maïbèche M, Chertemps T, Hilliou F, Siaussat D, Amselem J, Luyten I, Capdevielle-Dulac C, Labadie K, Merlin BL, Barbe V, de Boer JG, Marbouty M, Cônsoli FL, Dupas S, Hua-Van A, Le Goff G, Bézier A, Jacquin-Joly E, Whitfield JB, Vet LEM, Smid HM, Kaiser L, Koszul R, Huguet E, Herniou EA, Drezen JM, , Author Correction: Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization., Commun Biol 2021 Jul; 4(1): 940.

Rachez C, Legendre R, Costallat M, Varet H, Yi J, Kornobis E, Muchardt C, , HP1γ binding pre-mRNA intronic repeats modulates RNA splicing decisions., EMBO Rep 2021 Jul; (): e52320.

Xavier Montagutelli, Matthieu Prot, Grégory Jouvion, Laurine Levillayer, Laurine Conquet, Edouard Reyes-Gomez, Flora Donati, Melanie Albert, Sylvie van der Werf, Jean Jaubert, Etienne Simon-Lorière, A mouse-adapted SARS-CoV-2 strain replicating in standard laboratory mice, 2021.

Rotival M, Cossart P, Quintana-Murci L, , Reconstructing 50,000 years of human history from our DNA: lessons from modern genomics., C R Biol 2021 Jul; 344(2): 177-187.

Haudiquet M, Buffet A, Rendueles O, Rocha EPC, , Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae., PLoS Biol 2021 Jul; 19(7): e3001276.

Najjar I, Motreff L, Ma L, Lemée L, Briolat V, Monot M, , How Did Institut Pasteur’s NGS Core Facility, Biomics, Manage the Coronavirus Disease 2019 Crisis?, J Biomol Tech 2021 07; 32(2): 50-56.

Armand-Lefèvre L, Rondinaud E, Desvillechabrol D, Mullaert J, Clermont O, Petitjean M, Ruppe E, Cokelaer T, Bouchier C, Tenaillon O, Ma L, Nooroya Y, Matheron S, The Voyag-R Study Group , Andremont A, Denamur E, Kennedy SP, , Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad., Microb Genom 2021 Jul; 7(7): .

Thannesberger J, Rascovan N, Eisenmann A, Klymiuk I, Zittra C, Fuehrer HP, Scantlebury-Manning T, Gittens-St Hilaire M, Austin S, Landis RC, Steininger C, , Viral metagenomics reveals the presence of novel Zika virus variants in Aedes mosquitoes from Barbados., Parasit Vectors 2021 Jun; 14(1): 343.

Danko D, Bezdan D, Afshin EE, Ahsanuddin S, [70 authors], Rascovan N, [23 authors], Mason CE, , , A global metagenomic map of urban microbiomes and antimicrobial resistance., Cell 2021 Jun; 184(13): 3376-3393.e17.

Torbensen K, Baroud CN, Ristori S, Abou-Hassan A, , Tip Streaming of a Lipid-Stabilized Double Emulsion Generated in a Microfluidic Channel., Langmuir 2021 06; 37(24): 7442-7448.

Tremblay YDN, Durand BAR, Hamiot A, Martin-Verstraete I, Oberkampf M, Monot M, Dupuy B, Metabolic adaption to extracellular pyruvate triggers biofilm formation in Clostridioides difficile., ISME J 2021 Jun; (): .

Cockram C, Thierry A, Koszul R, , Generation of gene-level resolution chromosome contact maps in bacteria and archaea., STAR Protoc 2021 Jun; 2(2): 100512.

Bardou M, Postat J, Loaec C, Lemaître F, Ronteix G, Garcia Z, Bousso P, , Quorum sensing governs collective dendritic cell activation in vivo., EMBO J 2021 Jun; (): e107176.

Robbe-Saule M, Foulon M, Poncin I, Esnault L, Varet H, Legendre R, Besnard A, Grzegorzewicz AE, Jackson M, Canaan S, Marsollier L, Marion E, Transcriptional adaptation of Mycobacterium ulcerans in an original mouse model: New insights into the regulation of mycolacton, Virulence . 2021 Dec;12(1):1438-1451.

Vit C, Richard E, Fournes F, Whiteway C, Eyer X, Lapaillerie D, Parissi V, Mazel D, Loot C, Cassette recruitment in the chromosomal Integron of Vibrio cholerae., Nucleic Acids Res 2021 Jun; 49(10): 5654-5670.

de Melo GD, Lazarini F, Levallois S, Hautefort C, Michel V, Larrous F, Verillaud B, Aparicio C, Wagner S, Gheusi G, Kergoat L, Kornobis E, Donati F, Cokelaer T, Hervochon R, Madec Y, Roze E, Salmon D, Bourhy H, Lecuit M, Lledo PM, , COVID-19-related anosmia is associated with viral persistence and inflammation in human olfactory epithelium and brain infection in hamsters., Sci Transl Med 2021 Jun; 13(596): .

Liu Z, Raj S, van Rhijn N, Fraczek M, Michel JP, Sismeiro O, Legendre R, Varet H, Fontaine T, Bromley M, Latgé JP, , Functional Genomic and Biochemical Analysis Reveals Pleiotropic Effect of Congo Red on Aspergillus fumigatus., mBio 2021 May; 12(3): .

Jan Madacki, Mickael Orgeur, Guillem Mas Fiol, Wafa Frigui, Laurence Ma, Roland Brosch, ESX-1-Independent Horizontal Gene Transfer by Mycobacterium tuberculosis Complex Strains, mBio, 2021, 12 (3), ⟨10.1128/mBio.00965-21⟩.

Peng K, Safonova Y, Shugay M, Popejoy AB, Rodriguez OL, Breden F, Brodin P, Burkhardt AM, Bustamante C, Cao-Lormeau VM, Corcoran MM, Duffy D, Fuentes-Guajardo M, Fujita R, Greiff V, Jönsson VD, Liu X, Quintana-Murci L, Rossetti M, Xie J, Yaari G, Zhang W, Abedalthagafi MS, Adekoya KO, Ahmed RA, Chang WC, Gray C, Nakamura Y, Lees WD, Khatri P, Alachkar H, Scheepers C, Watson CT, Karlsson Hedestam GB, Mangul S, , Diversity in immunogenomics: the value and the challenge., Nat Methods 2021 May; (): .

Municio C, Antosz W, Grasser KD, Kornobis E, Van Bel M, Eguinoa I, Coppens F, Bräutigam A, Lermontova I, Bruckmann A, Zelkowska K, Houben A, Schubert V, , The Arabidopsis condensin CAP-D subunits arrange interphase chromatin., New Phytol 2021 05; 230(3): 972-987.

Lamy-Besnier Q, Koszul R, Debarbieux L, Marbouty M, , Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community., Microbiol Resour Announc 2021 Apr; 10(17): .

Tejada-Arranz A, Matos RG, Quentin Y, Bouilloux-Lafont M, Galtier E, Briolat V, Kornobis E, Douché T, Matondo M, Arraiano CM, Raynal B, De Reuse H, , RNase R is associated in a functional complex with the RhpA DEAD-box RNA helicase in Helicobacter pylori., Nucleic Acids Res 2021 49:5249-5264.

Choin J, Mendoza-Revilla J, Arauna LR, Cuadros-Espinoza S, Cassar O, Larena M, Ko AM, Harmant C, Laurent R, Verdu P, Laval G, Boland A, Olaso R, Deleuze JF, Valentin F, Ko YC, Jakobsson M, Gessain A, Excoffier L, Stoneking M, Patin E, Quintana-Murci L, , Genomic insights into population history and biological adaptation in Oceania., Nature 2021 Apr; 592(7855): 583-589.

Azimdine Habib, Lova Andrianonimiadana, Maheninasy Rakotondrainipiana, Prisca Andriantsalama, Ravaka Randriamparany, Rindra Vatosoa Randremanana, Rado Rakotoarison, Inès Vigan‑womas, Armand Rafalimanantsoa, Pascale Vonaesch, Philippe J. Sansonetti, Jean-Marc Collard, The Afribiota Investigators, High prevalence of intestinal parasite infestations among stunted and control children aged 2 to 5 years old in two neighborhoods of Antananarivo, Madagascar, PLoS Neglected Tropical Diseases, 2021, 15 (4), pp.e0009333. ⟨10.1371/journal.pntd.0009333⟩.

Flores-Bello A, Bauduer F, Salaberria J, Oyharçabal B, Calafell F, Bertranpetit J, Quintana-Murci L, Comas D, , Genetic origins, singularity, and heterogeneity of Basques., Curr Biol 2021 Mar; (): .

Roberts HE, Lopopolo M, Pagnamenta AT, Sharma E, Parkes D, Lonie L, Freeman C, Knight SJL, Lunter G, Dreau H, Lockstone H, Taylor JC, Schuh A, Bowden R, Buck D, Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma., Sci Rep 2021 Mar; 11(1): 6408.

Pfeifer E, Moura de Sousa JA, Touchon M, Rocha EPC, , Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires., Nucleic Acids Res 2021 03; 49(5): 2655-2673.

Xavier Montagutelli, Matthieu Prot, Laurine Levillayer, Eduard Baquero Salazar, Grégory Jouvion, Laurine Conquet, Maxime Beretta, Flora Donati, Mélanie Albert, Fabiana Gambaro, Sylvie Behillil, Vincent Enouf, Dominique Rousset, Hugo Mouquet, Jean Jaubert, Felix Rey, Sylvie van Der Werf, Etienne Simon-Loriere, Variants with the N501Y mutation extend SARS-CoV-2 host range to mice, with contact transmission, 2021.

Font-Porterias N, Caro-Consuegra R, Lucas-Sánchez M, Lopez M, Giménez A, Carballo A, Bosch E, Calafell F, Quintana-Murci L, Comas D, , The counteracting effects of demography on functional genomic variation: the Roma paradigm., Mol Biol Evol 2021 Mar; (): .

Dupont MSJ, Guillemot V, Campagne P, Serafini N, Marie S, Montagutelli X, Di Santo JP, Vosshenrich CAJ, , Host genetic control of natural killer cell diversity revealed in the Collaborative Cross., Proc Natl Acad Sci U S A 2021 Mar; 118(10): .

Nagaraja S, Cai MW, Sun J, Varet H, Sarid L, Trebicz-Geffen M, Shaulov Y, Mazumdar M, Legendre R, Coppée JY, Begley TJ, Dedon PC, Gourinath S, Guillen N, Saito-Nakano Y, Shimokawa C, Hisaeda H, Ankri S, , Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator., mBio 2021 Mar; 12(2): .

Kerner G, Laval G, Patin E, Boisson-Dupuis S, Abel L, Casanova JL, Quintana-Murci L, , Human ancient DNA analyses reveal the high burden of tuberculosis in Europeans over the last 2,000 years., Am J Hum Genet 2021 Mar; 108(3): 517-524.

Stressmann FA, Bernal-Bayard J, Perez-Pascual D, Audrain B, Rendueles O, Briolat V, Bruchmann S, Volant S, Ghozlane A, Häussler S, Duchaud E, Levraud JP, Ghigo JM, , Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection., ISME J 2021 Mar; 15(3): 702-719.

Rousset F, Cabezas-Caballero J, Piastra-Facon F, Fernández-Rodríguez J, Clermont O, Denamur E, Rocha EPC, Bikard D, , The impact of genetic diversity on gene essentiality within the Escherichia coli species., Nat Microbiol 2021 03; 6(3): 301-312.

Quistrebert J, Orlova M, Kerner G, Ton LT, Luong NT, Danh NT, Vincent QB, Jabot-Hanin F, Seeleuthner Y, Bustamante J, Boisson-Dupuis S, Huong NT, Ba NN, Casanova JL, Delacourt C, Hoal EG, Alcaïs A, Thai VH, Thành LT, Abel L, Schurr E, Cobat A, , Genome-wide association study of resistance to Mycobacterium tuberculosis infection identifies a locus at 10q26.2 in three distinct populations., PLoS Genet 2021 Mar; 17(3): e1009392.

Marbouty M, Thierry A, Millot GA, Koszul R, , MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut., Elife 2021 Feb; 10(): .

Huot N, Rascle P, Petitdemange C, Contreras V, Stürzel CM, Baquero E, Harper JL, Passaes C, Legendre R, Varet H, Madec Y, Sauermann U, Stahl-Hennig C, Nattermann J, Saez-Cirion A, Le Grand R, Keith Reeves R, Paiardini M, Kirchhoff F, Jacquelin B, Müller-Trutwin M, , SIV-induced terminally differentiated adaptive NK cells in lymph nodes associated with enhanced MHC-E restricted activity., Nat Commun 2021 02; 12(1): 1282.

Machado L, Geara P, Camps J, Dos Santos M, Teixeira-Clerc F, Van Herck J, Varet H, Legendre R, Pawlotsky JM, Sampaolesi M, Voet T, Maire P, Relaix F, Mourikis P, , Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation., Cell Stem Cell 2021 Feb; (): .

Poggi L, Richard GF, , Alternative DNA Structures In Vivo: Molecular Evidence and Remaining Questions., Microbiol Mol Biol Rev 2021 Feb; 85(1): .

Ruault M, Scolari VF, Lazar-Stefanita L, Hocher A, Loïodice I, Koszul R, Taddei A, , Sir3 mediates long-range chromosome interactions in budding yeast., Genome Res 2021 Feb; (): .

de Sousa JAM, Pfeifer E, Touchon M, Rocha EPC, , Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa., Mol Biol Evol 2021 Feb; (): .

Aubry F, Jacobs S, Darmuzey M, Lequime S, Delang L, Fontaine A, Jupatanakul N, Miot EF, Dabo S, Manet C, Montagutelli X, Baidaliuk A, Gámbaro F, Simon-Lorière E, Gilsoul M, Romero-Vivas CM, Cao-Lormeau VM, Jarman RG, Diagne CT, Faye O, Faye O, Sall AA, Neyts J, Nguyen L, Kaptein SJF, Lambrechts L, , Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains., Nat Commun 2021 02; 12(1): 916.

Quintana-Murci L, , Dangerous liaisons: human genetic adaptation to infectious agents., C R Biol 2021 Feb; 343(3): 297-309.

Rosado J, Pelleau S, Cockram C, Merkling SH, Nekkab N, Demeret C, Meola A, Kerneis S, Terrier B, Fafi-Kremer S, de Seze J, Bruel T, Dejardin F, Petres S, Longley R, Fontanet A, Backovic M, Mueller I, White MT, , Multiplex assays for the identification of serological signatures of SARS-CoV-2 infection: an antibody-based diagnostic and machine learning study., Lancet Microbe 2021 Feb; 2(2): e60-e69.

Orgeur M, Frigui W, Pawlik A, Clark S, Williams A, Ates LS, Ma L, Bouchier C, Parkhill J, Brodin P, Brosch R, , Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts., Microb Genom 2021 02; 7(2): .

Mournetas V, Massouridès E, Dupont JB, Kornobis E, Polvèche H, Jarrige M, Dorval ARL, Gosselin MRF, Manousopoulou A, Garbis SD, Górecki DC, Pinset C, , Myogenesis modelled by human pluripotent stem cells: a multi-omic study of Duchenne myopathy early onset., J Cachexia Sarcopenia Muscle 2021 02; 12(1): 209-232.

Houzelstein D, Simon-Chazottes D, Batista L, Tokuda S, Langa Vives F, Flamand M, Montagutelli X, Panthier JJ, , The ring finger protein 213 gene (Rnf213) contributes to Rift Valley fever resistance in mice., Mamm Genome 2021 02; 32(1): 30-37.

Keyser C, Zvénigorosky V, Gonzalez A, Fausser JL, Jagorel F, Gérard P, Tsagaan T, Duchesne S, Crubézy E, Ludes B, Genetic evidence suggests a sense of family, parity and conquest in the Xiongnu Iron Age nomads of Mongolia., Hum Genet 2021 Feb; 140(2): 349-359.

Gauthier J, Boulain H, van Vugt JJFA, Baudry L, Persyn E, Aury JM, Noel B, Bretaudeau A, Legeai F, Warris S, Chebbi MA, Dubreuil G, Duvic B, Kremer N, Gayral P, Musset K, Josse T, Bigot D, Bressac C, Moreau S, Periquet G, Harry M, Montagné N, Boulogne I, Sabeti-Azad M, Maïbèche M, Chertemps T, Hilliou F, Siaussat D, Amselem J, Luyten I, Capdevielle-Dulac C, Labadie K, Merlin BL, Barbe V, de Boer JG, Marbouty M, Cônsoli FL, Dupas S, Hua-Van A, Le Goff G, Bézier A, Jacquin-Joly E, Whitfield JB, Vet LEM, Smid HM, Kaiser L, Koszul R, Huguet E, Herniou EA, Drezen JM, , Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization., Commun Biol 2021 Jan; 4(1): 104.

Rapaport F, Boisson B, Gregor A, Béziat V, Boisson-Dupuis S, Bustamante J, Jouanguy E, Puel A, Rosain J, Zhang Q, Zhang SY, Gleeson JG, Quintana-Murci L, Casanova JL, Abel L, Patin E, , Negative selection on human genes underlying inborn errors depends on disease outcome and both the mode and mechanism of inheritance., Proc Natl Acad Sci U S A 2021 Jan; 118(3): .

Sun Z, Vaisvila R, Hussong LM, Yan B, Baum C, Saleh L, Samaranayake M, Guan S, Dai N, Corrêa IR, Pradhan S, Davis TB, Evans TC, Ettwiller LM, Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution., Genome Res 2021 Jan; 31(2): 291-300.

Danion F, van Rhijn NV, Dufour AC, Legendre R, Sismeiro O, Varet H, Olivo-Marin JC, Mouyna I, Chamilos G, Bromley M, Beauvais A, Latgé JP, Aspergillus fumigatus, One Uninucleate Species with Disparate Offspring., J Fungi (Basel) 2021 Jan; 7(1): .

Proutière A, du Merle L, Périchon B, Varet H, Gominet M, Trieu-Cuot P, Dramsi S, , Characterization of a Four-Component Regulatory System Controlling Bacteriocin Production in Streptococcus gallolyticus., mBio 2021 01; 12(1): .

Sabrina Kalia, Corinne Jallet, Saliha Azebi, Thomas Cokelaer, Juliana Pipoli Da Fonseca, Yu Wu, Julien Barbier , Jean-Christophe Cintrat, Daniel Gillet, Noël Tordo, Broad spectrum compounds targeting early stages of RABV infection, Antiviral Res 188 (2021) 105016.

Byrd AL, Liu M, Fujimura KE, Lyalina S, Nagarkar DR, Charbit B, Bergstedt J, Patin E, Harrison OJ, Quintana-Murci L, Mellman I, Duffy D, Albert ML, , , Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers., J Exp Med 2021 Jan; 218(1): .

Bos J, Cisneros LH, Mazel D, , Real-time tracking of bacterial membrane vesicles reveals enhanced membrane traffic upon antibiotic exposure., Sci Adv 2021 Jan; 7(4): .

Huot N, Rascle P, Planchais C, Contreras V, Passaes C, Le Grand R, Beignon AS, Kornobis E, Legendre R, Varet H, Saez-Cirion A, Mouquet H, Jacquelin B, Müller-Trutwin M, , CD32+CD4+ T Cells Sharing B Cell Properties Increase With Simian Immunodeficiency Virus Replication in Lymphoid Tissues., Front Immunol 2021 ; 12(): 695148.

O'Neill MB, Quach H, Pothlichet J, Aquino Y, Bisiaux A, Zidane N, Deschamps M, Libri V, Hasan M, Zhang SY, Zhang Q, Matuozzo D, Cobat A, Abel L, Casanova JL, Naffakh N, Rotival M, Quintana-Murci L, , Single-Cell and Bulk RNA-Sequencing Reveal Differences in Monocyte Susceptibility to Influenza A Virus Infection Between Africans and Europeans., Front Immunol 2021 ; 12(): 768189.

Bernheim A, Millman A, Ofir G, Meitav G, Avraham C, Shomar H, Rosenberg MM, Tal N, Melamed S, Amitai G, Sorek R, , Prokaryotic viperins produce diverse antiviral molecules., Nature 2021 Jan; 589(7840): 120-124.

Yang R, Mele F, Worley L, Langlais D, Rosain J, Benhsaien I, Elarabi H, Croft CA, Doisne JM, Zhang P, Weisshaar M, Jarrossay D, Latorre D, Shen Y, Han J, Ogishi M, Gruber C, Markle J, Al Ali F, Rahman M, Khan T, Seeleuthner Y, Kerner G, Husquin LT, Maclsaac JL, Jeljeli M, Errami A, Ailal F, Kobor MS, Oleaga-Quintas C, Roynard M, Bourgey M, El Baghdadi J, Boisson-Dupuis S, Puel A, Batteux F, Rozenberg F, Marr N, Pan-Hammarström Q, Bogunovic D, Quintana-Murci L, Carroll T, Ma CS, Abel L, Bousfiha A, Di Santo JP, Glimcher LH, Gros P, Tangye SG, Sallusto F, Bustamante J, Casanova JL, , Human T-bet Governs Innate and Innate-like Adaptive IFN-γ Immunity against Mycobacteria., Cell 2020 12; 183(7): 1826-1847.e31.

Cockram C, Thierry A, Gorlas A, Lestini R, Koszul R, , Euryarchaeal genomes are folded into SMC-dependent loops and domains, but lack transcription-mediated compartmentalization., Mol Cell 2021 02; 81(3): 459-472.e10.

Escudero JA, Nivina A, Kemble HE, Loot C, Tenaillon O, Mazel D, Primary and promiscuous functions coexist during evolutionary innovation through whole protein domain acquisitions., Elife 2020 Dec; 9(): .

Partula V, Deschasaux-Tanguy M, Mondot S, Victor-Bala A, Bouchemal N, Lécuyer L, Bobin-Dubigeon C, Torres MJ, Kesse-Guyot E, Charbit B, Patin E, Assmann KE, Latino-Martel P, Julia C, Galan P, Hercberg S, Quintana-Murci L, Albert ML, Duffy D, Lantz O, Savarin P, Triba MN, Touvier M, , , Associations between untargeted plasma metabolomic signatures and gut microbiota composition in the Milieu Intérieur population of healthy adults., Br J Nutr 2020 Dec; (): 1-11.

Millman A, Bernheim A, Stokar-Avihail A, Fedorenko T, Voichek M, Leavitt A, Oppenheimer-Shaanan Y, Sorek R, , Bacterial Retrons Function In Anti-Phage Defense., Cell 2020 Dec; 183(6): 1551-1561.e12.

Kratzat H, Mackens-Kiani T, Ameismeier M, Potocnjak M, Cheng J, Dacheux E, Namane A, Berninghausen O, Herzog F, Fromont-Racine M, Becker T, Beckmann R, , A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes., EMBO J 2021 01; 40(1): e105179.

Gaultney RA, Vincent AT, Lorioux C, Coppée JY, Sismeiro O, Varet H, Legendre R, Cockram CA, Veyrier FJ, Picardeau M, , 4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans., Nucleic Acids Res 2020 Dec; 48(21): 12102-12115.

Bourdon M, Manet C, Montagutelli X, , Host genetic susceptibility to viral infections: the role of type I interferon induction., Genes Immun 2020 12; 21(6-8): 365-379.

Saint-Sardos A, Sart S, Lippera K, Brient-Litzler E, Michelin S, Amselem G, Baroud CN, , High-Throughput Measurements of Intra-Cellular and Secreted Cytokine from Single Spheroids Using Anchored Microfluidic Droplets., Small 2020 12; 16(49): e2002303.

de Sousa JAM, Buffet A, Haudiquet M, Rocha EPC, Rendueles O, , Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation., ISME J 2020 Dec; 14(12): 2980-2996.

Aubry F, Dabo S, Manet C, Filipović I, Rose NH, Miot EF, Martynow D, Baidaliuk A, Merkling SH, Dickson LB, Crist AB, Anyango VO, Romero-Vivas CM, Vega-Rúa A, Dusfour I, Jiolle D, Paupy C, Mayanja MN, Lutwama JJ, Kohl A, Duong V, Ponlawat A, Sylla M, Akorli J, Otoo S, Lutomiah J, Sang R, Mutebi JP, Cao-Lormeau VM, Jarman RG, Diagne CT, Faye O, Faye O, Sall AA, McBride CS, Montagutelli X, Rašić G, Lambrechts L, , Enhanced Zika virus susceptibility of globally invasive Aedes aegypti populations., Science 2020 11; 370(6519): 991-996.

Mornico D, Hon CC, Koutero M, Weber C, Coppee JY, Dillies MA, Guillen N, , Genomic determinants for initiation and length of natural antisense transcripts in Entamoeba histolytica., Sci Rep 2020 11; 10(1): 20190.

Matthey-Doret C, Baudry L, Breuer A, Montagne R, Guiglielmoni N, Scolari V, Jean E, Campeas A, Chanut PH, Oriol E, Méot A, Politis L, Vigouroux A, Moreau P, Koszul R, Cournac A, , Computer vision for pattern detection in chromosome contact maps., Nat Commun 2020 11; 11(1): 5795.

Székely R, Rengifo-Gonzalez M, Singh V, Riabova O, Benjak A, Piton J, Cimino M, Kornobis E, Mizrahi V, Johnsson K, Manina G, Makarov V, Cole ST, , 6,11-Dioxobenzo[f]pyrido[1,2-a]indoles Kill Mycobacterium tuberculosis by Targeting Iron-Sulfur Protein Rv0338c (IspQ), A Putative Redox Sensor., ACS Infect Dis 2020 11; 6(11): 3015-3025.

Assouvie A, Rotival M, Hamroune J, Busso D, Romeo PH, Quintana-Murci L, Rousselet G, , A genetic variant controls interferon-β gene expression in human myeloid cells by preventing C/EBP-β binding on a conserved enhancer., PLoS Genet 2020 Nov; 16(11): e1009090.

Lacerda Mariano L, Rousseau M, Varet H, Legendre R, Gentek R, Saenz Coronilla J, Bajenoff M, Gomez Perdiguero E, Ingersoll MA, , Functionally distinct resident macrophage subsets differentially shape responses to infection in the bladder., Sci Adv 2020 Nov; 6(48): .

Parey E, Louis A, Cabau C, Guiguen Y, Roest Crollius H, Berthelot C, , Synteny-Guided Resolution of Gene Trees Clarifies the Functional Impact of Whole-Genome Duplications., Mol Biol Evol 2020 11; 37(11): 3324-3337.

Rodríguez-Rubio L, Serna C, Ares-Arroyo M, Matamoros BR, Delgado-Blas JF, Montero N, Bernabe-Balas C, Wedel EF, Mendez IS, Muniesa M, Gonzalez-Zorn B, , Extensive antimicrobial resistance mobilization via multicopy plasmid encapsidation mediated by temperate phages., J Antimicrob Chemother 2020 Nov; 75(11): 3173-3180.

Bastard P, Rosen LB, Zhang Q, Michailidis E, Hoffmann HH, Zhang Y, Dorgham K, Philippot Q, Rosain J, Béziat V, Manry J, Shaw E, Haljasmägi L, Peterson P, Lorenzo L, Bizien L, Trouillet-Assant S, Dobbs K, de Jesus AA, Belot A, Kallaste A, Catherinot E, Tandjaoui-Lambiotte Y, Le Pen J, Kerner G, Bigio B, Seeleuthner Y, Yang R, Bolze A, Spaan AN, Delmonte OM, Abers MS, Aiuti A, Casari G, Lampasona V, Piemonti L, Ciceri F, Bilguvar K, Lifton RP, Vasse M, Smadja DM, Migaud M, Hadjadj J, Terrier B, Duffy D, Quintana-Murci L, van de Beek D, Roussel L, Vinh DC, Tangye SG, Haerynck F, Dalmau D, Martinez-Picado J, Brodin P, Nussenzweig MC, Boisson-Dupuis S, Rodríguez-Gallego C, Vogt G, Mogensen TH, Oler AJ, Gu J, Burbelo PD, Cohen JI, Biondi A, Bettini LR, D'Angio M, Bonfanti P, Rossignol P, Mayaux J, Rieux-Laucat F, Husebye ES, Fusco F, Ursini MV, Imberti L, Sottini A, Paghera S, Quiros-Roldan E, Rossi C, Castagnoli R, Montagna D, Licari A, Marseglia GL, Duval X, Ghosn J, , , , , , , , , , , Tsang JS, Goldbach-Mansky R, Kisand K, Lionakis MS, Puel A, Zhang SY, Holland SM, Gorochov G, Jouanguy E, Rice CM, Cobat A, Notarangelo LD, Abel L, Su HC, Casanova JL, Autoantibodies against type I IFNs in patients with life-threatening COVID-19., Science 2020 Oct; 370(6515): .

Freel KC, Fouteau S, Roche D, Farasin J, Huber A, Koechler S, Peres M, Chiboub O, Varet H, Proux C, Deschamps J, Briandet R, Torchet R, Cruveiller S, Lièvremont D, Coppée JY, Barbe V, Arsène-Ploetze F, , Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2., Microb Genom 2020 Oct; (): .

Zavala-Alvarado C, Sismeiro O, Legendre R, Varet H, Bussotti G, Bayram J, G Huete S, Rey G, Coppée JY, Picardeau M, Benaroudj N, The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress., PLoS Pathog 2020 Oct; 16(10): e1008904.

Thannesberger J, Rascovan N, Eisenmann A, Klymiuk I, Zittra C, Fuehrer HP, Scantlebury-Manning T, Gittens-St Hilaire M, Austin S, Landis RC, Steininger C, , Highly Sensitive Virome Characterization of Aedes aegypti and Culex pipiens Complex from Central Europe and the Caribbean Reveals Potential for Interspecies Viral Transmission., Pathogens 2020 Aug; 9(9): .

Johansen MD, Irving A, Montagutelli X, Tate MD, Rudloff I, Nold MF, Hansbro NG, Kim RY, Donovan C, Liu G, Faiz A, Short KR, Lyons JG, McCaughan GW, Gorrell MD, Cole A, Moreno C, Couteur D, Hesselson D, Triccas J, Neely GG, Gamble JR, Simpson SJ, Saunders BM, Oliver BG, Britton WJ, Wark PA, Nold-Petry CA, Hansbro PM, , Animal and translational models of SARS-CoV-2 infection and COVID-19., Mucosal Immunol 2020 Aug; (): .

Volant S, Lechat P, Woringer P, Motreff L, Campagne P, Malabat C, Kennedy S, Ghozlane A, , SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis., BMC Bioinformatics 2020 Aug; 21(1): 345.

Aguilar-Rojas A, Castellanos-Castro S, Matondo M, Gianetto QG, Varet H, Sismeiro O, Legendre R, Fernandes J, Hardy D, Coppée JY, Olivo-Marin JC, Guillen N, , Insights into amebiasis using a human 3D-intestinal model., Cell Microbiol 2020 Aug; 22(8): e13203.

Petter Brodin, Lluis Quintana-Murci, Editorial overview: Evolutionary and systems immunology – methods to understand human immune system variation, Current Opinion in Immunology, 2020, 65, ⟨10.1016/j.coi.2020.11.001⟩.

Jorge A. Moura de Sousa, Amandine Buffet, Matthieu Haudiquet, Eduardo P.C. Rocha & Olaya Rendueles, Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation, ISME J (2020). https://doi.org/10.1038/s41396-020-0726-z.

Rotival M, Siddle KJ, Silvert M, Pothlichet J, Quach H, Quintana-Murci L, , Population variation in miRNAs and isomiRs and their impact on human immunity to infection., Genome Biol. 2020 Jul; 21(1): 187.

Huus KE, Rodriguez-Pozo A, Kapel N, Nestoret A, Habib A, Dede M, Manges A, Collard JM, Sansonetti PJ, Vonaesch P, Finlay BB, Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study., Microbiome 2020 Jul; 8(1): 113.

Trung V. Phan, Ryan Morris, Matthew E. Black, Tuan K. Do, Ke-Chih Lin, Krisztina Nagy, James C. Sturm, Julia Bos, and Robert H. Austin, Bacterial Route Finding and Collective Escape in Mazes and Fractals, Phys. Rev. X 10, 031017.

Redondo-Salvo S, Fernández-López R, Ruiz R, Vielva L, de Toro M, Rocha EPC, Garcillán-Barcia MP, de la Cruz F, , Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids., Nat Commun 2020 07; 11(1): 3602.

Jain S, Cachoux VML, Narayana GHNS, de Beco S, D'Alessandro J, Cellerin V, Chen T, Heuzé ML, Marcq P, Mège RM, Kabla AJ, Lim CT, Ladoux B, The role of single cell mechanical behavior and polarity in driving collective cell migration., Nat Phys 2020 Jul; 16(7): 802-809.

Aleksandra Nivina, Maj Svea Grieb, Céline Loot, David Bikard, Jean Cury, Laila Shehata, Juliana Bernardes, Didier Mazel, Structure-specific DNA recombination sites: Design, validation, and machine learning–based refinement, Science Advances , 2020, 6 (30), pp.eaay2922. ⟨10.1126/sciadv.aay2922⟩.

Léger P, Nachman E, Richter K, Tamietti C, Koch J, Burk R, Kummer S, Xin Q, Stanifer M, Bouloy M, Boulant S, Kräusslich HG, Montagutelli X, Flamand M, Nussbaum-Krammer C, Lozach PY, , NSs amyloid formation is associated with the virulence of Rift Valley fever virus in mice., Nat Commun 2020 07; 11(1): 3281.

Patin E, , Plague as a cause for familial Mediterranean fever., Nat. Immunol. 2020 Jun; (): .

Bianco E, Laval G, Font-Porterias N, García-Fernandez C, Dobon B, Sabido-Vera R, Stefanovska ES, Kučinskas V, Makukh H, Pamjav H, Quintana-Murci L, Netea MG, Bertranpetit J, Calafell F, Comas D, , Recent common origin, reduced population size, and marked admixture have shaped European Roma genomes., Mol. Biol. Evol. 2020 Jun; (): .

Vázquez-Rosas-Landa M, Ponce-Soto GY, Aguirre-Liguori JA, Thakur S, Scheinvar E, Barrera-Redondo J, Ibarra-Laclette E, Guttman DS, Eguiarte LE, Souza V, Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation., BMC Genomics 2020 Jun; 21(1): 418.

Pereira M, Ko JH, Logan J, Protheroe H, Kim KB, Tan ALM, Croucher PI, Park KS, Rotival M, Petretto E, Bassett JD, Williams GR, Behmoaras J, , A trans-eQTL network regulates osteoclast multinucleation and bone mass., Elife 2020 06; 9(): .

Baudry L, Guiglielmoni N, Marie-Nelly H, Cormier A, Marbouty M, Avia K, Mie YL, Godfroy O, Sterck L, Cock JM, Zimmer C, Coelho SM, Koszul R, , instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder., Genome Biol 2020 06; 21(1): 148.

Rausell A, Luo Y, Lopez M, Seeleuthner Y, Rapaport F, Favier A, Stenson PD, Cooper DN, Patin E, Casanova JL, Quintana-Murci L, Abel L, , Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes., Proc. Natl. Acad. Sci. U.S.A. 2020 Jun; 117(24): 13626-13636.

Casanova JL, Su HC, , , A Global Effort to Define the Human Genetics of Protective Immunity to SARS-CoV-2 Infection., Cell 2020 06; 181(6): 1194-1199.

Madin JS, Nielsen DA, Brbic M, Corkrey R, Danko D, Edwards K, Engqvist MKM, Fierer N, Geoghegan JL, Gillings M, Kyrpides NC, Litchman E, Mason CE, Moore L, Nielsen SL, Paulsen IT, Price ND, Reddy TBK, Richards MA, Rocha EPC, Schmidt TM, Shaaban H, Shukla M, Supek F, Tetu SG, Vieira-Silva S, Wattam AR, Westfall DA, Westoby M, , A synthesis of bacterial and archaeal phenotypic trait data., Sci Data 2020 06; 7(1): 170.

Busetto V, Barbosa I, Basquin J, Marquenet É, Hocq R, Hennion M, Paternina JA, Namane A, Conti E, Bensaude O, Le Hir H, , Structural and functional insights into CWC27/CWC22 heterodimer linking the exon junction complex to spliceosomes., Nucleic Acids Res. 2020 06; 48(10): 5670-5683.

Baudry L, Millot GA, Thierry A, Koszul R, Scolari VF, , Serpentine: a flexible 2D binning method for differential Hi-C analysis., Bioinformatics 2020 Jun; 36(12): 3645-3651.

Touchon M, Perrin A, de Sousa JAM, Vangchhia B, Burn S, O'Brien CL, Denamur E, Gordon D, Rocha EP, , Phylogenetic background and habitat drive the genetic diversification of Escherichia coli., PLoS Genet. 2020 Jun; 16(6): e1008866.

Barreiro LB, Quintana-Murci L, , Evolutionary and population (epi)genetics of immunity to infection., Hum. Genet. 2020 Jun; 139(6-7): 723-732.

Tomasi RF, Sart S, Champetier T, Baroud CN, , Individual Control and Quantification of 3D Spheroids in a High-Density Microfluidic Droplet Array., Cell Rep 2020 05; 31(8): 107670.

Batista L, Jouvion G, Simon-Chazottes D, Houzelstein D, Burlen-Defranoux O, Boissière M, Tokuda S, do Valle TZ, Cumano A, Flamand M, Montagutelli X, Panthier JJ, , Genetic dissection of Rift Valley fever pathogenesis: Rvfs2 locus on mouse chromosome 11 enables survival to early-onset hepatitis., Sci Rep 2020 May; 10(1): 8734.

Pourpre R, Naudon L, Meziane H, Lakisic G, Jouneau L, Varet H, Legendre R, Wendling O, Selloum M, Proux C, Coppée JY, Herault Y, Bierne H, BAHD1 haploinsufficiency results in anxiety-like phenotypes in male mice, PLoS ONE 2020;15(5):e0232789.

Sheppard D, Berry JL, Denise R, Rocha EPC, Matthews S, Pelicic V, , The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold., J. Biol. Chem. 2020 May; 295(19): 6594-6604.

Partula V, Deschasaux M, Druesne-Pecollo N, Latino-Martel P, Desmetz E, Chazelas E, Kesse-Guyot E, Julia C, Fezeu LK, Galan P, Hercberg S, Mondot S, Lantz O, Quintana-Murci L, Albert ML, Duffy D, , Srour B, Touvier M, , Associations between consumption of dietary fibers and the risk of cardiovascular diseases, cancers, type 2 diabetes, and mortality in the prospective NutriNet-Santé cohort., Am. J. Clin. Nutr. 2020 May; (): .

Peyrusson F, Varet H, Nguyen TK, Legendre R, Sismeiro O, Coppée JY, Wolz C, Tenson T, Van Bambeke F, Intracellular Staphylococcus aureus persisters upon antibiotic exposure, Nat Commun 2020 May;11(1):2200.

Denise R, Abby SS, Rocha EPC, , The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries., Trends Microbiol. 2020 May; 28(5): 372-386.

Soler-Bistué A, Aguilar-Pierlé S, Garcia-Garcerá M, Val ME, Sismeiro O, Varet H, Sieira R, Krin E, Skovgaard O, Comerci DJ, Rocha EPC, Mazel D, Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae., BMC Biol 2020 Apr; 18(1): 43.

Makarenko R, Denis C, Francesconi S, Gangloff S, Arcangioli B, , Nitrogen starvation reveals the mitotic potential of mutants in the S/MAPK pathways., Nat Commun 2020 04; 11(1): 1973.

Rey C, Chang YY, Latour-Lambert P, Varet H, Proux C, Legendre R, Coppée JY, Enninga J, Transcytosis subversion by M cell-to-enterocyte spread promotes Shigella flexneri and Listeria monocytogenes intracellular bacterial dissemination, PLoS Pathog. 2020 Apr;16(4):e1008446.

Tracey LJ, Noll KE, Montagutelli X, , 33rd international mammalian genome conference: meeting highlights., Mamm. Genome 2020 04; 31(3-4): 69-76.

O'Neill MB, Laval G, Teixeira JC, Palmenberg AC, Pepperell CS, , Genetic susceptibility to severe childhood asthma and rhinovirus-C maintained by balancing selection in humans for 150 000 years., Hum. Mol. Genet. 2020 Mar; 29(5): 736-744.

Böhm K, Giacomelli G, Schmidt A, Imhof A, Koszul R, Marbouty M, Bramkamp M, , Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum., Nat Commun 2020 Mar; 11(1): 1485.

Morgan MD, Patin E, Jagla B, Hasan M, Quintana-Murci L, Marioni JC, Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels, PLoS Genet. 2020 Mar;16(3):e1008686.

Sart S, Tomasi RF, Barizien A, Amselem G, Cumano A, Baroud CN, , Mapping the structure and biological functions within mesenchymal bodies using microfluidics., Sci Adv 2020 03; 6(10): eaaw7853.

Liu Y, Cheng J, Siejka-Zielińska P, Weldon C, Roberts H, Lopopolo M, Magri A, D'Arienzo V, Harris JM, McKeating JA, Song CX, Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS., Genome Biol 2020 Mar; 21(1): 54.

Jihène Klibi, Shamin Li, Ludivine Amable, Claudine Joseph, Stéphane Brunet, Marc Delord, Véronique Parietti, Jean Jaubert, Julien C. Marie, Saoussen Karray, Gérard Eberl, Bruno Lucas, Antoine Toubert, Kamel Benlagha, Characterization of the developmental landscape of murine RORγt+ iNKT cells, International Immunology, 2019, 32 (2), pp.105-116. ⟨10.1093/intimm/dxz064⟩.

Planchenault C, Pons MC, Schiavon C, Siguier P, Rech J, Guynet C, Dauverd-Girault J, Cury J, Rocha EPC, Junier I, Cornet F, Espéli O, , Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells., J. Mol. Biol. 2020 02; 432(3): 745-761.

Garcia-Garcera M, Rocha EPC, , Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria., Nat Commun 2020 02; 11(1): 758.

Bottai D, Frigui W, Sayes F, Di Luca M, Spadoni D, Pawlik A, Zoppo M, Orgeur M, Khanna V, Hardy D, Mangenot S, Barbe V, Medigue C, Ma L, Bouchier C, Tavanti A, Larrouy-Maumus G, Brosch R, TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages, Nat Commun 2020 Feb;11(1):684.

Brewer TE, Albertsen M, Edwards A, Kirkegaard RH, Rocha EPC, Fierer N, , Unlinked rRNA genes are widespread among bacteria and archaea., ISME J 2020 02; 14(2): 597-608.

Bernheim A, Sorek R, , The pan-immune system of bacteria: antiviral defence as a community resource., Nat Rev Microbiol 2020 Feb; 18(2): 113-119.

Dauban L, Montagne R, Thierry A, Lazar-Stefanita L, Bastié N, Gadal O, Cournac A, Koszul R, Beckouët F, Regulation of Cohesin-Mediated Chromosome Folding by Eco1 and Other Partners, Mol. Cell 2020 Jan;.

Aude Bernheim, David Bikard, Marie Touchon, Eduardo Rocha, Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements, Nucleic Acids Research, 2020, 48, pp.748 - 760. ⟨10.1093/nar/gkz1091⟩.

Mugherli L, Lety-Stefanska A, Landreau N, Tomasi RF, Baroud CN, , Quantifying the sol-gel process and detecting toxic gas in an array of anchored microfluidic droplets., Lab Chip 2020 Jan; 20(2): 236-243.

Manet C, Simon-Lorière E, Jouvion G, Hardy D, Prot M, Conquet L, Flamand M, Panthier JJ, Sakuntabhai A, Montagutelli X, , Genetic Diversity of Collaborative Cross Mice Controls Viral Replication, Clinical Severity, and Brain Pathology Induced by Zika Virus Infection, Independently of Oas1b., J Virol 2020 01; 94(3): .

Rotival M, Quintana-Murci L, Functional consequences of archaic introgression and their impact on fitness, Genome Biol. 2020 01;21(1):3.

Li Z, Rotival M, Patin E, Michel F, Pellegrini S, , Two common disease-associated TYK2 variants impact exon splicing and TYK2 dosage., PLoS One 2020 ; 15(1): e0225289.

Lecoeur H, Rosazza T, Kokou K, Varet H, Coppée JY, Lari A, Commère PH, Weil R, Meng G, Milon G, Späth GF, Prina E, , Leishmania amazonensis Subverts the Transcription Factor Landscape in Dendritic Cells to Avoid Inflammasome Activation and Stall Maturation., Front Immunol 2020 ; 11(): 1098.

Cury J, Abby SS, Doppelt-Azeroual O, Néron B, Rocha EPC, , Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan., Methods Mol. Biol. 2020 ; 2075(): 265-283.

Vit C, Loot C, Escudero JA, Nivina A, Mazel D, Integron Identification in Bacterial Genomes and Cassette Recombination Assays., Methods Mol Biol 2020 ; 2075(): 189-208.

Libante V, Nombre Y, Coluzzi C, Staub J, Guédon G, Gottschalk M, Teatero S, Fittipaldi N, Leblond-Bourget N, Payot S, , Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes., Pathogens 2019 Dec; 9(1): .

Nollmann M, Koszul R, Perspectives on Chromosome Organization, J. Mol. Biol. 2019 Dec;.

Jing Zhang, Megan Teh, Jamie Kim, Megan Eva, Romain Cayrol, Rachel Meade, Anastasia Nijnik, Xavier Montagutelli, Danielle Malo, Jean Jaubert, A Loss-of-Function Mutation in the Integrin Alpha L ( Itgal ) Gene Contributes to Susceptibility to Salmonella enterica Serovar Typhimurium Infection in Collaborative Cross Strain CC042, Infection and Immunity, 2019, 88 (1), pp.e00656-19. ⟨10.1128/IAI.00656-19⟩.

Taccoen N, Dollet B, Baroud CN, , Order to Disorder Transition in a Coarsening Two-Dimensional Foam., Phys. Rev. Lett. 2019 Dec; 123(23): 238006.

Lafaille FG, Harschnitz O, Lee YS, Zhang P, Hasek ML, Kerner G, Itan Y, Ewaleifoh O, Rapaport F, Carlile TM, Carter-Timofte ME, Paquet D, Dobbs K, Zimmer B, Gao D, Rojas-Duran MF, Kwart D, Rattina V, Ciancanelli MJ, McAlpine JL, Lorenzo L, Boucherit S, Rozenberg F, Halwani R, Henry B, Amenzoui N, Alsum Z, Marques L, Church JA, Al-Muhsen S, Tardieu M, Bousfiha AA, Paludan SR, Mogensen TH, Quintana-Murci L, Tessier-Lavigne M, Smith GA, Notarangelo LD, Studer L, Gilbert W, Abel L, Casanova JL, Zhang SY, Human SNORA31 variations impair cortical neuron-intrinsic immunity to HSV-1 and underlie herpes simplex encephalitis, Nat. Med. 2019 12;25(12):1873-1884.

Levraud JP, Jouneau L, Briolat V, Laghi V, Boudinot P, , IFN-Stimulated Genes in Zebrafish and Humans Define an Ancient Arsenal of Antiviral Immunity., J. Immunol. 2019 12; 203(12): 3361-3373.

Dubois V, Pawlik A, Bories A, Le Moigne V, Sismeiro O, Legendre R, Varet H, Rodríguez-Ordóñez MDP, Gaillard JL, Coppée JY, Brosch R, Herrmann JL, Girard-Misguich F, Mycobacterium abscessus virulence traits unraveled by transcriptomic profiling in amoeba and macrophages, PLoS Pathog. 2019 Nov;15(11):e1008069.

Clark DW, Okada Y, Moore KHS, Mason D, Pirastu N, Gandin I, Mattsson H, Barnes CLK, Lin K, Zhao JH, Deelen P, Rohde R, Schurmann C, Guo X, Giulianini F, Zhang W, Medina-Gomez C, Karlsson R, Bao Y, Bartz TM, Baumbach C, Biino G, Bixley MJ, Brumat M, Chai JF, Corre T, Cousminer DL, Dekker AM, Eccles DA, van Eijk KR, Fuchsberger C, Gao H, Germain M, Gordon SD, de Haan HG, Harris SE, Hofer E, Huerta-Chagoya A, Igartua C, Jansen IE, Jia Y, Kacprowski T, Karlsson T, Kleber ME, Li SA, Li-Gao R, Mahajan A, Matsuda K, Meidtner K, Meng W, Montasser ME, van der Most PJ, Munz M, Nutile T, Palviainen T, Prasad G, Prasad RB, Priyanka TDS, Rizzi F, Salvi E, Sapkota BR, Shriner D, Skotte L, Smart MC, Smith AV, van der Spek A, Spracklen CN, Strawbridge RJ, Tajuddin SM, Trompet S, Turman C, Verweij N, Viberti C, Wang L, Warren HR, Wootton RE, Yanek LR, Yao J, Yousri NA, Zhao W, Adeyemo AA, Afaq S, Aguilar-Salinas CA, Akiyama M, Albert ML, Allison MA, Alver M, Aung T, Azizi F, Bentley AR, Boeing H, Boerwinkle E, Borja JB, de Borst GJ, Bottinger EP, Broer L, Campbell H, Chanock S, Chee ML, Chen G, Chen YI, Chen Z, Chiu YF, Cocca M, Collins FS, Concas MP, Corley J, Cugliari G, van Dam RM, Damulina A, Daneshpour MS, Day FR, Delgado GE, Dhana K, Doney ASF, Dörr M, Doumatey AP, Dzimiri N, Ebenesersdóttir SS, Elliott J, Elliott P, Ewert R, Felix JF, Fischer K, Freedman BI, Girotto G, Goel A, Gögele M, Goodarzi MO, Graff M, Granot-Hershkovitz E, Grodstein F, Guarrera S, Gudbjartsson DF, Guity K, Gunnarsson B, Guo Y, Hagenaars SP, Haiman CA, Halevy A, Harris TB, Hedayati M, van Heel DA, Hirata M, Höfer I, Hsiung CA, Huang J, Hung YJ, Ikram MA, Jagadeesan A, Jousilahti P, Kamatani Y, Kanai M, Kerrison ND, Kessler T, Khaw KT, Khor CC, de Kleijn DPV, Koh WP, Kolcic I, Kraft P, Krämer BK, Kutalik Z, Kuusisto J, Langenberg C, Launer LJ, Lawlor DA, Lee IT, Lee WJ, Lerch MM, Li L, Liu J, Loh M, London SJ, Loomis S, Lu Y, Luan J, Mägi R, Manichaikul AW, Manunta P, Másson G, Matoba N, Mei XW, Meisinger C, Meitinger T, Mezzavilla M, Milani L, Millwood IY, Momozawa Y, Moore A, Morange PE, Moreno-Macías H, Mori TA, Morrison AC, Muka T, Murakami Y, Murray AD, de Mutsert R, Mychaleckyj JC, Nalls MA, Nauck M, Neville MJ, Nolte IM, Ong KK, Orozco L, Padmanabhan S, Pálsson G, Pankow JS, Pattaro C, Pattie A, Polasek O, Poulter N, Pramstaller PP, Quintana-Murci L, Räikkönen K, Ralhan S, Rao DC, van Rheenen W, Rich SS, Ridker PM, Rietveld CA, Robino A, van Rooij FJA, Ruggiero D, Saba Y, Sabanayagam C, Sabater-Lleal M, Sala CF, Salomaa V, Sandow K, Schmidt H, Scott LJ, Scott WR, Sedaghati-Khayat B, Sennblad B, van Setten J, Sever PJ, Sheu WH, Shi Y, Shrestha S, Shukla SR, Sigurdsson JK, Sikka TT, Singh JR, Smith BH, Stančáková A, Stanton A, Starr JM, Stefansdottir L, Straker L, Sulem P, Sveinbjornsson G, Swertz MA, Taylor AM, Taylor KD, Terzikhan N, Tham YC, Thorleifsson G, Thorsteinsdottir U, Tillander A, Tracy RP, Tusié-Luna T, Tzoulaki I, Vaccargiu S, Vangipurapu J, Veldink JH, Vitart V, Völker U, Vuoksimaa E, Wakil SM, Waldenberger M, Wander GS, Wang YX, Wareham NJ, Wild S, Yajnik CS, Yuan JM, Zeng L, Zhang L, Zhou J, Amin N, Asselbergs FW, Bakker SJL, Becker DM, Lehne B, Bennett DA, van den Berg LH, Berndt SI, Bharadwaj D, Bielak LF, Bochud M, Boehnke M, Bouchard C, Bradfield JP, Brody JA, Campbell A, Carmi S, Caulfield MJ, Cesarini D, Chambers JC, Chandak GR, Cheng CY, Ciullo M, Cornelis M, Cusi D, Smith GD, Deary IJ, Dorajoo R, van Duijn CM, Ellinghaus D, Erdmann J, Eriksson JG, Evangelou E, Evans MK, Faul JD, Feenstra B, Feitosa M, Foisy S, Franke A, Friedlander Y, Gasparini P, Gieger C, Gonzalez C, Goyette P, Grant SFA, Griffiths LR, Groop L, Gudnason V, Gyllensten U, Hakonarson H, Hamsten A, van der Harst P, Heng CK, Hicks AA, Hochner H, Huikuri H, Hunt SC, Jaddoe VWV, De Jager PL, Johannesson M, Johansson Å, Jonas JB, Jukema JW, Junttila J, Kaprio J, Kardia SLR, Karpe F, Kumari M, Laakso M, van der Laan SW, Lahti J, Laudes M, Lea RA, Lieb W, Lumley T, Martin NG, März W, Matullo G, McCarthy MI, Medland SE, Merriman TR, Metspalu A, Meyer BF, Mohlke KL, Montgomery GW, Mook-Kanamori D, Munroe PB, North KE, Nyholt DR, O'connell JR, Ober C, Oldehinkel AJ, Palmas W, Palmer C, Pasterkamp GG, Patin E, Pennell CE, Perusse L, Peyser PA, Pirastu M, Polderman TJC, Porteous DJ, Posthuma D, Psaty BM, Rioux JD, Rivadeneira F, Rotimi C, Rotter JI, Rudan I, Den Ruijter HM, Sanghera DK, Sattar N, Schmidt R, Schulze MB, Schunkert H, Scott RA, Shuldiner AR, Sim X, Small N, Smith JA, Sotoodehnia N, Tai ES, Teumer A, Timpson NJ, Toniolo D, Tregouet DA, Tuomi T, Vollenweider P, Wang CA, Weir DR, Whitfield JB, Wijmenga C, Wong TY, Wright J, Yang J, Yu L, Zemel BS, Zonderman AB, Perola M, Magnusson PKE, Uitterlinden AG, Kooner JS, Chasman DI, Loos RJF, Franceschini N, Franke L, Haley CS, Hayward C, Walters RG, Perry JRB, Esko T, Helgason A, Stefansson K, Joshi PK, Kubo M, Wilson JF, Associations of autozygosity with a broad range of human phenotypes, Nat Commun 2019 10;10(1):4957.

Ramírez-Nava EJ, Ortega-Cuellar D, González-Valdez A, Castillo-Rodríguez RA, Ponce-Soto GY, Hernández-Ochoa B, Cárdenas-Rodríguez N, Martínez-Rosas V, Morales-Luna L, Serrano-Posada H, Sierra-Palacios E, Arreguin-Espinosa R, Cuevas-Cruz M, Rocha-Ramírez LM, Pérez de la Cruz V, Marcial-Quino J, Gómez-Manzo S, Molecular Cloning and Exploration of the Biochemical and Functional Analysis of Recombinant Glucose-6-Phosphate Dehydrogenase from Gluconoacetobacter diazotrophicus PAL5., Int J Mol Sci 2019 Oct; 20(21): .

Carballido Lopez A, Cunrath O, Forster A, Pérard J, Graulier G, Legendre R, Varet H, Sismeiro O, Perraud Q, Pesset B, Saint Auguste P, Bumann D, Mislin GLA, Coppee JY, Michaud-Soret I, Fechter P, Schalk IJ, Non-specific interference of cobalt with siderophore-dependent iron uptake pathways, Metallomics 2019 Nov;11(11):1937-1951.

Garcia-Luis J, Lazar-Stefanita L, Gutierrez-Escribano P, Thierry A, Cournac A, García A, González S, Sánchez M, Jarmuz A, Montoya A, Dore M, Kramer H, Karimi MM, Antequera F, Koszul R, Aragon L, FACT mediates cohesin function on chromatin, Nat. Struct. Mol. Biol. 2019 Oct;26(10):970-979.

Scepanovic P, Hodel F, Mondot S, Partula V, Byrd A, Hammer C, Alanio C, Bergstedt J, Patin E, Touvier M, Lantz O, Albert ML, Duffy D, Quintana-Murci L, Fellay J, A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals., Microbiome 2019 Sep; 7(1): 130.

Rotival M, , Characterising the genetic basis of immune response variation to identify causal mechanisms underlying disease susceptibility., HLA 2019 09; 94(3): 275-284.

Martínez-Carranza E, Ponce-Soto GY, Servín-González L, Alcaraz LD, Soberón-Chávez G, Evolution of bacteria seen through their essential genes: the case of Pseudomonas aeruginosa and Azotobacter vinelandii., Microbiology (Reading) 2019 Sep; 165(9): 976-984.

Baudry L, Foutel-Rodier T, Thierry A, Koszul R, Marbouty M, MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries, Front Genet 2019;10:753.

Fabienne Levi-Acobas, Adam Katolik, Pascal Röthlisberger, Thomas Cokelaer, Ivo Sarac, Masad J. Damha, Christian J. Leumann and Marcel Hollenstein*, Compatibility of 5-ethynyl-2’F-ANA UTP with in vitro selection for the generation of base-modified, nuclease resistant aptamers, Org. Biomol. Chem. 2019, 17, 8083 - 8087.

Tarantola A, Horwood PF, Goarant C, Bertrand S, Merilles OEA, Pedron T, Klement-Frutos E, Sansonetti P, Quintana-Murci L, Richard V, Counting Oceanians of Non-European, Non-Asian Descent (ONENA) in the South Pacific to Make Them Count in Global Health, Trop Med Infect Dis 2019 Aug;4(3).

Lopez M, Choin J, Sikora M, Siddle K, Harmant C, Costa HA, Silvert M, Mouguiama-Daouda P, Hombert JM, Froment A, Le Bomin S, Perry GH, Barreiro LB, Bustamante CD, Verdu P, Patin E, Quintana-Murci L, Genomic Evidence for Local Adaptation of Hunter-Gatherers to the African Rainforest, Curr. Biol. 2019 Sep;29(17):2926-2935.e4.

García-Ulloa M, Ponce-Soto GY, González-Valdez A, González-Pedrajo B, Díaz-Guerrero M, Souza V, Soberón-Chávez G, Two Pseudomonas aeruginosa clonal groups belonging to the PA14 clade are indigenous to the Churince system in Cuatro Ciénegas Coahuila, México., Environ Microbiol 2019 Aug; 21(8): 2964-2976.

Harrison GF, Sanz J, Boulais J, Mina MJ, Grenier JC, Leng Y, Dumaine A, Yotova V, Bergey CM, Nsobya SL, Elledge SJ, Schurr E, Quintana-Murci L, Perry GH, Barreiro LB, Natural selection contributed to immunological differences between hunter-gatherers and agriculturalists, Nat Ecol Evol 2019 Aug;3(8):1253-1264.

Denise R, Abby SS, Rocha EPC, Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility, PLoS Biol. 2019 Jul;17(7):e3000390.

Oya E, Durand-Dubief M, Cohen A, Maksimov V, Schurra C, Nakayama JI, Weisman R, Arcangioli B, Ekwall K, Leo1 is essential for the dynamic regulation of heterochromatin and gene expression during cellular quiescence, Epigenetics Chromatin 2019 07;12(1):45.

Buchrieser J, Degrelle SA, Couderc T, Nevers Q, Disson O, Manet C, Donahue DA, Porrot F, Hillion KH, Perthame E, Arroyo MV, Souquere S, Ruigrok K, Dupressoir A, Heidmann T, Montagutelli X, Fournier T, Lecuit M, Schwartz O, , IFITM proteins inhibit placental syncytiotrophoblast formation and promote fetal demise., Science 2019 Jul; 365(6449): 176-180.

Negro V, Krin E, Aguilar Pierlé S, Chaze T, Giai Gianetto Q, Kennedy SP, Matondo M, Mazel D, Baharoglu Z, , RadD Contributes to R-Loop Avoidance in Sub-MIC Tobramycin., mBio 2019 07; 10(4): .

Hommel B, Sturny-Leclère A, Volant S, Veluppillai N, Duchateau M, Yu CH, Hourdel V, Varet H, Matondo M, Perfect JR, Casadevall A, Dromer F, Alanio A, Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype., PLoS Pathog 2019 Jul; 15(7): e1007945.

Brodin P, Duffy D, Quintana-Murci L, A Call for Blood-In Human Immunology, Immunity 2019 Jun;50(6):1335-1336.

Zhang E, Khanna V, Dacheux E, Namane A, Doyen A, Gomard M, Turcotte B, Jacquier A, Fromont-Racine M, A specialised SKI complex assists the cytoplasmic RNA exosome in the absence of direct association with ribosomes, EMBO J. 2019 07;38(14):e100640.

Galli E, Ferat JL, Desfontaines JM, Val ME, Skovgaard O, Barre FX, Possoz C, Replication termination without a replication fork trap., Sci Rep 2019 Jun; 9(1): 8315.

Schwacke R, Ponce-Soto GY, Krause K, Bolger AM, Arsova B, Hallab A, Gruden K, Stitt M, Bolger ME, Usadel B, MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis., Mol Plant 2019 Jun; 12(6): 879-892.

Silvert M, Quintana-Murci L, Rotival M, Impact and Evolutionary Determinants of Neanderthal Introgression on Transcriptional and Post-Transcriptional Regulation, Am. J. Hum. Genet. 2019 Jun;104(6):1241-1250.

Guérin TM, Béneut C, Barinova N, López V, Lazar-Stefanita L, Deshayes A, Thierry A, Koszul R, Dubrana K, Marcand S, Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis, Mol. Cell 2019 07;75(1):131-144.e3.

Piazza A, Heyer WD, Moving forward one step back at a time: reversibility during homologous recombination, Curr. Genet. 2019 May;.

Pribis JP, García-Villada L, Zhai Y, Lewin-Epstein O, Wang AZ, Liu J, Xia J, Mei Q, Fitzgerald DM, Bos J, Austin RH, Herman C, Bates D, Hadany L, Hastings PJ, Rosenberg SM, , Gamblers: An Antibiotic-Induced Evolvable Cell Subpopulation Differentiated by Reactive-Oxygen-Induced General Stress Response., Mol Cell 2019 05; 74(4): 785-800.e7.

Van den Bossche A, Varet H, Sury A, Sismeiro O, Legendre R, Coppee JY, Mathys V, Ceyssens PJ, Transcriptional profiling of a laboratory and clinical Mycobacterium tuberculosis strain suggests respiratory poisoning upon exposure to delamanid, Tuberculosis (Edinb) 2019 Jul;117:18-23.

Aude Bernheim, David Bikard, Marie Touchon, Eduardo P C Rocha, A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria, Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, 374 (1772), pp.20180088. ⟨10.1098/rstb.2018.0088⟩.

Dubois T, Tremblay YDN, Hamiot A, Martin-Verstraete I, Deschamps J, Monot M, Briandet R, Dupuy B, , A microbiota-generated bile salt induces biofilm formation in Clostridium difficile., NPJ Biofilms Microbiomes 2019 05; 5(1): 14.

Kerner G, Ramirez-Alejo N, Seeleuthner Y, Yang R, Ogishi M, Cobat A, Patin E, Quintana-Murci L, Boisson-Dupuis S, Casanova JL, Abel L, Homozygosity for P1104A underlies tuberculosis in about 1% of patients in a cohort of European ancestry, Proc. Natl. Acad. Sci. U.S.A. 2019 May;.

Partula V, Mondot S, Torres MJ, Kesse-Guyot E, Deschasaux M, Assmann K, Latino-Martel P, Buscail C, Julia C, Galan P, Hercberg S, Rouilly V, Thomas S, Quintana-Murci L, Albert ML, Duffy D, Lantz O, Touvier M, , , Associations between usual diet and gut microbiota composition: results from the Milieu Intérieur cross-sectional study., Am J Clin Nutr 2019 May; 109(5): 1472-1483.

Dávila Felipe M, Domelevo Entfellner JB, Lemoine F, Truszkowski J, Gascuel O, , Distribution and asymptotic behavior of the phylogenetic transfer distance., J Math Biol 2019 07; 79(2): 485-508.

Barizien A, Suryateja Jammalamadaka MS, Amselem G, Baroud CN, , Growing from a few cells: combined effects of initial stochasticity and cell-to-cell variability., J R Soc Interface 2019 04; 16(153): 20180935.

Rotival M, Quach H, Quintana-Murci L, Defining the genetic and evolutionary architecture of alternative splicing in response to infection, Nat Commun 2019 04;10(1):1671.

Mary L, Zvénigorosky V, Kovalev A, Gonzalez A, Fausser JL, Jagorel F, Kilunovskaya M, Semenov V, Crubézy E, Ludes B, Keyser C, Genetic kinship and admixture in Iron Age Scytho-Siberians., Hum Genet 2019 Apr; 138(4): 411-423.

Nemat-Gorgani N, Guethlein LA, Henn BM, Norberg SJ, Chiaroni J, Sikora M, Quintana-Murci L, Mountain JL, Norman PJ, Parham P, Diversity of Killer Cell Ig-Like Receptor, HLA Class I, and Their Interactions in Seven Populations of Sub-Saharan Africans, J. Immunol. 2019 Mar;.

Tesina P, Heckel E, Cheng J, Fromont-Racine M, Buschauer R, Kater L, Beatrix B, Berninghausen O, Jacquier A, Becker T, Beckmann R, Structure of the 80S ribosome-Xrn1 nuclease complex, Nat. Struct. Mol. Biol. 2019 04;26(4):275-280.

Quintana-Murci L, Human Immunology through the Lens of Evolutionary Genetics, Cell 2019 Mar;177(1):184-199.

Laval G, Peyrégne S, Zidane N, Harmant C, Renaud F, Patin E, Prugnolle F, Quintana-Murci L, Recent Adaptive Acquisition by African Rainforest Hunter-Gatherers of the Late Pleistocene Sickle-Cell Mutation Suggests Past Differences in Malaria Exposure, Am. J. Hum. Genet. 2019 Mar;104(3):553-561.

Mukhortava A, Pöge M, Grieb MS, Nivina A, Loot C, Mazel D, Schlierf M, Structural heterogeneity of attC integron recombination sites revealed by optical tweezers., Nucleic Acids Res 2019 Feb; 47(4): 1861-1870.

Piazza A, Shah SS, Wright WD, Gore SK, Koszul R, Heyer WD, Dynamic Processing of Displacement Loops during Recombinational DNA Repair, Mol. Cell 2019 03;73(6):1255-1266.e4.

Bradley P, den Bakker HC, Rocha EPC, McVean G, Iqbal Z, Ultrafast search of all deposited bacterial and viral genomic data, Nat. Biotechnol. 2019 Feb;37(2):152-159.

Tan ALM, Langley SR, Tan CF, Chai JF, Khoo CM, Leow MK, Khoo EYH, Moreno-Moral A, Pravenec M, Rotival M, Sadananthan SA, Velan SS, Venkataraman K, Chong YS, Lee YS, Sim X, Stunkel W, Liu MH, Tai ES, Petretto E, , Ethnicity-Specific Skeletal Muscle Transcriptional Signatures and Their Relevance to Insulin Resistance in Singapore., J. Clin. Endocrinol. Metab. 2019 02; 104(2): 465-486.

Lopez-Igual R., Bernal-Bayard J., Rodriguez-Paton A., Ghigo J.-M., and Mazel D., Engineered toxin-intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations, Nat Biotechnol. 2019 Jul;37(7):755-760. doi: 10.1038/s41587-019-0105-3. Epub 2019 Apr 15..

Rascovan N, Sjögren KG, Kristiansen K, Nielsen R, Willerslev E, Desnues C, Rasmussen S, , Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline., Cell 2019 01; 176(1-2): 295-305.e10.

Sart, S., Tomasi,R.F.-X., Barizien, A., Amselem, G., Cumano, A. & Baroud, C.N., Mapping structure and biological functions within mesenchymal bodies using microfluidics, bioRxiv 514158; doi: https://doi.org/10.1101/514158.

Weill FX, Domman D, Njamkepo E, Almesbahi AA, Naji M, Nasher SS, Rakesh A, Assiri AM, Sharma NC, Kariuki S, Pourshafie MR, Rauzier J, Abubakar A, Carter JY, Wamala JF, Seguin C, Bouchier C, Malliavin T, Bakhshi B, Abulmaali HHN, Kumar D, Njoroge SM, Malik MR, Kiiru J, Luquero FJ, Azman AS, Ramamurthy T, Thomson NR, Quilici ML, , Genomic insights into the 2016-2017 cholera epidemic in Yemen., Nature 2019 01; 565(7738): 230-233.

Berthelot C, Clarke J, Desvignes T, William Detrich H, Flicek P, Peck LS, Peters M, Postlethwait JH, Clark MS, , Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine?, Genome Biol Evol 2019 01; 11(1): 220-231.

Maffucci P, Bigio B, Rapaport F, Cobat A, Borghesi A, Lopez M, Patin E, Bolze A, Shang L, Bendavid M, Scott EM, Stenson PD, Cunningham-Rundles C, Cooper DN, Gleeson JG, Fellay J, Quintana-Murci L, Casanova JL, Abel L, Boisson B, Itan Y, Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis, Proc. Natl. Acad. Sci. U.S.A. 2019 Jan;116(3):950-959.

Martínez-Barricarte R, Markle JG, Ma CS, Deenick EK, Ramírez-Alejo N, Mele F, Latorre D, Mahdaviani SA, Aytekin C, Mansouri D, Bryant VL, Jabot-Hanin F, Deswarte C, Nieto-Patlán A, Surace L, Kerner G, Itan Y, Jovic S, Avery DT, Wong N, Rao G, Patin E, Okada S, Bigio B, Boisson B, Rapaport F, Seeleuthner Y, Schmidt M, Ikinciogullari A, Dogu F, Tanir G, Tabarsi P, Bloursaz MR, Joseph JK, Heer A, Kong XF, Migaud M, Lazarov T, Geissmann F, Fleckenstein B, Arlehamn CL, Sette A, Puel A, Emile JF, van de Vosse E, Quintana-Murci L, Di Santo JP, Abel L, Boisson-Dupuis S, Bustamante J, Tangye SG, Sallusto F, Casanova JL, , Human IFN-γ immunity to mycobacteria is governed by both IL-12 and IL-23., Sci Immunol 2018 12; 3(30): .

Boisson-Dupuis S, Ramirez-Alejo N, Li Z, Patin E, Rao G, Kerner G, Lim CK, Krementsov DN, Hernandez N, Ma CS, Zhang Q, Markle J, Martinez-Barricarte R, Payne K, Fisch R, Deswarte C, Halpern J, Bouaziz M, Mulwa J, Sivanesan D, Lazarov T, Naves R, Garcia P, Itan Y, Boisson B, Checchi A, Jabot-Hanin F, Cobat A, Guennoun A, Jackson CC, Pekcan S, Caliskaner Z, Inostroza J, Costa-Carvalho BT, de Albuquerque JAT, Garcia-Ortiz H, Orozco L, Ozcelik T, Abid A, Rhorfi IA, Souhi H, Amrani HN, Zegmout A, Geissmann F, Michnick SW, Muller-Fleckenstein I, Fleckenstein B, Puel A, Ciancanelli MJ, Marr N, Abolhassani H, Balcells ME, Condino-Neto A, Strickler A, Abarca K, Teuscher C, Ochs HD, Reisli I, Sayar EH, El-Baghdadi J, Bustamante J, Hammarström L, Tangye SG, Pellegrini S, Quintana-Murci L, Abel L, Casanova JL, Tuberculosis and impaired IL-23-dependent IFN-γ immunity in humans homozygous for a common missense variant, Sci Immunol 2018 Dec;3(30).

Rendueles O, de Sousa JAM, Bernheim A, Touchon M, Rocha EPC, Genetic exchanges are more frequent in bacteria encoding capsules, PLoS Genet. 2018 12;14(12):e1007862.

Husquin LT, Rotival M, Fagny M, Quach H, Zidane N, McEwen LM, MacIsaac JL, Kobor MS, Aschard H, Patin E, Quintana-Murci L, , Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation., Genome Biol 2018 12; 19(1): 222.

Phan TV, Morris RJ, Lam HT, Hulamm P, Black ME, Bos J, Austin RH, , Emergence of Escherichia coli critically buckled motile helices under stress., Proc Natl Acad Sci U S A 2018 12; 115(51): 12979-12984.

Duval M, Dar D, Carvalho F, Rocha EPC, Sorek R, Cossart P, HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance, Proc. Natl. Acad. Sci. U.S.A. 2018 12;115(52):13359-13364.

Etienne Patin, Lluis Quintana-Murci, The demographic and adaptive history of central African hunter-gatherers and farmers, Current Opinion in Genetics and Development, 2018, 53, pp.90-97. ⟨10.1016/j.gde.2018.07.008⟩.

Brenna Henn, Lluis Quintana-Murci, Editorial overview: The history, geography and adaptation of human genes: A tribute to L. Luca Cavalli-Sforza, Current Opinion in Genetics and Development, 2018, 53, pp.iii-v. ⟨10.1016/j.gde.2018.11.004⟩.

Piazza A, Heyer WD, Homologous Recombination and the Formation of Complex Genomic Rearrangements, Trends Cell Biol. 2019 Feb;29(2):135-149.

Bergey CM, Lopez M, Harrison GF, Patin E, Cohen JA, Quintana-Murci L, Barreiro LB, Perry GH, Polygenic adaptation and convergent evolution on growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers, Proc. Natl. Acad. Sci. U.S.A. 2018 Nov;115(48):E11256-E11263.

de Lemos Martins F, Fournes F, Mazzuoli MV, Mazel D, Val ME, Vibrio cholerae chromosome 2 copy number is controlled by the methylation-independent binding of its monomeric initiator to the chromosome 1 crtS site., Nucleic Acids Res 2018 Nov; 46(19): 10145-10156.

de Lemos Martins F, Fournes F, Mazzuoli MV, Mazel D, Val ME, , Vibrio cholerae chromosome 2 copy number is controlled by the methylation-independent binding of its monomeric initiator to the chromosome 1 crtS site., Nucleic Acids Res 2018 11; 46(19): 10145-10156.

Fourati et al, A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection., Nat Commun. 2018 Oct 24;9(1):4418.

Sacerdot C, Louis A, Bon C, Berthelot C, Roest Crollius H, , Chromosome evolution at the origin of the ancestral vertebrate genome., Genome Biol 2018 10; 19(1): 166.

McEwen LM, Jones MJ, Lin DTS, Edgar RD, Husquin LT, MacIsaac JL, Ramadori KE, Morin AM, Rider CF, Carlsten C, Quintana-Murci L, Horvath S, Kobor MS, Systematic evaluation of DNA methylation age estimation with common preprocessing methods and the Infinium MethylationEPIC BeadChip array, Clin Epigenetics 2018 Oct;10(1):123.

Moreau P, Cournac A, Palumbo GA, Marbouty M, Mortaza S, Thierry A, Cairo S, Lavigne M, Koszul R, Neuveut C, , Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin., Nat Commun 2018 Oct; 9(1): 4268.

Freiherr von Boeselager R, Pfeifer E, Frunzke J, Cytometry meets next-generation sequencing – RNA-Seq of sorted subpopulations reveals regional replication and iron-triggered prophage induction in Corynebacterium glutamicum, Sci Rep 2018 Oct;8(1):14856.

Baudement MO, Cournac A, Court F, Seveno M, Parrinello H, Reynes C, Sabatier R, Bouschet T, Yi Z, Sallis S, Tancelin M, Rebouissou C, Cathala G, Lesne A, Mozziconacci J, Journot L, Forné T, High-salt-recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies, Genome Res. 2018 Oct;.

Legrand M, Bachellier-Bassi S, Lee KK, Chaudhari Y, Tournu H, Arbogast L, Boyer H, Chauvel M, Cabral V, Maufrais C, Nesseir A, Maslanka I, Permal E, Rossignol T, Walker LA, Zeidler U, Znaidi S, Schoeters F, Majgier C, Julien RA, Ma L, Tichit M, Bouchier C, Van Dijck P, Munro CA, d'Enfert C, Erratum: Generating genomic platforms to study Candida albicans pathogenesis, Nucleic Acids Res. 2018 09;46(16):8664.

Foutel-Rodier T, Thierry A, Koszul R, Marbouty M, Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut Microbiota, Meth. Enzymol. 2018;612:183-195.

Louka P, Vasudevan KK, Guha M, Joachimiak E, Wloga D, Tomasi RF, Baroud CN, Dupuis-Williams P, Galati DF, Pearson CG, Rice LM, Moresco JJ, Yates JR, Jiang YY, Lechtreck K, Dentler W, Gaertig J, , Proteins that control the geometry of microtubules at the ends of cilia., J Cell Biol 2018 12; 217(12): 4298-4313.

Dimitri Desvillechabrol, Christiane Bouchier, Sean Kennedy, Thomas Cokelaer, Sequana Coverage: Detection and Characterization of Genomic Variations using Running Median and Mixture Models, GigaScience, giy110, https://doi.org/10.1093/gigascience/giy110.

Clave E, Araujo IL, Alanio C, Patin E, Bergstedt J, Urrutia A, Lopez-Lastra S, Li Y, Charbit B, MacPherson CR, Hasan M, Melo-Lima BL, Douay C, Saut N, Germain M, Trégouët DA, Morange PE, Fontes M, Duffy D, Di Santo JP, Quintana-Murci L, Albert ML, Toubert A, , , Human thymopoiesis is influenced by a common genetic variant within the TCRA-TCRD locus., Sci Transl Med 2018 Sep; 10(457): .

Hugo Varet, Jean-Yves Coppée, checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes, Bioinformatics, 2018.

Jianqiang Bao, Carlos Perez, Jeesun Kim, Huan Zhang, Caitlin Murphy, Tewfik Hamidi, Jean Jaubert, Craig Platt, Janet Chou, Meichun Deng, Meng-Hua Zhou, Yuying Huang, Héctor Gaitán-Peñas, Jean-Louis Guénet, Kevin Lin, Yue Lu, Taiping Chen, Mark Bedford, Sharon Y.R. Dent, John Richburg, Raúl Estévez, Hui-Lin Pan, Raif Geha, Qinghua Shi, Fernando Benavides, Deficient LRRC8A-dependent volume-regulated anion channel activity is associated with male infertility in mice, JCI Insight, 2018, 3 (16), pp.e99767. ⟨10.1172/jci.insight.99767⟩.

Stoddard D, Zhao Y, Bayless BA, Gui L, Louka P, Dave D, Suryawanshi S, Tomasi RF, Dupuis-Williams P, Baroud CN, Gaertig J, Winey M, Nicastro D, , Tetrahymena RIB72A and RIB72B are microtubule inner proteins in the ciliary doublet microtubules., Mol Biol Cell 2018 10; 29(21): 2566-2577.

Legrand M, Bachellier-Bassi S, Lee KK, Chaudhari Y, Tournu H, Arbogast L, Boyer H, Chauvel M, Cabral V, Maufrais C, Nesseir A, Maslanka I, Permal E, Rossignol T, Walker LA, Zeidler U, Znaidi S, Schoeters F, Majgier C, Julien RA, Ma L, Tichit M, Bouchier C, Van Dijck P, Munro CA, d'Enfert C, , Generating genomic platforms to study Candida albicans pathogenesis., Nucleic Acids Res 2018 08; 46(14): 6935-6949.

Maataoui, Naouale; Mayet, Aurélie; Duron, Sandrine; Delacour, Hervé; Mentré, France; Laouenan, Cédric; Desvillechabrol, Dimitri; Cokelaer, Thomas; Meynard, Jean Baptiste; Ducher, Annie, High Acquisition Rate of ESBL-Producing Enterobacteriaceae among French Military Personnel on Mission Abroad, without Evidence of Inter-Individual Transmission., Maataoui et al, Clinical Microbiology and Infection, 2018.

Angebault C, Ghozlane A, Volant S, Botterel F, d'Enfert C, Bougnoux ME, Combined bacterial and fungal intestinal microbiota analyses: Impact of storage conditions and DNA extraction protocols, PLoS ONE 2018;13(8):e0201174.

Scolari VF, Mercy G, Koszul R, Lesne A, Mozziconacci J, Kinetic Signature of Cooperativity in the Irreversible Collapse of a Polymer, Phys. Rev. Lett. 2018 Aug;121(5):057801.

Tarantola A, Horwood P, Richard V, Quintana-Murci L, Host and viral genetic diversity can help explain mortality during the 1918-21 influenza pandemic in the Pacific region, Lancet Infect Dis 2018 Aug;18(8):833-834.

Manet C, Roth C, Tawfik A, Cantaert T, Sakuntabhai A, Montagutelli X, , Host genetic control of mosquito-borne Flavivirus infections., Mamm Genome 2018 08; 29(7-8): 384-407.

Kang E, Crouse A, Chevallier L, Pontier SM, Alzahrani A, Silué N, Campbell-Valois FX, Montagutelli X, Gruenheid S, Malo D, , Enterobacteria and host resistance to infection., Mamm. Genome 2018 08; 29(7-8): 558-576.

Scepanovic P, Alanio C, Hammer C, Hodel F, Bergstedt J, Patin E, Thorball CW, Chaturvedi N, Charbit B, Abel L, Quintana-Murci L, Duffy D, Albert ML, Fellay J, , , Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines., Genome Med 2018 Jul; 10(1): 59.

Muller H, Scolari VF, Agier N, Piazza A, Thierry A, Mercy G, Descorps-Declere S, Lazar-Stefanita L, Espeli O, Llorente B, Fischer G, Mozziconacci J, Koszul R, Characterizing meiotic chromosomes’ structure and pairing using a designer sequence optimized for Hi-C, Mol. Syst. Biol. 2018 07;14(7):e8293.

David Couvin, Aude Bernheim, Claire Toffano-Nioche, Marie Touchon, Juraj Michalik, Bertrand Néron, Eduardo P C Rocha, Gilles Vergnaud, Daniel Gautheret, Christine Pourcel, CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins, Nucleic Acids Research, 2018, 46 (W1), pp.W246-W251. ⟨10.1093/nar/gky425⟩.

Bernheim A, Sorek R, , Viruses cooperate to defeat bacteria., Nature 2018 Jul; 559(7715): 482-484.

Wielgoss S, Fiegna F, Rendueles O, Yu YN, Velicer GJ, Kin discrimination and outer membrane exchange in Myxococcus xanthus: A comparative analysis among natural isolates, Mol. Ecol. 2018 Jun;.

Cury J, Oliveira PH, de la Cruz F, Rocha EPC, Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements, Mol. Biol. Evol. 2018 Jun;.

Varet H, Shaulov Y, Sismeiro O, Trebicz-Geffen M, Legendre R, Coppée JY, Ankri S, Guillen N, Enteric bacteria boost defences against oxidative stress in Entamoeba histolytica, Sci Rep 2018 Jun;8(1):9042.

Clerissi C, Touchon M, Capela D, Tang M, Cruveiller S, Genthon C, Lopez-Roques C, Parker MA, Moulin L, Masson-Boivin C, Rocha EPC, Parallels between experimental and natural evolution of legume symbionts, Nat Commun 2018 06;9(1):2264.

Ropars J, Maufrais C, Diogo D, Marcet-Houben M, Perin A, Sertour N, Mosca K, Permal E, Laval G, Bouchier C, Ma L, Schwartz K, Voelz K, May RC, Poulain J, Battail C, Wincker P, Borman AM, Chowdhary A, Fan S, Kim SH, Le Pape P, Romeo O, Shin JH, Gabaldon T, Sherlock G, Bougnoux ME, d'Enfert C, Gene flow contributes to diversification of the major fungal pathogen Candida albicans, Nat Commun 2018 06;9(1):2253.

Patin E, Hasan M, Bergstedt J, Rouilly V, Libri V, Urrutia A, Alanio C, Scepanovic P, Hammer C, Jönsson F, Beitz B, Quach H, Lim YW, Hunkapiller J, Zepeda M, Green C, Piasecka B, Leloup C, Rogge L, Huetz F, Peguillet I, Lantz O, Fontes M, Di Santo JP, Thomas S, Fellay J, Duffy D, Quintana-Murci L, Albert ML, , , Publisher Correction: Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors., Nat Immunol 2018 06; 19(6): 645.

Rocha EPC, Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics, Mol. Biol. Evol. 2018 Jun;35(6):1338-1347.

Krin E, Pierlé SA, Sismeiro O, Jagla B, Dillies MA, Varet H, Irazoki O, Campoy S, Rouy Z, Cruveiller S, Médigue C, Coppée JY, Mazel D, Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation, BMC Genomics 2018 May;19(1):373.

Cui L, Vigouroux A, Rousset F, Varet H, Khanna V, Bikard D, A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9, Nat Commun. 2018 May 15;9(1):1912. doi: 10.1038/s41467-018-04209-5.

Frenoy A, Bonhoeffer S, Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria, PLoS Biol. 2018 May;16(5):e2005056.

Bernal-Bayard J, Gomez-Valero L, Wessel A, Khanna V, Bouchier C, Ghigo JM, Short genome report of cellulose-producing commensal Escherichia coli 1094., Stand Genomic Sci 2018 ; 13(): 13.

Piazza A1,2, Heyer WD1, Multi-Invasion-Induced Rearrangements as a Pathway for Physiological and Pathological Recombination, Bioessays. 2018 May;40(5):e1700249..

Jing Zhang, Danielle Malo, Richard P Mott, Jean-Jacques Panthier, Xavier Montagutelli, Jean Jaubert, Identification of new loci involved in the host susceptibility to Salmonella Typhimurium in collaborative cross mice, BMC Genomics, 2018, 19 (1), pp.303. ⟨10.1186/s12864-018-4667-0⟩.

Portnoi MF, Dumargne MC, Rojo S, Witchel SF, Duncan AJ, Eozenou C, Bignon-Topalovic J, Yatsenko SA, Rajkovic A, Reyes-Mugica M, Almstrup K, Fusee L, Srivastava Y, Chantot-Bastaraud S, Hyon C, Louis-Sylvestre C, Validire P, de Malleray Pichard C, Ravel C, Christin-Maitre S, Brauner R, Rossetti R, Persani L, Charreau EH, Dain L, Chiauzzi VA, Mazen I, Rouba H, Schluth-Bolard C, MacGowan S, McLean WHI, Patin E, Rajpert-De Meyts E, Jauch R, Achermann JC, Siffroi JP, McElreavey K, Bashamboo A, Mutations involving the SRY-related gene SOX8 are associated with a spectrum of human reproductive anomalies, Hum. Mol. Genet. 2018 04;27(7):1228-1240.

Dickson LB, Ghozlane A, Volant S, Bouchier C, Ma L, Vega-Rúa A, Dusfour I, Jiolle D, Paupy C, Mayanja MN, Kohl A, Lutwama JJ, Duong V, Lambrechts L, Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome, Parasit Vectors 2018 03;11(1):207.

Guérin A, Kerner G, Marr N, Markle JG, Fenollar F, Wong N, Boughorbel S, Avery DT, Ma CS, Bougarn S, Bouaziz M, Béziat V, Della Mina E, Oleaga-Quintas C, Lazarov T, Worley L, Nguyen T, Patin E, Deswarte C, Martinez-Barricarte R, Boucherit S, Ayral X, Edouard S, Boisson-Dupuis S, Rattina V, Bigio B, Vogt G, Geissmann F, Quintana-Murci L, Chaussabel D, Tangye SG, Raoult D, Abel L, Bustamante J, Casanova JL, IRF4 haploinsufficiency in a family with Whipple’s disease, Elife 2018 Mar;7.

Lopez M, Kousathanas A, Quach H, Harmant C, Mouguiama-Daouda P, Hombert JM, Froment A, Perry GH, Barreiro LB, Verdu P, Patin E, Quintana-Murci L, The demographic history and mutational load of African hunter-gatherers and farmers, Nat Ecol Evol 2018 Apr;2(4):721-730.

Patin E, Hasan M, Bergstedt J, Rouilly V, Libri V, Urrutia A, Alanio C, Scepanovic P, Hammer C, Jönsson F, Beitz B, Quach H, Lim YW, Hunkapiller J, Zepeda M, Green C, Piasecka B, Leloup C, Rogge L, Huetz F, Peguillet I, Lantz O, Fontes M, Di Santo JP, Thomas S, Fellay J, Duffy D, Quintana-Murci L, Albert ML, , , Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors., Nat Immunol 2018 Mar; 19(3): 302-314.

Piazza A, Koszul R, Heyer WD, A Proximity Ligation-Based Method for Quantitative Measurement of D-Loop Extension in S. cerevisiae, Meth. Enzymol. 2018;601:27-44.

Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy and Thomas Cokelaer, Sequanix: A Dynamic Graphical Interface for Snakemake Workflows, https://doi.org/10.1093/bioinformatics/bty034.

Vitor MT, Sart S, Barizien A, Torre LG, Baroud CN, Tracking the Evolution of Transiently Transfected Individual Cells in a Microfluidic Platform, Sci Rep 2018 Jan;8(1):1225.

Liascukiene I, Amselem G, Gunes DZ, Baroud CN, , Capture of colloidal particles by a moving microfluidic bubble., Soft Matter 2018 Feb; 14(6): 992-1000.

Piasecka B, Duffy D, Urrutia A, Quach H, Patin E, Posseme C, Bergstedt J, Charbit B, Rouilly V, MacPherson CR, Hasan M, Albaud B, Gentien D, Fellay J, Albert ML, Quintana-Murci L, , , Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges., Proc Natl Acad Sci U S A 2018 Jan; 115(3): E488-E497.

Raimondi C, Jagla B, Proux C, Waxin H, Gangloff S, Arcangioli B, Molecular signature of the imprintosome complex at the mating-type locus in fission yeast, Microb Cell 2018 Jan;5(4):169-183.

Lioy VS*, Cournac A*, Marbouty M, Duigou S, Mozziconacci J, Espéli O, Boccard F, Koszul R, Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins, Cell 2018 Jan;.

Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Graziano J, Emery B, Bell M, Loparev V, Juieng P, Gartin J, Bizet C, Clermont D, Criscuolo A, Brisse S, McQuiston JR, , Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov., Antonie Van Leeuwenhoek 2018 Jan; 111(1): 55-72.

Escudero JA, Nivina A, Cambray G, López-Igual R, Loot C, Mazel D, Recoding of synonymous genes to expand evolutionary landscapes requires control of secondary structure affecting translation., Biotechnol Bioeng 2018 Jan; 115(1): 184-191.

Fournes F, Val ME, Skovgaard O, Mazel D, Replicate Once Per Cell Cycle: Replication Control of Secondary Chromosomes., Front Microbiol 2018 ; 9(): 1833.

Borriss R, Danchin A, Harwood CR, Médigue C, Rocha EPC, Sekowska A, Vallenet D, Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement, Microb Biotechnol 2018 01;11(1):3-17.

Bos J, Austin RH, , A bacterial antibiotic resistance accelerator and applications., Methods Cell Biol 2018 ; 147(): 41-57.

Vivanco L, Rascovan N, Austin AT, , Plant, fungal, bacterial, and nitrogen interactions in the litter layer of a native Patagonian forest., PeerJ 2018 ; 6(): e4754.

Berthelot C, Villar D, Horvath JE, Odom DT, Flicek P, , Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression., Nat Ecol Evol 2018 Jan; 2(1): 152-163.

Ares-Arroyo M, Bernabe-Balas C, Santos-Lopez A, Baquero MR, Prasad KN, Cid D, Martin-Espada C, San Millan A, Gonzalez-Zorn B, , PCR-Based Analysis of ColE1 Plasmids in Clinical Isolates and Metagenomic Samples Reveals Their Importance as Gene Capture Platforms., Front Microbiol 2018 ; 9(): 469.

Martínez-Carranza E, Barajas H, Alcaraz LD, Servín-González L, Ponce-Soto GY, Soberón-Chávez G, Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli., Front Microbiol 2018 ; 9(): 1059.

Martínez-Carranza E, Ponce-Soto GY, Díaz-Pérez AL, Cadenas E, Souza V, Campos-García J, Involvement of cyclodipeptides in the competition of bacterial communities in the oligotrophic Churince aquatic system of Cuatro Ciénegas Basin dominated by Gammaproteobacteria., Extremophiles 2018 Jan; 22(1): 73-85.

Martínez-Carranza E, Barajas H, Alcaraz LD, Servín-González L, Ponce-Soto GY, Soberón-Chávez G, Corrigendum: Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli., Front Microbiol 2018 ; 9(): 2330.

Nejad C, Pillman KA, Siddle KJ, Pepin G, Änkö ML, McCoy CE, Beilharz T, Quintana-Murci L, Goodall GJ, Bracken CP, Gantier MP, miR-222 isoforms are differentially regulated by type-I interferon, RNA 2017 Dec;.

Raquin V, Merkling SH, Gausson V, Moltini-Conclois I, Frangeul L, Varet H, Dillies MA, Saleh MC, Lambrechts L, , Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut., PLoS Negl Trop Dis 2017 12; 11(12): e0006152.

Gangloff S, Achaz G, Francesconi S, Villain A, Miled S, Denis C, Arcangioli B, Quiescence unveils a novel mutational force in fission yeast, Elife 2017 Dec;6.

Aude Bernheim, Alicia Calvo Villamanan, Clovis Basier, Lun Cui, Eduardo P. C. Rocha, Marie Touchon, David Bikard, Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria, Nature Communications 8, 2094..

Aude Bernheim, Alicia Calvo-Villamañán, Clovis Basier, Lun Cui, Eduardo P C Rocha, Marie Touchon, David Bikard, Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria, Nature Communications, 2017, 8, pp.2094. ⟨10.1038/s41467-017-02350-1⟩.

Pfeifer E, Gätgens C, Polen T, Frunzke J, Adaptive laboratory evolution of Corynebacterium glutamicum towards higher growth rates on glucose minimal medium, Sci Rep 2017 Dec;7(1):16780.

Wang Y, Gao X, Ghozlane A, Hu H, Li X, Xiao Y, Li D, Yu G, Zhang T, Characteristics of Fecal Microbiota in Pediatric Crohn’s Disease and Their Dynamic Changes During Infliximab Therapy, J Crohns Colitis 2017 Nov;.

de Gunzburg J, Ghozlane A, Ducher A, Le Chatelier E, Duval X, Ruppé E, Armand-Lefevre L, Sablier-Gallis F, Burdet C, Alavoine L, Chachaty E, Augustin V, Varastet M, Levenez F, Kennedy S, Pons N, Mentré F, Andremont A, Protection of the human gut microbiome from antibiotics, J. Infect. Dis. 2017 Nov;.

Maestroni L, Audry J, Matmati S, Arcangioli B, Géli V, Coulon S, Eroded telomeres are rearranged in quiescent fission yeast cells through duplications of subtelomeric sequences, Nat Commun 2017 11;8(1):1684.

Guédon G, Libante V, Coluzzi C, Payot S, Leblond-Bourget N, , The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems., Genes (Basel) 2017 Nov; 8(11): .

Léo Machado, Joana Esteves de Lima, Odile Fabre, Caroline Proux, Rachel Legendre, Anikó Szegedi, Hugo Varet, Lars Roed Ingerslev, Romain Barrès, Frédéric Relaix, Philippos Mourikis, In Situ Fixation Redefines Quiescence and Early Activation of Skeletal Muscle Stem Cells, Cell Reports , Volume 21 , Issue 7 , 1982 - 1993.

Laso-Jadart R, Harmant C, Quach H, Zidane N, Tyler-Smith C, Mehdi Q, Ayub Q, Quintana-Murci L, Patin E, The Genetic Legacy of the Indian Ocean Slave Trade: Recent Admixture and Post-admixture Selection in the Makranis of Pakistan, Am. J. Hum. Genet. 2017 Dec;101(6):977-984.

Pasquier J, Braasch I, Batzel P, Cabau C, Montfort J, Nguyen T, Jouanno E, Berthelot C, Klopp C, Journot L, Postlethwait JH, Guiguen Y, Bobe J, , Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome., J Exp Zool B Mol Dev Evol 2017 Nov; 328(7): 709-721.

Martins RM, Macpherson CR, Claes A, Scheidig-Benatar C, Sakamoto H, Yam XY, Preiser P, Goel S, Wahlgren M, Sismeiro O, Coppée JY, Scherf A, An ApiAP2 member regulates expression of clonally variant genes of the human malaria parasite Plasmodium falciparum, Sci Rep 2017 Oct;7(1):14042.

Oliveira PH, Touchon M, Cury J, Rocha EPC, The chromosomal organization of horizontal gene transfer in bacteria, Nat Commun 2017 Oct;8(1):841.

Garcia-Garcera M, Touchon M, Brisse S, Rocha EPC, Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter, Environ. Microbiol. 2017 Oct;.

Stressmann FA, Couve-Deacon E, Chainier D, Chauhan A, Wessel A, Durand-Fontanier S, Escande MC, Kriegel I, Francois B, Ploy MC, Beloin C, Ghigo JM, Comparative Analysis of Bacterial Community Composition and Structure in Clinically Symptomatic and Asymptomatic Central Venous Catheters, mSphere 2017 Sep-Oct;2(5).

Capela D, Marchetti M, Clérissi C, Perrier A, Guetta D, Gris C, Valls M, Jauneau A, Cruveiller S, Rocha EPC, Masson-Boivin C., Recruitment of a lineage-specific virulence regulatory pathway promotes intracellular infection by a plant pathogen experimentally evolved into a legume symbiont., Mol Biol Evol. 2017 May 23. doi: 10.1093/molbev/msx165.

Emilia Pachulec, Rym Ben Abdelwahed Bagga, Lucie Chevallier, Hope O'Donnell, Chloé Guillas, Jean Jaubert, Xavier Montagutelli, Elisabeth Carniel, Christian E. Demeure, Enhanced Macrophage M1 Polarization and Resistance to Apoptosis Enable Resistance to Plague, Journal of Infectious Diseases, 2017, 216 (6), pp.761-770. ⟨10.1093/infdis/jix348⟩.

Tepekule B, Uecker H, Derungs I, Frenoy A, Bonhoeffer S, Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies, PLoS Comput. Biol. 2017 Sep;13(9):e1005745.

Beltramo PJ, Gupta M, Alicke A, Liascukiene I, Gunes DZ, Baroud CN, Vermant J, , Arresting dissolution by interfacial rheology design., Proc Natl Acad Sci U S A 2017 09; 114(39): 10373-10378.

Sart S, Tomasi RF, Amselem G, Baroud CN, Multiscale cytometry and regulation of 3D cell cultures on a chip, Nat Commun 2017 09;8(1):469.

Cury J, Touchon M, Rocha EPC, Integrative and conjugative elements and their hosts: composition, distribution and organization, Nucleic Acids Res. 2017 Sep;45(15):8943-8956.

Hurtado-Ortiz R, Nazimoudine A, Criscuolo A, Hugon P, Mornico D, Brisse S, Bizet C, Clermont D, , Psychrobacter pasteurii and Psychrobacter piechaudii sp. nov., two novel species within the genus Psychrobacter., Int J Syst Evol Microbiol 2017 Sep; 67(9): 3192-3197.

Thomas Cokelaer, Dimitri Desvillechabrol, Rachel Legendre, Mélissa Cardon, Sequana: a set of snakemake NGS pipelines, J. Open Source Softw, 2 p352.

Jamet A, Touchon M, Ribeiro-Gonçalves B, Carriço JA, Charbit A, Nassif X, Ramirez M, Rocha EPC, A widespread family of polymorphic toxins encoded by temperate phages, BMC Biol. 2017 Aug;15(1):75.

Roche B, Arcangioli B, Martienssen R, New roles for Dicer in the nucleolus and its relevance to cancer, Cell Cycle 2017 Sep;16(18):1643-1653.

Dickson LB, Jiolle D, Minard G, Moltini-Conclois I, Volant S, Ghozlane A, Bouchier C, Ayala D, Paupy C, Moro CV, Lambrechts L, Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector, Sci Adv 2017 Aug;3(8):e1700585.

P. Parize, E. Muth, C. Richaud, M. Gratigny, B. Pilmis, A. Lamamy, J.-L. Mainardi, J. Cheval, L. de Visser, F. Jagorel, L. Ben Yahia, G. Bamba, M. Dubois, O. Join-Lambert, M. Leruez-Ville, X. Nassif, A. Lefort, F. Lanternier, F. Suarez, O. Lortholary, M. Lecuit, Marc Eloit, Untargeted next-generation sequencing-based first-line diagnosis of infection in immunocompromised adults: a multicentre, blinded, prospective study, Clinical Microbiology and Infection, 2017, 23 (8), pp.574.e1-574.e6. ⟨10.1016/j.cmi.2017.02.006⟩.

Vázquez-Rosas-Landa M, Ponce-Soto GY, Eguiarte LE, Souza V, Comparative genomics of free-living Gammaproteobacteria: pathogenesis-related genes or interaction-related genes?, Pathog Dis 2017 Jul; 75(5): .

Grieb MS, Nivina A, Cheeseman BL, Hartmann A, Mazel D and Schlierf M, Dynamic stepwise opening of integron attC DNA hairpins by SSB prevents toxicity and ensures functionality, Nucleic Acids Research (2017) 45(18):10555-10563. doi: 10.1093/nar/gkx670 .

Bialek-Davenet S, Mayer N, Vergalli J, Duprilot M, Brisse S, Pagès JM, Nicolas-Chanoine MH, In-vivo loss of carbapenem resistance by extensively drug-resistant Klebsiella pneumoniae during treatment via porin expression modification, Sci Rep 2017 Jul;7(1):6722.

Rendueles O, Garcia-Garcerà M, Néron B, Touchon M, Rocha EPC, Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens, PLoS Pathog. 2017 Jul;13(7):e1006525.

Lazar-Stefanita L, Scolari VF, Mercy G, Muller H, Guérin TM, Thierry A, Mozziconacci J, Koszul R, Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle, EMBO J. 2017 09;36(18):2684-2697.

Bland MJ, Ducos-Galand M, Val ME, Mazel D, An att site-based recombination reporter system for genome engineering and synthetic DNA assembly., BMC Biotechnol 2017 Jul; 17(1): 62.

Bisiaux A, Boussier J, Duffy D, Quintana-Murci L, Fontes M, Albert ML, , Deconvolution of the Response to Bacillus Calmette-Guérin Reveals NF-κB-Induced Cytokines As Autocrine Mediators of Innate Immunity, Front Immunol 2017;8:796.

Saffarian A, Touchon M, Mulet C, Tournebize R, Passet V, Brisse S, Rocha EPC, Sansonetti PJ, Pédron T, Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts, BMC Genomics 2017 07;18(1):525.

Passoni G, Langevin C, Palha N, Mounce BC, Briolat V, Affaticati P, De Job E, Joly JS, Vignuzzi M, Saleh MC, Herbomel P, Boudinot P, Levraud JP, , Imaging of viral neuroinvasion in the zebrafish reveals that Sindbis and chikungunya viruses favour different entry routes., Dis Model Mech 2017 Jul; 10(7): 847-857.

Kim J, Michelin S, Hilbers M, Martinelli L, Chaudan E, Amselem G, Fradet E, Boilot JP, Brouwer AM, Baroud CN, Peretti J, Gacoin T, Monitoring the orientation of rare-earth-doped nanorods for flow shear tomography, Nat Nanotechnol 2017 Sep;12(9):914-919.

Frénoy A, Taddei F, Misevic D, Second-order cooperation: Cooperative offspring as a living public good arising from second-order selection on non-cooperative individuals, Evolution 2017 07;71(7):1802-1814.

Jourdier E, Baudry L, Poggi-Parodi D, Vicq Y, Koszul R, Margeot A, Marbouty M, Bidard F, Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes, Biotechnol Biofuels 2017;10:151.

Urbieta MS, Rascovan N, Vázquez MP, Donati E, , Genome analysis of the thermoacidophilic archaeon Acidianus copahuensis focusing on the metabolisms associated to biomining activities., BMC Genomics 2017 06; 18(1): 445.

Chen TD, Rotival M, Chiu LY, Bagnati M, Ko JH, Srivastava PK, Petretto E, Pusey CD, Lai PC, Aitman TJ, Cook HT, Behmoaras J, , Identification of Ceruloplasmin as a Gene that Affects Susceptibility to Glomerulonephritis Through Macrophage Function., Genetics 2017 06; 206(2): 1139-1151.

Langevin C, Aleksejeva E, Houel A, Briolat V, Torhy C, Lunazzi A, Levraud JP, Boudinot P, , FTR83, a Member of the Large Fish-Specific finTRIM Family, Triggers IFN Pathway and Counters Viral Infection., Front Immunol 2017 ; 8(): 617.

Perrin A, Larsonneur E, Nicholson AC, Edwards DJ, Gundlach KM, Whitney AM, Gulvik CA, Bell ME, Rendueles O, Cury J, Hugon P, Clermont D, Enouf V, Loparev V, Juieng P, Monson T, Warshauer D, Elbadawi LI, Walters MS, Crist MB, Noble-Wang J, Borlaug G, Rocha EPC, Criscuolo A, Touchon M, Davis JP, Holt KE, McQuiston JR, Brisse S, , Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain., Nat Commun 2017 05; 8(): 15483.

Gopalan S, Carja O, Fagny M, Patin E, Myrick JW, McEwen LM, Mah SM, Kobor MS, Froment A, Feldman MW, Quintana-Murci L, Henn BM, Trends in DNA Methylation with Age Replicate Across Diverse Human Populations, Genetics 2017 07;206(3):1659-1674.

Defenouillère Q, Fromont-Racine M, The ribosome-bound quality control complex: from aberrant peptide clearance to proteostasis maintenance, Curr. Genet. 2017 Dec;63(6):997-1005.

Roche B, Arcangioli B, Martienssen R, Transcriptional reprogramming in cellular quiescence, RNA Biol 2017 07;14(7):843-853.

Patin E., Lopez M, Grollemund R., Verdu P., Harmant C., Quach H., Laval G., Perry GH, Barreiro LB, Froment A., Evelyne H., Massougbodji A., Fortes-Lima C., Migot-Nabias F., Bellis G., Dugoujon JM, Pereira JB, Fernandes V., Pereira L., Van der Veen L., Mouguiama-Daouda P., Bustamante CD., Hombert JM., Quintana-Murci L., Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America, Science. 2017 May; 356(6337);543-546.

Villa L, Feudi C, Fortini D, Brisse S, Passet V, Bonura C, Endimiani A, Mammina C, Ocampo AM, Jimenez JN, Doumith M, Woodford N, Hopkins K, Carattoli A, Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone, Microb Genom 2017 Apr;3(4):e000110.

Touchon M, Moura de Sousa JA, Rocha EPC, Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer, Curr Opin Microbiol. 2017 May 17;38:66-73.

Eduati F, Doldàn-Martelli V, Klinger B, Cokelaer T, Sieber A, Kogera F, Dorel M, Garnett MJ, Blüthgen N, Saez-Rodriguez J, Drug resistance mechanisms in colorectal cancer dissected with cell type-specific dynamic logic models, Cancer Res. 2017 Apr;.

Leroy M, Piton J, Gilet L, Pellegrini O, Proux C, Coppée JY, Figaro S, Condon C, Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis, EMBO J. 2017 May;36(9):1167-1181.

Céline Loot, Aleksandra Nivina, Jean Cury, José Antonio Escudero, Magaly Ducos-Galand, David Bikard, Eduardo P C Rocha, Didier Mazel, Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance., mBio, 2017, 8 (2), pp.e02296-16. ⟨10.1128/mBio.02296-16⟩.

Quach H, Quintana-Murci L, Living in an adaptive world: Genomic dissection of the genus Homo and its immune response, J. Exp. Med. 2017 Apr;214(4):877-894.

Ryan J Morris1 , Trung V Phan , Matthew Black , Ke-Chih Lin , Ioannis G Kevrekidis , Julia Bos and Robert H Austin, Bacterial population solitary waves can defeat rings of funnels, New J. Phys. 19 (2017) 035002.

Defenouillère Q, Namane A, Mouaikel J, Jacquier A, Fromont-Racine M, The ribosome-bound quality control complex remains associated to aberrant peptides during their proteasomal targeting and interacts with Tom1 to limit protein aggregation, Mol. Biol. Cell 2017 May;28(9):1165-1176.

Nagle N, van Oven M, Wilcox S, van Holst Pellekaan S, Tyler-Smith C, Xue Y, Ballantyne KN, Wilcox L, Papac L, Cooke K, van Oorschot RA, McAllister P, Williams L, Kayser M, Mitchell RJ,, Aboriginal Australian mitochondrial genome variation – an increased understanding of population antiquity and diversity, Sci Rep 2017 Mar;7:43041.

Mercy G, Mozziconacci J, Scolari VF, Yang K, Zhao G, Thierry A, Luo Y, Mitchell LA, Shen M, Shen Y, Walker R, Zhang W, Wu Y, Xie ZX, Luo Z, Cai Y, Dai J, Yang H, Yuan YJ, Boeke JD, Bader JS, Muller H, Koszul R, 3D organization of synthetic and scrambled chromosomes, Science 2017 03;355(6329).

Shen Y, Wang Y, Chen T, Gao F, Gong J, Abramczyk D, Walker R, Zhao H, Chen S, Liu W, Luo Y, Müller CA, Paul-Dubois-Taine A, Alver B, Stracquadanio G, Mitchell LA, Luo Z, Fan Y, Zhou B, Wen B, Tan F, Wang Y, Zi J, Xie Z, Li B, Yang K, Richardson SM, Jiang H, French CE, Nieduszynski CA, Koszul R, Marston AL, Yuan Y, Wang J, Bader JS, Dai J, Boeke JD, Xu X, Cai Y, Yang H, Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome, Science 2017 Mar;355(6329).

Blin C, Passet V, Touchon M, Rocha EPC, Brisse S, Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae, Environ. Microbiol. 2017 May;19(5):1881-1898.

Abby SS, Rocha EPC, Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder, Methods Mol Biol. 2017;1615:1-21.

Srivastava PK, Bagnati M, Delahaye-Duriez A, Ko JH, Rotival M, Langley SR, Shkura K, Mazzuferi M, Danis B, van Eyll J, Foerch P, Behmoaras J, Kaminski RM, Petretto E, Johnson MR, , Genome-wide analysis of differential RNA editing in epilepsy., Genome Res. 2017 03; 27(3): 440-450.

Soler-Bistué Alfonso, Timmermans Michaël, Mazel Didier, The Proximity of Ribosomal Protein Genes to oriC Enhances Vibrio cholerae Fitness in the Absence of Multifork Replication, MBio. 2017 Feb 28;8(1). pii: e00097-17. doi: 10.1128/mBio.00097-17..

Marbouty M, Baudry L, Cournac A, Koszul R, Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay, Sci Adv 2017 Feb;3(2):e1602105.

Julien Farasin, Sandrine Koechler, Hugo Varet, Julien Deschamps, Marie-Agnès Dillies, Caroline Proux, Mathieu Erhardt, Aline Huber, Bernd Jagla, Romain Briandet, Jean-Yves Coppée, Florence Arsène-Ploetze, Comparison of biofilm formation and motility processes in arsenic-resistant Thiomonas spp. strains revealed divergent response to arsenite, Microb Biotechnol. 2017 Feb 7. doi: 10.1111/1751-7915.12556.

Santos-Lopez A, Bernabe-Balas C, Ares-Arroyo M, Ortega-Huedo R, Hoefer A, San Millan A, Gonzalez-Zorn B, , A Naturally Occurring Single Nucleotide Polymorphism in a Multicopy Plasmid Produces a Reversible Increase in Antibiotic Resistance., Antimicrob Agents Chemother 2017 Feb; 61(2): .

Gangloff Serge, Arcangioli Benoit, DNA Repair and Mutations During Quiescence in Yeast, FEMS Yeast Res. 2017 Jan;.

Billard-Pomares T, Rouyer C, Walewski V, Badell-Ocando E, Dumas M, Zumelzu C, Jaureguy F, Brisse S, Caux F, Bouchaud O, Carbonnelle E, , Diagnosis in France of a Non-Toxigenic tox Gene-Bearing Strain of Corynebacterium diphtheriae in a Young Male Back From Senegal., Open Forum Infect Dis 2017 ; 4(1): ofw271.

Deschamps M, Quintana-Murci L, [Innate immunity and human diseases: from archaic introgression to natural selection], Med Sci (Paris) 2016 Dec;32(12):1079-1086.

Marbouty M, Koszul R, Generation and Analysis of Chromosomal Contact Maps of Bacteria, Methods Mol. Biol. 2017;1624:75-84.

Ribeiro TG, Clermont D, Branquinho R, Machado E, Peixe L, Brisse S, , Citrobacter europaeus sp. nov., isolated from water and human faecal samples., Int J Syst Evol Microbiol 2017 Jan; 67(1): 170-173.

Coluzzi C, Guédon G, Devignes MD, Ambroset C, Loux V, Lacroix T, Payot S, Leblond-Bourget N, , A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins., Front Microbiol 2017 ; 8(): 443.

Soberón-Chávez G, Alcaraz LD, Morales E, Ponce-Soto GY, Servín-González L, The Transcriptional Regulators of the CRP Family Regulate Different Essential Bacterial Functions and Can Be Inherited Vertically and Horizontally., Front Microbiol 2017 ; 8(): 959.

Schmidt C, Kowalinski E, Shanmuganathan V, Defenouillère Q, Braunger K, Heuer A, Pech M, Namane A, Berninghausen O, Fromont-Racine M, Jacquier A, Conti E, Becker T, Beckmann R, The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex, Science 2016 12;354(6318):1431-1433.

Melot B, Brisse S, Breurec S, Passet V, Malpote E, Lamaury I, Thiery G, Hoen B, Community-acquired meningitis caused by a CG86 hypervirulent Klebsiella pneumoniae strain: first case report in the Caribbean, BMC Infect. Dis. 2016 Dec;16(1):736.

Belyy A*, Raoux-Barbot D*, Saveanu C*, Namane A, Ogryzko V, Worpenberg L, David V, Henriot V, Fellous S, Merrifield C, Assayag E, Ladant D, Renault L, Mechold U, Actin activates Pseudomonas aeruginosa ExoY nucleotidyl cyclase toxin and ExoY-like effector domains from MARTX toxins, Nat Commun 2016 Dec;7:13582.

Nagle N, Ballantyne KN, van Oven M, Tyler-Smith C, Xue Y, Wilcox S, Wilcox L, Turkalov R, van Oorschot RA, van Holst Pellekaan S, Schurr TG, McAllister P, Williams L, Kayser M, Mitchell RJ,, Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania, J. Hum. Genet. 2017 Mar;62(3):343-353.

Lopopolo M, Børsting C, Pereira V, Morling N, A study of the peopling of Greenland using next generation sequencing of complete mitochondrial genomes., Am J Phys Anthropol 2016 Dec; 161(4): 698-704.

Grosso-Becerra MV, González-Valdez A, Granados-Martínez MJ, Morales E, Servín-González L, Méndez JL, Delgado G, Morales-Espinosa R, Ponce-Soto GY, Cocotl-Yañez M, Soberón-Chávez G, Pseudomonas aeruginosa ATCC 9027 is a non-virulent strain suitable for mono-rhamnolipids production., Appl Microbiol Biotechnol 2016 Dec; 100(23): 9995-10004.

Lebreton A, Stavru F, Brisse S, Cossart P, 1926-2016: 90 Years of listeriology, Microbes Infect. 2016 Dec;18(12):711-723.

Dreyer M, Aguilar-Bultet L, Rupp S, Guldimann C, Stephan R, Schock A, Otter A, Schüpbach G, Brisse S, Lecuit M, Frey J, Oevermann A, , Listeria monocytogenes sequence type 1 is predominant in ruminant rhombencephalitis., Sci Rep 2016 Nov; 6(): 36419.

Quintana-Murci L, Understanding rare and common diseases in the context of human evolution, Genome Biol. 2016 Nov;17(1):225.

Witkowski B, Duru V, Khim N, Ross LS, Saintpierre B, Beghain J, Chy S, Kim S, Ke S, Kloeung N, Eam R, Khean C, Ken M, Loch K, Bouillon A, Domergue A, Ma L, Bouchier C, Leang R, Huy R, Nuel G, Barale JC, Legrand E, Ringwald P, Fidock DA, Mercereau-Puijalon O, Ariey F, Ménard D, A surrogate marker of piperaquine-resistant Plasmodium falciparum malaria: a phenotype-genotype association study, Lancet Infect Dis 2017 Feb;17(2):174-183.

Ouadani H, Ben-Mustapha I, Ben-Ali M, Larguèche B, Jovanic T, Garcia S, Arcangioli B, Elloumi-Zghal H, Fathallah D, Hachicha M, Masmoudi H, Rougeon F, Barbouche MR, , Activation induced cytidine deaminase mutant (AID-His130Pro) from Hyper IgM 2 patient retained mutagenic activity on SHM artificial substrate., Mol Immunol 2016 11; 79(): 77-82.

Christian Weber, Mikael Koutero, Marie-Agnes Dillies, Hugo Varet, Cesar Lopez-Camarillo, Jean Yves Coppée, Chung-Chau Hon, Nancy Guillén, Extensive transcriptome analysis correlates the plasticity of Entamoeba histolytica pathogenesis to rapid phenotype changes depending on the environment, Sci Rep. 2016 Oct 21;6:35852. doi: 10.1038/srep35852..

van Wijlick L, Geissen R, Hilbig JS, Lagadec Q, Cantero PD, Pfeifer E, Juchimiuk M, Kluge S, Wickert S, Alepuz P, Ernst JF, Dom34 Links Translation to Protein O-mannosylation, PLoS Genet. 2016 Oct;12(10):e1006395.

Quach H, Rotival M, Pothlichet J, Loh YE, Dannemann M, Zidane N, Laval G, Patin E, Harmant C, Lopez M, Deschamps M, Naffakh N, Duffy D, Coen A, Leroux-Roels G, Clément F, Boland A, Deleuze JF, Kelso J, Albert ML, Quintana-Murci L, Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations, Cell 2016 Oct;167(3):643-656.e17.

Martin RM, Cao J, Brisse S, Passet V, Wu W, Zhao L, Malani PN, Rao K, Bachman MA, Molecular Epidemiology of Colonizing and Infecting Isolates of Klebsiella pneumoniae, mSphere 2016 Sep-Oct;1(5).

Amselem G, Guermonprez C, Drogue B, Michelin S, Baroud CN, Universal microfluidic platform for bioassays in anchored droplets, Lab Chip 2016 Oct;16(21):4200-4211.

Roche B, Rougeron V, Quintana-Murci L, Renaud F, Abbate JL, Prugnolle F, Might Interspecific Interactions between Pathogens Drive Host Evolution? The Case of Plasmodium Species and Duffy-Negativity in Human Populations, Trends Parasitol. 2016 Oct;.

Roche B, Arcangioli B, Martienssen RA, RNA interference is essential for cellular quiescence, Science 2016 11;354(6313).

Moura A, Criscuolo A, Pouseele H, Maury MM, Leclercq A, Tarr C, Björkman JT, Dallman T, Reimer A, Enouf V, Larsonneur E, Carleton H, Bracq-Dieye H, Katz LS, Jones L, Touchon M, Tourdjman M, Walker M, Stroika S, Cantinelli T, Chenal-Francisque V, Kucerova Z, Rocha EP, Nadon C, Grant K, Nielsen EM, Pot B, Gerner-Smidt P, Lecuit M, Brisse S, , Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes., Nat Microbiol 2016 Oct; 2(): 16185.

Njamkepo E, Fawal N, Tran-Dien A, Hawkey J, Strockbine N, Jenkins C, Talukder KA, Bercion R, Kuleshov K, Kolínská R, Russell JE, Kaftyreva L, Accou-Demartin M, Karas A, Vandenberg O, Mather AE, Mason CJ, Page AJ, Ramamurthy T, Bizet C, Gamian A, Carle I, Sow AG, Bouchier C, Wester AL, Lejay-Collin M, Fonkoua MC, Le Hello S, Blaser MJ, Jernberg C, Ruckly C, Mérens A, Page AL, Aslett M, Roggentin P, Fruth A, Denamur E, Venkatesan M, Bercovier H, Bodhidatta L, Chiou CS, Clermont D, Colonna B, Egorova S, Pazhani GP, Ezernitchi AV, Guigon G, Harris SR, Izumiya H, Korzeniowska-Kowal A, Lutyńska A, Gouali M, Grimont F, Langendorf C, Marejková M, Peterson LA, Perez-Perez G, Ngandjio A, Podkolzin A, Souche E, Makarova M, Shipulin GA, Ye C, Žemličková H, Herpay M, Grimont PA, Parkhill J, Sansonetti P, Holt KE, Brisse S, Thomson NR, Weill FX, Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1, Nat Microbiol 2016 10;1(11):16209.

Laissue P, Lakhal B, Vatin M, Batista F, Burgio G, Mercier E, Santos ED, Buffat C, Sierra-Diaz DC, Renault G, Montagutelli X, Salmon J, Monget P, Veitia RA, Méhats C, Fellous M, Gris JC, Cocquet J, Vaiman D, Association of FOXD1 variants with adverse pregnancy outcomes in mice and humans, Open Biol 2016 Oct;6(10).

Rascovan N, Telke A, Raoult D, Rolain JM, Desnues C, , Exploring divergent antibiotic resistance genes in ancient metagenomes and discovery of a novel beta-lactamase family., Environ Microbiol Rep 2016 Oct; 8(5): 886-895.

Mathieu A, Fleurier S, Frénoy A, Dairou J, Bredeche MF, Sanchez-Vizuete P, Song X, Matic I, Discovery and Function of a General Core Hormetic Stress Response in E. coli Induced by Sublethal Concentrations of Antibiotics, Cell Rep 2016 09;17(1):46-57.

Rendueles O, Velicer GJ, Evolution by flight and fight: diverse mechanisms of adaptation by actively motile microbes, ISME J 2017 02;11(2):555-568.

Nivina A, Escudero JA, Vit C, Mazel D, Loot C, Efficiency of integron cassette insertion in correct orientation is ensured by the interplay of the three unpaired features of attC recombination sites., Nucleic Acids Res 2016 Sep; 44(16): 7792-803.

Wang Y, Ma CS, Ling Y, Bousfiha A, Camcioglu Y, Jacquot S, Payne K, Crestani E, Roncagalli R, Belkadi A, Kerner G, Lorenzo L, Deswarte C, Chrabieh M, Patin E, Vincent QB, Müller-Fleckenstein I, Fleckenstein B, Ailal F, Quintana-Murci L, Fraitag S, Alyanakian MA, Leruez-Ville M, Picard C, Puel A, Bustamante J, Boisson-Dupuis S, Malissen M, Malissen B, Abel L, Hovnanian A, Notarangelo LD, Jouanguy E, Tangye SG, Béziat V, Casanova JL, Dual T cell- and B cell-intrinsic deficiency in humans with biallelic RLTPR mutations, J. Exp. Med. 2016 10;213(11):2413-2435.

Rascovan N, Duraisamy R, Desnues C, , Metagenomics and the Human Virome in Asymptomatic Individuals., Annu Rev Microbiol 2016 09; 70(): 125-41.

Gonzalez-Hilarion S, Paulet D, Lee KT, Hon CC, Lechat P, Mogensen E, Moyrand F, Proux C, Barboux R, Bussotti G, Hwang J, Coppée JY, Bahn YS, Janbon G, Intron retention-dependent gene regulation in Cryptococcus neoformans, Sci Rep 2016 08;6:32252.

Alejandra Urrutia, Darragh Duffy, Vincent Rouilly, Céline Posseme, Raouf Djebali, Gabriel Illanes, Valentina Libri, Benoit Albaud, David Gentien, Barbara Piasecka, Milena Hasan, Magnus Fontes, Lluis Quintana-Murcic, Matthew L. Albert, Milieu Intérieur Consortium , Standardized Whole-Blood Transcriptional Profiling Enables the Deconvolution of Complex Induced Immune Responses, DOI: http://dx.doi.org/10.1016/j.celrep.2016.08.011 show.

Frot C, Taccoen N, Baroud CN, Frugal Droplet Microfluidics Using Consumer Opto-Electronics, PLoS ONE 2016;11(8):e0161490.

Horvath S, Gurven M, Levine ME, Trumble BC, Kaplan H, Allayee H, Ritz BR, Chen B, Lu AT, Rickabaugh TM, Jamieson BD, Sun D, Li S, Chen W, Quintana-Murci L, Fagny M, Kobor MS, Tsao PS, Reiner AP, Edlefsen KL, Absher D, Assimes TL, An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease, Genome Biol. 2016 Aug;17(1):171.

Asmar S, Rascovan N, Robert C, Drancourt M, , Draft Genome Sequence of Mycobacterium acapulcensis Strain CSURP1424., Genome Announc 2016 Aug; 4(4): .

Pfeifer E, Hünnefeld M, Popa O, Polen T, Kohlheyer D, Baumgart M, Frunzke J, Silencing of cryptic prophages in Corynebacterium glutamicum, Nucleic Acids Res. 2016 12;44(21):10117-10131.

Breurec S, Criscuolo A, Diancourt L, Rendueles O, Vandenbogaert M, Passet V, Caro V, Rocha EP, Touchon M, Brisse S, Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis, Sci Rep 2016;6:30379.

Chaput C, Ecobichon C, Pouradier N, Rousselle JC, Namane A, Boneca IG, Role of the N-Acetylmuramoyl-l-Alanyl Amidase, AmiA, of Helicobacter pylori in Peptidoglycan Metabolism, Daughter Cell Separation, and Virulence, Microb. Drug Resist. 2016 Sep;22(6):477-86.

Pasi M, Mornico D, Volant S, Juchet A, Batisse J, Bouchier C, Parissi V, Ruff M, Lavery R, Lavigne M, DNA minicircles clarify the specific role of DNA structure on retroviral integration, Nucleic Acids Res. 2016 Jul;.

Demarta-Gatsi C, Smith L, Thiberge S, Peronet R, Commere PH, Matondo M, Apetoh L, Bruhns P, Ménard R, Mécheri S, , Protection against malaria in mice is induced by blood stage-arresting histamine-releasing factor (HRF)-deficient parasites., J Exp Med 2016 07; 213(8): 1419-28.

Rey O, Danchin E, Mirouze M, Loot C, Blanchet S, Adaptation to Global Change: A Transposable Element-Epigenetics Perspective., Trends Ecol Evol 2016 Jul; 31(7): 514-526.

Rascovan N, Carbonetto B, Perrig D, Díaz M, Canciani W, Abalo M, Alloati J, González-Anta G, Vazquez MP, , Integrated analysis of root microbiomes of soybean and wheat from agricultural fields., Sci Rep 2016 06; 6(): 28084.

Mazuet C, Legeay C, Sautereau J, Ma L, Bouchier C, Bouvet P, Popoff MR, Diversity of Group I and II Clostridium botulinum Strains from France Including Recently Identified Subtypes, Genome Biol Evol 2016 06;8(6):1643-60.

Hugo Varet, Loraine Brillet-Guéguen, Jean-Yves Coppée, Marie-Agnès Dillies, SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data, PLoS One. 2016 Jun 9;11(6):e0157022. doi: 10.1371/journal.pone.0157022. eCollection 2016.

Koszul R, Beyond the bounds of evolution: Synthetic chromosomes… How and what for?, C. R. Biol. 2016 Jun;.

Rascovan N, Monteil Bouchard S, Grob JJ, Collet-Villette AM, Gaudy-Marqueste C, Penicaud M, Lepidi H, Raoult D, Desnues C, , Human Polyomavirus-6 Infecting Lymph Nodes of a Patient With an Angiolymphoid Hyperplasia With Eosinophilia or Kimura Disease., Clin Infect Dis 2016 06; 62(11): 1419-21.

Tang A, Dadaglio G, Oberkampf M, Di Carlo S, Peduto L, Laubreton D, Desrues B, Sun CM, Montagutelli X, Leclerc C, B cells promote tumor progression in a mouse model of HPV-mediated cervical cancer, Int. J. Cancer 2016 Sep;139(6):1358-71.

Maganga GD, Relmy A, Bakkali-Kassimi L, Ngoubangoye B, Tsoumbou T, Bouchier C, N'Dilimabaka N, Leroy EM, Zientara S, Berthet N, Molecular characterization of Orf virus in goats in Gabon, Central Africa, Virol. J. 2016;13:79.

Quintana-Murci L, Genetic and epigenetic variation of human populations: An adaptive tale, C. R. Biol. 2016 Jul-Aug;339(7-8):278-83.

Thierry A, Khanna V, Dujon B, Massive Amplification at an Unselected Locus Accompanies Complex Chromosomal Rearrangements in Yeast, G3 (Bethesda) 2016 05;6(5):1201-15.

Pedro H. Oliveira, Marie Touchon, and Eduardo P. C. Rocha, Regulation of genetic flux between bacteria by restriction-modification systems., Proc Natl Acad Sci U S A. 2016 May 17;113(20):5658-63. doi: 10.1073/pnas.1603257113. .

Jean Cury, Thomas Jové, Marie Touchon, Bertrand Néron, and Eduardo PC Rocha, Identification and analysis of integrons and cassette arrays in bacterial genomes., Nucleic Acids Res. 2016 Apr 29. pii: gkw319..

Mazuet C, Yoon EJ, Boyer S, Pignier S, Blanc T, Doehring I, Meziane-Cherif D, Dumant-Forest C, Sautereau J, Legeay C, Bouvet P, Bouchier C, Quijano-Roy S, Pestel-Caron M, Courvalin P, Popoff MR, A penicillin- and metronidazole-resistant Clostridium botulinum strain responsible for an infant botulism case, Clin. Microbiol. Infect. 2016 Jul;22(7):644.e7-644.e12.

Defenouillère Q, Zhang E, Namane A, Mouaikel J, Jacquier A, Fromont-Racine M, Rqc1 and Ltn1 Prevent C-terminal Alanine-Threonine Tail (CAT-tail)-induced Protein Aggregation by Efficient Recruitment of Cdc48 on Stalled 60S Subunits, J. Biol. Chem. 2016 Jun;291(23):12245-53.

Mee ET, Preston MD, Minor PD, Schepelmann S, Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing., Vaccine 2016 Apr; 34(17): 2035-43.

Val ME, Marbouty M, de Lemos Martins F, Kennedy SP, Kemble H, Bland MJ, Possoz C, Koszul R, Skovgaard O, Mazel D, A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae., Sci Adv 2016 Apr; 2(4): e1501914.

Skurnik D, Clermont O, Guillard T, Launay A, Danilchanka O, Pons S, Diancourt L, Lebreton F, Kadlec K, Roux D, Jiang D, Dion S, Aschard H, Denamur M, Cywes-Bentley C, Schwarz S, Tenaillon O, Andremont A, Picard B, Mekalanos J, Brisse S, Denamur E, , Emergence of Antimicrobial-Resistant Escherichia coli of Animal Origin Spreading in Humans., Mol Biol Evol 2016 Apr; 33(4): 898-914.

Touchon M, Bernheim A, Rocha EPC, Genetic and life-history traits associated with the distribution of prophages in bacteria., ISME J. 2016 Mar 25. doi: 10.1038/ismej.2016.47. .

Njamkepo E, Fawal N, Tran-Dien A, Hawkey J, Strockbine N, Jenkins C, Talukder KA, Bercion R, Kuleshov K, Kolínská R, Russell JE, Kaftyreva L, Accou-Demartin M, Karas A, Vandenberg O, Mather AE, Mason CJ, Page AJ, Ramamurthy T, Bizet C, Gamian A, Carle I, Sow AG, Bouchier C, Wester AL, Lejay-Collin M, Fonkoua MC, Le Hello S, Blaser MJ, Jernberg C, Ruckly C, Mérens A, Page AL, Aslett M, Roggentin P, Fruth A, Denamur E, Venkatesan M, Bercovier H, Bodhidatta L, Chiou CS, Clermont D, Colonna B, Egorova S, Pazhani GP, Ezernitchi AV, Guigon G, Harris SR, Izumiya H, Korzeniowska-Kowal A, Lutyńska A, Gouali M, Grimont F, Langendorf C, Marejková M, Peterson LA, Perez-Perez G, Ngandjio A, Podkolzin A, Souche E, Makarova M, Shipulin GA, Ye C, Žemličková H, Herpay M, Grimont PA, Parkhill J, Sansonetti P, Holt KE, Brisse S, Thomson NR, Weill FX, , Global phylogeography and evolutionary history of Shigella dysenteriae type 1., Nat Microbiol 2016 03; 1(): 16027.

Eduardo PC Rocha, Using Sex to Cure the Genome, PLoS Biol 14(3): e1002417. doi:10.1371/ journal.pbio.1002417.

Sophie S. Abby, Jean Cury, Julien Guglielmini, Bertrand Néron, Marie Touchon & Eduardo P. C. Rocha, Identification of protein secretion systems in bacterial genomes, Scientific Reports 6, 23080 (2016).

Escudero JA, Loot C, Parissi V, Nivina A, Bouchier C, Mazel D, Unmasking the ancestral activity of integron integrases reveals a smooth evolutionary transition during functional innovation., Nat Commun 2016 Mar; 7(): 10937.

Segura I, Lange C, Knevels E, Moskalyuk A, Pulizzi R, Eelen G, Chaze T, Tudor C, Boulegue C, Holt M, Daelemans D, Matondo M, Ghesquière B, Giugliano M, Ruiz de Almodovar C, Dewerchin M, Carmeliet P, The Oxygen Sensor PHD2 Controls Dendritic Spines and Synapses via Modification of Filamin A, Cell Rep 2016 Mar;14(11):2653-67.

Beal J, Haddock-Angelli T, Gershater M, de Mora K, Lizarazo M, Hollenhorst J, and Rettberg R; Deshmukh Gopaul as iGEM Interlab Study Contributors., Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli, PLoS One. 2016 Mar 3;11(3):e0150182. doi: 10.1371/journal.pone.0150182. eCollection 2016..

Maury MM, Tsai YH, Charlier C, Touchon M, Chenal-Francisque V, Leclercq A, Criscuolo A, Gaultier C, Roussel S, Brisabois A, Disson O, Rocha EPC, Brisse S, Lecuit M, , Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity., Nat Genet 2016 Mar; 48(3): 308-313.

Marguerite Lapierre, Camille Blin, Amaury Lambert, Guillaume Achaz and Eduardo P. C. Rocha, The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography, Mol Biol Evol (2016) doi: 10.1093/molbev/msw048 .

Breurec S, Melot B, Hoen B, Passet V, Schepers K, Bastian S, Brisse S, Liver Abscess Caused by Infection with Community-Acquired Klebsiella quasipneumoniae subsp. quasipneumoniae, Emerging Infect. Dis. 2016 Mar;22(3):529-31.

Persson J, Steglich B, Smialowska A, Boyd M, Bornholdt J, Andersson R, Schurra C, Arcangioli B, Sandelin A, Nielsen O, Ekwall K, Regulating retrotransposon activity through the use of alternative transcription start sites, EMBO Rep. 2016 05;17(5):753-68.

Sapriel G, Konjek J, Orgeur M, Bouri L, Frézal L, Roux AL, Dumas E, Brosch R, Bouchier C, Brisse S, Vandenbogaert M, Thiberge JM, Caro V, Ngeow YF, Tan JL, Herrmann JL, Gaillard JL, Heym B, Wirth T, Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications., BMC Genomics 2016 Feb; 17(): 118.

Glaser P, Martins-Simões P, Villain A, Barbier M, Tristan A, Bouchier C, Ma L, Bes M, Laurent F, Guillemot D, Wirth T, Vandenesch F, Demography and Intercontinental Spread of the USA300 Community-Acquired Methicillin-Resistant Staphylococcus aureus Lineage, MBio 2016 Feb;7(1):e02183-15.

Itan Y, Shang L, Boisson B, Ciancanelli MJ, Markle JG, Martinez-Barricarte R, Scott E, Shah I, Stenson PD, Gleeson J, Cooper DN, Quintana-Murci L, Zhang SY, Abel L, Casanova JL, The mutation significance cutoff: gene-level thresholds for variant predictions, Nat. Methods 2016 Feb;13(2):109-10.

Rascovan N, Maldonado J, Vazquez MP, Eugenia Farías M, , Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea., ISME J 2016 Feb; 10(2): 299-309.

Boritsch EC, Frigui W, Cascioferro A, Malaga W, Etienne G, Laval F, Pawlik A, Le Chevalier F, Orgeur M, Ma L, Bouchier C, Stinear TP, Supply P, Majlessi L, Daffé M, Guilhot C, Brosch R, pks5-recombination-mediated surface remodelling in Mycobacterium tuberculosis emergence, Nat Microbiol 2016 Jan;1:15019.

Maya Spichal, Alice Brion, Sébastien Herbert, Axel Cournac, Martial Marbouty, Christophe Zimmer, Romain Koszul, Emmanuelle Fabre, Evidence for actin dual role in regulating chromosome organization and dynamics in yeast, J Cell Sci 2016 : doi: 10.1242/jcs.175745.

Touchon M, Rocha EPC, Coevolution of the Organization and Structure of Prokaryotic Genomes., Cold Spring Harb Perspect Biol. 2016 Jan 4;8(1).

Cournac A, Marbouty M, Mozziconacci J, Koszul R, Generation and Analysis of Chromosomal Contact Maps of Yeast Species, Methods Mol Biol. 2016;1361:227-45.

Deschamps M, Laval G, Fagny M, Itan Y, Abel L, Casanova JL, Patin E, Quintana-Murci L, Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes, Am. J. Hum. Genet. 2016 Jan;98(1):5-21.

Rascovan N, Huynh H, Chouin G, Adekola K, Georges-Zimmermann P, Signoli M, Desfosses Y, Aboudharam G, Drancourt M, Desnues C, , Tracing back ancient oral microbiomes and oral pathogens using dental pulps from ancient teeth., NPJ Biofilms Microbiomes 2016 ; 2(): 6.

Bernut A, Viljoen A, Dupont C, Sapriel G, Blaise M, Bouchier C, Brosch R, de Chastellier C, Herrmann JL, Kremer L, Insights into the smooth-to-rough transitioning in Mycobacterium bolletii unravels a functional Tyr residue conserved in all mycobacterial MmpL family members, Mol. Microbiol. 2016 Mar;99(5):866-83.

Gennaris A, Ezraty B, Henry C, Agrebi R, Vergnes A, Oheix E, Bos J, Leverrier P, Espinosa L, Szewczyk J, Vertommen D, Iranzo O, Collet JF, Barras F, , Repairing oxidized proteins in the bacterial envelope using respiratory chain electrons., Nature 2015 Dec; 528(7582): 409-412.

Berthet N, Frangeul L, Olaussen KA, Brambilla E, Dorvault N, Girard P, Validire P, Fadel E, Bouchier C, Gessain A, Soria JC, No evidence for viral sequences in five lepidic adenocarcinomas (former “BAC”) by a high-throughput sequencing approach, BMC Res Notes 2015;8:782.

Santos JC, Duchateau M, Fredlund J, Weiner A, Mallet A, Schmitt C, Matondo M, Hourdel V, Chamot-Rooke J, Enninga J, The COPII complex and lysosomal VAMP7 determine intracellular Salmonella localization and growth., Cell Microbiol 2015 Dec; 17(12): 1699-720.

Fagny M, Patin E, MacIsaac JL, Rotival M, Flutre T, Jones MJ, Siddle KJ, Quach H, Harmant C, McEwen LM, Froment A, Heyer E, Gessain A, Betsem E, Mouguiama-Daouda P, Hombert JM, Perry GH, Barreiro LB, Kobor MS, Quintana-Murci L, The epigenomic landscape of African rainforest hunter-gatherers and farmers, Nat Commun 2015 Nov;6:10047.

Lavergne A, de Thoisy B, Tirera S, Donato D, Bouchier C, Catzeflis F, Lacoste V, Identification of lymphocytic choriomeningitis mammarenavirus in house mouse (Mus musculus, Rodentia) in French Guiana, Infect. Genet. Evol. 2016 Jan;37:225-30.

Triska P, Soares P, Patin E, Fernandes V, Cerny V, Pereira L, Extensive Admixture and Selective Pressure Across the Sahel Belt, Genome Biol Evol 2015 Nov;7(12):3484-95.

Cournac A, Koszul R, Mozziconacci J, The 3D folding of metazoan genomes correlates with the association of similar repetitive elements, Nucleic Acids Res. 2015 Nov;.

Marbouty M, Koszul R, Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data, Trends Genet. 2015 Nov;.

Asmar S, Rascovan N, Robert C, Drancourt M, , Draft Genome Sequence of Mycobacterium mucogenicum Strain CSUR P2099., Genome Announc 2015 Nov; 3(6): .

Goudenège D, Travers MA, Lemire A, Petton B, Haffner P, Labreuche Y, Tourbiez D, Mangenot S, Calteau A, Mazel D, Nicolas JL, Jacq A, Le Roux F, A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters, Environ Microbiol. 2015 Nov;17(11):4189-99.

Fradet E, Bayer C, Hollfelder F, Baroud CN, Measuring Fast and Slow Enzyme Kinetics in Stationary Droplets, Anal. Chem. 2015 Dec;87(23):11915-22.

Tebbi A, Levillayer F, Jouvion G, Fiette L, Soubigou G, Varet H, Boudjadja N, Cairo S, Hashimoto K, Suzuki AM, Carninci P, Carissimo A, di Bernardo D, Wei Y, Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress, Carcinogenesis 2016 Jan;37(1):39-48.

Asmar S, Rascovan N, Robert C, Drancourt M, , Draft Genome Sequence of Mycobacterium peregrinum Strain CSUR P2098., Genome Announc 2015 Nov; 3(6): .

Barré-Sinoussi F, Montagutelli X, Animal models are essential to biological research: issues and perspectives, Future Sci OA 2015 Nov;1(4):FSO63.

Nagle N, Ballantyne KN, van Oven M, Tyler-Smith C, Xue Y, Taylor D, Wilcox S, Wilcox L, Turkalov R, van Oorschot RA, McAllister P, Williams L, Kayser M, Mitchell RJ,, Antiquity and diversity of aboriginal Australian Y-chromosomes, Am. J. Phys. Anthropol. 2016 Mar;159(3):367-81.

Balloy V, Varet H, Dillies MA, Proux C, Jagla B, Coppée JY, Tabary O, Corvol H, Chignard M, Guillot L, Normal and Cystic Fibrosis Human Bronchial Epithelial Cells Infected with Pseudomonas aeruginosa Exhibit Distinct Gene Activation Patterns, PLoS ONE 2015;10(10):e0140979.

Itan Y, Shang L, Boisson B, Patin E, Bolze A, Moncada-Vélez M, Scott E, Ciancanelli MJ, Lafaille FG, Markle JG, Martinez-Barricarte R, de Jong SJ, Kong XF, Nitschke P, Belkadi A, Bustamante J, Puel A, Boisson-Dupuis S, Stenson PD, Gleeson JG, Cooper DN, Quintana-Murci L, Claverie JM, Zhang SY, Abel L, Casanova JL, The human gene damage index as a gene-level approach to prioritizing exome variants, Proc. Natl. Acad. Sci. U.S.A. 2015 Nov;112(44):13615-20.

Saffarian A, Mulet C, Naito T, Bouchier C, Tichit M, Ma L, Grompone G, Sansonetti PJ, Pédron T, Draft Genome Sequences of Acinetobacter parvus CM11, Acinetobacter radioresistens CM38, and Stenotrophomonas maltophilia BR12, Isolated from Murine Proximal Colonic Tissue, Genome Announc 2015;3(5).

Yue Cui, Katarzyna Franciszkiewicz, Yvonne K Mburu, Stanislas Mondot, Lionel Le Bourhis, Virginie Premel, Emmanuel Martin, Alexandra Kachaner, Livine Duban, Molly A Ingersoll, Sylvie Rabot, Jean Jaubert, Jean-Pierre de Villartay, Claire Soudais, Olivier Lantz, Mucosal-associated invariant T cell–rich congenic mouse strain allows functional evaluation, Journal of Clinical Investigation, 2015, 125 (11), pp.4171 - 4185. ⟨10.1172/JCI82424⟩.

Monot M, Eckert C, Lemire A, Hamiot A, Dubois T, Tessier C, Dumoulard B, Hamel B, Petit A, Lalande V, Ma L, Bouchier C, Barbut F, Dupuy B, Clostridium difficile: New Insights into the Evolution of the Pathogenicity Locus, Sci Rep 2015;5:15023.

Benn Torres J, Vilar MG, Torres GA, Gaieski JB, Bharath Hernandez R, Browne ZE, Stevenson M, Walters W, Schurr TG,, Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin, PLoS ONE 2015;10(10):e0139192.

Guermonprez C, Michelin S, Baroud CN, Flow distribution in parallel microfluidic networks and its effect on concentration gradient, Biomicrofluidics 2015 Sep;9(5):054119.

Chenal-Francisque V, Maury MM, Lavina M, Touchon M, Leclercq A, Lecuit M, Brisse S, , Clonogrouping, a Rapid Multiplex PCR Method for Identification of Major Clones of Listeria monocytogenes., J Clin Microbiol 2015 Oct; 53(10): 3355-8.

Ménard S, Ben Haddou T, Ramadani AP, Ariey F, Iriart X, Beghain J, Bouchier C, Witkowski B, Berry A, Mercereau-Puijalon O, Benoit-Vical F, Induction of Multidrug Tolerance in Plasmodium falciparum by Extended Artemisinin Pressure, Emerging Infect. Dis. 2015 Oct;21(10):1733-41.

Heloise Muller, Romain Koszul, Conception et synthèse de néochromosomes, 2015;17(4):228-236. doi:10.1684/mte.2015.0574.

Vembar SS, Macpherson CR, Sismeiro O, Coppée JY, Scherf A, The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages, Genome Biol. 2015;16:212.

Morello E, Mallet A, Konto-Ghiorghi Y, Chaze T, Mistou MY, Oliva G, Oliveira L, Di Guilmi AM, Trieu-Cuot P, Dramsi S, Evidence for the Sialylation of PilA, the PI-2a Pilus-Associated Adhesin of Streptococcus agalactiae Strain NEM316, PLoS ONE 2015;10(9):e0138103.

Guidi M, Ruault M, Marbouty M, Loïodice I, Cournac A, Billaudeau C, Hocher A, Mozziconacci J, Koszul R, Taddei A, , Spatial reorganization of telomeres in long-lived quiescent cells., Genome Biol 2015 Sep; 16(1): 206.

Martínez-Cruz B, Mendizabal I, Harmant C, de Pablo R, Ioana M, Angelicheva D, Kouvatsi A, Makukh H, Netea MG, Pamjav H, Zalán A, Tournev I, Marushiakova E, Popov V, Bertranpetit J, Kalaydjieva L, Quintana-Murci L, Comas D, Origins, admixture and founder lineages in European Roma, Eur. J. Hum. Genet. 2016 Jun;24(6):937-43.

Descorps-Declère S, Saguez C, Cournac A, Marbouty M, Rolland T, Ma L, Bouchier C, Moszer I, Dujon B, Koszul R, Richard GF, Genome-wide replication landscape of Candida glabrata, BMC Biol. 2015 Sep;13:69.

Izdebski R, Fiett J, Urbanowicz P, Baraniak A, Derde LP, Bonten MJ, Carmeli Y, Goossens H, Hryniewicz W, Brun-Buisson C, Brisse S, Gniadkowski M, ,, Phylogenetic lineages, clones and β-lactamases in an international collection of Klebsiella oxytoca isolates non-susceptible to expanded-spectrum cephalosporins, J. Antimicrob. Chemother. 2015 Dec;70(12):3230-7.

Mombo IM, Berthet N, Lukashev AN, Bleicker T, Brünink S, Léger L, Atencia R, Cox D, Bouchier C, Durand P, Arnathau C, Brazier L, Fair JN, Schneider BS, Drexler JF, Prugnolle F, Drosten C, Renaud F, Leroy EM, Rougeron V, First Detection of an Enterovirus C99 in a Captive Chimpanzee with Acute Flaccid Paralysis, from the Tchimpounga Chimpanzee Rehabilitation Center, Republic of Congo, PLoS ONE 2015;10(8):e0136700.

Helfrich S, Pfeifer E, Krämer C, Sachs CC, Wiechert W, Kohlheyer D, Nöh K, Frunzke J, Live cell imaging of SOS and prophage dynamics in isogenic bacterial populations, Mol. Microbiol. 2015 Nov;98(4):636-50.

Mozziconacci J, Koszul R, Filling the gap: Micro-C accesses the nucleosomal fiber at 100-1000 bp resolution, Genome Biol. 2015;16(1):169.

Carlos Perez, Lars Mecklenburg, Jean Jaubert, Lucia Martinez-Santamaria, Brian Iritani, Alexsandra Espejo, Eleonora Napoli, Gyu Song, Marcela del Rio, John Digiovanni, Cecilia Giulivi, Mark Bedford, Sharon Y.R. Dent, Richard Wood, Donna F. Kusewitt, Jean-Louis Guénet, Claudio Conti, Fernando Benavides, Increased Susceptibility to Skin Carcinogenesis Associated with a Spontaneous Mouse Mutation in the Palmitoyl Transferase Zdhhc13 Gene, Journal of Investigative Dermatology, 2015, 135 (12), pp.3133-3143. ⟨10.1038/jid.2015.314⟩.

Surinova S, Choi M, Tao S, Schüffler PJ, Chang CY, Clough T, Vysloužil K, Khoylou M, Srovnal J, Liu Y, Matondo M, Hüttenhain R, Weisser H, Buhmann JM, Hajdúch M, Brenner H, Vitek O, Aebersold R, Prediction of colorectal cancer diagnosis based on circulating plasma proteins, EMBO Mol Med 2015 Sep;7(9):1166-78.

San Millan A, Toll-Riera M, Escudero JA, Cantón R, Coque TM, MacLean RC, Sequencing of plasmids pAMBL1 and pAMBL2 from Pseudomonas aeruginosa reveals a blaVIM-1 amplification causing high-level carbapenem resistance, J. Antimicrob. Chemother. 2015 Jul;.

Guénet JL, Panthier JJ, Avner P, Heard E, Montagutelli X, [The legacy of Mary F. Lyon (1925-2014)], Med Sci (Paris) 2015 Jun-Jul;31(6-7):687-9.

Rendueles O, Zee PC, Dinkelacker I, Amherd M, Wielgoss S, Velicer GJ, Rapid and widespread de novo evolution of kin discrimination, Proc. Natl. Acad. Sci. U.S.A. 2015 Jul;112(29):9076-81.

Onori R, Gaiarsa S, Comandatore F, Pongolini S, Brisse S, Colombo A, Cassani G, Marone P, Grossi P, Minoja G, Bandi C, Sassera D, Toniolo A, Tracking Nosocomial Klebsiella pneumoniae Infections and Outbreaks by Whole-Genome Analysis: Small-Scale Italian Scenario within a Single Hospital, J. Clin. Microbiol. 2015 Sep;53(9):2861-8.

Simon-Loriere E, Faye O, Faye O, Koivogui L, Magassouba N, Keita S, Thiberge JM, Diancourt L, Bouchier C, Vandenbogaert M, Caro V, Fall G, Buchmann JP, Matranga CB, Sabeti PC, Manuguerra JC, Holmes EC, Sall AA, Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic, Nature 2015 Aug;524(7563):102-4.

Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, Jenney A, Connor TR, Hsu LY, Severin J, Brisse S, Cao H, Wilksch J, Gorrie C, Schultz MB, Edwards DJ, Nguyen KV, Nguyen TV, Dao TT, Mensink M, Minh VL, Nhu NT, Schultsz C, Kuntaman K, Newton PN, Moore CE, Strugnell RA, Thomson NR, Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health, Proc. Natl. Acad. Sci. U.S.A. 2015 Jul;112(27):E3574-81.

Sacco E, Cortes M, Josseaume N, Bouchier C, Dubée V, Hugonnet JE, Mainardi JL, Rice LB, Arthur M, Mutation landscape of acquired cross-resistance to glycopeptide and β-lactam antibiotics in Enterococcus faecium, Antimicrob. Agents Chemother. 2015 Sep;59(9):5306-15.

Rendueles O, Amherd M, Velicer GJ, Positively Frequency-Dependent Interference Competition Maintains Diversity and Pervades a Natural Population of Cooperative Microbes, Curr. Biol. 2015 Jun;25(13):1673-81.

Rendueles O, Ghigo JM, Mechanisms of Competition in Biofilm Communities, Microbiol Spectr 2015 Jun;3(3).

Rosinski-Chupin I, Sauvage E, Sismeiro O, Villain A, Da Cunha V, Caliot ME, Dillies MA, Trieu-Cuot P, Bouloc P, Lartigue MF, Glaser P, Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae, BMC Genomics 2015 May;16:419.

ArunKumar G, Tatarinova TV, Duty J, Rollo D, Syama A, Arun VS, Kavitha VJ, Triska P, Greenspan B, Wells RS, Pitchappan R, , Genome-wide signatures of male-mediated migration shaping the Indian gene pool, J. Hum. Genet. 2015 May;.

Oliveira PH, Mairhofer J, Alves PM, Lara AR, Kontoravdi C, Advances in the Development of Biotherapeutics, Biomed Res Int 2015;2015:793876.

Xue H, Cordero OX, Camas FM, Trimble W, Meyer F, Guglielmini J, Rocha EP, Polz MF, Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations, MBio 2015;6(3):e00552-15.

Clermont D, Motreff L, Passet V, Fernandez JC, Bizet C, Brisse S, , Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov., Int J Syst Evol Microbiol 2015 May; 65(Pt 5): 1486-1490.

Dequivre M, Diel B, Villard C, Sismeiro O, Durot M, Coppée JY, Nesme X, Vial L, Hommais F, Small RNA Deep-Sequencing Analyses Reveal a New Regulator of Virulence in Agrobacterium fabrum C58, Mol. Plant Microbe Interact. 2015 May;28(5):580-9.

Flot JF, Marie-Nelly H, Koszul R, Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures, FEBS Lett. 2015 Apr;.

Donovan C, Heyer A, Pfeifer E, Polen T, Wittmann A, Krämer R, Frunzke J, Bramkamp M, A prophage-encoded actin-like protein required for efficient viral DNA replication in bacteria, Nucleic Acids Res. 2015 May;43(10):5002-16.

Iqbal N, Guérout AM, Krin E, Le Roux F, Mazel D, Comprehensive Functional Analysis of the 18 Vibrio cholerae N16961 Toxin-Antitoxin Systems Substantiates Their Role in Stabilizing the Superintegron, J. Bacteriol. 2015 Jul;197(13):2150-9.

Davies-Sala C, Soler-Bistué A, Bonomo RA, Zorreguieta A, Tolmasky ME, External guide sequence technology: a path to development of novel antimicrobial therapeutics, Ann. N. Y. Acad. Sci. 2015 Apr;.

Mazuet C, Bouchier C, Popoff MR, Draft Genome Sequence of Clostridium botulinum Strain 277-00 Type B2, Genome Announc 2015;3(2).

Soler-Bistué A, Mondotte JA, Bland MJ, Val ME, Saleh MC, Mazel D, Genomic location of the major ribosomal protein gene locus determines Vibrio cholerae global growth and infectivity., PLoS Genet 2015 Apr; 11(4): e1005156.

Chen X, Hasan M, Libri V, Urrutia A, Beitz B, Rouilly V, Duffy D, Patin É, Chalmond B, Rogge L, Quintana-Murci L, Albert ML, Schwikowski B, , , Automated flow cytometric analysis across large numbers of samples and cell types., Clin Immunol 2015 Apr; 157(2): 249-60.

Hasan M, Beitz B, Rouilly V, Libri V, Urrutia A, Duffy D, Cassard L, Di Santo JP, Mottez E, Quintana-Murci L, Albert ML, Rogge L, , , Semi-automated and standardized cytometric procedures for multi-panel and multi-parametric whole blood immunophenotyping., Clin Immunol 2015 Apr; 157(2): 261-76.

Thomas S, Rouilly V, Patin E, Alanio C, Dubois A, Delval C, Marquier LG, Fauchoux N, Sayegrih S, Vray M, Duffy D, Quintana-Murci L, Albert ML, , , The Milieu Intérieur study – an integrative approach for study of human immunological variance., Clin Immunol 2015 Apr; 157(2): 277-93.

Escudero JA, Loot C, Nivina A, Mazel D, The Integron: Adaptation On Demand., Microbiol Spectr 2015 Apr; 3(2): MDNA3-0019-2014.

Berthelot C, Muffato M, Abecassis J, Roest Crollius H, , The 3D organization of chromatin explains evolutionary fragile genomic regions., Cell Rep 2015 Mar; 10(11): 1913-24.

Berthet N, Périchon B, Mazuet C, Chapetón-Montes D, Bouchier C, Bouvet P, Legeay C, Popoff MR, Courvalin P, A vanG-type locus in Clostridium argentinense, J. Antimicrob. Chemother. 2015 Jul;70(7):1942-5.

Siddle KJ, Tailleux L, Deschamps M, Loh YH, Deluen C, Gicquel B, Antoniewski C, Barreiro LB, Farinelli L, Quintana-Murci L, bacterial infection drives the expression dynamics of microRNAs and their isomiRs, PLoS Genet. 2015 Mar;11(3):e1005064.

Khater F, Balestrino D, Charbonnel N, Dufayard JF, Brisse S, Forestier C, In silico analysis of usher encoding genes in Klebsiella pneumoniae and characterization of their role in adhesion and colonization, PLoS ONE 2015;10(3):e0116215.

Misevic D, Frénoy A, Lindner AB, Taddei F, Shape matters: lifecycle of cooperative patches promotes cooperation in bulky populations, Evolution 2015 Mar;69(3):788-802.

Wang J, McIntosh F, Radomski N, Dewar K, Simeone R, Enninga J, Brosch R, Rocha EP, Veyrier FJ, Behr MA, Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii, Genome Biol Evol 2015 Mar;7(3):856-70.

Kasher PR, Jenkinson EM, Briolat V, Gent D, Morrissey C, Zeef LA, Rice GI, Levraud JP, Crow YJ, , Characterization of samhd1 morphant zebrafish recapitulates features of the human type I interferonopathy Aicardi-Goutières syndrome., J. Immunol. 2015 Mar; 194(6): 2819-25.

Thierry A, Khanna V, Créno S, Lafontaine I, Ma L, Bouchier C, Dujon B, Macrotene chromosomes provide insights to a new mechanism of high-order gene amplification in eukaryotes, Nat Commun 2015 Jan;6:6154.

Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, Turner JM, Bertelsen MF, Murchison EP, Flicek P, Odom DT, , Enhancer evolution across 20 mammalian species., Cell 2015 Jan; 160(3): 554-66.

Da Cunha V, Davies MR, Douarre PE, Rosinski-Chupin I, Margarit I, Spinali S, Perkins T, Lechat P, Dmytruk N, Sauvage E, Ma L, Romi B, Tichit M, Lopez-Sanchez MJ, Descorps-Declere S, Souche E, Buchrieser C, Trieu-Cuot P, Moszer I, Clermont D, Maione D, Bouchier C, McMillan DJ, Parkhill J, Telford JL, Dougan G, Walker MJ, Holden MT, Poyart C, Glaser P, Corrigendum: Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline, Nat Commun 2015 Jan;6:6108.

Passet V, Brisse S, Association of tellurite resistance with hypervirulent clonal groups of Klebsiella pneumoniae, J. Clin. Microbiol. 2015 Apr;53(4):1380-2.

Marbouty M, Le Gall A, Cattoni DI, Cournac A, Koh A, Fiche JB, Mozziconacci J, Murray H, Koszul R, Nollmann M, Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging, Mol. Cell 2015 Aug;59(4):588-602.

Bouvet P, Sautereau J, Le Coustumier A, Mory F, Bouchier C, Popoff MR, Foot Infection by Clostridium sordellii: Case Report and Review of 15 Cases in France, J. Clin. Microbiol. 2015 Apr;53(4):1423-7.

Balaresque P, Poulet N, Cussat-Blanc S, Gerard P, Quintana-Murci L, Heyer E, Jobling MA, Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations, Eur. J. Hum. Genet. 2015 Jan;.

Lévi-Meyrueis C, Monteil V, Sismeiro O, Dillies MA, Kolb A, Monot M, Dupuy B, Duarte SS, Jagla B, Coppée JY, Beraud M, Norel F, Repressor activity of the RpoS/σS-dependent RNA polymerase requires DNA binding, Nucleic Acids Res. 2015 Feb;43(3):1456-68.

Tokuda S, Do Valle TZ, Batista L, Simon-Chazottes D, Guillemot L, Bouloy M, Flamand M, Montagutelli X, Panthier JJ, The genetic basis for susceptibility to Rift Valley fever disease in MBT/Pas mice, Genes Immun. 2015 Apr-May;16(3):206-12.

Nemec A, Krizova L, Maixnerova M, Sedo O, Brisse S, Higgins PG, Acinetobacter seifertii sp. nov., a member of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex isolated from human clinical specimens, Int. J. Syst. Evol. Microbiol. 2015 Mar;65(Pt 3):934-42.

Bos J, Zhang Q, Vyawahare S, Rogers E, Rosenberg SM, Austin RH, , Emergence of antibiotic resistance from multinucleated bacterial filaments., Proc Natl Acad Sci U S A 2015 Jan; 112(1): 178-83.

Jean-Louis Guénet, Jean-Jacques Panthier, Fernando Benavides, Xavier Montagutelli, Genetics of the mouse, Springer-Verlag, 2015, XVII Chapters, 408 pages..

Funfak A, Fisch C, Abdel Motaal HT, Diener J, Combettes L, Baroud CN, Dupuis-Williams P, Paramecium swimming and ciliary beating patterns: a study on four RNA interference mutations, Integr Biol (Camb) 2015 Jan;7(1):90-100.

Ambroset C, Coluzzi C, Guédon G, Devignes MD, Loux V, Lacroix T, Payot S, Leblond-Bourget N, , New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration., Front Microbiol 2015 ; 6(): 1483.

Ponce-Soto GY, Aguirre-von-Wobeser E, Eguiarte LE, Elser JJ, Lee ZM, Souza V, Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment., Front Microbiol 2015 ; 6(): 246.

Guilbaud M, Piveteau P, Desvaux M, Brisse S, Briandet R, Exploring the diversity of Listeria monocytogenes biofilm architecture by high-throughput confocal laser scanning microscopy and the predominance of the honeycomb-like morphotype, Appl. Environ. Microbiol. 2015 Mar;81(5):1813-9.

Marie-Nelly H, Marbouty M, Cournac A, Flot JF, Liti G, Parodi DP, Syan S, Guillén N, Margeot A, Zimmer C, Koszul R, , High-quality genome (re)assembly using chromosomal contact data., Nat Commun 2014 Dec; 5(): 5695.

Jeannot K, Diancourt L, Vaux S, Thouverez M, Ribeiro A, Coignard B, Courvalin P, Brisse S, Molecular epidemiology of carbapenem non-susceptible Acinetobacter baumannii in France, PLoS ONE 2014;9(12):e115452.

Marbouty M, Cournac A, Flot JF, Marie-Nelly H, Mozziconacci J, Koszul R, Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms, Elife 2014;3:e03318.

Vaux S, Criscuolo A, Desnos-Ollivier M, Diancourt L, Tarnaud C, Vandenbogaert M, Brisse S, Coignard B, Dromer F, , , Multicenter outbreak of infections by Saprochaete clavata, an unrecognized opportunistic fungal pathogen., mBio 2014 Dec; 5(6): .

Almelli T, Nuel G, Bischoff E, Aubouy A, Elati M, Wang CW, Dillies MA, Coppée JY, Ayissi GN, Basco LK, Rogier C, Ndam NT, Deloron P, Tahar R, Differences in gene transcriptomic pattern of Plasmodium falciparum in children with cerebral malaria and asymptomatic carriers, PLoS ONE 2014;9(12):e114401.

Wasels F, Monot M, Spigaglia P, Barbanti F, Ma L, Bouchier C, Dupuy B, Mastrantonio P, Inter- and intraspecies transfer of a Clostridium difficile conjugative transposon conferring resistance to MLSB, Microb. Drug Resist. 2014 Dec;20(6):555-60.

Val ME, Soler-Bistué A, Bland MJ, Mazel D, Management of multipartite genomes: the Vibrio cholerae model., Curr Opin Microbiol 2014 Dec; 22(): 120-6.

Colombo RP, Fernández Bidondo L, Silvani VA, Carbonetto MB, Rascovan N, Bompadre MJ, Pérgola M, Cuenca G, Godeas AM, , Diversity of arbuscular mycorrhizal fungi in soil from the Pampa Ondulada, Argentina, assessed by pyrosequencing and morphological techniques., Can J Microbiol 2014 Dec; 60(12): 819-27.

Mazuet C, Sautereau J, Legeay C, Bouchier C, Bouvet P, Popoff MR, An atypical outbreak of food-borne botulism due to Clostridium botulinum types B and E from ham, J. Clin. Microbiol. 2015 Feb;53(2):722-6.

Maatallah M, Vading M, Kabir MH, Bakhrouf A, Kalin M, Nauclér P, Brisse S, Giske CG, Klebsiella variicola is a frequent cause of bloodstream infection in the stockholm area, and associated with higher mortality compared to K. pneumoniae, PLoS ONE 2014;9(11):e113539.

Salissou A, Zamanka H, Biyghe Binze B, Rivière T, Tichit M, Ibrahim ML, Fandeur T, Low Prevalence of Pfcrt Resistance Alleles among Patients with Uncomplicated Falciparum Malaria in Niger Six Years after Chloroquine Withdrawal, Malar Res Treat 2014;2014:614190.

Khan ME, Borde C, Rocha EP, Mériaux V, Maréchal V, Escoll P, Goyard S, Cavaillon JM, Manoury B, Doyen N, TLR9 activation is triggered by the excess of stimulatory versus inhibitory motifs present in Trypanosomatidae DNA, PLoS Negl Trop Dis 2014 Nov;8(11):e3308.

Berthet N, Falguières M, Filippone C, Bertolus C, Bole-Feysot C, Brisse S, Gessain A, Heard I, Favre M, Resequencing microarray technology for genotyping human papillomavirus in cervical smears, PLoS ONE 2014;9(11):e109301.

Thuan Beng Saw*, Shreyansh Jain*, Benoit Ladoux & Chwee Teck Lim (* equal contribution), Mechanobiology of Collective Cell Migration, Cellular and Molecular Bioengineering 8, no. 1 (March 2015): 3–13.

N' Dilimabaka N, Berthet N, Rougeron V, Mangombi JB, Durand P, Maganga GD, Bouchier C, Schneider BS, Fair J, Renaud F, Leroy EM, Evidence of lymphocytic choriomeningitis virus (LCMV) in domestic mice in Gabon: risk of emergence of LCMV encephalitis in Central Africa, J. Virol. 2015 Jan;89(2):1456-60.

Baharoglu Z, Mazel D, , SOS, the formidable strategy of bacteria against aggressions., FEMS Microbiol Rev 2014 Nov; 38(6): 1126-45.

Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas-Chanoine MH, Decré D, Brisse S, Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups, Emerging Infect. Dis. 2014 Nov;20(11):1812-20.

Oliveira PH, da Silva CL, Cabral JM, Concise review: Genomic instability in human stem cells: current status and future challenges, Stem Cells 2014 Nov;32(11):2824-32.

Mazel D, Colwell R, Klose K, Oliver J, Crumlish M, McDougald D, Bland MJ, Austin B, VIBRIO 2014 meeting report, Res. Microbiol. 2014 Dec;165(10):857-64.

McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L, Minx P, Murphy D, O'Quin KE, Rétaux S, Rohner N, Searle SM, Stahl BA, Tabin C, Volff JN, Yoshizawa M, Warren WC, The cavefish genome reveals candidate genes for eye loss, Nat Commun 2014;5:5307.

Abby SS, Néron B, Ménager H, Touchon M, Rocha EP, MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems, PLoS ONE 2014;9(10):e110726.

Touchon M, Cury J, Yoon EJ, Krizova L, Cerqueira GC, Murphy C, Feldgarden M, Wortman J, Clermont D, Lambert T, Grillot-Courvalin C, Nemec A, Courvalin P, Rocha EP, , The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences., Genome Biol Evol 2014 Oct; 6(10): 2866-82.

Touchon M, Bobay LM, Rocha EP, The chromosomal accommodation and domestication of mobile genetic elements, Curr. Opin. Microbiol. 2014 Dec;22:22-9.

Compain F, Babosan A, Brisse S, Genel N, Audo J, Ailloud F, Kassis-Chikhani N, Arlet G, Decré D, Multiplex PCR for detection of seven virulence factors and K1/K2 capsular serotypes of Klebsiella pneumoniae, J. Clin. Microbiol. 2014 Dec;52(12):4377-80.

Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Nicolas-Chanoine MH, Decré D, Brisse S, Development of a multiplex PCR assay for identification of Klebsiella pneumoniae hypervirulent clones of capsular serotype K2, J. Med. Microbiol. 2014 Dec;63(Pt 12):1608-14.

Bourhy P, Collet L, Brisse S, Picardeau M, Leptospira mayottensis sp. nov., a pathogenic species of the genus Leptospira isolated from humans, Int. J. Syst. Evol. Microbiol. 2014 Dec;64(Pt 12):4061-7.

Lesne A, Riposo J, Roger P, Cournac A, Mozziconacci J, 3D genome reconstruction from chromosomal contacts, Nat. Methods 2014 Nov;11(11):1141-3.

Barreiro LB, Quintana-Murci L, Editorial Overview: immunogenetics and transplantation: bringing evolution and genomics to human immunology, Curr. Opin. Immunol. 2014 Oct;30:v-vii.

Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R, A repository of assays to quantify 10,000 human proteins by SWATH-MS, Sci Data 2014;1:140031.

Rüeger S, Bochud PY, Dufour JF, Müllhaupt B, Semela D, Heim MH, Moradpour D, Cerny A, Malinverni R, Booth DR, Suppiah V, George J, Argiro L, Halfon P, Bourlière M, Talal AH, Jacobson IM, Patin E, Nalpas B, Poynard T, Pol S, Abel L, Kutalik Z, Negro F, Impact of common risk factors of fibrosis progression in chronic hepatitis C, Gut 2015 Oct;64(10):1605-15.

Bialek-Davenet S, Lavigne JP, Guyot K, Mayer N, Tournebize R, Brisse S, Leflon-Guibout V, Nicolas-Chanoine MH, Differential contribution of AcrAB and OqxAB efflux pumps to multidrug resistance and virulence in Klebsiella pneumoniae, J. Antimicrob. Chemother. 2015 Jan;70(1):81-8.

Ségurel L, Quintana-Murci L, Preserving immune diversity through ancient inheritance and admixture, Curr. Opin. Immunol. 2014 Oct;30:79-84.

Remigi P, Capela D, Clerissi C, Tasse L, Torchet R, Bouchez O, Batut J, Cruveiller S, Rocha EP, Masson-Boivin C, Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer, PLoS Biol. 2014 Sep;12(9):e1001942.

Leblond CS, Nava C, Polge A, Gauthier J, Huguet G, Lumbroso S, Giuliano F, Stordeur C, Depienne C, Mouzat K, Pinto D, Howe J, Lemière N, Durand CM, Guibert J, Ey E, Toro R, Peyre H, Mathieu A, Amsellem F, Rastam M, Gillberg IC, Rappold GA, Holt R, Monaco AP, Maestrini E, Galan P, Heron D, Jacquette A, Afenjar A, Rastetter A, Brice A, Devillard F, Assouline B, Laffargue F, Lespinasse J, Chiesa J, Rivier F, Bonneau D, Regnault B, Zelenika D, Delepine M, Lathrop M, Sanlaville D, Schluth-Bolard C, Edery P, Perrin L, Tabet AC, Schmeisser MJ, Boeckers TM, Coleman M, Sato D, Szatmari P, Scherer SW, Rouleau GA, Betancur C, Leboyer M, Gillberg C, Delorme R, Bourgeron T, , Meta-analysis of SHANK Mutations in Autism Spectrum Disorders: a gradient of severity in cognitive impairments., PLoS Genet 2014 Sep; 10(9): e1004580.

Coeuret S, de La Blanchardière A, Saguet-Rysanek V, Chèze S, Tavernier M, Arsène D, Criscuolo A, Brisse S, Vergnaud M, Verdon R, Lecuit M, , Campylobacter coli cultured from the stools of a patient with immunoproliferative small intestinal disease., Clin Microbiol Infect 2014 Sep; 20(9): 908-11.

Zhang Q, Bos J, Tarnopolskiy G, Sturm JC, Kim H, Pourmand N, Austin RH, , You cannot tell a book by looking at the cover: Cryptic complexity in bacterial evolution., Biomicrofluidics 2014 Sep; 8(5): 052004.

Yamada A, Lee S, Bassereau P, Baroud CN, Trapping and release of giant unilamellar vesicles in microfluidic wells, Soft Matter 2014 Aug;10(32):5878-85.

Siddle KJ, Quintana-Murci L, The Red Queen’s long race: human adaptation to pathogen pressure, Curr. Opin. Genet. Dev. 2014 Dec;29:31-8.

Perry GH, Foll M, Grenier JC, Patin E, Nédélec Y, Pacis A, Barakatt M, Gravel S, Zhou X, Nsobya SL, Excoffier L, Quintana-Murci L, Dominy NJ, Barreiro LB, Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers, Proc. Natl. Acad. Sci. U.S.A. 2014 09;111(35):E3596-603.

Scornec H, Tichit M, Bouchier C, Pédron T, Cavin JF, Sansonetti PJ, Licandro-Seraut H, Rapid 96-well plates DNA extraction and sequencing procedures to identify genome-wide transposon insertion sites in a difficult to lyse bacterium: Lactobacillus casei, J. Microbiol. Methods 2014 Nov;106:78-82.

Oliveira PH, Touchon M, Rocha EP, The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts, Nucleic Acids Res. 2014;42(16):10618-31.

Genth H, Pauillac S, Schelle I, Bouvet P, Bouchier C, Varela-Chavez C, Just I, Popoff MR, Haemorrhagic toxin and lethal toxin from Clostridium sordellii strain vpi9048: molecular characterization and comparative analysis of substrate specificity of the large clostridial glucosylating toxins, Cell. Microbiol. 2014 Nov;16(11):1706-21.

Bobay LM, Touchon M, Rocha EP, Pervasive domestication of defective prophages by bacteria, Proc. Natl. Acad. Sci. U.S.A. 2014 Aug;111(33):12127-32.

Qin N, Yang F, Li A, Prifti E, Chen Y, Shao L, Guo J, Le Chatelier E, Yao J, Wu L, Zhou J, Ni S, Liu L, Pons N, Batto JM, Kennedy SP, Leonard P, Yuan C, Ding W, Chen Y, Hu X, Zheng B, Qian G, Xu W, Ehrlich SD, Zheng S, Li L, Alterations of the human gut microbiome in liver cirrhosis, Nature 2014 Sep;513(7516):59-64.

Marine Livrozet, Sophie Vandermeersch, Laurent Mesnard, Elizabeth Thioulouse, Jean Jaubert, Jean-Jacques Boffa, Jean-Philippe Haymann, Laurent Baud, Dominique Bazin, Michel Daudon, Letavernier Emmanuel, An Animal Model of Type A Cystinuria Due to Spontaneous Mutation in 129S2/SvPasCrl Mice, PLoS ONE, 2014, 9 (7), pp.e102700. ⟨10.1371/journal.pone.0102700⟩.

Heikkinen AT, Friedlein A, Matondo M, Hatley OJ, Petsalo A, Juvonen R, Galetin A, Rostami-Hodjegan A, Aebersold R, Lamerz J, Dunkley T, Cutler P, Parrott N, Quantitative ADME proteomics – CYP and UGT enzymes in the Beagle dog liver and intestine, Pharm. Res. 2015 Jan;32(1):74-90.

Bolotin A, de Wouters T, Schnupf P, Bouchier C, Loux V, Rhimi M, Jamet A, Dervyn R, Boudebbouze S, Blottière HM, Sorokin A, Snel J, Cerf-Bensussan N, Gaboriau-Routhiau V, van de Guchte M, Maguin E, Genome Sequence of “Candidatus Arthromitus” sp. Strain SFB-Mouse-NL, a Commensal Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions, Genome Announc 2014;2(4).

Mombo IM, Berthet N, Bouchier C, Fair JN, Schneider BS, Renaud F, Leroy EM, Rougeron V, Characterization of a genogroup I sapovirus isolated from chimpanzees in the republic of congo, Genome Announc 2014;2(4).

Vilar MG, Melendez C, Sanders AB, Walia A, Gaieski JB, Owings AC, Schurr TG, , Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies, Am. J. Phys. Anthropol. 2014 Nov;155(3):352-68.

Althaus D, Lehner A, Brisse S, Maury M, Tasara T, Stephan R, Characterization of Listeria monocytogenes strains isolated during 2011-2013 from human infections in Switzerland, Foodborne Pathog. Dis. 2014 Oct;11(10):753-8.

Hespeels B, Knapen M, Hanot-Mambres D, Heuskin AC, Pineux F, LUCAS S, Koszul R, Van Doninck K, Gateway to genetic exchange? DNA double-strand breaks in the bdelloid rotifer Adineta vaga submitted to desiccation, J. Evol. Biol. 2014 Jul;27(7):1334-45.

Brisse S, Passet V, Grimont PA, Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola, Int. J. Syst. Evol. Microbiol. 2014 Sep;64(Pt 9):3146-52.

Ma L, Shen CJ, Cohen ÉA, Xiong SD, Wang JH, miRNA-1236 inhibits HIV-1 infection of monocytes by repressing translation of cellular factor VprBP, PLoS ONE 2014;9(6):e99535.

Baharoglu Z, Mazel D, Influence of very short patch mismatch repair on SOS inducing lesions after aminoglycoside treatment in Escherichia coli, Res. Microbiol. 2014 Jul-Aug;165(6):476-80.

Magalie Duchateau, Thomas J.D. Jørgensen, Ophélie Robine, Edith Nicol, Christian Malosse, Julia Chamot-Rooke, Guillaume van der Rest, Ion source parameters and hydrogen scrambling in the ECD of selectively deuterated peptides, IJMS, 2014, 367, 21:27.

Fromont-Racine, M; Saveanu, C, mRNA Degradation and Decay (book chapter), Fungal RNA Biology.

Criscuolo A, Brisse S, AlienTrimmer removes adapter oligonucleotides with high sensitivity in short-insert paired-end reads. Commentary on Turner (2014) Assessment of insert sizes and adapter content in FASTQ data from NexteraXT libraries, Front Genet 2014;5:130.

Jang SM, Azebi S, Soubigou G, Muchardt C, DYRK1A phoshorylates histone H3 to differentially regulate the binding of HP1 isoforms and antagonize HP1-mediated transcriptional repression, EMBO Rep. 2014 Jun;15(6):686-94.

Lévi-Meyrueis C, Monteil V, Sismeiro O, Dillies MA, Monot M, Jagla B, Coppée JY, Dupuy B, Norel F, Expanding the RpoS/σS-network by RNA sequencing and identification of σS-controlled small RNAs in Salmonella, PLoS ONE 2014;9(5):e96918.

Urbieta MS, Rascovan N, Castro C, Revale S, Giaveno MA, Vazquez M, Donati ER, , Draft Genome Sequence of the Novel Thermoacidophilic Archaeon Acidianus copahuensis Strain ALE1, Isolated from the Copahue Volcanic Area in Neuquen, Argentina., Genome Announc 2014 May; 2(3): .

Chaze T, Guillot A, Valot B, Langella O, Chamot-Rooke J, Di Guilmi AM, Trieu-Cuot P, Dramsi S, Mistou MY, O-Glycosylation of the N-terminal region of the serine-rich adhesin Srr1 of Streptococcus agalactiae explored by mass spectrometry, Mol. Cell Proteomics 2014 Sep;13(9):2168-82.

Aguirre-von-Wobeser E, Soberón-Chávez G, Eguiarte LE, Ponce-Soto GY, Vázquez-Rosas-Landa M, Souza V, Two-role model of an interaction network of free-living γ-proteobacteria from an oligotrophic environment., Environ Microbiol 2014 May; 16(5): 1366-77.

Hernández N, Escudero JA, San Millán Á, González-Zorn B, Lobo JM, Verdú JR, Suárez M, Culturable aerobic and facultative bacteria from the gut of the polyphagic dung beetle Thorectes lusitanicus, Insect Sci. 2015 Apr;22(2):178-90.

Elhaik E, Tatarinova T, Chebotarev D, Piras IS, Maria Calò C, De Montis A, Atzori M, Marini M, Tofanelli S, Francalacci P, Pagani L, Tyler-Smith C, Xue Y, Cucca F, Schurr TG, Gaieski JB, Melendez C, Vilar MG, Owings AC, Gómez R, Fujita R, Santos FR, Comas D, Balanovsky O, Balanovska E, Zalloua P, Soodyall H, Pitchappan R, Ganeshprasad A, Hammer M, Matisoo-Smith L, Wells RS, , Geographic population structure analysis of worldwide human populations infers their biogeographical origins, Nat Commun 2014;5:3513.

Gonçalves GA, Oliveira PH, Gomes AG, Prather KL, Lewis LA, Prazeres DM, Monteiro GA, Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters, Appl. Microbiol. Biotechnol. 2014 Aug;98(15):6609-19.

Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, Noël B, Bento P, Da Silva C, Labadie K, Alberti A, Aury JM, Louis A, Dehais P, Bardou P, Montfort J, Klopp C, Cabau C, Gaspin C, Thorgaard GH, Boussaha M, Quillet E, Guyomard R, Galiana D, Bobe J, Volff JN, Genêt C, Wincker P, Jaillon O, Roest Crollius H, Guiguen Y, , The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates., Nat Commun 2014 Apr; 5(): 3657.

Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM, Corander J, Dufour M, Ringwood T, Savin C, Bouchier C, Martin L, Miettinen M, Shubin M, Riehm JM, Laukkanen-Ninios R, Sihvonen LM, Siitonen A, Skurnik M, Falcão JP, Fukushima H, Scholz HC, Prentice MB, Wren BW, Parkhill J, Carniel E, Achtman M, McNally A, Thomson NR, Parallel independent evolution of pathogenicity within the genus Yersinia, Proc. Natl. Acad. Sci. U.S.A. 2014 May;111(18):6768-73.

Compain F, Frangeul L, Drieux L, Verdet C, Brisse S, Arlet G, Decré D, Complete nucleotide sequence of two multidrug-resistant IncR plasmids from Klebsiella pneumoniae, Antimicrob. Agents Chemother. 2014 Jul;58(7):4207-10.

Bellini A, Girard PM, Tessier L, Sage E, Francesconi S, Fission yeast Rad52 phosphorylation restrains error prone recombination pathways, PLoS ONE 2014;9(4):e95788.

Subota I, Julkowska D, Vincensini L, Reeg N, Buisson J, Blisnick T, Huet D, Perrot S, Santi-Rocca J, Duchateau M, Hourdel V, Rousselle JC, Cayet N, Namane A, Chamot-Rooke J, Bastin P, Proteomic analysis of intact flagella of procyclic Trypanosoma brucei cells identifies novel flagellar proteins with unique sub-localization and dynamics, Mol. Cell Proteomics 2014 Jul;13(7):1769-86.

Marie-Nelly H, Marbouty M, Cournac A, Liti G, Fischer G, Zimmer C, Koszul R, , Filling annotation gaps in yeast genomes using genome-wide contact maps., Bioinformatics 2014 Aug; 30(15): 2105-13.

Itan Y, Mazel M, Mazel B, Abhyankar A, Nitschke P, Quintana-Murci L, Boisson-Dupuis S, Boisson B, Abel L, Zhang SY, Casanova JL, HGCS: an online tool for prioritizing disease-causing gene variants by biological distance, BMC Genomics 2014;15:256.

Janbon G, Ormerod KL, Paulet D, Byrnes EJ, Yadav V, Chatterjee G, Mullapudi N, Hon CC, Billmyre RB, Brunel F, Bahn YS, Chen W, Chen Y, Chow EW, Coppée JY, Floyd-Averette A, Gaillardin C, Gerik KJ, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh YP, Ianiri G, Jones S, Kodira CD, Kozubowski L, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wollschlaeger C, Wood IA, Zeng Q, Neuvéglise C, Newlon CS, Perfect JR, Lodge JK, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA, Cuomo CA, Dietrich FS, , Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation., PLoS Genet 2014 Apr; 10(4): e1004261.

Fagny M, Patin E, Enard D, Barreiro LB, Quintana-Murci L, Laval G, Exploring the occurrence of classic selective sweeps in humans using whole-genome sequencing data sets, Mol. Biol. Evol. 2014 Jul;31(7):1850-68.

Eshghi A, Becam J, Lambert A, Sismeiro O, Dillies MA, Jagla B, Wunder EA, Ko AI, Coppee JY, Goarant C, Picardeau M, A putative regulatory genetic locus modulates virulence in the pathogen Leptospira interrogans, Infect. Immun. 2014 Jun;82(6):2542-52.

Briolat V, Jouneau L, Carvalho R, Palha N, Langevin C, Herbomel P, Schwartz O, Spaink HP, Levraud JP, Boudinot P, , Contrasted innate responses to two viruses in zebrafish: insights into the ancestral repertoire of vertebrate IFN-stimulated genes., J. Immunol. 2014 May; 192(9): 4328-41.

Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, Martin JA, Bilgel M, Bohutski P, Boulier KM, Capaldo BJ, Chang J, Charoen K, Choi WJ, Deng P, DiCarlo JE, Doong J, Dunn J, Feinberg JI, Fernandez C, Floria CE, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau CY, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Ma H, Mao J, McDade JE, McMillan A, Moore AM, Oh WC, Ouyang Y, Patel R, Paul M, Paulsen LC, Qiu J, Rhee A, Rubashkin MG, Soh IY, Sotuyo NE, Srinivas V, Suarez A, Wong A, Wong R, Xie WR, Xu Y, Yu AT, Koszul R, Bader JS, Boeke JD, Chandrasegaran S, Total synthesis of a functional designer eukaryotic chromosome, Science 2014 Apr;344(6179):55-8.

Marbouty M, Ermont C, Dujon B, Richard GF, Koszul R, Purification of G1 daughter cells from different Saccharomycetes species through an optimized centrifugal elutriation procedure, Yeast 2014 May;31(5):159-66.

Bécavin C, Bouchier C, Lechat P, Archambaud C, Creno S, Gouin E, Wu Z, Kühbacher A, Brisse S, Pucciarelli MG, García-del Portillo F, Hain T, Portnoy DA, Chakraborty T, Lecuit M, Pizarro-Cerdá J, Moszer I, Bierne H, Cossart P, , Comparison of widely used Listeria monocytogenes strains EGD, 10403S, and EGD-e highlights genomic variations underlying differences in pathogenicity., mBio 2014 Mar; 5(2): e00969-14.

Darragh Duffy, Vincent Rouilly, Valentina Libri, Milena Hasan, Benoit Beitz, Mikael David, Alejandra Urrutia, Aurélie Bisiaux, Samuel T Labrie, Annick Dubois, Ivo G Boneca, Cécile Delval, Stéphanie Thomas, Lars Rogge, Manfred Schmolz, Lluis Quintana-Murci, Matthew L Albert, Laurent Abel, Andres Alcover, Philippe Bousso, Ana Cumano, Marc Daëron, Caroline Demangel, Ludovic Deriano, James Di santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Antonio Freitas, Ivo Gomperts-Boneca, Serge Hercberg, Olivier Lantz, Claude Leclerc, Hugo Mouquet, Sandra Pellegrini, Stanislas Pol, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Vassili Soumelis, Frédéric Tangy, Eric Tartour, Antoine Toubert, Marie-Noëlle Ungeheuer, Functional analysis via standardized whole-blood stimulation systems defines the boundaries of a healthy immune response to complex stimuli., Immunity, 2014, 40 (3), pp.436-50. ⟨10.1016/j.immuni.2014.03.002⟩.

Diago-Navarro E, Chen L, Passet V, Burack S, Ulacia-Hernando A, Kodiyanplakkal RP, Levi MH, Brisse S, Kreiswirth BN, Fries BC, Carbapenem-resistant Klebsiella pneumoniae exhibit variability in capsular polysaccharide and capsule associated virulence traits, J. Infect. Dis. 2014 Sep;210(5):803-13.

Criscuolo A, de la Blanchardière A, Coeuret S, Passet V, Saguet-Rysanek V, Vergnaud M, Verdon R, Leclercq A, Lecuit M, Brisse S, , Draft Genome Sequence of Campylobacter coli Strain IPSID-1 Isolated from a Patient with Immunoproliferative Small Intestinal Disease., Genome Announc 2014 Mar; 2(2): .

Rentsch CA, Birkhäuser FD, Biot C, Gsponer JR, Bisiaux A, Wetterauer C, Lagranderie M, Marchal G, Orgeur M, Bouchier C, Bachmann A, Ingersoll MA, Brosch R, Albert ML, Thalmann GN, Bacillus Calmette-Guérin strain differences have an impact on clinical outcome in bladder cancer immunotherapy, Eur. Urol. 2014 Oct;66(4):677-88.

Guglielmini J, Néron B, Abby SS, Garcillán-Barcia MP, de la Cruz F, Rocha EP, Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion, Nucleic Acids Res. 2014 May;42(9):5715-27.

Krin E, Cambray G, Mazel D, The superintegron integrase and the cassette promoters are co-regulated in Vibrio cholerae, PLoS ONE 2014;9(3):e91194.

Dubois-Colas N, Petit-Jentreau L, Barreiro LB, Durand S, Soubigou G, Lecointe C, Klibi J, Rezaï K, Lokiec F, Coppée JY, Gicquel B, Tailleux L, Extracellular adenosine triphosphate affects the response of human macrophages infected with Mycobacterium tuberculosis, J. Infect. Dis. 2014 Sep;210(5):824-33.

Huguet G, Nava C, Lemière N, Patin E, Laval G, Ey E, Brice A, Leboyer M, Szepetowski P, Gillberg C, Depienne C, Delorme R, Bourgeron T, Heterogeneous pattern of selective pressure for PRRT2 in human populations, but no association with autism spectrum disorders, PLoS ONE 2014;9(3):e88600.

Siegel TN, Hon CC, Zhang Q, Lopez-Rubio JJ, Scheidig-Benatar C, Martins RM, Sismeiro O, Coppée JY, Scherf A, Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum, BMC Genomics 2014;15:150.

Savin C, Martin L, Bouchier C, Filali S, Chenau J, Zhou Z, Becher F, Fukushima H, Thomson NR, Scholz HC, Carniel E, The Yersinia pseudotuberculosis complex: characterization and delineation of a new species, Yersinia wautersii, Int. J. Med. Microbiol. 2014 May;304(3-4):452-63.

Burguener GF, Maldonado MJ, Revale S, Fernández Do Porto D, Rascován N, Vázquez M, Farías ME, Marti MA, Turjanski AG, , Draft Genome Sequence of the Polyextremophilic Halorubrum sp. Strain AJ67, Isolated from Hyperarsenic Lakes in the Argentinian Puna., Genome Announc 2014 Feb; 2(1): .

Der Sarkissian C, Brotherton P, Balanovsky O, Templeton JE, Llamas B, Soubrier J, Moiseyev V, Khartanovich V, Cooper A, Haak W, , Mitochondrial genome sequencing in Mesolithic North East Europe Unearths a new sub-clade within the broadly distributed human haplogroup C1, PLoS ONE 2014;9(2):e87612.

Val ME, Kennedy SP, Soler-Bistué AJ, Barbe V, Bouchier C, Ducos-Galand M, Skovgaard O, Mazel D, Fuse or die: how to survive the loss of Dam in Vibrio cholerae., Mol Microbiol 2014 Feb; 91(4): 665-78.

Baharoglu Z, Babosan A, Mazel D, , Identification of genes involved in low aminoglycoside-induced SOS response in Vibrio cholerae: a role for transcription stalling and Mfd helicase., Nucleic Acids Res 2014 Feb; 42(4): 2366-79.

Loot C, Parissi V, Escudero JA, Amarir-Bouhram J, Bikard D, Mazel D, The integron integrase efficiently prevents the melting effect of Escherichia coli single-stranded DNA-binding protein on folded attC sites., J Bacteriol 2014 Feb; 196(4): 762-71.

Brisse S, Brehony C, Conceição T, Cubero M, Glasner C, Le Gouil M, Renvoisé A, Sheppard S, Weinert LA, Microbial molecular markers and epidemiological surveillance in the era of high throughput sequencing: an update from the IMMEM-10 conference, Res. Microbiol. 2014 Feb-Mar;165(2):140-53.

Siddle KJ, Deschamps M, Tailleux L, Nédélec Y, Pothlichet J, Lugo-Villarino G, Libri V, Gicquel B, Neyrolles O, Laval G, Patin E, Barreiro LB, Quintana-Murci L, A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection, Genome Res. 2014 May;24(5):850-9.

Clarke AC, Prost S, Stanton JA, White WT, Kaplan ME, Matisoo-Smith EA, , From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes, BMC Genomics 2014;15:68.

Rendueles O, Beloin C, Latour-Lambert P, Ghigo JM, A new biofilm-associated colicin with increased efficiency against biofilm bacteria, ISME J 2014 Jun;8(6):1275-88.

Sesto N, Touchon M, Andrade JM, Kondo J, Rocha EP, Arraiano CM, Archambaud C, Westhof É, Romby P, Cossart P, A PNPase dependent CRISPR System in Listeria, PLoS Genet. 2014 Jan;10(1):e1004065.

Mozzetta C, Pontis J, Fritsch L, Robin P, Portoso M, Proux C, Margueron R, Ait-Si-Ali S, The histone H3 lysine 9 methyltransferases G9a and GLP regulate polycomb repressive complex 2-mediated gene silencing, Mol. Cell 2014 Jan;53(2):277-89.

Guyet A, Benaroudj N, Proux C, Gominet M, Coppée JY, Mazodier P, Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism., BMC Microbiol 2014 Apr; 14(): 81.

Patin E, Siddle KJ, Laval G, Quach H, Harmant C, Becker N, Froment A, Régnault B, Lemée L, Gravel S, Hombert JM, Van der Veen L, Dominy NJ, Perry GH, Barreiro LB, Verdu P, Heyer E, Quintana-Murci L, The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists, Nat Commun 2014;5:3163.

Kunze G, Gaillardin C, Czernicka M, Durrens P, Martin T, Böer E, Gabaldón T, Cruz JA, Talla E, Marck C, Goffeau A, Barbe V, Baret P, Baronian K, Beier S, Bleykasten C, Bode R, Casaregola S, Despons L, Fairhead C, Giersberg M, Gierski PP, Hähnel U, Hartmann A, Jankowska D, Jubin C, Jung P, Lafontaine I, Leh-Louis V, Lemaire M, Marcet-Houben M, Mascher M, Morel G, Richard GF, Riechen J, Sacerdot C, Sarkar A, Savel G, Schacherer J, Sherman DJ, Stein N, Straub ML, Thierry A, Trautwein-Schult A, Vacherie B, Westhof E, Worch S, Dujon B, Souciet JL, Wincker P, Scholz U, Neuvéglise C, , The complete genome of Blastobotrys (Arxula) adeninivorans LS3 – a yeast of biotechnological interest., Biotechnol Biofuels 2014 ; 7(): 66.

Carbonetto B, Rascovan N, Álvarez R, Mentaberry A, Vázquez MP, , Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas., PLoS One 2014 ; 9(6): e99949.

Macheras E, Konjek J, Roux AL, Thiberge JM, Bastian S, Leão SC, Palaci M, Sivadon-Tardy V, Gutierrez C, Richter E, Rüsch-Gerdes S, Pfyffer GE, Bodmer T, Jarlier V, Cambau E, Brisse S, Caro V, Rastogi N, Gaillard JL, Heym B, Multilocus sequence typing scheme for the Mycobacterium abscessus complex, Res. Microbiol. 2014 Feb-Mar;165(2):82-90.

Thibeaux R, Weber C, Hon CC, Dillies MA, Avé P, Coppée JY, Labruyère E, Guillén N, Identification of the virulence landscape essential for Entamoeba histolytica invasion of the human colon, PLoS Pathog. 2013;9(12):e1003824.

Ariey F, Witkowski B, Amaratunga C, Beghain J, Langlois AC, Khim N, Kim S, Duru V, Bouchier C, Ma L, Lim P, Leang R, Duong S, Sreng S, Suon S, Chuor CM, Bout DM, Ménard S, Rogers WO, Genton B, Fandeur T, Miotto O, Ringwald P, Le Bras J, Berry A, Barale JC, Fairhurst RM, Benoit-Vical F, Mercereau-Puijalon O, Ménard D, A molecular marker of artemisinin-resistant Plasmodium falciparum malaria, Nature 2014 Jan;505(7481):50-5.

Archambaud C, Sismeiro O, Toedling J, Soubigou G, Bécavin C, Lechat P, Lebreton A, Ciaudo C, Cossart P, The intestinal microbiota interferes with the microRNA response upon oral Listeria infection, MBio 2013;4(6):e00707-13.

Vatin M, Bouvier S, Bellazi L, Montagutelli X, Laissue P, Ziyyat A, Serres C, De Mazancourt P, Dieudonné MN, Mornet E, Vaiman D, Gris JC, Polymorphisms of human placental alkaline phosphatase are associated with in vitro fertilization success and recurrent pregnancy loss, Am. J. Pathol. 2014 Feb;184(2):362-8.

Fradet E, Abbyad P, Vos MH, Baroud CN, Parallel measurements of reaction kinetics using ultralow-volumes, Lab Chip 2013 Nov;13(22):4326-30.

Frénoy A, Taddei F, Misevic D, Genetic architecture promotes the evolution and maintenance of cooperation, PLoS Comput. Biol. 2013;9(11):e1003339.

Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte EM, Aebersold R, Bühlmann P, Statistical approach to protein quantification, Mol. Cell Proteomics 2014 Feb;13(2):666-77.

Cantinelli T, Chenal-Francisque V, Diancourt L, Frezal L, Leclercq A, Wirth T, Lecuit M, Brisse S, “Epidemic clones” of Listeria monocytogenes are widespread and ancient clonal groups., J Clin Microbiol 2013 Nov; 51(11): 3770-9.

Arcangioli B, How to choose the right mate, PLoS Genet. 2013 Oct;9(10):e1003881.

Rabhi I, Rabhi S, Ben-Othman R, Aniba MR, , Trentin B, Piquemal D, Regnault B, Guizani-Tabbane L, Comparative analysis of resistant and susceptible macrophage gene expression response to Leishmania major parasite, BMC Genomics 2013;14:723.

Ben-Mustapha I, Ben-Ali M, Mekki N, Patin E, Harmant C, Bouguila J, Elloumi-Zghal H, Harbi A, Béjaoui M, Boughammoura L, Chemli J, Barbouche MR, A 1,100-year-old founder effect mutation in IL12B gene is responsible for Mendelian susceptibility to mycobacterial disease in Tunisian patients, Immunogenetics 2014 Jan;66(1):67-71.

Saba CK, Escudero JA, Herrera-Leon S, Porrero MC, Suarez M, Dominguez L, Demuyakor B, Gonzalez-Zorn B, First identification of Salmonella Urbana and Salmonella Ouakam in humans in Africa, J Infect Dev Ctries 2013;7(10):691-5.

Tordjman S, Najjar I, Bellissant E, Anderson GM, Barburoth M, Cohen D, Jaafari N, Schischmanoff O, Fagard R, Lagdas E, Kermarrec S, Ribardiere S, Botbol M, Fougerou C, Bronsard G, Vernay-Leconte J, Advances in the research of melatonin in autism spectrum disorders: literature review and new perspectives, Int J Mol Sci 2013 Oct;14(10):20508-42.

Brandt G, Haak W, Adler CJ, Roth C, Szécsényi-Nagy A, Karimnia S, Möller-Rieker S, Meller H, Ganslmeier R, Friederich S, Dresely V, Nicklisch N, Pickrell JK, Sirocko F, Reich D, Cooper A, Alt KW, , Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity, Science 2013 Oct;342(6155):257-61.

Girard PM, Graindorge D, Smirnova V, Rigolet P, Francesconi S, Scanlon S, Sage E, Oxidative stress in mammalian cells impinges on the cysteines redox state of human XRCC3 protein and on its cellular localization, PLoS ONE 2013;8(10):e75751.

Audrain B, Ferrières L, Zairi A, Soubigou G, Dobson C, Coppée JY, Beloin C, Ghigo JM, Induction of the Cpx envelope stress pathway contributes to Escherichia coli tolerance to antimicrobial peptides, Appl. Environ. Microbiol. 2013 Dec;79(24):7770-9.

Lemaire J, Mkannez G, Guerfali FZ, Gustin C, Attia H, Sghaier RM, , Dellagi K, Laouini D, Renard P, MicroRNA expression profile in human macrophages in response to Leishmania major infection, PLoS Negl Trop Dis 2013;7(10):e2478.

Casanova JL, Abel L, Quintana-Murci L, Immunology taught by human genetics, Cold Spring Harb. Symp. Quant. Biol. 2013;78:157-72.

Bouvet P, Ruimy R, Bouchier C, Faucher N, Mazuet C, Popoff MR, An atypical Clostridium strain related to the Clostridium botulinum group III strain isolated from a human blood culture, J. Clin. Microbiol. 2014 Jan;52(1):339-43.

Brisse S, Passet V, Haugaard AB, Babosan A, Kassis-Chikhani N, Struve C, Decré D, wzi Gene sequencing, a rapid method for determination of capsular type for Klebsiella strains, J. Clin. Microbiol. 2013 Dec;51(12):4073-8.

Bobay LM, Touchon M, Rocha EP, Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability, PLoS Genet. 2013;9(9):e1003825.

Aimé C, Laval G, Patin E, Verdu P, Ségurel L, Chaix R, Hegay T, Quintana-Murci L, Heyer E, Austerlitz F, Human genetic data reveal contrasting demographic patterns between sedentary and nomadic populations that predate the emergence of farming, Mol. Biol. Evol. 2013 Dec;30(12):2629-44.

Pawlik A, Garnier G, Orgeur M, Tong P, Lohan A, Le Chevalier F, Sapriel G, Roux AL, Conlon K, Honoré N, Dillies MA, Ma L, Bouchier C, Coppée JY, Gaillard JL, Gordon SV, Loftus B, Brosch R, Herrmann JL, Identification and characterization of the genetic changes responsible for the characteristic smooth-to-rough morphotype alterations of clinically persistent Mycobacterium abscessus, Mol. Microbiol. 2013 Nov;90(3):612-29.

Gabaldón T, Martin T, Marcet-Houben M, Durrens P, Bolotin-Fukuhara M, Lespinet O, Arnaise S, Boisnard S, Aguileta G, Atanasova R, Bouchier C, Couloux A, Creno S, Almeida Cruz J, Devillers H, Enache-Angoulvant A, Guitard J, Jaouen L, Ma L, Marck C, Neuvéglise C, Pelletier E, Pinard A, Poulain J, Recoquillay J, Westhof E, Wincker P, Dujon B, Hennequin C, Fairhead C, Comparative genomics of emerging pathogens in the Candida glabrata clade, BMC Genomics 2013;14:623.

Palha N, Guivel-Benhassine F, Briolat V, Lutfalla G, Sourisseau M, Ellett F, Wang CH, Lieschke GJ, Herbomel P, Schwartz O, Levraud JP, , Real-time whole-body visualization of Chikungunya Virus infection and host interferon response in zebrafish., PLoS Pathog. 2013 ; 9(9): e1003619.

Nicolas-Chanoine MH, Robert J, Vigan M, Laouénan C, Brisse S, Mentré F, Jarlier V, , Different factors associated with CTX-M-producing ST131 and non-ST131 Escherichia coli clinical isolates, PLoS ONE 2013;8(9):e72191.

Cousin S, Clermont D, Creno S, Ma L, Loux V, Bizet C, Bouchier C, , Draft Genome Sequence of Lactobacillus pasteurii CRBIP 24.76T., Genome Announc 2013 Aug; 1(4): .

Cousin S, Creno S, Ma L, Clermont D, Loux V, Bizet C, Bouchier C, , Draft Genome Sequence of Lactobacillus hominis Strain CRBIP 24.179T, Isolated from Human Intestine., Genome Announc 2013 Aug; 1(4): .

Cousin S, Loux V, Ma L, Creno S, Clermont D, Bizet C, Bouchier C, , Draft Genome Sequences of Lactobacillus equicursoris CIP 110162T and Lactobacillus sp. Strain CRBIP 24.137, Isolated from Thoroughbred Racehorse Feces and Human Urine, Respectively., Genome Announc 2013 Aug; 1(4): .

Falentin H, Cousin S, Clermont D, Creno S, Ma L, Chuat V, Loux V, Rüdiger P, Bizet C, Bouchier C, Draft Genome Sequences of Five Strains of Lactobacillus acidophilus, Strain CIP 76.13T, Isolated from Humans, Strains CIRM-BIA 442 and CIRM-BIA 445, Isolated from Dairy Products, and Strains DSM 20242 and DSM 9126 of Unknown Origin, Genome Announc 2013 Aug;1(4).

Babiano R, Badis G, Saveanu C, Namane A, Doyen A, Díaz-Quintana A, Jacquier A, Fromont-Racine M, de la Cruz J, Yeast ribosomal protein L7 and its homologue Rlp7 are simultaneously present at distinct sites on pre-60S ribosomal particles, Nucleic Acids Res. 2013 Nov;41(20):9461-70.

Eskandarian HA, Impens F, Nahori MA, Soubigou G, Coppée JY, Cossart P, Hamon MA, A role for SIRT2-dependent histone H3K18 deacetylation in bacterial infection, Science 2013 Aug;341(6145):1238858.

Poznik GD, Henn BM, Yee MC, Sliwerska E, Euskirchen GM, Lin AA, Snyder M, Quintana-Murci L, Kidd JM, Underhill PA, Bustamante CD, Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females, Science 2013 Aug;341(6145):562-5.

Criscuolo A, Brisse S, AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads, Genomics 2013 Nov-Dec;102(5-6):500-6.

Angebault C, Djossou F, Abélanet S, Permal E, Ben Soltana M, Diancourt L, Bouchier C, Woerther PL, Catzeflis F, Andremont A, d'Enfert C, Bougnoux ME, Candida albicans is not always the preferential yeast colonizing humans: a study in Wayampi Amerindians, J. Infect. Dis. 2013 Nov;208(10):1705-16.

Rascovan N, Carbonetto B, Revale S, Reinert MD, Alvarez R, Godeas AM, Colombo R, Aguilar M, Novas MV, Iannone L, Zelada AM, Pardo A, Schrauf G, Mentaberry A, Vazquez MP, , The PAMPA datasets: a metagenomic survey of microbial communities in Argentinean pampean soils., Microbiome 2013 Jul; 1(1): 21.

Buffet JP, Pisanu B, Brisse S, Roussel S, Félix B, Halos L, Chapuis JL, Vayssier-Taussat M, Deciphering bartonella diversity, recombination, and host specificity in a rodent community, PLoS ONE 2013;8(7):e68956.

Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EG, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthélémy RM, Bast J, Bazykin GA, Chabrol O, Couloux A, Da Rocha M, Da Silva C, Gladyshev E, Gouret P, Hallatschek O, Hecox-Lea B, Labadie K, Lejeune B, Piskurek O, Poulain J, Rodriguez F, Ryan JF, Vakhrusheva OA, Wajnberg E, Wirth B, Yushenova I, Kellis M, Kondrashov AS, Mark Welch DB, Pontarotti P, Weissenbach J, Wincker P, Jaillon O, Van Doninck K, Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga, Nature 2013 Aug;500(7463):453-7.

Smokvina T, Wels M, Polka J, Chervaux C, Brisse S, Boekhorst J, van Hylckama Vlieg JE, Siezen RJ, Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity, PLoS ONE 2013;8(7):e68731.

Quach H, Wilson D, Laval G, Patin E, Manry J, Guibert J, Barreiro LB, Nerrienet E, Verschoor E, Gessain A, Przeworski M, Quintana-Murci L, Different selective pressures shape the evolution of Toll-like receptors in human and African great ape populations, Hum. Mol. Genet. 2013 Dec;22(23):4829-40.

Oliveira PH, Mairhofer J, Marker-free plasmids for biotechnological applications – implications and perspectives, Trends Biotechnol. 2013 Sep;31(9):539-47.

Beuzelin C, Evnouchidou I, Rigolet P, Cauvet-Burgevin A, Girard PM, Dardalhon D, Culina S, Gdoura A, van Endert P, Francesconi S, Deletion of the fission yeast homologue of human insulinase reveals a TORC1-dependent pathway mediating resistance to proteotoxic stress, PLoS ONE 2013;8(6):e67705.

Goudenège D, Labreuche Y, Krin E, Ansquer D, Mangenot S, Calteau A, Médigue C, Mazel D, Polz MF, Le Roux F, Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits, ISME J 2013 Oct;7(10):1985-96.

Travier L, Rendueles O, Ferrières L, Herry JM, Ghigo JM, Escherichia coli resistance to nonbiocidal antibiofilm polysaccharides is rare and mediated by multiple mutations leading to surface physicochemical modifications, Antimicrob. Agents Chemother. 2013 Aug;57(8):3960-8.

Chenal-Francisque V, Diancourt L, Cantinelli T, Passet V, Tran-Hykes C, Bracq-Dieye H, Leclercq A, Pourcel C, Lecuit M, Brisse S, , Optimized Multilocus variable-number tandem-repeat analysis assay and its complementarity with pulsed-field gel electrophoresis and multilocus sequence typing for Listeria monocytogenes clone identification and surveillance., J Clin Microbiol 2013 Jun; 51(6): 1868-80.

Baharoglu Z, Garriss G, Mazel D, , Multiple Pathways of Genome Plasticity Leading to Development of Antibiotic Resistance., Antibiotics (Basel) 2013 May; 2(2): 288-315.

Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, Sanz P, Yang-Yao D, Manry J, Ciani G, Luiselli D, Quintana-Murci L, Comas D, Pettener D, , Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata, PLoS ONE 2013;8(5):e65441.

Quax TE, Voet M, Sismeiro O, Dillies MA, Jagla B, Coppée JY, Sezonov G, Forterre P, van der Oost J, Lavigne R, Prangishvili D, Massive activation of archaeal defense genes during viral infection, J. Virol. 2013 Aug;87(15):8419-28.

Lebeaux D, Chauhan A, Rendueles O, Beloin C, From in vitro to in vivo Models of Bacterial Biofilm-Related Infections, Pathogens 2013;2(2):288-356.

Soutourina OA, Monot M, Boudry P, Saujet L, Pichon C, Sismeiro O, Semenova E, Severinov K, Le Bouguenec C, Coppée JY, Dupuy B, Martin-Verstraete I, Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile, PLoS Genet. 2013 May;9(5):e1003493.

Quereda JJ, Pucciarelli MG, Botello-Morte L, Calvo E, Carvalho F, Bouchier C, Vieira A, Mariscotti JF, Chakraborty T, Cossart P, Hain T, Cabanes D, García-Del Portillo F, Occurrence of mutations impairing sigma factor B (SigB) function upon inactivation of Listeria monocytogenes genes encoding surface proteins, Microbiology (Reading, Engl.) 2013 Jul;159(Pt 7):1328-39.

Escudero JA, San Millan A, Montero N, Gutierrez B, Ovejero CM, Carrilero L, González-Zorn B, SatR is a repressor of fluoroquinolone efflux pump SatAB, Antimicrob. Agents Chemother. 2013 Jul;57(7):3430-3.

Schughart K, Libert C, , Kas MJ, Controlling complexity: the clinical relevance of mouse complex genetics, Eur. J. Hum. Genet. 2013 Nov;21(11):1191-6.

Matsuki T, Pédron T, Regnault B, Mulet C, Hara T, Sansonetti PJ, Epithelial cell proliferation arrest induced by lactate and acetate from Lactobacillus casei and Bifidobacterium breve, PLoS ONE 2013;8(4):e63053.

Daub JT, Hofer T, Cutivet E, Dupanloup I, Quintana-Murci L, Robinson-Rechavi M, Excoffier L, Evidence for polygenic adaptation to pathogens in the human genome, Mol. Biol. Evol. 2013 Jul;30(7):1544-58.

Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch GJ, White S, Chow W, Kilian B, Quintais LT, Guerra-Assunção JA, Zhou Y, Gu Y, Yen J, Vogel JH, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird GK, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliot D, Eliott D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Mortimer B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper J, Cooper J, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley CM, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster SC, Carter NP, Harrow J, Ning Z, Herrero J, Searle SM, Enright A, Geisler R, Plasterk RH, Lee C, Westerfield M, de Jong PJ, Zon LI, Postlethwait JH, Nüsslein-Volhard C, Hubbard TJ, Roest Crollius H, Rogers J, Stemple DL, , The zebrafish reference genome sequence and its relationship to the human genome., Nature 2013 Apr; 496(7446): 498-503.

Zhou Z, McCann A, Litrup E, Murphy R, Cormican M, Fanning S, Brown D, Guttman DS, Brisse S, Achtman M, Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona, PLoS Genet. 2013 Apr;9(4):e1003471.

Joffret ML, Bouchier C, Grandadam M, Zeller H, Maufrais C, Bourhy H, Despres P, Delpeyroux F, Dacheux L, Genomic characterization of Sebokele virus 1 (SEBV1) reveals a new candidate species among the genus Parechovirus, J. Gen. Virol. 2013 Jul;94(Pt 7):1547-53.

Rosinski-Chupin I, Sauvage E, Mairey B, Mangenot S, Ma L, Da Cunha V, Rusniok C, Bouchier C, Barbe V, Glaser P, Reductive evolution in Streptococcus agalactiae and the emergence of a host adapted lineage, BMC Genomics 2013;14:252.

Bolze A, Mahlaoui N, Byun M, Turner B, Trede N, Ellis SR, Abhyankar A, Itan Y, Patin E, Brebner S, Sackstein P, Puel A, Picard C, Abel L, Quintana-Murci L, Faust SN, Williams AP, Baretto R, Duddridge M, Kini U, Pollard AJ, Gaud C, Frange P, Orbach D, Emile JF, Stephan JL, Sorensen R, Plebani A, Hammarstrom L, Conley ME, Selleri L, Casanova JL, Ribosomal protein SA haploinsufficiency in humans with isolated congenital asplenia, Science 2013 May;340(6135):976-8.

Lartigue MF, Nordmann P, Edelstein MV, Cuzon G, Brisse S, Poirel L, Characterization of an extended-spectrum class A β-lactamase from a novel enterobacterial species taxonomically related to Rahnella spp./Ewingella spp, J. Antimicrob. Chemother. 2013 Aug;68(8):1733-6.

Komarova AV, Combredet C, Sismeiro O, Dillies MA, Jagla B, Sanchez David RY, Vabret N, Coppée JY, Vidalain PO, Tangy F, Identification of RNA partners of viral proteins in infected cells., RNA Biol 2013 Jun; 10(6): 944-56.

Fevre C, Almeida AS, Taront S, Pedron T, Huerre M, Prevost MC, Kieusseian A, Cumano A, Brisse S, Sansonetti PJ, Tournebize R, A novel murine model of rhinoscleroma identifies Mikulicz cells, the disease signature, as IL-10 dependent derivatives of inflammatory monocytes, EMBO Mol Med 2013 Apr;5(4):516-30.

Pothlichet J, Quintana-Murci L, The genetics of innate immunity sensors and human disease, Int. Rev. Immunol. 2013 Apr;32(2):157-208.

Oliveira PH, da Silva CL, Cabral JM, An appraisal of human mitochondrial DNA instability: new insights into the role of non-canonical DNA structures and sequence motifs, PLoS ONE 2013;8(3):e59907.

Itan Y, Zhang SY, Vogt G, Abhyankar A, Herman M, Nitschke P, Fried D, Quintana-Murci L, Abel L, Casanova JL, The human gene connectome as a map of short cuts for morbid allele discovery, Proc. Natl. Acad. Sci. U.S.A. 2013 Apr;110(14):5558-63.

Defenouillère Q, Yao Y, Mouaikel J, Namane A, Galopier A, Decourty L, Doyen A, Malabat C, Saveanu C, Jacquier A, Fromont-Racine M, Cdc48-associated complex bound to 60S particles is required for the clearance of aberrant translation products, Proc. Natl. Acad. Sci. U.S.A. 2013 Mar;110(13):5046-51.

Andres P, Lucero C, Soler-Bistué A, Guerriero L, Albornoz E, Tran T, Zorreguieta A, , Galas M, Corso A, Tolmasky ME, Petroni A, Differential distribution of plasmid-mediated quinolone resistance genes in clinical enterobacteria with unusual phenotypes of quinolone susceptibility from Argentina, Antimicrob. Agents Chemother. 2013 Jun;57(6):2467-75.

Guérout AM, Iqbal N, Mine N, Ducos-Galand M, Van Melderen L, Mazel D, Characterization of the phd-doc and ccd toxin-antitoxin cassettes from Vibrio superintegrons, J. Bacteriol. 2013 May;195(10):2270-83.

Quintana-Murci L, Clark AG, Population genetic tools for dissecting innate immunity in humans, Nat. Rev. Immunol. 2013 Apr;13(4):280-93.

Clavaud C, Jourdain R, Bar-Hen A, Tichit M, Bouchier C, Pouradier F, El Rawadi C, Guillot J, Ménard-Szczebara F, Breton L, Latgé JP, Mouyna I, Dandruff is associated with disequilibrium in the proportion of the major bacterial and fungal populations colonizing the scalp, PLoS ONE 2013;8(3):e58203.

Machado LS, de Oliveira FG, Rocha EP, dos Santos PH, Briso AL, Sundefeld ML, Sundfeld RH, Clinical trial evaluating color change and tooth sensitivity throughout and following in-office bleaching, Int J Periodontics Restorative Dent 2013 Mar-Apr;33(2):209-15.

Rocha EP, Evolution. With a little help from prokaryotes, Science 2013 Mar;339(6124):1154-5.

Guérillot R, Da Cunha V, Sauvage E, Bouchier C, Glaser P, Modular evolution of TnGBSs, a new family of integrative and conjugative elements associating insertion sequence transposition, plasmid replication, and conjugation for their spreading, J. Bacteriol. 2013 May;195(9):1979-90.

Savin C, Frangeul L, Ma L, Bouchier C, Moszer I, Carniel E, Draft Genome Sequence of a Clinical Strain of Yersinia enterocolitica (IP10393) of Bioserotype 4/O:3 from France, Genome Announc 2013 Jan;1(1).

Der Sarkissian C, Balanovsky O, Brandt G, Khartanovich V, Buzhilova A, Koshel S, Zaporozhchenko V, Gronenborn D, Moiseyev V, Kolpakov E, Shumkin V, Alt KW, Balanovska E, Cooper A, Haak W, , Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe, PLoS Genet. 2013;9(2):e1003296.

Casetti L, Martin-Lannerée S, Najjar I, Plo I, Augé S, Roy L, Chomel JC, Lauret E, Turhan AG, Dusanter-Fourt I, Differential contributions of STAT5A and STAT5B to stress protection and tyrosine kinase inhibitor resistance of chronic myeloid leukemia stem/progenitor cells, Cancer Res. 2013 Apr;73(7):2052-8.

Burkovics P, Sebesta M, Sisakova A, Plault N, Szukacsov V, Robert T, Pinter L, Marini V, Kolesar P, Haracska L, Gangloff S, Krejci L, Srs2 mediates PCNA-SUMO-dependent inhibition of DNA repair synthesis, EMBO J. 2013 Mar;32(5):742-55.

Hon CC, Weber C, Sismeiro O, Proux C, Koutero M, Deloger M, Das S, Agrahari M, Dillies MA, Jagla B, Coppee JY, Bhattacharya A, Guillen N, Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica, Nucleic Acids Res. 2013 Feb;41(3):1936-52.

Badro DA, Douaihy B, Haber M, Youhanna SC, Salloum A, Ghassibe-Sabbagh M, Johnsrud B, Khazen G, Matisoo-Smith E, Soria-Hernanz DF, Wells RS, Tyler-Smith C, Platt DE, Zalloua PA, , Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern Middle Eastern populations with European and African populations, PLoS ONE 2013;8(1):e54616.

N'guessan CA, Brisse S, Le Roux-Nio AC, Poussier S, Koné D, Wicker E, Development of variable number of tandem repeats typing schemes for Ralstonia solanacearum, the agent of bacterial wilt, banana Moko disease and potato brown rot, J. Microbiol. Methods 2013 Mar;92(3):366-74.

Struelens MJ, Brisse S, From molecular to genomic epidemiology: transforming surveillance and control of infectious diseases, Euro Surveill. 2013;18(4):20386.

Vasseur E, Quintana-Murci L, The impact of natural selection on health and disease: uses of the population genetics approach in humans, Evol Appl 2013 Jun;6(4):596-607.

Verdu P, Becker NS, Froment A, Georges M, Grugni V, Quintana-Murci L, Hombert JM, Van der Veen L, Le Bomin S, Bahuchet S, Heyer E, Austerlitz F, Sociocultural behavior, sex-biased admixture, and effective population sizes in Central African Pygmies and non-Pygmies, Mol. Biol. Evol. 2013 Apr;30(4):918-37.

Supply P, Marceau M, Mangenot S, Roche D, Rouanet C, Khanna V, Majlessi L, Criscuolo A, Tap J, Pawlik A, Fiette L, Orgeur M, Fabre M, Parmentier C, Frigui W, Simeone R, Boritsch EC, Debrie AS, Willery E, Walker D, Quail MA, Ma L, Bouchier C, Salvignol G, Sayes F, Cascioferro A, Seemann T, Barbe V, Locht C, Gutierrez MC, Leclerc C, Bentley SD, Stinear TP, Brisse S, Médigue C, Parkhill J, Cruveiller S, Brosch R, Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis, Nat. Genet. 2013 Feb;45(2):172-9.

Bernier SP, Lebeaux D, DeFrancesco AS, Valomon A, Soubigou G, Coppée JY, Ghigo JM, Beloin C, Starvation, together with the SOS response, mediates high biofilm-specific tolerance to the fluoroquinolone ofloxacin, PLoS Genet. 2013;9(1):e1003144.

Dangla R, Kayi SC, Baroud CN, Droplet microfluidics driven by gradients of confinement, Proc. Natl. Acad. Sci. U.S.A. 2013 Jan;110(3):853-8.

Andres J, Arsène-Ploetze F, Barbe V, Brochier-Armanet C, Cleiss-Arnold J, Coppée JY, Dillies MA, Geist L, Joublin A, Koechler S, Lassalle F, Marchal M, Médigue C, Muller D, Nesme X, Plewniak F, Proux C, Ramírez-Bahena MH, Schenowitz C, Sismeiro O, Vallenet D, Santini JM, Bertin PN, Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26, Genome Biol Evol 2013;5(5):934-53.

Cousin S, Motreff L, Gulat-Okalla ML, Gouyette C, Spröer C, Schumann P, Begaud E, Bouchier C, Clermont D, Bizet C, , Lactobacillus pasteurii sp. nov. and Lactobacillus hominis sp. nov., Int J Syst Evol Microbiol 2013 Jan; 63(Pt 1): 53-59.

Bikard D, Mazel D, Shuffling of DNA cassettes in a synthetic integron, Methods Mol. Biol. 2013;1073:169-74.

Baharoglu Z, Krin E, Mazel D, , RpoS plays a central role in the SOS induction by sub-lethal aminoglycoside concentrations in Vibrio cholerae., PLoS Genet 2013 ; 9(4): e1003421.

Elhaik E, Greenspan E, Staats S, Krahn T, Tyler-Smith C, Xue Y, Tofanelli S, Francalacci P, Cucca F, Pagani L, Jin L, Li H, Schurr TG, Greenspan B, Spencer Wells R, , The GenoChip: a new tool for genetic anthropology, Genome Biol Evol 2013;5(5):1021-31.

Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Jane Adler C, Richards SM, Sarkissian CD, Ganslmeier R, Friederich S, Dresely V, van Oven M, Kenyon R, Van der Hoek MB, Korlach J, Luong K, Ho SY, Quintana-Murci L, Behar DM, Meller H, Alt KW, Cooper A, , Adhikarla S, Ganesh Prasad AK, Pitchappan R, Varatharajan Santhakumari A, Balanovska E, Balanovsky O, Bertranpetit J, Comas D, Martínez-Cruz B, Melé M, Clarke AC, Matisoo-Smith EA, Dulik MC, Gaieski JB, Owings AC, Schurr TG, Vilar MG, Hobbs A, Soodyall H, Javed A, Parida L, Platt DE, Royyuru AK, Jin L, Li S, Kaplan ME, Merchant NC, John Mitchell R, Renfrew C, Lacerda DR, Santos FR, Soria Hernanz DF, Spencer Wells R, Swamikrishnan P, Tyler-Smith C, Paulo Vieira P, Ziegle JS, Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans, Nat Commun 2013;4:1764.

Manry J, Quintana-Murci L, A genome-wide perspective of human diversity and its implications in infectious disease, Cold Spring Harb Perspect Med 2013 Jan;3(1):a012450.

Nuñez PA, Romero H, Farber MD, Rocha EP, Natural selection for operons depends on genome size, Genome Biol Evol 2013;5(11):2242-54.

Brito PH, Rocha EP, Xavier KB, Gordo I, Natural genome diversity of AI-2 quorum sensing in Escherichia coli: conserved signal production but labile signal reception, Genome Biol Evol 2013;5(1):16-30.

Gutierrez A, Laureti L, Crussard S, Abida H, Rodríguez-Rojas A, Blázquez J, Baharoglu Z, Mazel D, Darfeuille F, Vogel J, Matic I, β-Lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity, Nat Commun 2013;4:1610.

Bos J, Duverger Y, Thouvenot B, Chiaruttini C, Branlant C, Springer M, Charpentier B, Barras F, , The sRNA RyhB regulates the synthesis of the Escherichia coli methionine sulfoxide reductase MsrB but not MsrA., PLoS One 2013 ; 8(5): e63647.

Farías ME, Rascovan N, Toneatti DM, Albarracín VH, Flores MR, Poiré DG, Collavino MM, Aguilar OM, Vazquez MP, Polerecky L, , The discovery of stromatolites developing at 3570 m above sea level in a high-altitude volcanic lake Socompa, Argentinean Andes., PLoS One 2013 ; 8(1): e53497.

Baudoin M, Song Y, Manneville P, Baroud CN, Airway reopening through catastrophic events in a hierarchical network, Proc. Natl. Acad. Sci. U.S.A. 2013 Jan;110(3):859-64.

Patillon B, Luisi P, Blanché H, Patin E, Cann HM, Génin E, Sabbagh A, Positive selection in the chromosome 16 VKORC1 genomic region has contributed to the variability of anticoagulant response in humans, PLoS ONE 2012;7(12):e53049.

Manry J, Quintana-Murci L, [Population genetics and human immunity: the interferon paradigm], Med Sci (Paris) 2012 Dec;28(12):1095-101.

Holmes A, Roseaulin L, Schurra C, Waxin H, Lambert S, Zaratiegui M, Martienssen RA, Arcangioli B, Lsd1 and lsd2 control programmed replication fork pauses and imprinting in fission yeast, Cell Rep 2012 Dec;2(6):1513-20.

Giraud E, Lecoeur H, Soubigou G, Coppée JY, Milon G, Prina E, Lang T, Distinct transcriptional signatures of bone marrow-derived C57BL/6 and DBA/2 dendritic leucocytes hosting live Leishmania amazonensis amastigotes, PLoS Negl Trop Dis 2012;6(12):e1980.

Bobay LM, Rocha EP, Touchon M, The adaptation of temperate bacteriophages to their host genomes, Mol. Biol. Evol. 2013 Apr;30(4):737-51.

Andriantsoanirina V, Khim N, Ratsimbasoa A, Witkowski B, Benedet C, Canier L, Bouchier C, Tichit M, Durand R, Ménard D, Plasmodium falciparum Na+/H+ exchanger (pfnhe-1) genetic polymorphism in Indian Ocean malaria-endemic areas, Am. J. Trop. Med. Hyg. 2013 Jan;88(1):37-42.

Arunkumar G, Soria-Hernanz DF, Kavitha VJ, Arun VS, Syama A, Ashokan KS, Gandhirajan KT, Vijayakumar K, Narayanan M, Jayalakshmi M, Ziegle JS, Royyuru AK, Parida L, Wells RS, Renfrew C, Schurr TG, Smith CT, Platt DE, Pitchappan R, , Population differentiation of southern Indian male lineages correlates with agricultural expansions predating the caste system, PLoS ONE 2012;7(11):e50269.

Nogueira T, Touchon M, Rocha EP, Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria, PLoS ONE 2012;7(11):e49403.

Léger P, Lara E, Jagla B, Sismeiro O, Mansuroglu Z, Coppée JY, Bonnefoy E, Bouloy M, Dicer-2- and Piwi-mediated RNA interference in Rift Valley fever virus-infected mosquito cells, J. Virol. 2013 Feb;87(3):1631-48.

Viana LV, Leitão CB, Grillo Mde F, Rocha EP, Brenner JK, Friedman R, Gross JL, Are diabetes management guidelines applicable in ‘real life’?, Diabetol Metab Syndr 2012;4(1):47.

Lucie Chevallier, Charlène Blanchet, Jean Jaubert, Emilia Pachulec, Christian E. Demeure, Elisabeth Carniel, Jean-Jacques Panthier, Xavier Montagutelli, Resistance to plague of Mus spretus SEG/Pas mice requires the combined action of at least four genetic factors, Genes and Immunity, 2013, 14 (1), pp.35-41. ⟨10.1038/gene.2012.50⟩.

Cousin S, Ma L, Creno S, Clermont D, Loux V, Bizet C, Bouchier C, , Draft genome sequence of Lactobacillus gigeriorum CRBIP 24.85T, isolated from a chicken crop., J Bacteriol 2012 Nov; 194(21): 5973.

Bellini A, Girard PM, Lambert S, Tessier L, Sage E, Francesconi S, Stress activated protein kinase pathway modulates homologous recombination in fission yeast, PLoS ONE 2012;7(10):e47987.

Martini AP, Barros RM, Júnior AC, Rocha EP, de Almeida EO, Ferraz CC, Pellegrin MC, Anchieta RB, Influence of platform and abutment angulation on peri-implant bone. A three-dimensional finite element stress analysis, J Oral Implantol 2013 Dec;39(6):663-9.

Bos J, Yakhnina AA, Gitai Z, , BapE DNA endonuclease induces an apoptotic-like response to DNA damage in Caulobacter., Proc Natl Acad Sci U S A 2012 Oct; 109(44): 18096-101.

Sala CD, Soler-Bistué AJ, Korprapun L, Zorreguieta A, Tolmasky ME, Inhibition of cell division induced by external guide sequences (EGS Technology) targeting ftsZ, PLoS ONE 2012;7(10):e47690.

Kassis-Chikhani N, Frangeul L, Drieux L, Sengelin C, Jarlier V, Brisse S, Arlet G, Decré D, Complete nucleotide sequence of the first KPC-2- and SHV-12-encoding IncX plasmid, pKpS90, from Klebsiella pneumoniae, Antimicrob. Agents Chemother. 2013 Jan;57(1):618-20.

Touchon M, Charpentier S, Pognard D, Picard B, Arlet G, Rocha EP, Denamur E, Branger C, Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements, Microbiology (Reading, Engl.) 2012 Dec;158(Pt 12):2997-3004.

Mazel D, Mobashery S, Antibiotics as physiological stress inducers and bacterial response to the challenge, Curr. Opin. Microbiol. 2012 Oct;15(5):553-4.

Ghorbal M, Scheidig-Benatar C, Bouizem S, Thomas C, Paisley G, Faltermeier C, Liu M, Scherf A, Lopez-Rubio JJ, Gopaul DN, Initial characterization of the Pf-Int recombinase from the malaria parasite Plasmodium falciparum, PLoS ONE 2012;7(10):e46507.

Haase JK, Brown DJ, Weill FX, Mather H, Foster G, Brisse S, Wain J, Achtman M, Population genetic structure of 4,12:a:- Salmonella enterica strains from harbor porpoises, Appl. Environ. Microbiol. 2012 Dec;78(24):8829-33.

Marcade G, Brisse S, Bialek S, Marcon E, Leflon-Guibout V, Passet V, Moreau R, Nicolas-Chanoine MH, The emergence of multidrug-resistant Klebsiella pneumoniae of international clones ST13, ST16, ST35, ST48 and ST101 in a teaching hospital in the Paris region, Epidemiol. Infect. 2013 Aug;141(8):1705-12.

Traglia GM, Sala CD, Fuxman Bass JI, Soler-Bistué AJ, Zorreguieta A, Ramírez MS, Tolmasky ME, Internalization of Locked Nucleic Acids/DNA Hybrid Oligomers into Escherichia coli, Biores Open Access 2012 Oct;1(5):260-3.

Burgio G, Baylac M, Heyer E, Montagutelli X, Exploration of the genetic organization of morphological modularity on the mouse mandible using a set of interspecific recombinant congenic strains between C57BL/6 and mice of the Mus spretus species, G3 (Bethesda) 2012 Oct;2(10):1257-68.

Abby SS, Rocha EP, The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems, PLoS Genet. 2012 Sep;8(9):e1002983.

Bialek-Davenet S, Nicolas-Chanoine MH, Decré D, Brisse S, Microbiological and clinical characteristics of bacteraemia caused by the hypermucoviscosity phenotype of Klebsiella pneumoniae in Korea, Epidemiol. Infect. 2013 Jan;141(1):188.

Guglielmini J, de la Cruz F, Rocha EP, Evolution of conjugation and type IV secretion systems, Mol. Biol. Evol. 2013 Feb;30(2):315-31.

Rębała K, Martínez-Cruz B, Tönjes A, Kovacs P, Stumvoll M, Lindner I, Büttner A, Wichmann HE, Siváková D, Soták M, Quintana-Murci L, Szczerkowska Z, Comas D, , Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements, Eur. J. Hum. Genet. 2013 Apr;21(4):415-22.

Loot C, Ducos-Galand M, Escudero JA, Bouvier M, Mazel D, Replicative resolution of integron cassette insertion., Nucleic Acids Res 2012 Sep; 40(17): 8361-70.

González-Zorn B, Escudero JA, Ecology of antimicrobial resistance: humans, animals, food and environment, Int. Microbiol. 2012 Sep;15(3):101-9.

Wong H, Marie-Nelly H, Herbert S, Carrivain P, Blanc H, Koszul R, Fabre E, Zimmer C, A predictive computational model of the dynamic 3D interphase yeast nucleus, Curr. Biol. 2012 Oct;22(20):1881-90.

Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J, Normalization of a chromosomal contact map, BMC Genomics 2012;13:436.

Crequer A, Picard C, Patin E, D'Amico A, Abhyankar A, Munzer M, Debré M, Zhang SY, de Saint-Basile G, Fischer A, Abel L, Orth G, Casanova JL, Jouanguy E, Inherited MST1 deficiency underlies susceptibility to EV-HPV infections, PLoS ONE 2012;7(8):e44010.

Deghorain M, Bobay LM, Smeesters PR, Bousbata S, Vermeersch M, Perez-Morga D, Drèze PA, Rocha EP, Touchon M, Van Melderen L, Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages, J. Bacteriol. 2012 Nov;194(21):5829-39.

Rabhi I, Rabhi S, Ben-Othman R, Rasche A, Daskalaki A, Trentin B, Piquemal D, Regnault B, Descoteaux A, Guizani-Tabbane L, , Transcriptomic signature of Leishmania infected mice macrophages: a metabolic point of view, PLoS Negl Trop Dis 2012;6(8):e1763.

Dhamgaye S, Bernard M, Lelandais G, Sismeiro O, Lemoine S, Coppée JY, Le Crom S, Prasad R, Devaux F, RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans, BMC Genomics 2012;13:396.

Vatin M, Burgio G, Renault G, Laissue P, Firlej V, Mondon F, Montagutelli X, Vaiman D, Serres C, Ziyyat A, Refined mapping of a quantitative trait locus on chromosome 1 responsible for mouse embryonic death, PLoS ONE 2012;7(8):e43356.

Cimino M, Thomas C, Namouchi A, Dubrac S, Gicquel B, Gopaul DN, Identification of DNA binding motifs of the Mycobacterium tuberculosis PhoP/PhoR two-component signal transduction system, PLoS ONE 2012;7(8):e42876.

Crequer A, Troeger A, Patin E, Ma CS, Picard C, Pedergnana V, Fieschi C, Lim A, Abhyankar A, Gineau L, Mueller-Fleckenstein I, Schmidt M, Taieb A, Krueger J, Abel L, Tangye SG, Orth G, Williams DA, Casanova JL, Jouanguy E, Human RHOH deficiency causes T cell defects and susceptibility to EV-HPV infections, J. Clin. Invest. 2012 Sep;122(9):3239-47.

Patin E, Kutalik Z, Guergnon J, Bibert S, Nalpas B, Jouanguy E, Munteanu M, Bousquet L, Argiro L, Halfon P, Boland A, Müllhaupt B, Semela D, Dufour JF, Heim MH, Moradpour D, Cerny A, Malinverni R, Hirsch H, Martinetti G, Suppiah V, Stewart G, Booth DR, George J, Casanova JL, Bréchot C, Rice CM, Talal AH, Jacobson IM, Bourlière M, Theodorou I, Poynard T, Negro F, Pol S, Bochud PY, Abel L, , , , Genome-wide association study identifies variants associated with progression of liver fibrosis from HCV infection, Gastroenterology 2012 Nov;143(5):1244-52.e1-12.

Rendueles O, Ferrières L, Frétaud M, Bégaud E, Herbomel P, Levraud JP, Ghigo JM, A new zebrafish model of oro-intestinal pathogen colonization reveals a key role for adhesion in protection by probiotic bacteria, PLoS Pathog. 2012;8(7):e1002815.

Martinez-Cruz B, Ioana M, Calafell F, Arauna LR, Sanz P, Ionescu R, Boengiu S, Kalaydjieva L, Pamjav H, Makukh H, Plantinga T, van der Meer JW, Comas D, Netea MG, , Y-chromosome analysis in individuals bearing the Basarab name of the first dynasty of Wallachian kings, PLoS ONE 2012;7(7):e41803.

Oliveira PH, Boura JS, Abecasis MM, Gimble JM, da Silva CL, Cabral JM, Impact of hypoxia and long-term cultivation on the genomic stability and mitochondrial performance of ex vivo expanded human stem/stromal cells, Stem Cell Res 2012 Nov;9(3):225-36.

Quintero NV, Song Y, Manneville P, Baroud CN, Behavior of liquid plugs at bifurcations in a microfluidic tree network, Biomicrofluidics 2012 Sep;6(3):34105.

Chassain B, Lemée L, Didi J, Thiberge JM, Brisse S, Pons JL, Pestel-Caron M, Multilocus sequence typing analysis of Staphylococcus lugdunensis implies a clonal population structure, J. Clin. Microbiol. 2012 Sep;50(9):3003-9.

Nickerson NN, Abby SS, Rocha EP, Chami M, Pugsley AP, A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin, J. Bacteriol. 2012 Sep;194(18):4951-8.

Brisse S, Diancourt L, Laouénan C, Vigan M, Caro V, Arlet G, Drieux L, Leflon-Guibout V, Mentré F, Jarlier V, Nicolas-Chanoine MH, , Phylogenetic distribution of CTX-M- and non-extended-spectrum-β-lactamase-producing Escherichia coli isolates: group B2 isolates, except clone ST131, rarely produce CTX-M enzymes, J. Clin. Microbiol. 2012 Sep;50(9):2974-81.

Merlet A, Cazanave C, Dutronc H, de Barbeyrac B, Brisse S, Dupon M, Primary liver abscess due to CC23-K1 virulent clone of Klebsiella pneumoniae in France, Clin. Microbiol. Infect. 2012 Sep;18(9):E338-9.

Vasseur E, Boniotto M, Patin E, Laval G, Quach H, Manry J, Crouau-Roy B, Quintana-Murci L, The evolutionary landscape of cytosolic microbial sensors in humans, Am. J. Hum. Genet. 2012 Jul;91(1):27-37.

Morris D, Boyle F, Morris C, Condon I, Delannoy-Vieillard AS, Power L, Khan A, Morris-Downes M, Finnegan C, Powell J, Monahan R, Burns K, O'Connell N, Boyle L, O'Gorman A, Humphreys H, Brisse S, Turton J, Woodford N, Cormican M, Inter-hospital outbreak of Klebsiella pneumoniae producing KPC-2 carbapenemase in Ireland, J. Antimicrob. Chemother. 2012 Oct;67(10):2367-72.

Rendueles O, Kaplan JB, Ghigo JM, Antibiofilm polysaccharides, Environ. Microbiol. 2013 Feb;15(2):334-46.

Achtman M, Wain J, Weill FX, Nair S, Zhou Z, Sangal V, Krauland MG, Hale JL, Harbottle H, Uesbeck A, Dougan G, Harrison LH, Brisse S,, Multilocus sequence typing as a replacement for serotyping in Salmonella enterica, PLoS Pathog. 2012;8(6):e1002776.

Alanio A, Cabaret O, Sitterlé E, Costa JM, Brisse S, Cordonnier C, Bretagne S, , Azole preexposure affects the Aspergillus fumigatus population in patients., Antimicrob. Agents Chemother. 2012 Sep; 56(9): 4948-50.

Hocquet D, Llanes C, Thouverez M, Kulasekara HD, Bertrand X, Plésiat P, Mazel D, Miller SI, Evidence for induction of integron-based antibiotic resistance by the SOS response in a clinical setting, PLoS Pathog. 2012;8(6):e1002778.

Janssens FA, Koszul R, Zickler D, The chiasmatype theory. A new interpretation of the maturation divisions. 1909, Genetics 2012 Jun;191(2):319-46.

Koszul R, Meselson M, Van Doninck K, Vandenhaute J, Zickler D, The centenary of Janssens’s chiasmatype theory, Genetics 2012 Jun;191(2):309-17.

Burgio G, Baylac M, Heyer E, Montagutelli X, Nasal bone shape is under complex epistatic genetic control in mouse interspecific recombinant congenic strains, PLoS ONE 2012;7(5):e37721.

Martinez-Jéhanne V, Pichon C, du Merle L, Poupel O, Cayet N, Bouchier C, Le Bouguénec C, Role of the vpe carbohydrate permease in Escherichia coli urovirulence and fitness in vivo, Infect. Immun. 2012 Aug;80(8):2655-66.

Fabre L, Zhang J, Guigon G, Le Hello S, Guibert V, Accou-Demartin M, de Romans S, Lim C, Roux C, Passet V, Diancourt L, Guibourdenche M, Issenhuth-Jeanjean S, Achtman M, Brisse S, Sola C, Weill FX, CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections, PLoS ONE 2012;7(5):e36995.

Dulik MC, Owings AC, Gaieski JB, Vilar MG, Andre A, Lennie C, Mackenzie MA, Kritsch I, Snowshoe S, Wright R, Martin J, Gibson N, Andrews TD, Schurr TG, , Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations, Proc. Natl. Acad. Sci. U.S.A. 2012 May;109(22):8471-6.

Morris D, McGarry E, Cotter M, Passet V, Lynch M, Ludden C, Hannan MM, Brisse S, Cormican M, Detection of OXA-48 carbapenemase in the pandemic clone Escherichia coli O25b:H4-ST131 in the course of investigation of an outbreak of OXA-48-producing Klebsiella pneumoniae, Antimicrob. Agents Chemother. 2012 Jul;56(7):4030-1.

Schurr TG, Dulik MC, Owings AC, Zhadanov SI, Gaieski JB, Vilar MG, Ramos J, Moss MB, Natkong F, , Clan, language, and migration history has shaped genetic diversity in Haida and Tlingit populations from Southeast Alaska, Am. J. Phys. Anthropol. 2012 Jul;148(3):422-35.

Luciano P, Coulon S, Faure V, Corda Y, Bos J, Brill SJ, Gilson E, Simon MN, Géli V, , RPA facilitates telomerase activity at chromosome ends in budding and fission yeasts., EMBO J 2012 Apr; 31(8): 2034-46.

Jourdren L, Bernard M, Dillies MA, Le Crom S, Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses, Bioinformatics 2012 Jun;28(11):1542-3.

Sahr T, Rusniok C, Dervins-Ravault D, Sismeiro O, Coppee JY, Buchrieser C, Deep sequencing defines the transcriptional map of L. pneumophila and identifies growth phase-dependent regulated ncRNAs implicated in virulence, RNA Biol 2012 Apr;9(4):503-19.

Baharoglu Z, Krin E, Mazel D, , Connecting environment and genome plasticity in the characterization of transformation-induced SOS regulation and carbon catabolite control of the Vibrio cholerae integron integrase., J Bacteriol 2012 Apr; 194(7): 1659-67.

Haber M, Platt DE, Ashrafian Bonab M, Youhanna SC, Soria-Hernanz DF, Martínez-Cruz B, Douaihy B, Ghassibe-Sabbagh M, Rafatpanah H, Ghanbari M, Whale J, Balanovsky O, Wells RS, Comas D, Tyler-Smith C, Zalloua PA, , Afghanistan’s ethnic groups share a Y-chromosomal heritage structured by historical events, PLoS ONE 2012;7(3):e34288.

Vieira J, Jones AR, Danon A, Sakuma M, Hoang N, Robles D, Tait S, Heyes DJ, Picot M, Yoshii T, Helfrich-Förster C, Soubigou G, Coppee JY, Klarsfeld A, Rouyer F, Scrutton NS, Ahmad M, Human cryptochrome-1 confers light independent biological activity in transgenic Drosophila correlated with flavin radical stability, PLoS ONE 2012;7(3):e31867.

Martínez-Cruz B, Harmant C, Platt DE, Haak W, Manry J, Ramos-Luis E, Soria-Hernanz DF, Bauduer F, Salaberria J, Oyharçabal B, Quintana-Murci L, Comas D, , Evidence of pre-Roman tribal genetic structure in Basques from uniparentally inherited markers, Mol. Biol. Evol. 2012 Sep;29(9):2211-22.

Rendueles O, Ghigo JM, Multi-species biofilms: how to avoid unfriendly neighbors, FEMS Microbiol. Rev. 2012 Sep;36(5):972-89.

Breurec S, Guessennd N, Timinouni M, Le TA, Cao V, Ngandjio A, Randrianirina F, Thiberge JM, Kinana A, Dufougeray A, Perrier-Gros-Claude JD, Boisier P, Garin B, Brisse S, Klebsiella pneumoniae resistant to third-generation cephalosporins in five African and two Vietnamese major towns: multiclonal population structure with two major international clonal groups, CG15 and CG258, Clin. Microbiol. Infect. 2013 Apr;19(4):349-55.

Legrand E, Yrinesi J, Ekala MT, Péneau J, Volney B, Berger F, Bouchier C, Bertani S, Musset L, Meynard JB, Mercereau-Puijalon O, , Discordant temporal evolution of Pfcrt and Pfmdr1 genotypes and Plasmodium falciparum in vitro drug susceptibility to 4-aminoquinolines after drug policy change in French Guiana., Antimicrob Agents Chemother 2012 Mar; 56(3): 1382-9.

Lepeule R, Ruppé E, Le P, Massias L, Chau F, Nucci A, Lefort A, Fantin B, Cefoxitin as an alternative to carbapenems in a murine model of urinary tract infection due to Escherichia coli harboring CTX-M-15-type extended-spectrum β-lactamase., Antimicrob Agents Chemother 2012 Mar; 56(3): 1376-81.

Namouchi A, Didelot X, Schöck U, Gicquel B, Rocha EP, After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection, Genome Res. 2012 Apr;22(4):721-34.

Rosenfeld N, Bouchier C, Courvalin P, Périchon B, Expression of the resistance-nodulation-cell division pump AdeIJK in Acinetobacter baumannii is regulated by AdeN, a TetR-type regulator, Antimicrob. Agents Chemother. 2012 May;56(5):2504-10.

Gayraud-Morel B, Chrétien F, Jory A, Sambasivan R, Negroni E, Flamant P, Soubigou G, Coppée JY, Di Santo J, Cumano A, Mouly V, Tajbakhsh S, Myf5 haploinsufficiency reveals distinct cell fate potentials for adult skeletal muscle stem cells, J. Cell. Sci. 2012 Apr;125(Pt 7):1738-49.

Santi-Rocca J, Smith S, Weber C, Pineda E, Hon CC, Saavedra E, Olivos-García A, Rousseau S, Dillies MA, Coppée JY, Guillén N, Endoplasmic reticulum stress-sensing mechanism is activated in Entamoeba histolytica upon treatment with nitric oxide, PLoS ONE 2012;7(2):e31777.

Behar DM, Harmant C, Manry J, van Oven M, Haak W, Martinez-Cruz B, Salaberria J, Oyharçabal B, Bauduer F, Comas D, Quintana-Murci L, , The Basque paradigm: genetic evidence of a maternal continuity in the Franco-Cantabrian region since pre-Neolithic times, Am. J. Hum. Genet. 2012 Mar;90(3):486-93.

Quintana-Murci L, Genetics. Gene losses in the human genome, Science 2012 Feb;335(6070):806-7.

Gutierrez B, Escudero JA, San Millan A, Hidalgo L, Carrilero L, Ovejero CM, Santos-Lopez A, Thomas-Lopez D, Gonzalez-Zorn B, Fitness cost and interference of Arm/Rmt aminoglycoside resistance with the RsmF housekeeping methyltransferases, Antimicrob. Agents Chemother. 2012 May;56(5):2335-41.

Leblond CS, Heinrich J, Delorme R, Proepper C, Betancur C, Huguet G, Konyukh M, Chaste P, Ey E, Rastam M, Anckarsäter H, Nygren G, Gillberg IC, Melke J, Toro R, Regnault B, Fauchereau F, Mercati O, Lemière N, Skuse D, Poot M, Holt R, Monaco AP, Järvelä I, Kantojärvi K, Vanhala R, Curran S, Collier DA, Bolton P, Chiocchetti A, Klauck SM, Poustka F, Freitag CM, Waltes R, Kopp M, Duketis E, Bacchelli E, Minopoli F, Ruta L, Battaglia A, Mazzone L, Maestrini E, Sequeira AF, Oliveira B, Vicente A, Oliveira G, Pinto D, Scherer SW, Zelenika D, Delepine M, Lathrop M, Bonneau D, Guinchat V, Devillard F, Assouline B, Mouren MC, Leboyer M, Gillberg C, Boeckers TM, Bourgeron T, , Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders., PLoS Genet 2012 Feb; 8(2): e1002521.

Green B, Bouchier C, Fairhead C, Craig NL, Cormack BP, Insertion site preference of Mu, Tn5, and Tn7 transposons, Mob DNA 2012;3(1):3.

Gama JA, Abby SS, Vieira-Silva S, Dionisio F, Rocha EP, Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens, PLoS Pathog. 2012 Feb;8(2):e1002503.

Cousin S, Gulat-Okalla ML, Motreff L, Gouyette C, Bouchier C, Clermont D, Bizet C, , Lactobacillus gigeriorum sp. nov., isolated from chicken crop., Int J Syst Evol Microbiol 2012 Feb; 62(Pt 2): 330-334.

Louis VL, Despons L, Friedrich A, Martin T, Durrens P, Casarégola S, Neuvéglise C, Fairhead C, Marck C, Cruz JA, Straub ML, Kugler V, Sacerdot C, Uzunov Z, Thierry A, Weiss S, Bleykasten C, De Montigny J, Jacques N, Jung P, Lemaire M, Mallet S, Morel G, Richard GF, Sarkar A, Savel G, Schacherer J, Seret ML, Talla E, Samson G, Jubin C, Poulain J, Vacherie B, Barbe V, Pelletier E, Sherman DJ, Westhof E, Weissenbach J, Baret PV, Wincker P, Gaillardin C, Dujon B, Souciet JL, Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization, G3 (Bethesda) 2012 Feb;2(2):299-311.

Lu Y, Wang C, Qin Z, Wen B, Farina SE, Jin L, Li H, , Mitochondrial origin of the matrilocal Mosuo people in China, Mitochondrial DNA 2012 Feb;23(1):13-9.

Tran T, Andres P, Petroni A, Soler-Bistué A, Albornoz E, Zorreguieta A, Reyes-Lamothe R, Sherratt DJ, Corso A, Tolmasky ME, Small plasmids harboring qnrB19: a model for plasmid evolution mediated by site-specific recombination at oriT and Xer sites, Antimicrob. Agents Chemother. 2012 Apr;56(4):1821-7.

Panthier JJ, Montagutelli X, [The Collaborative Cross, a groundbreaking tool to tackle complex traits], Med Sci (Paris) 2012 Jan;28(1):103-8.

Lewis LA, Astatke M, Umekubo PT, Alvi S, Saby R, Afrose J, Oliveira PH, Monteiro GA, Prazeres DM, Protein-DNA interactions define the mechanistic aspects of circle formation and insertion reactions in IS2 transposition, Mob DNA 2012;3(1):1.

Landraud L, Jauréguy F, Frapy E, Guigon G, Gouriou S, Carbonnelle E, Clermont O, Denamur E, Picard B, Lemichez E, Brisse S, Nassif X, Severity of Escherichia coli bacteraemia is independent of the intrinsic virulence of the strains assessed in a mouse model, Clin. Microbiol. Infect. 2013 Jan;19(1):85-90.

Lesic B, Zouine M, Ducos-Galand M, Huon C, Rosso ML, Prévost MC, Mazel D, Carniel E, A natural system of chromosome transfer in Yersinia pseudotuberculosis., PLoS Genet 2012 ; 8(3): e1002529.

Val ME, Skovgaard O, Ducos-Galand M, Bland MJ, Mazel D, Genome engineering in Vibrio cholerae: a feasible approach to address biological issues., PLoS Genet 2012 Jan; 8(1): e1002472.

Permal E, Flutre T, Quesneville H, Roadmap for annotating transposable elements in eukaryote genomes, Methods Mol. Biol. 2012;859:53-68.

Jouneau A, Ciaudo C, Sismeiro O, Brochard V, Jouneau L, Vandormael-Pournin S, Coppée JY, Zhou Q, Heard E, Antoniewski C, Cohen-Tannoudji M, Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles, RNA 2012 Feb;18(2):253-64.

Bochud PY, Bibert S, Kutalik Z, Patin E, Guergnon J, Nalpas B, Goossens N, Kuske L, Müllhaupt B, Gerlach T, Heim MH, Moradpour D, Cerny A, Malinverni R, Regenass S, Dollenmaier G, Hirsch H, Martinetti G, Gorgiewski M, Bourlière M, Poynard T, Theodorou I, Abel L, Pol S, Dufour JF, Negro F, , , IL28B alleles associated with poor hepatitis C virus (HCV) clearance protect against inflammation and fibrosis in patients infected with non-1 HCV genotypes, Hepatology 2012 Feb;55(2):384-94.

Manry J, Laval G, Patin E, Fornarino S, Itan Y, Fumagalli M, Sironi M, Tichit M, Bouchier C, Casanova JL, Barreiro LB, Quintana-Murci L, Evolutionary genetic dissection of human interferons, J. Exp. Med. 2011 Dec;208(13):2747-59.

Bourhy P, Collet L, Lernout T, Zinini F, Hartskeerl RA, van der Linden H, Thiberge JM, Diancourt L, Brisse S, Giry C, Pettinelli F, Picardeau M, Human leptospira isolates circulating in Mayotte (Indian Ocean) have unique serological and molecular features, J. Clin. Microbiol. 2012 Feb;50(2):307-11.

Gommet C, Billecocq A, Jouvion G, Hasan M, Zaverucha do Valle T, Guillemot L, Blanchet C, van Rooijen N, Montagutelli X, Bouloy M, Panthier JJ, Tissue tropism and target cells of NSs-deleted rift valley fever virus in live immunodeficient mice, PLoS Negl Trop Dis 2011 Dec;5(12):e1421.

Kim S, Nguon C, Guillard B, Duong S, Chy S, Sum S, Nhem S, Bouchier C, Tichit M, Christophel E, Taylor WR, Baird JK, Menard D, Performance of the CareStart™ G6PD deficiency screening test, a point-of-care diagnostic for primaquine therapy screening, PLoS ONE 2011;6(12):e28357.

Vieira-Silva S, Touchon M, Abby SS, Rocha EP, Investment in rapid growth shapes the evolutionary rates of essential proteins, Proc. Natl. Acad. Sci. U.S.A. 2011 Dec;108(50):20030-5.

Khim N, Kim S, Bouchier C, Tichit M, Ariey F, Fandeur T, Chim P, Ke S, Sum S, Man S, Ratsimbasoa A, Durand R, Ménard D, Reduced impact of pyrimethamine drug pressure on Plasmodium malariae dihydrofolate reductase gene, Antimicrob. Agents Chemother. 2012 Feb;56(2):863-8.

Kang L, Lu Y, Wang C, Hu K, Chen F, Liu K, Li S, Jin L, Li H, , Y-chromosome O3 haplogroup diversity in Sino-Tibetan populations reveals two migration routes into the eastern Himalayas, Ann. Hum. Genet. 2012 Jan;76(1):92-9.

Zhang Q, Huang Y, Zhang Y, Fang X, Claes A, Duchateau M, Namane A, Lopez-Rubio JJ, Pan W, Scherf A, A critical role of perinuclear filamentous actin in spatial repositioning and mutually exclusive expression of virulence genes in malaria parasites, Cell Host Microbe 2011 Nov;10(5):451-63.

Christian E. Demeure, Charlène Blanchet, Catherine Fitting, Corinne Fayolle, Huot Khun, Marek Szatanik, Geneviève Milon, Jean-Jacques Panthier, Jean Jaubert, Xavier Montagutelli, Michel Huerre, Jean-Marc Cavaillon, Elisabeth Carniel, Early Systemic Bacterial Dissemination and a Rapid Innate Immune Response Characterize Genetic Resistance to Plague of SEG Mice, Journal of Infectious Diseases, 2012, 205 (1), pp.134-143. ⟨10.1093/infdis/jir696⟩.

L'Hôte D, Vatin M, Auer J, Castille J, Passet B, Montagutelli X, Serres C, Vaiman D, Fidgetin-like1 is a strong candidate for a dynamic impairment of male meiosis leading to reduced testis weight in mice, PLoS ONE 2011;6(11):e27582.

Fradet E, McDougall C, Abbyad P, Dangla R, McGloin D, Baroud CN, Combining rails and anchors with laser forcing for selective manipulation within 2D droplet arrays, Lab Chip 2011 Dec;11(24):4228-34.

Boniotto M, Tailleux L, Lomma M, Gicquel B, Buchrieser C, Garcia S, Quintana-Murci L, Population variation in NAIP functional copy number confers increased cell death upon Legionella pneumophila infection, Hum. Immunol. 2012 Feb;73(2):196-200.

Javed A, Melé M, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Arunkumar G, Pitchappan R, Bertranpetit J, Calafell F, Parida L, , Recombination networks as genetic markers in a human variation study of the Old World, Hum. Genet. 2012 Apr;131(4):601-13.

Zaratiegui M, Castel SE, Irvine DV, Kloc A, Ren J, Li F, de Castro E, Marín L, Chang AY, Goto D, Cande WZ, Antequera F, Arcangioli B, Martienssen RA, RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II, Nature 2011 Nov;479(7371):135-8.

Khim N, Siv S, Kim S, Mueller T, Fleischmann E, Singh B, Divis PC, Steenkeste N, Duval L, Bouchier C, Duong S, Ariey F, Menard D, Plasmodium knowlesi infection in humans, Cambodia, 2007-2010, Emerging Infect. Dis. 2011 Oct;17(10):1900-2.

Stanojcic S, Gimenez S, Permal E, Cousserans F, Quesneville H, Fournier P, d'Alençon E, Correlation of LNCR rasiRNAs expression with heterochromatin formation during development of the holocentric insect Spodoptera frugiperda, PLoS ONE 2011;6(9):e24746.

Martini E, Borde V, Legendre M, Audic S, Regnault B, Soubigou G, Dujon B, Llorente B, Genome-wide analysis of heteroduplex DNA in mismatch repair-deficient yeast cells reveals novel properties of meiotic recombination pathways, PLoS Genet. 2011 Sep;7(9):e1002305.

Andriantsoanirina V, Durand R, Pradines B, Baret E, Bouchier C, Ratsimbasoa A, Ménard D, In vitro susceptibility to pyrimethamine of DHFR I164L single mutant Plasmodium falciparum, Malar. J. 2011 Sep;10:283.

Escudero JA, San Millan A, Gutierrez B, Hidalgo L, La Ragione RM, AbuOun M, Galimand M, Ferrándiz MJ, Domínguez L, de la Campa AG, Gonzalez-Zorn B, Fluoroquinolone efflux in Streptococcus suis is mediated by SatAB and not by SmrA, Antimicrob. Agents Chemother. 2011 Dec;55(12):5850-60.

Touchon M, Barbier P, Bernardet JF, Loux V, Vacherie B, Barbe V, Rocha EP, Duchaud E, Complete genome sequence of the fish pathogen Flavobacterium branchiophilum, Appl. Environ. Microbiol. 2011 Nov;77(21):7656-62.

Dangla R, Lee S, Baroud CN, Trapping microfluidic drops in wells of surface energy, Phys. Rev. Lett. 2011 Sep;107(12):124501.

Sage E, Girard PM, Francesconi S, Unravelling UVA-induced mutagenesis, Photochem. Photobiol. Sci. 2012 Jan;11(1):74-80.

Melé M, Javed A, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Pitchappan RM, Arunkumar G, Parida L, Calafell F, Bertranpetit J, , Recombination gives a new insight in the effective population size and the history of the old world human populations, Mol. Biol. Evol. 2012 Jan;29(1):25-30.

Cheval J, Sauvage V, Frangeul L, Dacheux L, Guigon G, Dumey N, Pariente K, Rousseaux C, Dorange F, Berthet N, Brisse S, Moszer I, Bourhy H, Manuguerra CJ, Lecuit M, Burguiere A, Caro V, Eloit M, , Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples., J Clin Microbiol 2011 Sep; 49(9): 3268-75.

Cai X, Qin Z, Wen B, Xu S, Wang Y, Lu Y, Wei L, Wang C, Li S, Huang X, Jin L, Li H, , Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes, PLoS ONE 2011;6(8):e24282.

Jagla B, Wiswedel B, Coppée JY, Extending KNIME for next-generation sequencing data analysis, Bioinformatics 2011 Oct;27(20):2907-9.

Gaieski JB, Owings AC, Vilar MG, Dulik MC, Gaieski DF, Gittelman RM, Lindo J, Gau L, Schurr TG, , Genetic ancestry and indigenous heritage in a Native American descendant community in Bermuda, Am. J. Phys. Anthropol. 2011 Nov;146(3):392-405.

Vasseur E, Patin E, Laval G, Pajon S, Fornarino S, Crouau-Roy B, Quintana-Murci L, The selective footprints of viral pressures at the human RIG-I-like receptor family, Hum. Mol. Genet. 2011 Nov;20(22):4462-74.

Granier SA, Hidalgo L, San Millan A, Escudero JA, Gutierrez B, Brisabois A, Gonzalez-Zorn B, ArmA methyltransferase in a monophasic Salmonella enterica isolate from food, Antimicrob. Agents Chemother. 2011 Nov;55(11):5262-6.

Guérin E, Jové T, Tabesse A, Mazel D, Ploy MC, High-level gene cassette transcription prevents integrase expression in class 1 integrons, J. Bacteriol. 2011 Oct;193(20):5675-82.

Guglielmini J, Quintais L, Garcillán-Barcia MP, de la Cruz F, Rocha EP, The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation, PLoS Genet. 2011 Aug;7(8):e1002222.

Breurec S, Guillard B, Hem S, Papadakos KS, Brisse S, Huerre M, Monchy D, Oung C, Sgouras DN, Tan TS, Thiberge JM, Vong S, Raymond J, Linz B, Expansion of European vacA and cagA alleles to East-Asian Helicobacter pylori strains in Cambodia, Infect. Genet. Evol. 2011 Dec;11(8):1899-905.

Breurec S, Guillard B, Hem S, Brisse S, Dieye FB, Huerre M, Oung C, Raymond J, Tan TS, Thiberge JM, Vong S, Monchy D, Linz B, Evolutionary history of Helicobacter pylori sequences reflect past human migrations in Southeast Asia, PLoS ONE 2011;6(7):e22058.

Polge C, Heng AE, Jarzaguet M, Ventadour S, Claustre A, Combaret L, Béchet D, Matondo M, Uttenweiler-Joseph S, Monsarrat B, Attaix D, Taillandier D, Muscle actin is polyubiquitinylated in vitro and in vivo and targeted for breakdown by the E3 ligase MuRF1, FASEB J. 2011 Nov;25(11):3790-802.

Lyoumi S, Abitbol M, Rainteau D, Karim Z, Bernex F, Oustric V, Millot S, Lettéron P, Heming N, Guillmot L, Montagutelli X, Berdeaux G, Gouya L, Poupon R, Deybach JC, Beaumont C, Puy H, Protoporphyrin retention in hepatocytes and Kupffer cells prevents sclerosing cholangitis in erythropoietic protoporphyria mouse model, Gastroenterology 2011 Oct;141(4):1509-19, 1519.e1-3.

Breurec S, Michel R, Seck A, Brisse S, Côme D, Dieye FB, Garin B, Huerre M, Mbengue M, Fall C, Sgouras DN, Thiberge JM, Dia D, Raymond J, Clinical relevance of cagA and vacA gene polymorphisms in Helicobacter pylori isolates from Senegalese patients, Clin. Microbiol. Infect. 2012 Feb;18(2):153-9.

Flutre T, Permal E, Quesneville H, In search of lost trajectories: Recovering the diversification of transposable elements, Mob Genet Elements 2011 Jul;1(2):151-154.

Simon-Chazottes D, Frenkiel MP, Montagutelli X, Guénet JL, Desprès P, Panthier JJ, Transgenic expression of full-length 2′,5′-oligoadenylate synthetase 1b confers to BALB/c mice resistance against West Nile virus-induced encephalitis, Virology 2011 Aug;417(1):147-53.

Decré D, Verdet C, Emirian A, Le Gourrierec T, Petit JC, Offenstadt G, Maury E, Brisse S, Arlet G, Emerging severe and fatal infections due to Klebsiella pneumoniae in two university hospitals in France, J. Clin. Microbiol. 2011 Aug;49(8):3012-4.

Fornarino S, Laval G, Barreiro LB, Manry J, Vasseur E, Quintana-Murci L, Evolution of the TIR domain-containing adaptors in humans: swinging between constraint and adaptation, Mol. Biol. Evol. 2011 Nov;28(11):3087-97.

Clermont O, Gordon DM, Brisse S, Walk ST, Denamur E, Characterization of the cryptic Escherichia lineages: rapid identification and prevalence, Environ. Microbiol. 2011 Sep;13(9):2468-77.

Heyer E, Brazier L, Ségurel L, Hegay T, Austerlitz F, Quintana-Murci L, Georges M, Pasquet P, Veuille M, Lactase persistence in central Asia: phenotype, genotype, and evolution, Hum. Biol. 2011 Jun;83(3):379-92.

Ben-Ali M, Corre B, Manry J, Barreiro LB, Quach H, Boniotto M, Pellegrini S, Quintana-Murci L, Functional characterization of naturally occurring genetic variants in the human TLR1-2-6 gene family, Hum. Mutat. 2011 Jun;32(6):643-52.

Chenal-Francisque V, Lopez J, Cantinelli T, Caro V, Tran C, Leclercq A, Lecuit M, Brisse S, , Worldwide distribution of major clones of Listeria monocytogenes., Emerg Infect Dis 2011 Jun; 17(6): 1110-2.

Fevre C, Passet V, Deletoile A, Barbe V, Frangeul L, Almeida AS, Sansonetti P, Tournebize R, Brisse S, PCR-based identification of Klebsiella pneumoniae subsp. rhinoscleromatis, the agent of rhinoscleroma, PLoS Negl Trop Dis 2011 May;5(5):e1052.

Leclercq A, Chenal-Francisque V, Dieye H, Cantinelli T, Drali R, Brisse S, Lecuit M, , Characterization of the novel Listeria monocytogenes PCR serogrouping profile IVb-v1., Int J Food Microbiol 2011 May; 147(1): 74-7.

Balanovsky O, Dibirova K, Dybo A, Mudrak O, Frolova S, Pocheshkhova E, Haber M, Platt D, Schurr T, Haak W, Kuznetsova M, Radzhabov M, Balaganskaya O, Romanov A, Zakharova T, Soria Hernanz DF, Zalloua P, Koshel S, Ruhlen M, Renfrew C, Wells RS, Tyler-Smith C, Balanovska E, , Parallel evolution of genes and languages in the Caucasus region, Mol. Biol. Evol. 2011 Oct;28(10):2905-20.

Rendueles O, Travier L, Latour-Lambert P, Fontaine T, Magnus J, Denamur E, Ghigo JM, Screening of Escherichia coli species biodiversity reveals new biofilm-associated antiadhesion polysaccharides, MBio 2011;2(3):e00043-11.

Baharoglu Z, Mazel D, , Vibrio cholerae triggers SOS and mutagenesis in response to a wide range of antibiotics: a route towards multiresistance., Antimicrob Agents Chemother 2011 May; 55(5): 2438-41.

Mauclère P, Afonso PV, Meertens L, Plancoulaine S, Calattini S, Froment A, Van Beveren M, de Thé G, Quintana-Murci L, Mahieux R, Gessain A, HTLV-2B strains, similar to those found in several Amerindian tribes, are endemic in central African Bakola Pygmies, J. Infect. Dis. 2011 May;203(9):1316-23.

Cambray G, Sanchez-Alberola N, Campoy S, Guerin E, Da Re S, González-Zorn B, Ploy MC, Barbé J, Mazel D, Erill I, Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons, Mob DNA 2011;2(1):6.

Carretto E, Barbarini D, Dijkshoorn L, van der Reijden TJ, Brisse S, Passet V, Farina C, , Widespread carbapenem resistant Acinetobacter baumannii clones in Italian hospitals revealed by a multicenter study, Infect. Genet. Evol. 2011 Aug;11(6):1319-26.

Bradley AS, Baharoglu Z, Niewiarowski A, Michel B, Tsaneva IR, Formation of a stable RuvA protein double tetramer is required for efficient branch migration in vitro and for replication fork reversal in vivo, J. Biol. Chem. 2011 Jun;286(25):22372-83.

Truman RW, Singh P, Sharma R, Busso P, Rougemont J, Paniz-Mondolfi A, Kapopoulou A, Brisse S, Scollard DM, Gillis TP, Cole ST, Probable zoonotic leprosy in the southern United States, N. Engl. J. Med. 2011 Apr;364(17):1626-33.

Yan S, Wang CC, Li H, Li SL, Jin L, , An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4, Eur. J. Hum. Genet. 2011 Sep;19(9):1013-5.

Souissi I, Najjar I, Ah-Koon L, Schischmanoff PO, Lesage D, Le Coquil S, Roger C, Dusanter-Fourt I, Varin-Blank N, Cao A, Metelev V, Baran-Marszak F, Fagard R, A STAT3-decoy oligonucleotide induces cell death in a human colorectal carcinoma cell line by blocking nuclear transfer of STAT3 and STAT3-bound NF-κB, BMC Cell Biol. 2011 Apr;12:14.

Deplaine G, Lavazec C, Bischoff E, Natalang O, Perrot S, Guillotte-Blisnick M, Coppée JY, Pradines B, Mercereau-Puijalon O, David PH, Artesunate tolerance in transgenic Plasmodium falciparum parasites overexpressing a tryptophan-rich protein, Antimicrob. Agents Chemother. 2011 Jun;55(6):2576-84.

Hamel A, Fisch C, Combettes L, Dupuis-Williams P, Baroud CN, Transitions between three swimming gaits in Paramecium escape, Proc. Natl. Acad. Sci. U.S.A. 2011 May;108(18):7290-5.

Breurec S, Fall C, Pouillot R, Boisier P, Brisse S, Diene-Sarr F, Djibo S, Etienne J, Fonkoua MC, Perrier-Gros-Claude JD, Ramarokoto CE, Randrianirina F, Thiberge JM, Zriouil SB, , Garin B, Laurent F, Epidemiology of methicillin-susceptible Staphylococcus aureus lineages in five major African towns: high prevalence of Panton-Valentine leukocidin genes, Clin. Microbiol. Infect. 2011 Apr;17(4):633-9.

Manry J, Laval G, Patin E, Fornarino S, Tichit M, Bouchier C, Barreiro LB, Quintana-Murci L, Evolutionary genetics evidence of an essential, nonredundant role of the IFN-γ pathway in protective immunity, Hum. Mutat. 2011 Jun;32(6):633-42.

Touchon M, Charpentier S, Clermont O, Rocha EP, Denamur E, Branger C, CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection, J. Bacteriol. 2011 May;193(10):2460-7.

Warnecke T, Rocha EP, Function-specific accelerations in rates of sequence evolution suggest predictable epistatic responses to reduced effective population size, Mol. Biol. Evol. 2011 Aug;28(8):2339-49.

Selevsek N, Matondo M, Sanchez Carbayo M, Aebersold R, Domon B, Systematic quantification of peptides/proteins in urine using selected reaction monitoring, Proteomics 2011 Mar;11(6):1135-47.

Court M, Selevsek N, Matondo M, Allory Y, Garin J, Masselon CD, Domon B, Toward a standardized urine proteome analysis methodology, Proteomics 2011 Mar;11(6):1160-71.

Oliveira PH, Prather KL, Prazeres DM, Monteiro GA, Mutation detection in plasmid-based biopharmaceuticals, Biotechnol J 2011 Apr;6(4):378-91.

Clermont O, Olier M, Hoede C, Diancourt L, Brisse S, Keroudean M, Glodt J, Picard B, Oswald E, Denamur E, Animal and human pathogenic Escherichia coli strains share common genetic backgrounds, Infect. Genet. Evol. 2011 Apr;11(3):654-62.

Nemec A, Krizova L, Maixnerova M, van der Reijden TJ, Deschaght P, Passet V, Vaneechoutte M, Brisse S, Dijkshoorn L, Genotypic and phenotypic characterization of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex with the proposal of Acinetobacter pittii sp. nov. (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis sp. nov. (formerly Acinetobacter genomic species 13TU), Res. Microbiol. 2011 May;162(4):393-404.

Deschaght P, Van Simaey L, Decat E, Van Mechelen E, Brisse S, Vaneechoutte M, Rapid genotyping of Achromobacter xylosoxidans, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia isolates using melting curve analysis of RAPD-generated DNA fragments (McRAPD), Res. Microbiol. 2011 May;162(4):386-92.

Ludwig M, Palha N, Torhy C, Briolat V, Colucci-Guyon E, Brémont M, Herbomel P, Boudinot P, Levraud JP, , Whole-body analysis of a viral infection: vascular endothelium is a primary target of infectious hematopoietic necrosis virus in zebrafish larvae., PLoS Pathog. 2011 Feb; 7(2): e1001269.

Coulibaly-N'Golo GM, Ekaza E, Coulibaly B, Aka N, N'guessan RK, Thiberge JM, Caro V, Brisse S, Bretin-Dosso M, Multilocus VNTR analysis of Mycobacterium ulcerans strains isolated in Côte d’Ivoire, J Infect Dev Ctries 2011 Feb;5(1):59-63.

Di Popolo A, Giannouli M, Triassi M, Brisse S, Zarrilli R, Molecular epidemiological investigation of multidrug-resistant Acinetobacter baumannii strains in four Mediterranean countries with a multilocus sequence typing scheme, Clin. Microbiol. Infect. 2011 Feb;17(2):197-201.

Breurec S, Zriouil SB, Fall C, Boisier P, Brisse S, Djibo S, Etienne J, Fonkoua MC, Perrier-Gros-Claude JD, Pouillot R, Ramarokoto CE, Randrianirina F, Tall A, Thiberge JM, , Laurent F, Garin B, Epidemiology of methicillin-resistant Staphylococcus aureus lineages in five major African towns: emergence and spread of atypical clones, Clin. Microbiol. Infect. 2011 Feb;17(2):160-5.

Treangen TJ, Rocha EP, Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes, PLoS Genet. 2011;7(1):e1001284.

Lebreton A, Lakisic G, Job V, Fritsch L, Tham TN, Camejo A, Matteï PJ, Regnault B, Nahori MA, Cabanes D, Gautreau A, Ait-Si-Ali S, Dessen A, Cossart P, Bierne H, A bacterial protein targets the BAHD1 chromatin complex to stimulate type III interferon response, Science 2011 Mar;331(6022):1319-21.

Huebner AM, Abell C, Huck WT, Baroud CN, Hollfelder F, Monitoring a reaction at submillisecond resolution in picoliter volumes, Anal. Chem. 2011 Feb;83(4):1462-8.

Dittami SM, Proux C, Rousvoal S, Peters AF, Cock JM, Coppée JY, Boyen C, Tonon T, Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae), BMC Mol. Biol. 2011;12:2.

Roux AL, Ray A, Pawlik A, Medjahed H, Etienne G, Rottman M, Catherinot E, Coppée JY, Chaoui K, Monsarrat B, Toubert A, Daffé M, Puzo G, Gaillard JL, Brosch R, Dulphy N, Nigou J, Herrmann JL, Overexpression of proinflammatory TLR-2-signalling lipoproteins in hypervirulent mycobacterial variants, Cell. Microbiol. 2011 May;13(5):692-704.

Casanova JL, Abel L, Quintana-Murci L, Human TLRs and IL-1Rs in host defense: natural insights from evolutionary, epidemiological, and clinical genetics, Annu. Rev. Immunol. 2011;29:447-91.

Yang K, Zheng H, Qin Z, Lu Y, Farina SE, Li S, Jin L, Li D, Li H, , Positive selection on mitochondrial M7 lineages among the Gelong people in Hainan, J. Hum. Genet. 2011 Mar;56(3):253-6.

Laouari D, Burtin M, Phelep A, Martino C, Pillebout E, Montagutelli X, Friedlander G, Terzi F, TGF-alpha mediates genetic susceptibility to chronic kidney disease, J. Am. Soc. Nephrol. 2011 Feb;22(2):327-35.

Berthet N, Deletoile A, Passet V, Kennedy GC, Manuguerra JC, Cole ST, Brisse S, Reconstructed ancestral sequences improve pathogen identification using resequencing DNA microarrays, PLoS ONE 2010;5(12):e15243.

Cleiss-Arnold J, Koechler S, Proux C, Fardeau ML, Dillies MA, Coppee JY, Arsène-Ploetze F, Bertin PN, Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans, BMC Genomics 2010;11:709.

Forquin MP, Hébert A, Roux A, Aubert J, Proux C, Heilier JF, Landaud S, Junot C, Bonnarme P, Martin-Verstraete I, Global regulation of the response to sulfur availability in the cheese-related bacterium Brevibacterium aurantiacum, Appl. Environ. Microbiol. 2011 Feb;77(4):1449-59.

Bernstein KA, Gangloff S, Rothstein R, The RecQ DNA helicases in DNA repair, Annu. Rev. Genet. 2010;44:393-417.

Zaratiegui M, Vaughn MW, Irvine DV, Goto D, Watt S, Bähler J, Arcangioli B, Martienssen RA, CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR, Nature 2011 Jan;469(7328):112-5.

Lagha M, Sato T, Regnault B, Cumano A, Zuniga A, Licht J, Relaix F, Buckingham M, Transcriptome analyses based on genetic screens for Pax3 myogenic targets in the mouse embryo., BMC Genomics 2010 Dec; 11(): 696.

Bikard D, Loot C, Baharoglu Z, Mazel D, Folded DNA in action: hairpin formation and biological functions in prokaryotes., Microbiol Mol Biol Rev 2010 Dec; 74(4): 570-88.

Quintana-Murci L, Barreiro LB, The role played by natural selection on Mendelian traits in humans, Ann. N. Y. Acad. Sci. 2010 Dec;1214:1-17.

Haber M, Platt DE, Badro DA, Xue Y, El-Sibai M, Bonab MA, Youhanna SC, Saade S, Soria-Hernanz DF, Royyuru A, Wells RS, Tyler-Smith C, Zalloua PA, , Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon, Eur. J. Hum. Genet. 2011 Mar;19(3):334-40.

Qin Z, Yang Y, Kang L, Yan S, Cho K, Cai X, Lu Y, Zheng H, Zhu D, Fei D, Li S, Jin L, Li H, , A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum, Am. J. Phys. Anthropol. 2010 Dec;143(4):555-69.

Melé M, Javed A, Pybus M, Calafell F, Parida L, Bertranpetit J, , A new method to reconstruct recombination events at a genomic scale, PLoS Comput. Biol. 2010;6(11):e1001010.

Alcaïs A, Quintana-Murci L, Thaler DS, Schurr E, Abel L, Casanova JL, Life-threatening infectious diseases of childhood: single-gene inborn errors of immunity?, Ann. N. Y. Acad. Sci. 2010 Dec;1214:18-33.

Song Y, Baudoin M, Manneville P, Baroud CN, The air-liquid flow in a microfluidic airway tree, Med Eng Phys 2011 Sep;33(7):849-56.

Haak W, Balanovsky O, Sanchez JJ, Koshel S, Zaporozhchenko V, Adler CJ, Der Sarkissian CS, Brandt G, Schwarz C, Nicklisch N, Dresely V, Fritsch B, Balanovska E, Villems R, Meller H, Alt KW, Cooper A, , Ancient DNA from European early neolithic farmers reveals their near eastern affinities, PLoS Biol. 2010;8(11):e1000536.

Barbier F, Lebeaux D, Hernandez D, Delannoy AS, Caro V, François P, Schrenzel J, Ruppé E, Gaillard K, Wolff M, Brisse S, Andremont A, Ruimy R, High prevalence of the arginine catabolic mobile element in carriage isolates of methicillin-resistant Staphylococcus epidermidis, J. Antimicrob. Chemother. 2011 Jan;66(1):29-36.

Abbyad P, Dangla R, Alexandrou A, Baroud CN, Rails and anchors: guiding and trapping droplet microreactors in two dimensions, Lab Chip 2011 Mar;11(5):813-21.

Batini C, Lopes J, Behar DM, Calafell F, Jorde LB, van der Veen L, Quintana-Murci L, Spedini G, Destro-Bisol G, Comas D, Insights into the demographic history of African Pygmies from complete mitochondrial genomes, Mol. Biol. Evol. 2011 Feb;28(2):1099-110.

San Millan A, Giufré M, Escudero JA, Hidalgo L, Gutierrez B, Cerquetti M, Gonzalez-Zorn B, Contribution of ROB-1 and PBP3 mutations to the resistance phenotype of a β-lactamase-positive amoxicillin/clavulanic acid-resistant Haemophilus influenzae carrying plasmid pB1000 in Italy, J. Antimicrob. Chemother. 2011 Jan;66(1):96-9.

Baharoglu Z, Bikard D, Mazel D, , Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation., PLoS Genet 2010 Oct; 6(10): e1001165.

Andriantsoanirina V, Ratsimbasoa A, Bouchier C, Tichit M, Jahevitra M, Rabearimanana S, Raherinjafy R, Mercereau-Puijalon O, Durand R, Ménard D, Chloroquine clinical failures in P. falciparum malaria are associated with mutant Pfmdr-1, not Pfcrt in Madagascar, PLoS ONE 2010 Oct;5(10):e13281.

Rapp JB, Noguchi C, Das MM, Wong LK, Ansbach AB, Holmes AM, Arcangioli B, Noguchi E, Checkpoint-dependent and -independent roles of Swi3 in replication fork recovery and sister chromatid cohesion in fission yeast, PLoS ONE 2010;5(10):e13379.

do Valle TZ, Billecocq A, Guillemot L, Alberts R, Gommet C, Geffers R, Calabrese K, Schughart K, Bouloy M, Montagutelli X, Panthier JJ, A new mouse model reveals a critical role for host innate immunity in resistance to Rift Valley fever, J. Immunol. 2010 Nov;185(10):6146-56.

Ferrières L, Hémery G, Nham T, Guérout AM, Mazel D, Beloin C, Ghigo JM, Silent mischief: bacteriophage Mu insertions contaminate products of Escherichia coli random mutagenesis performed using suicidal transposon delivery plasmids mobilized by broad-host-range RP4 conjugative machinery, J. Bacteriol. 2010 Dec;192(24):6418-27.

Sangal V, Harbottle H, Mazzoni CJ, Helmuth R, Guerra B, Didelot X, Paglietti B, Rabsch W, Brisse S, Weill FX, Roumagnac P, Achtman M, Evolution and population structure of Salmonella enterica serovar Newport, J. Bacteriol. 2010 Dec;192(24):6465-76.

Champlot S, Berthelot C, Pruvost M, Bennett EA, Grange T, Geigl EM, , An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications., PLoS One 2010 Sep; 5(9): .

Charlène Blanchet, Jean Jaubert, Elisabeth Carniel, Corinne Fayolle, Geneviève Milon, Marek Szatanik, Jean-Jacques Panthier, Xavier Montagutelli, Mus spretus SEG/Pas mice resist virulent Yersinia pestis, under multigenic control, Genes and Immunity, 2011, 12 (1), pp.23-30. ⟨10.1038/gene.2010.45⟩.

Song Y, Manneville P, Baroud CN, Local interactions and the global organization of a two-phase flow in a branching tree, Phys. Rev. Lett. 2010 Sep;105(13):134501.

Santos J, González-Sánchez L, Villa-Morales M, Ors I, López-Nieva P, Vaquero C, González-Gugel E, Fernández-Navarro P, Roncero AM, Guenet JL, Montagutelli X, Fernández-Piqueras J, , The stromal gene encoding the CD274 antigen as a genetic modifier controlling survival of mice with γ-radiation-induced T-cell lymphoblastic lymphomas., Oncogene 2010 Sep; 29(38): 5265-73.

Dangla R, Gallaire F, Baroud CN, Microchannel deformations due to solvent-induced PDMS swelling, Lab Chip 2010 Nov;10(21):2972-8.

Enache-Angoulvant A, Bourget M, Brisse S, Stockman-Pannier C, Diancourt L, François N, Rimek D, Fairhead C, Poulain D, Hennequin C, Multilocus microsatellite markers for molecular typing of Candida glabrata: application to analysis of genetic relationships between bloodstream and digestive system isolates, J. Clin. Microbiol. 2010 Nov;48(11):4028-34.

Rocha EP, Feil EJ, Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?, PLoS Genet. 2010 Sep;6(9):e1001104.

Martínez-Cruz B, Vitalis R, Ségurel L, Austerlitz F, Georges M, Théry S, Quintana-Murci L, Hegay T, Aldashev A, Nasyrova F, Heyer E, In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations, Eur. J. Hum. Genet. 2011 Feb;19(2):216-23.

Le Roux F, Labreuche Y, Davis BM, Iqbal N, Mangenot S, Goarant C, Mazel D, Waldor MK, Virulence of an emerging pathogenic lineage of Vibrio nigripulchritudo is dependent on two plasmids, Environ. Microbiol. 2011 Feb;13(2):296-306.

Thompson FL, Thompson CC, Vicente AC, Klose KE, , Vibrio2009: the third international conference on the biology of Vibrios, Mol. Microbiol. 2010 Sep;77(5):1065-71.

Smillie C, Garcillán-Barcia MP, Francia MV, Rocha EP, de la Cruz F, Mobility of plasmids, Microbiol. Mol. Biol. Rev. 2010 Sep;74(3):434-52.

Brocas C, Charbonnier JB, Dhérin C, Gangloff S, Maloisel L, Stable interactions between DNA polymerase δ catalytic and structural subunits are essential for efficient DNA repair, DNA Repair (Amst.) 2010 Oct;9(10):1098-111.

Carlos Perez, Jean Jaubert, Jean-Louis Guénet, Kirstin Barnhart, Catherine Ross-Inta, Vicente Quintanilla, Isabelle Aubin, Jimi Brandon, Nancy Otto, John Digiovanni, Irma Gimenez-Conti, Cecilia Giulivi, Donna F. Kusewitt, Claudio Conti, Fernando Benavides, Two Hypomorphic Alleles of Mouse Ass1 as a New Animal Model of Citrullinemia Type I and Other Hyperammonemic Syndromes, American Journal of Pathology, 2010, 177 (4), pp.1958-1968. ⟨10.2353/ajpath.2010.100118⟩.

Loot C, Bikard D, Rachlin A, Mazel D, Cellular pathways controlling integron cassette site folding., EMBO J 2010 Aug; 29(15): 2623-34.

Zhadanov SI, Dulik MC, Markley M, Jennings GW, Gaieski JB, Elias G, Schurr TG, , Genetic heritage and native identity of the Seaconke Wampanoag tribe of Massachusetts, Am. J. Phys. Anthropol. 2010 Aug;142(4):579-89.

Labreuche Y, Le Roux F, Henry J, Zatylny C, Huvet A, Lambert C, Soudant P, Mazel D, Nicolas JL, Vibrio aestuarianus zinc metalloprotease causes lethality in the Pacific oyster Crassostrea gigas and impairs the host cellular immune defenses, Fish Shellfish Immunol. 2010 Nov;29(5):753-8.

Abbyad P, Tharaux PL, Martin JL, Baroud CN, Alexandrou A, Sickling of red blood cells through rapid oxygen exchange in microfluidic drops, Lab Chip 2010 Oct;10(19):2505-12.

Nalpas B, Lavialle-Meziani R, Plancoulaine S, Jouanguy E, Nalpas A, Munteanu M, Charlotte F, Ranque B, Patin E, Heath S, Fontaine H, Vallet-Pichard A, Pontoire D, Bourlière M, Casanova JL, Lathrop M, Bréchot C, Poynard T, Matsuda F, Pol S, Abel L, Interferon gamma receptor 2 gene variants are associated with liver fibrosis in patients with chronic hepatitis C infection, Gut 2010 Aug;59(8):1120-6.

Baroud CN, Gallaire F, Dangla R, Dynamics of microfluidic droplets, Lab Chip 2010 Aug;10(16):2032-45.

Touchon M, Rocha EP, The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella, PLoS ONE 2010;5(6):e11126.

Thiberge JM, Boursaux-Eude C, Lehours P, Dillies MA, Creno S, Coppée JY, Rouy Z, Lajus A, Ma L, Burucoa C, Ruskoné-Foumestraux A, Courillon-Mallet A, De Reuse H, Boneca IG, Lamarque D, Mégraud F, Delchier JC, Médigue C, Bouchier C, Labigne A, Raymond J, From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma, BMC Genomics 2010;11:368.

Bikard D, Julié-Galau S, Cambray G, Mazel D, The synthetic integron: an in vivo genetic shuffling device, Nucleic Acids Res. 2010 Aug;38(15):e153.

Oliveira PH, Prather KJ, Prazeres DM, Monteiro GA, Analysis of DNA repeats in bacterial plasmids reveals the potential for recurrent instability events, Appl. Microbiol. Biotechnol. 2010 Aug;87(6):2157-67.

Baharoglu Z, Lestini R, Duigou S, Michel B, RNA polymerase mutations that facilitate replication progression in the rep uvrD recF mutant lacking two accessory replicative helicases, Mol. Microbiol. 2010 Jul;77(2):324-36.

Skurnik D, Nucci A, Ruimy R, Lasocki S, Muller-Serieys C, Montravers P, Andremont A, Courvalin P, Emergence of carbapenem-resistant Hafnia: the fall of the last soldier., Clin Infect Dis 2010 May; 50(10): 1429-31.

Andriantsoanirina V, Ménard D, Rabearimanana S, Hubert V, Bouchier C, Tichit M, Bras JL, Durand R, Association of microsatellite variations of Plasmodium falciparum Na+/H+ exchanger (Pfnhe-1) gene with reduced in vitro susceptibility to quinine: lack of confirmation in clinical isolates from Africa, Am. J. Trop. Med. Hyg. 2010 May;82(5):782-7.

Czeher C, Labbo R, Vieville G, Arzika I, Bogreau H, Rogier C, Diancourt L, Brisse S, Ariey F, Duchemin JB, Population genetic structure of Anopheles gambiae and Anopheles arabiensis in Niger, J. Med. Entomol. 2010 May;47(3):355-66.

Laval G, Patin E, Barreiro LB, Quintana-Murci L, Formulating a historical and demographic model of recent human evolution based on resequencing data from noncoding regions, PLoS ONE 2010;5(4):e10284.

d'Alençon E, Sezutsu H, Legeai F, Permal E, Bernard-Samain S, Gimenez S, Gagneur C, Cousserans F, Shimomura M, Brun-Barale A, Flutre T, Couloux A, East P, Gordon K, Mita K, Quesneville H, Fournier P, Feyereisen R, Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements, Proc. Natl. Acad. Sci. U.S.A. 2010 Apr;107(17):7680-5.

Vieira-Silva S, Touchon M, Rocha EP, No evidence for elemental-based streamlining of prokaryotic genomes, Trends Ecol. Evol. (Amst.) 2010 Jun;25(6):319-20; author reply 320-1.

Diancourt L, Passet V, Nemec A, Dijkshoorn L, Brisse S, The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool, PLoS ONE 2010;5(4):e10034.

Yao Y, Demoinet E, Saveanu C, Lenormand P, Jacquier A, Fromont-Racine M, Ecm1 is a new pre-ribosomal factor involved in pre-60S particle export, RNA 2010 May;16(5):1007-17.

Quintana-Murci L, Harmant C, Quach H, Balanovsky O, Zaporozhchenko V, Bormans C, van Helden PD, Hoal EG, Behar DM, Strong maternal Khoisan contribution to the South African coloured population: a case of gender-biased admixture, Am. J. Hum. Genet. 2010 Apr;86(4):611-20.

Rankin DJ, Rocha EP, Brown SP, What traits are carried on mobile genetic elements, and why?, Heredity (Edinb) 2011 Jan;106(1):1-10.

Bob NS, Diop BM, Renaud F, Marrama L, Durand P, Tall A, Ka B, Ekala MT, Bouchier C, Mercereau-Puijalon O, Jambou R, Parasite polymorphism and severe malaria in Dakar (Senegal): a West African urban area, PLoS ONE 2010;5(3):e9817.

Andriantsoanirina V, Bouchier C, Tichit M, Jahevitra M, Rabearimanana S, Randrianjafy R, Ratsimbasoa A, Mercereau-Puijalon O, Durand R, Ménard D, Origins of the recent emergence of Plasmodium falciparum pyrimethamine resistance alleles in Madagascar, Antimicrob. Agents Chemother. 2010 Jun;54(6):2323-9.

Ménard D, Barnadas C, Bouchier C, Henry-Halldin C, Gray LR, Ratsimbasoa A, Thonier V, Carod JF, Domarle O, Colin Y, Bertrand O, Picot J, King CL, Grimberg BT, Mercereau-Puijalon O, Zimmerman PA, Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people, Proc. Natl. Acad. Sci. U.S.A. 2010 Mar;107(13):5967-71.

Najjar I, Deglesne PA, Schischmanoff PO, Fabre EE, Boisson-Dupuis S, Nimmerjahn F, Bornkamm GW, Dusanter-Fourt I, Fagard R, STAT1-dependent IgG cell-surface expression in a human B cell line derived from a STAT1-deficient patient, J. Leukoc. Biol. 2010 Jun;87(6):1145-52.

Lesage S, Patin E, Condroyer C, Leutenegger AL, Lohmann E, Giladi N, Bar-Shira A, Belarbi S, Hecham N, Pollak P, Ouvrard-Hernandez AM, Bardien S, Carr J, Benhassine T, Tomiyama H, Pirkevi C, Hamadouche T, Cazeneuve C, Basak AN, Hattori N, Dürr A, Tazir M, Orr-Urtreger A, Quintana-Murci L, Brice A, , Parkinson’s disease-related LRRK2 G2019S mutation results from independent mutational events in humans, Hum. Mol. Genet. 2010 May;19(10):1998-2004.

Lim P, Wongsrichanalai C, Chim P, Khim N, Kim S, Chy S, Sem R, Nhem S, Yi P, Duong S, Bouth DM, Genton B, Beck HP, Gobert JG, Rogers WO, Coppee JY, Fandeur T, Mercereau-Puijalon O, Ringwald P, Le Bras J, Ariey F, Decreased in vitro susceptibility of Plasmodium falciparum isolates to artesunate, mefloquine, chloroquine, and quinine in Cambodia from 2001 to 2007, Antimicrob. Agents Chemother. 2010 May;54(5):2135-42.

Pallafacchina G, François S, Regnault B, Czarny B, Dive V, Cumano A, Montarras D, Buckingham M, An adult tissue-specific stem cell in its niche: a gene profiling analysis of in vivo quiescent and activated muscle satellite cells., Stem Cell Res 2010 Mar; 4(2): 77-91.

Cassar O, Bassot S, Plancoulaine S, Quintana-Murci L, Harmant C, Gurtsevitch V, Senyuta NB, Yakovleva LS, de The G, Gessain A, Human herpesvirus 8, Southern Siberia, Emerging Infect. Dis. 2010 Mar;16(3):580-2.

Aguilera A, Souza-Egipsy V, González-Toril E, Rendueles O, Amils R, Eukaryotic microbial diversity of phototrophic microbial mats in two Icelandic geothermalhot springs, Int. Microbiol. 2010 Mar;13(1):21-32.

Arsène-Ploetze F, Koechler S, Marchal M, Coppée JY, Chandler M, Bonnefoy V, Brochier-Armanet C, Barakat M, Barbe V, Battaglia-Brunet F, Bruneel O, Bryan CG, Cleiss-Arnold J, Cruveiller S, Erhardt M, Heinrich-Salmeron A, Hommais F, Joulian C, Krin E, Lieutaud A, Lièvremont D, Michel C, Muller D, Ortet P, Proux C, Siguier P, Roche D, Rouy Z, Salvignol G, Slyemi D, Talla E, Weiss S, Weissenbach J, Médigue C, Bertin PN, Structure, function, and evolution of the Thiomonas spp. genome, PLoS Genet. 2010 Feb;6(2):e1000859.

Giannouli M, Cuccurullo S, Crivaro V, Di Popolo A, Bernardo M, Tomasone F, Amato G, Brisse S, Triassi M, Utili R, Zarrilli R, Molecular epidemiology of multidrug-resistant Acinetobacter baumannii in a tertiary care hospital in Naples, Italy, shows the emergence of a novel epidemic clone, J. Clin. Microbiol. 2010 Apr;48(4):1223-30.

Ramirez MS, Don M, Merkier AK, Bistué AJ, Zorreguieta A, Centrón D, Tolmasky ME, Naturally competent Acinetobacter baumannii clinical isolate as a convenient model for genetic studies, J. Clin. Microbiol. 2010 Apr;48(4):1488-90.

, Genome sequence of the pea aphid Acyrthosiphon pisum, PLoS Biol. 2010 Feb;8(2):e1000313.

Cazalet C, Gomez-Valero L, Rusniok C, Lomma M, Dervins-Ravault D, Newton HJ, Sansom FM, Jarraud S, Zidane N, Ma L, Bouchier C, Etienne J, Hartland EL, Buchrieser C, Analysis of the Legionella longbeachae genome and transcriptome uncovers unique strategies to cause Legionnaires’ disease., PLoS Genet 2010 Feb; 6(2): e1000851.

Koechler S, Cleiss-Arnold J, Proux C, Sismeiro O, Dillies MA, Goulhen-Chollet F, Hommais F, Lièvremont D, Arsène-Ploetze F, Coppée JY, Bertin PN, Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans, BMC Microbiol. 2010;10:53.

Najjar I, Fagard R, STAT1 and pathogens, not a friendly relationship, Biochimie 2010 May;92(5):425-44.

Rusniok C, Couvé E, Da Cunha V, El Gana R, Zidane N, Bouchier C, Poyart C, Leclercq R, Trieu-Cuot P, Glaser P, Genome sequence of Streptococcus gallolyticus: insights into its adaptation to the bovine rumen and its ability to cause endocarditis, J. Bacteriol. 2010 Apr;192(8):2266-76.

Chayot R, Montagne B, Mazel D, Ricchetti M, , An end-joining repair mechanism in Escherichia coli., Proc Natl Acad Sci U S A 2010 Feb; 107(5): 2141-6.

L'Hôte D, Laissue P, Serres C, Montagutelli X, Veitia RA, Vaiman D, , Interspecific resources: a major tool for quantitative trait locus cloning and speciation research., Bioessays 2010 Feb; 32(2): 132-42.

Das B, Bischerour J, Val ME, Barre FX, Molecular keys of the tropism of integration of the cholera toxin phage., Proc Natl Acad Sci U S A 2010 Mar; 107(9): 4377-82.

San Millan A, Garcia-Cobos S, Escudero JA, Hidalgo L, Gutierrez B, Carrilero L, Campos J, Gonzalez-Zorn B, Haemophilus influenzae clinical isolates with plasmid pB1000 bearing blaROB-1: fitness cost and interspecies dissemination, Antimicrob. Agents Chemother. 2010 Apr;54(4):1506-11.

Vieira-Silva S, Rocha EP, The systemic imprint of growth and its uses in ecological (meta)genomics, PLoS Genet. 2010 Jan;6(1):e1000808.

Duperthuy M, Binesse J, Le Roux F, Romestand B, Caro A, Got P, Givaudan A, Mazel D, Bachère E, Destoumieux-Garzón D, The major outer membrane protein OmpU of Vibrio splendidus contributes to host antimicrobial peptide resistance and is required for virulence in the oyster Crassostrea gigas, Environ. Microbiol. 2010 Apr;12(4):951-63.

Delétoile A, Passet V, Aires J, Chambaud I, Butel MJ, Smokvina T, Brisse S, Species delineation and clonal diversity in four Bifidobacterium species as revealed by multilocus sequencing, Res. Microbiol. 2010 Mar;161(2):82-90.

Jové T, Da Re S, Denis F, Mazel D, Ploy MC, Inverse correlation between promoter strength and excision activity in class 1 integrons, PLoS Genet. 2010 Jan;6(1):e1000793.

Ronan Jambou, Axel Martinelli, João Pinto, Simonetta Gribaldo, Eric Legrand, Makhtar Niang, Nimol Kim, Lim Pharath, Béatrice Volnay, Marie Therese Ekala, Christiane Bouchier, Thierry Fandeur, Pedro Berzosa, Agustin Benito, Isabel Dinis Ferreira, Cynthia Ferreira, Pedro Paulo Vieira, Maria das Graças Alecrim, Odile Mercereau-Puijalon, Pedro Cravo, Geographic structuring of the Plasmodium falciparum sarco(endo)plasmic reticulum Ca2+ ATPase (PfSERCA) gene diversity., PLoS ONE, 2010, 5 (2), pp.e9424. ⟨10.1371/journal.pone.0009424⟩.

Cambray G, Guerout AM, Mazel D, Integrons, Annu. Rev. Genet. 2010;44:141-66.

Guérin E, Cambray G, Da Re S, Mazel D, Ploy MC, [The SOS response controls antibiotic resistance by regulating the integrase of integrons], Med Sci (Paris) 2010 Jan;26(1):28-30.

Neyrolles O, Quintana-Murci L, Sexual inequality in tuberculosis, PLoS Med. 2009 Dec;6(12):e1000199.

Mil-Homens D, Rocha EP, Fialho AM, Genome-wide analysis of DNA repeats in Burkholderia cenocepacia J2315 identifies a novel adhesin-like gene unique to epidemic-associated strains of the ET-12 lineage, Microbiology (Reading, Engl.) 2010 Apr;156(Pt 4):1084-96.

Louicharoen C, Patin E, Paul R, Nuchprayoon I, Witoonpanich B, Peerapittayamongkol C, Casademont I, Sura T, Laird NM, Singhasivanon P, Quintana-Murci L, Sakuntabhai A, Positively selected G6PD-Mahidol mutation reduces Plasmodium vivax density in Southeast Asians, Science 2009 Dec;326(5959):1546-9.

Barreiro LB, Quintana-Murci L, From evolutionary genetics to human immunology: how selection shapes host defence genes, Nat. Rev. Genet. 2010 Jan;11(1):17-30.

Fagegaltier D, Bougé AL, Berry B, Poisot E, Sismeiro O, Coppée JY, Théodore L, Voinnet O, Antoniewski C, The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila, Proc. Natl. Acad. Sci. U.S.A. 2009 Dec;106(50):21258-63.

Thierry A, Dujon B, Richard GF, Megasatellites: a new class of large tandem repeats discovered in the pathogenic yeast Candida glabrata, Cell. Mol. Life Sci. 2010 Mar;67(5):671-6.

Kafasla P, Barrass JD, Thompson E, Fromont-Racine M, Jacquier A, Beggs JD, Lewis J, Interaction of yeast eIF4G with spliceosome components: implications in pre-mRNA processing events, RNA Biol 2009 Nov-Dec;6(5):563-74.

Frumerie C, Ducos-Galand M, Gopaul DN, Mazel D, The relaxed requirements of the integron cleavage site allow predictable changes in integron target specificity, Nucleic Acids Res. 2010 Jan;38(2):559-69.

Pothlichet J, Burtey A, Kubarenko AV, Caignard G, Solhonne B, Tangy F, Ben-Ali M, Quintana-Murci L, Heinzmann A, Chiche JD, Vidalain PO, Weber AN, Chignard M, Si-Tahar M, Study of human RIG-I polymorphisms identifies two variants with an opposite impact on the antiviral immune response, PLoS ONE 2009;4(10):e7582.

Koszul R, Kleckner N, Dynamic chromosome movements during meiosis: a way to eliminate unwanted connections?, Trends Cell Biol. 2009 Dec;19(12):716-24.

Noranate N, Prugnolle F, Jouin H, Tall A, Marrama L, Sokhna C, Ekala MT, Guillotte M, Bischoff E, Bouchier C, Patarapotikul J, Ohashi J, Trape JF, Rogier C, Mercereau-Puijalon O, Population diversity and antibody selective pressure to Plasmodium falciparum MSP1 block2 locus in an African malaria-endemic setting, BMC Microbiol. 2009;9:219.

Steenkeste N, Dillies MA, Khim N, Sismeiro O, Chy S, Lim P, Crameri A, Bouchier C, Mercereau-Puijalon O, Beck HP, Imwong M, Dondorp AM, Socheat D, Rogier C, Coppée JY, Ariey F, FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance, Malar. J. 2009;8:229.

Matondo M, Bousquet-Dubouch MP, Gallay N, Uttenweiler-Joseph S, Recher C, Payrastre B, Manenti S, Monsarrat B, Burlet-Schiltz O, Proteasome inhibitor-induced apoptosis in acute myeloid leukemia: a correlation with the proteasome status, Leuk. Res. 2010 Apr;34(4):498-506.

Regnault B, Osorio Y Fortea J, Miao D, Eisenbarth G, Melanitou E, Early over expression of messenger RNA for multiple genes, including insulin, in the Pancreatic Lymph Nodes of NOD mice is associated with Islet Autoimmunity, BMC Med Genomics 2009;2:63.

Zagnoni M, Baroud CN, Cooper JM, Electrically initiated upstream coalescence cascade of droplets in a microfluidic flow, Phys Rev E Stat Nonlin Soft Matter Phys 2009 Oct;80(4 Pt 2):046303.

Souciet JL, Dujon B, Gaillardin C, Johnston M, Baret PV, Cliften P, Sherman DJ, Weissenbach J, Westhof E, Wincker P, Jubin C, Poulain J, Barbe V, Ségurens B, Artiguenave F, Anthouard V, Vacherie B, Val ME, Fulton RS, Minx P, Wilson R, Durrens P, Jean G, Marck C, Martin T, Nikolski M, Rolland T, Seret ML, Casarégola S, Despons L, Fairhead C, Fischer G, Lafontaine I, Leh V, Lemaire M, de Montigny J, Neuvéglise C, Thierry A, Blanc-Lenfle I, Bleykasten C, Diffels J, Fritsch E, Frangeul L, Goëffon A, Jauniaux N, Kachouri-Lafond R, Payen C, Potier S, Pribylova L, Ozanne C, Richard GF, Sacerdot C, Straub ML, Talla E, Comparative genomics of protoploid Saccharomycetaceae., Genome Res 2009 Oct; 19(10): 1696-709.

Nogueira T, Rankin DJ, Touchon M, Taddei F, Brown SP, Rocha EP, Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence, Curr. Biol. 2009 Nov;19(20):1683-91.

Monfort L, Caro V, Devaux Z, Delannoy AS, Brisse S, Sednaoui P, First neisseria gonorrhoeae genotyping analysis in france: identification of a strain cluster with reduced susceptibility to Ceftriaxone, J. Clin. Microbiol. 2009 Nov;47(11):3540-5.

Gutierrez B, Herrera-Leon S, Escudero JA, Hidalgo L, Gonzalez-Sanz R, Arroyo M, San Millan A, Echeita MA, Gonzalez-Zorn B, Novel genetic environment of qnrB2 associated with TEM-1 and SHV-12 on pB1004, an IncHI2 plasmid, in Salmonella Bredeney BB1047 from Spain, J. Antimicrob. Chemother. 2009 Dec;64(6):1334-6.

Elhani D, Bakir L, Aouni M, Passet V, Arlet G, Brisse S, Weill FX, Molecular epidemiology of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae strains in a university hospital in Tunis, Tunisia, 1999-2005, Clin. Microbiol. Infect. 2010 Feb;16(2):157-64.

Abraham AL, Pothier J, Rocha EP, Alternative to homo-oligomerisation: the creation of local symmetry in proteins by internal amplification, J. Mol. Biol. 2009 Dec;394(3):522-34.

Ortiz M, Guex N, Patin E, Martin O, Xenarios I, Ciuffi A, Quintana-Murci L, Telenti A, Evolutionary trajectories of primate genes involved in HIV pathogenesis, Mol. Biol. Evol. 2009 Dec;26(12):2865-75.

Bouvier M, Ducos-Galand M, Loot C, Bikard D, Mazel D, Structural features of single-stranded integron cassette attC sites and their role in strand selection., PLoS Genet 2009 Sep; 5(9): e1000632.

Heyer E, Balaresque P, Jobling MA, Quintana-Murci L, Chaix R, Segurel L, Aldashev A, Hegay T, Genetic diversity and the emergence of ethnic groups in Central Asia, BMC Genet. 2009;10:49.

Arcangioli B, Ben Hassine S, Unrepaired oxidative DNA damage induces an ATR/ATM apoptotic-like response in quiescent fission yeast, Cell Cycle 2009 Aug;8(15):2326-31.

Andriantsoanirina V, Ratsimbasoa A, Bouchier C, Jahevitra M, Rabearimanana S, Radrianjafy R, Andrianaranjaka V, Randriantsoa T, Rason MA, Tichit M, Rabarijaona LP, Mercereau-Puijalon O, Durand R, Ménard D, Plasmodium falciparum drug resistance in Madagascar: facing the spread of unusual pfdhfr and pfmdr-1 haplotypes and the decrease of dihydroartemisinin susceptibility, Antimicrob. Agents Chemother. 2009 Nov;53(11):4588-97.

El-Sibai M, Platt DE, Haber M, Xue Y, Youhanna SC, Wells RS, Izaabel H, Sanyoura MF, Harmanani H, Bonab MA, Behbehani J, Hashwa F, Tyler-Smith C, Zalloua PA, , Geographical structure of the Y-chromosomal genetic landscape of the Levant: a coastal-inland contrast, Ann. Hum. Genet. 2009 Nov;73(Pt 6):568-81.

Oliveira PH, Prazeres DM, Monteiro GA, Deletion formation mutations in plasmid expression vectors are unfavored by runaway amplification conditions and differentially selected under kanamycin stress, J. Biotechnol. 2009 Sep;143(4):231-8.

van Schaik W, Château A, Dillies MA, Coppée JY, Sonenshein AL, Fouet A, The global regulator CodY regulates toxin gene expression in Bacillus anthracis and is required for full virulence, Infect. Immun. 2009 Oct;77(10):4437-45.

Bierne H, Tham TN, Batsche E, Dumay A, Leguillou M, Kernéis-Golsteyn S, Regnault B, Seeler JS, Muchardt C, Feunteun J, Cossart P, Human BAHD1 promotes heterochromatic gene silencing, Proc. Natl. Acad. Sci. U.S.A. 2009 Aug;106(33):13826-31.

Oliveira PH, Prather KJ, Prazeres DM, Monteiro GA, Structural instability of plasmid biopharmaceuticals: challenges and implications, Trends Biotechnol. 2009 Sep;27(9):503-11.

Forquin MP, Duvergey H, Proux C, Loux V, Mounier J, Landaud S, Coppée JY, Gibrat JF, Bonnarme P, Martin-Verstraete I, Vallaeys T, Identification of brevibacteriaceae by multilocus sequence typing and comparative genomic hybridization analyses, Appl. Environ. Microbiol. 2009 Oct;75(19):6406-9.

Soler Bistué AJ, Martín FA, Vozza N, Ha H, Joaquín JC, Zorreguieta A, Tolmasky ME, Inhibition of aac(6′)-Ib-mediated amikacin resistance by nuclease-resistant external guide sequences in bacteria, Proc. Natl. Acad. Sci. U.S.A. 2009 Aug;106(32):13230-5.

Paragas N, Nickolas TL, Wyatt C, Forster CS, Sise M, Morgello S, Jagla B, Buchen C, Stella P, Sanna-Cherchi S, Carnevali ML, Mattei S, Bovino A, Argentiero L, Magnano A, Devarajan P, Schmidt-Ott KM, Allegri L, Klotman P, D'Agati V, Gharavi AG, Barasch J, Urinary NGAL marks cystic disease in HIV-associated nephropathy, J. Am. Soc. Nephrol. 2009 Aug;20(8):1687-92.

Ivanova EP, Christen R, Bizet C, Clermont D, Motreff L, Bouchier C, Zhukova NV, Crawford RJ, Kiprianova EA, , Pseudomonas brassicacearum subsp. neoaurantiaca subsp. nov., orange-pigmented bacteria isolated from soil and the rhizosphere of agricultural plants., Int J Syst Evol Microbiol 2009 Oct; 59(Pt 10): 2476-81.

Barreiro LB, Ben-Ali M, Quach H, Laval G, Patin E, Pickrell JK, Bouchier C, Tichit M, Neyrolles O, Gicquel B, Kidd JR, Kidd KK, Alcaïs A, Ragimbeau J, Pellegrini S, Abel L, Casanova JL, Quintana-Murci L, Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense, PLoS Genet. 2009 Jul;5(7):e1000562.

Bouchier C, Ma L, Créno S, Dujon B, Fairhead C, Complete mitochondrial genome sequences of three Nakaseomyces species reveal invasion by palindromic GC clusters and considerable size expansion, FEMS Yeast Res. 2009 Dec;9(8):1283-92.

Payen C, Fischer G, Marck C, Proux C, Sherman DJ, Coppée JY, Johnston M, Dujon B, Neuvéglise C, Unusual composition of a yeast chromosome arm is associated with its delayed replication, Genome Res. 2009 Oct;19(10):1710-21.

Barnadas C, Musset L, Legrand E, Tichit M, Briolant S, Fusai T, Rogier C, Bouchier C, Picot S, Ménard D, , High prevalence and fixation of Plasmodium vivax dhfr/dhps mutations related to sulfadoxine/pyrimethamine resistance in French Guiana., Am J Trop Med Hyg 2009 Jul; 81(1): 19-22.

Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy M, Vergassola M, Nahori MA, Soubigou G, Régnault B, Coppée JY, Lecuit M, Johansson J, Cossart P, , The Listeria transcriptional landscape from saprophytism to virulence., Nature 2009 Jun; 459(7249): 950-6.

San Millan A, Escudero JA, Gutierrez B, Hidalgo L, Garcia N, Llagostera M, Dominguez L, Gonzalez-Zorn B, Multiresistance in Pasteurella multocida is mediated by coexistence of small plasmids, Antimicrob. Agents Chemother. 2009 Aug;53(8):3399-404.

Soutourina O, Poupel O, Coppée JY, Danchin A, Msadek T, Martin-Verstraete I, CymR, the master regulator of cysteine metabolism in Staphylococcus aureus, controls host sulphur source utilization and plays a role in biofilm formation, Mol. Microbiol. 2009 Jul;73(2):194-211.

van Asten L, van der Lubben M, van den Wijngaard C, van Pelt W, Verheij R, Jacobi A, Overduin P, Meijer A, Luijt D, Claas E, Hermans M, Melchers W, Rossen J, Schuurman R, Wolffs P, Boucher C, Bouchier C, Schirm J, Kroes L, Leenders S, Galama J, Peeters M, van Loon A, Stobberingh E, Schutten M, Koopmans M, Strengthening the diagnostic capacity to detect Bio Safety Level 3 organisms in unusual respiratory viral outbreaks, J. Clin. Virol. 2009 Jul;45(3):185-90.

Burgio G, Baylac M, Heyer E, Montagutelli X, Genetic analysis of skull shape variation and morphological integration in the mouse using interspecific recombinant congenic strains between C57BL/6 and mice of the mus spretus species, Evolution 2009 Oct;63(10):2668-86.

Jacquier H, Zaoui C, Sanson-le Pors MJ, Mazel D, Berçot B, Translation regulation of integrons gene cassette expression by the attC sites, Mol. Microbiol. 2009 Jun;72(6):1475-86.

Andriantsoanirina V, Lascombes V, Ratsimbasoa A, Bouchier C, Hoffman J, Tichit M, Rabarijaona LP, Durand R, Ménard D, Rapid detection of point mutations in Plasmodium falciparum genes associated with antimalarial drugs resistance by using High-Resolution Melting analysis, J. Microbiol. Methods 2009 Aug;78(2):165-70.

Guerin E, Cambray G, Sanchez-Alberola N, Campoy S, Erill I, Da Re S, Gonzalez-Zorn B, Barbé J, Ploy MC, Mazel D, The SOS response controls integron recombination, Science 2009 May;324(5930):1034.

Verneuil E, Cordero M, Gallaire F, Baroud CN, Laser-induced force on a microfluidic drop: origin and magnitude, Langmuir 2009 May;25(9):5127-34.

Clermont D, Diard S, Bouchier C, Vivier C, Bimet F, Motreff L, Welker M, Kallow W, Bizet C, Microbacterium binotii sp. nov., isolated from human blood, Int. J. Syst. Evol. Microbiol. 2009 May;59(Pt 5):1016-22.

Treangen TJ, Abraham AL, Touchon M, Rocha EP, Genesis, effects and fates of repeats in prokaryotic genomes, FEMS Microbiol. Rev. 2009 May;33(3):539-71.

Dejager L, Libert C, Montagutelli X, , Thirty years of Mus spretus: a promising future., Trends Genet. 2009 May; 25(5): 234-41.

Berniell-Lee G, Calafell F, Bosch E, Heyer E, Sica L, Mouguiama-Daouda P, van der Veen L, Hombert JM, Quintana-Murci L, Comas D, Genetic and demographic implications of the Bantu expansion: insights from human paternal lineages, Mol. Biol. Evol. 2009 Jul;26(7):1581-9.

Patin E, Laval G, Barreiro LB, Salas A, Semino O, Santachiara-Benerecetti S, Kidd KK, Kidd JR, Van der Veen L, Hombert JM, Gessain A, Froment A, Bahuchet S, Heyer E, Quintana-Murci L, Inferring the demographic history of African farmers and pygmy hunter-gatherers using a multilocus resequencing data set, PLoS Genet. 2009 Apr;5(4):e1000448.

Le Roux F, Zouine M, Chakroun N, Binesse J, Saulnier D, Bouchier C, Zidane N, Ma L, Rusniok C, Lajus A, Buchrieser C, Médigue C, Polz MF, Mazel D, Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity, Environ. Microbiol. 2009 Aug;11(8):1959-70.

Treangen TJ, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EP, A novel heuristic for local multiple alignment of interspersed DNA repeats, IEEE/ACM Trans Comput Biol Bioinform 2009 Apr-Jun;6(2):180-9.

Brisse S, Fevre C, Passet V, Issenhuth-Jeanjean S, Tournebize R, Diancourt L, Grimont P, Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization, PLoS ONE 2009;4(3):e4982.

Osorio y Fortéa J, de La Llave E, Regnault B, Coppée JY, Milon G, Lang T, Prina E, Transcriptional signatures of BALB/c mouse macrophages housing multiplying Leishmania amazonensis amastigotes, BMC Genomics 2009;10:119.

Schor IE, Rascovan N, Pelisch F, Alló M, Kornblihtt AR, , Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing., Proc Natl Acad Sci U S A 2009 Mar; 106(11): 4325-30.

Santos J, González-Sánchez L, Matabuena-Deyzaguirre M, Villa-Morales M, Cozar P, López-Nieva P, Fernández-Navarro P, Fresno M, Díaz-Muñoz MD, Guenet JL, Montagutelli X, Fernández-Piqueras J, , A role for stroma-derived annexin A1 as mediator in the control of genetic susceptibility to T-cell lymphoblastic malignancies through prostaglandin E2 secretion., Cancer Res. 2009 Mar; 69(6): 2577-87.

Pagès F, Peyrefitte CN, Mve MT, Jarjaval F, Brisse S, Iteman I, Gravier P, Tolou H, Nkoghe D, Grandadam M, Aedes albopictus mosquito: the main vector of the 2007 Chikungunya outbreak in Gabon, PLoS ONE 2009;4(3):e4691.

Ibrahim ML, Steenkeste N, Khim N, Adam HH, Konaté L, Coppée JY, Ariey F, Duchemin JB, Field-based evidence of fast and global increase of Plasmodium falciparum drug-resistance by DNA-microarrays and PCR/RFLP in Niger, Malar. J. 2009;8:32.

Quach H, Barreiro LB, Laval G, Zidane N, Patin E, Kidd KK, Kidd JR, Bouchier C, Veuille M, Antoniewski C, Quintana-Murci L, Signatures of purifying and local positive selection in human miRNAs, Am. J. Hum. Genet. 2009 Mar;84(3):316-27.

Ishida K, Welker M, Christiansen G, Cadel-Six S, Bouchier C, Dittmann E, Hertweck C, Tandeau de Marsac N, Plasticity and evolution of aeruginosin biosynthesis in cyanobacteria, Appl. Environ. Microbiol. 2009 Apr;75(7):2017-26.

Ben Hassine S, Arcangioli B, Tdp1 protects against oxidative DNA damage in non-dividing fission yeast, EMBO J. 2009 Mar;28(6):632-40.

Verdu P, Austerlitz F, Estoup A, Vitalis R, Georges M, Théry S, Froment A, Le Bomin S, Gessain A, Hombert JM, Van der Veen L, Quintana-Murci L, Bahuchet S, Heyer E, Origins and genetic diversity of pygmy hunter-gatherers from Western Central Africa, Curr. Biol. 2009 Feb;19(4):312-8.

Bousquet-Dubouch MP, Baudelet E, Guérin F, Matondo M, Uttenweiler-Joseph S, Burlet-Schiltz O, Monsarrat B, Affinity purification strategy to capture human endogenous proteasome complexes diversity and to identify proteasome-interacting proteins, Mol. Cell Proteomics 2009 May;8(5):1150-64.

Dacheux L, Larrous F, Mailles A, Boisseleau D, Delmas O, Biron C, Bouchier C, Capek I, Muller M, Ilari F, Lefranc T, Raffi F, Goudal M, Bourhy H, European bat Lyssavirus transmission among cats, Europe, Emerging Infect. Dis. 2009 Feb;15(2):280-4.

Heyer E, Quintana-Murci L, Evolutionary genetics as a tool to target genes involved in phenotypes of medical relevance, Evol Appl 2009 Feb;2(1):71-80.

Ah-You N, Gagnevin L, Grimont PA, Brisse S, Nesme X, Chiroleu F, Bui Thi Ngoc L, Jouen E, Lefeuvre P, Vernière C, Pruvost O, Polyphasic characterization of xanthomonads pathogenic to members of the Anacardiaceae and their relatedness to species of Xanthomonas, Int. J. Syst. Evol. Microbiol. 2009 Feb;59(Pt 2):306-18.

Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EP, Denamur E, Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths, PLoS Genet. 2009 Jan;5(1):e1000344.

Brisse S, Pannier C, Angoulvant A, de Meeus T, Diancourt L, Faure O, Muller H, Peman J, Viviani MA, Grillot R, Dujon B, Fairhead C, Hennequin C, Uneven distribution of mating types among genotypes of Candida glabrata isolates from clinical samples, Eukaryotic Cell 2009 Mar;8(3):287-95.

Lim P, Alker AP, Khim N, Shah NK, Incardona S, Doung S, Yi P, Bouth DM, Bouchier C, Puijalon OM, Meshnick SR, Wongsrichanalai C, Fandeur T, Le Bras J, Ringwald P, Ariey F, Pfmdr1 copy number and arteminisin derivatives combination therapy failure in falciparum malaria in Cambodia, Malar. J. 2009;8:11.

Cordero ML, Verneuil E, Gallaire F, Baroud CN, Time-resolved temperature rise in a thin liquid film due to laser absorption, Phys Rev E Stat Nonlin Soft Matter Phys 2009 Jan;79(1 Pt 1):011201.

Koszul R, Kameoka S, Weiner BM, Real-time imaging of meiotic chromosomes in Saccharomyces cerevisiae, Methods Mol. Biol. 2009;558:81-9.

Laissue P, Burgio G, l'Hôte D, Renault G, Marchiol-Fournigault C, Fradelizi D, Fellous M, Serres C, Montagutelli X, Monget P, Vaiman D, , Identification of Quantitative Trait Loci responsible for embryonic lethality in mice assessed by ultrasonography., Int. J. Dev. Biol. 2009 ; 53(4): 623-9.

Diogo D, Bouchier C, d'Enfert C, Bougnoux ME, Loss of heterozygosity in commensal isolates of the asexual diploid yeast Candida albicans, Fungal Genet. Biol. 2009 Feb;46(2):159-68.

Bui TN, Vernière C, Jarne P, Brisse S, Guérin F, Boutry S, Gagnevin L, Pruvost O, From local surveys to global surveillance: three high-throughput genotyping methods for epidemiological monitoring of Xanthomonas citri pv. citri pathotypes, Appl. Environ. Microbiol. 2009 Feb;75(4):1173-84.

Muller H, Thierry A, Coppée JY, Gouyette C, Hennequin C, Sismeiro O, Talla E, Dujon B, Fairhead C, Genomic polymorphism in the population of Candida glabrata: gene copy-number variation and chromosomal translocations, Fungal Genet. Biol. 2009 Mar;46(3):264-76.

Rosso ML, Chauvaux S, Dessein R, Laurans C, Frangeul L, Lacroix C, Schiavo A, Dillies MA, Foulon J, Coppée JY, Médigue C, Carniel E, Simonet M, Marceau M, , Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression., BMC Microbiol. 2008 Dec; 8(): 211.

Delétoile A, Decré D, Courant S, Passet V, Audo J, Grimont P, Arlet G, Brisse S, Phylogeny and identification of Pantoea species and typing of Pantoea agglomerans strains by multilocus gene sequencing, J. Clin. Microbiol. 2009 Feb;47(2):300-10.

Koszul R, Fischer G, A prominent role for segmental duplications in modeling eukaryotic genomes, C. R. Biol. 2009 Feb-Mar;332(2-3):254-66.

Adams SM, Bosch E, Balaresque PL, Ballereau SJ, Lee AC, Arroyo E, López-Parra AM, Aler M, Grifo MS, Brion M, Carracedo A, Lavinha J, Martínez-Jarreta B, Quintana-Murci L, Picornell A, Ramon M, Skorecki K, Behar DM, Calafell F, Jobling MA, The genetic legacy of religious diversity and intolerance: paternal lineages of Christians, Jews, and Muslims in the Iberian Peninsula, Am. J. Hum. Genet. 2008 Dec;83(6):725-36.

Behar DM, Blue-Smith J, Soria-Hernanz DF, Tzur S, Hadid Y, Bormans C, Moen A, Tyler-Smith C, Quintana-Murci L, Wells RS, , A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals, Hum. Mutat. 2008 Dec;29(12):1387-91.

Jaureguy F, Landraud L, Passet V, Diancourt L, Frapy E, Guigon G, Carbonnelle E, Lortholary O, Clermont O, Denamur E, Picard B, Nassif X, Brisse S, Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains, BMC Genomics 2008;9:560.

Cambray G, Mazel D, Synonymous genes explore different evolutionary landscapes, PLoS Genet. 2008 Nov;4(11):e1000256.

Balbi KJ, Rocha EP, Feil EJ, The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp, Mol. Biol. Evol. 2009 Feb;26(2):345-55.

Zalloua PA, Platt DE, El Sibai M, Khalife J, Makhoul N, Haber M, Xue Y, Izaabel H, Bosch E, Adams SM, Arroyo E, López-Parra AM, Aler M, Picornell A, Ramon M, Jobling MA, Comas D, Bertranpetit J, Wells RS, Tyler-Smith C, , Identifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean, Am. J. Hum. Genet. 2008 Nov;83(5):633-42.

Mariette N, Barnadas C, Bouchier C, Tichit M, Ménard D, Country-wide assessment of the genetic polymorphism in Plasmodium falciparum and Plasmodium vivax antigens detected with rapid diagnostic tests for malaria, Malar. J. 2008 Oct;7:219.

Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeño-Tárraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EP, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J, The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients, J. Bacteriol. 2009 Jan;191(1):261-77.

Rocha EP, Evolutionary patterns in prokaryotic genomes, Curr. Opin. Microbiol. 2008 Oct;11(5):454-60.

Ngoc LB, Verniere C, Vital K, Guerin F, Gagnevin L, Brisse S, Ah-You N, Pruvost O, Development of 14 minisatellite markers for the citrus canker bacterium, Xanthomonas citri pv. citri, Mol Ecol Resour 2009 Jan;9(1):125-7.

Binesse J, Delsert C, Saulnier D, Champomier-Vergès MC, Zagorec M, Munier-Lehmann H, Mazel D, Le Roux F, Metalloprotease vsm is the major determinant of toxicity for extracellular products of Vibrio splendidus, Appl. Environ. Microbiol. 2008 Dec;74(23):7108-17.

Balaresque P, Bowden GR, Parkin EJ, Omran GA, Heyer E, Quintana-Murci L, Roewer L, Stoneking M, Nasidze I, Carvalho-Silva DR, Tyler-Smith C, de Knijff P, Jobling MA, Dynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis, Hum. Mutat. 2008 Oct;29(10):1171-80.

Vimont S, Mnif B, Fevre C, Brisse S, Comparison of PFGE and multilocus sequence typing for analysis of Klebsiella pneumoniae isolates, J. Med. Microbiol. 2008 Oct;57(Pt 10):1308-10.

Le Masson M, Baharoglu Z, Michel B, ruvA and ruvB mutants specifically impaired for replication fork reversal, Mol. Microbiol. 2008 Oct;70(2):537-48.

Ségurel L, Martínez-Cruz B, Quintana-Murci L, Balaresque P, Georges M, Hegay T, Aldashev A, Nasyrova F, Jobling MA, Heyer E, Vitalis R, Sex-specific genetic structure and social organization in Central Asia: insights from a multi-locus study, PLoS Genet. 2008;4(9):e1000200.

Wanat JJ, Kim KP, Koszul R, Zanders S, Weiner B, Kleckner N, Alani E, Csm4, in collaboration with Ndj1, mediates telomere-led chromosome dynamics and recombination during yeast meiosis, PLoS Genet. 2008;4(9):e1000188.

Val ME, Kennedy SP, El Karoui M, Bonné L, Chevalier F, Barre FX, FtsK-dependent dimer resolution on multiple chromosomes in the pathogen Vibrio cholerae., PLoS Genet 2008 Sep; 4(9): e1000201.

Weiss S, Carapito C, Cleiss J, Koechler S, Turlin E, Coppee JY, Heymann M, Kugler V, Stauffert M, Cruveiller S, Médigue C, Van Dorsselaer A, Bertin PN, Arsène-Ploetze F, Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data, Biochimie 2009 Feb;91(2):192-203.

Thierry A, Bouchier C, Dujon B, Richard GF, Megasatellites: a peculiar class of giant minisatellites in genes involved in cell adhesion and pathogenicity in Candida glabrata, Nucleic Acids Res. 2008 Oct;36(18):5970-82.

Barnadas C, Ratsimbasoa A, Tichit M, Bouchier C, Jahevitra M, Picot S, Ménard D, Plasmodium vivax resistance to chloroquine in Madagascar: clinical efficacy and polymorphisms in pvmdr1 and pvcrt-o genes, Antimicrob. Agents Chemother. 2008 Dec;52(12):4233-40.

Wirth T, Hildebrand F, Allix-Béguec C, Wölbeling F, Kubica T, Kremer K, van Soolingen D, Rüsch-Gerdes S, Locht C, Brisse S, Meyer A, Supply P, Niemann S, Origin, spread and demography of the Mycobacterium tuberculosis complex, PLoS Pathog. 2008;4(9):e1000160.

Lamarre C, Sokol S, Debeaupuis JP, Henry C, Lacroix C, Glaser P, Coppée JY, François JM, Latgé JP, Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia, BMC Genomics 2008;9:417.

Rosset S, Wells RS, Soria-Hernanz DF, Tyler-Smith C, Royyuru AK, Behar DM, , Maximum-likelihood estimation of site-specific mutation rates in human mitochondrial DNA from partial phylogenetic classification, Genetics 2008 Nov;180(3):1511-24.

Najjar I, Schischmanoff PO, Baran-Marszak F, Deglesne PA, Youlyouz-Marfak I, Pampin M, Feuillard J, Bornkamm GW, Chelbi-Alix MK, Fagard R, Novel function of STAT1beta in B cells: induction of cell death by a mechanism different from that of STAT1alpha, J. Leukoc. Biol. 2008 Dec;84(6):1604-12.

Payen C, Koszul R, Dujon B, Fischer G, Segmental duplications arise from Pol32-dependent repair of broken forks through two alternative replication-based mechanisms, PLoS Genet. 2008;4(9):e1000175.

Luca F, Bubba G, Basile M, Brdicka R, Michalodimitrakis E, Rickards O, Vershubsky G, Quintana-Murci L, Kozlov AI, Novelletto A, Multiple advantageous amino acid variants in the NAT2 gene in human populations, PLoS ONE 2008;3(9):e3136.

Ragon M, Wirth T, Hollandt F, Lavenir R, Lecuit M, Le Monnier A, Brisse S, , A new perspective on Listeria monocytogenes evolution., PLoS Pathog 2008 Sep; 4(9): e1000146.

Guermonprez H, Loot C, Casacuberta JM, Different strategies to persist: the pogo-like Lemi1 transposon produces miniature inverted-repeat transposable elements or typical defective elements in different plant genomes., Genetics 2008 Sep; 180(1): 83-92.

Natalang O, Bischoff E, Deplaine G, Proux C, Dillies MA, Sismeiro O, Guigon G, Bonnefoy S, Patarapotikul J, Mercereau-Puijalon O, Coppée JY, David PH, Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate, BMC Genomics 2008;9:388.

Niang M, Marrama L, Ekala MT, Alioune G, Tall A, Ndiaye JL, Sarr D, Dangou JM, Lehesran JY, Bouchier C, Mercereau-Puijalon O, Jambou R, Accumulation of CVIET Pfcrt allele of Plasmodium falciparum in placenta of pregnant women living in an urban area of Dakar, Senegal, J. Antimicrob. Chemother. 2008 Nov;62(5):921-8.

Oliveira PH, Lemos F, Monteiro GA, Prazeres DM, Recombination frequency in plasmid DNA containing direct repeats–predictive correlation with repeat and intervening sequence length, Plasmid 2008 Sep;60(2):159-65.

Achour I, Cavelier P, Tichit M, Bouchier C, Lafaye P, Rougeon F, Tetrameric and homodimeric camelid IgGs originate from the same IgH locus, J. Immunol. 2008 Aug;181(3):2001-9.

Ratelade J, Lavin TA, Muda AO, Morisset L, Mollet G, Boyer O, Chen DS, Henger A, Kretzler M, Hubner N, Théry C, Gubler MC, Montagutelli X, Antignac C, Esquivel EL, , Maternal environment interacts with modifier genes to influence progression of nephrotic syndrome., J. Am. Soc. Nephrol. 2008 Aug; 19(8): 1491-9.

Lebreton A, Rousselle JC, Lenormand P, Namane A, Jacquier A, Fromont-Racine M, Saveanu C, 60S ribosomal subunit assembly dynamics defined by semi-quantitative mass spectrometry of purified complexes, Nucleic Acids Res. 2008 Sep;36(15):4988-99.

Le Breton C, Dupaigne P, Robert T, Le Cam E, Gangloff S, Fabre F, Veaute X, Srs2 removes deadly recombination intermediates independently of its interaction with SUMO-modified PCNA, Nucleic Acids Res. 2008 Sep;36(15):4964-74.

Coppée JY, Do DNA microarrays have their future behind them?, Microbes Infect. 2008 Jul;10(9):1067-71.

Cadel-Six S, Dauga C, Castets AM, Rippka R, Bouchier C, Tandeau de Marsac N, Welker M, Halogenase genes in nonribosomal peptide synthetase gene clusters of Microcystis (cyanobacteria): sporadic distribution and evolution, Mol. Biol. Evol. 2008 Sep;25(9):2031-41.

Ribeiro SC, Oliveira PH, Prazeres DM, Monteiro GA, High frequency plasmid recombination mediated by 28 bp direct repeats, Mol. Biotechnol. 2008 Nov;40(3):252-60.

Ménard D, Andriantsoanirina V, Jahevitra M, Barnadas C, Tichit M, Bouchier C, Hopkins Sibley C, Dihydrofolate reductase I164L mutation in Plasmodium falciparum, Madagascar, Emerging Infect. Dis. 2008 Jul;14(7):1166-7.

Vivas JR, Regnault B, Michel V, Bussière FI, Avé P, Huerre M, Labigne A, D' Elios MM, Touati E, Interferon gamma-signature transcript profiling and IL-23 upregulation in response to Helicobacter pylori infection, Int J Immunopathol Pharmacol 2008 Jul-Sep;21(3):515-26.

Zhang J, Zhang X, Fu J, Bi Z, Arheart KL, Barreiro LB, Quintana-Murci L, Pahwa S, Liu H, Protective role of DC-SIGN (CD209) neck-region alleles with <5 repeat units in HIV-1 transmission, J. Infect. Dis. 2008 Jul;198(1):68-71.

Chaix R, Austerlitz F, Hegay T, Quintana-Murci L, Heyer E, Genetic traces of east-to-west human expansion waves in Eurasia, Am. J. Phys. Anthropol. 2008 Jul;136(3):309-17.

Babic A, Guérout AM, Mazel D, Construction of an improved RP4 (RK2)-based conjugative system, Res. Microbiol. 2008 Sep-Oct;159(7-8):545-9.

Koszul R, Kim KP, Prentiss M, Kleckner N, Kameoka S, Meiotic chromosomes move by linkage to dynamic actin cables with transduction of force through the nuclear envelope, Cell 2008 Jun;133(7):1188-201.

Rousseau P, Loot C, Turlan C, Nolivos S, Chandler M, Bias between the left and right inverted repeats during IS911 targeted insertion, J. Bacteriol. 2008 Sep;190(18):6111-8.

Baroud CN, Wang XC, Masson JB, Collective behavior during the exit of a wetting liquid through a network of channels, J Colloid Interface Sci 2008 Oct;326(2):445-50.

Vieira-Silva S, Rocha EP, An assessment of the impacts of molecular oxygen on the evolution of proteomes, Mol. Biol. Evol. 2008 Sep;25(9):1931-42.

Frangeul L, Quillardet P, Castets AM, Humbert JF, Matthijs HC, Cortez D, Tolonen A, Zhang CC, Gribaldo S, Kehr JC, Zilliges Y, Ziemert N, Becker S, Talla E, Latifi A, Billault A, Lepelletier A, Dittmann E, Bouchier C, de Marsac NT, Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium, BMC Genomics 2008;9:274.

Abraham AL, Rocha EP, Pothier J, Swelfe: a detector of internal repeats in sequences and structures, Bioinformatics 2008 Jul;24(13):1536-7.

Nemec A, Krízová L, Maixnerová M, Diancourt L, van der Reijden TJ, Brisse S, van den Broek P, Dijkshoorn L, Emergence of carbapenem resistance in Acinetobacter baumannii in the Czech Republic is associated with the spread of multidrug-resistant strains of European clone II, J. Antimicrob. Chemother. 2008 Sep;62(3):484-9.

Assunção WG, Tabata LF, Barão VA, Rocha EP, Comparison of stress distribution between complete denture and implant-retained overdenture-2D FEA, J Oral Rehabil 2008 Oct;35(10):766-74.

Guigon G, Cheval J, Cahuzac R, Brisse S, MLVA-NET–a standardised web database for bacterial genotyping and surveillance, Euro Surveill. 2008 May;13(19).

Delmas O, Holmes EC, Talbi C, Larrous F, Dacheux L, Bouchier C, Bourhy H, Genomic diversity and evolution of the lyssaviruses, PLoS ONE 2008 Apr;3(4):e2057.

Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, Metspalu E, Scozzari R, Makkan H, Tzur S, Comas D, Bertranpetit J, Quintana-Murci L, Tyler-Smith C, Wells RS, Rosset S, , The dawn of human matrilineal diversity, Am. J. Hum. Genet. 2008 May;82(5):1130-40.

Sperandio B, Regnault B, Guo J, Zhang Z, Stanley SL, Sansonetti PJ, Pédron T, Virulent Shigella flexneri subverts the host innate immune response through manipulation of antimicrobial peptide gene expression, J. Exp. Med. 2008 May;205(5):1121-32.

Blazquez S, Guigon G, Weber C, Syan S, Sismeiro O, Coppée JY, Labruyère E, Guillén N, Chemotaxis of Entamoeba histolytica towards the pro-inflammatory cytokine TNF is based on PI3K signalling, cytoskeleton reorganization and the Galactose/N-acetylgalactosamine lectin activity, Cell. Microbiol. 2008 Aug;10(8):1676-86.

Decourty L, Saveanu C, Zemam K, Hantraye F, Frachon E, Rousselle JC, Fromont-Racine M, Jacquier A, Linking functionally related genes by sensitive and quantitative characterization of genetic interaction profiles, Proc. Natl. Acad. Sci. U.S.A. 2008 Apr;105(15):5821-6.

Roseaulin L, Yamada Y, Tsutsui Y, Russell P, Iwasaki H, Arcangioli B, Mus81 is essential for sister chromatid recombination at broken replication forks, EMBO J. 2008 May;27(9):1378-87.

Fernandez MI, Regnault B, Mulet C, Tanguy M, Jay P, Sansonetti PJ, Pédron T, Maturation of paneth cells induces the refractory state of newborn mice to Shigella infection, J. Immunol. 2008 Apr;180(7):4924-30.

Osorio Y Fortéa J, Prina E, Lang T, Milon G, Davory C, Coppée JY, Regnault B, AffyGCQC: a web-based interface to detect outlying genechips with extreme studentized deviate tests, J Bioinform Comput Biol 2008 Apr;6(2):317-34.

Labalette C, Nouët Y, Sobczak-Thepot J, Armengol C, Levillayer F, Gendron MC, Renard CA, Regnault B, Chen J, Buendia MA, Wei Y, The LIM-only protein FHL2 regulates cyclin D1 expression and cell proliferation, J. Biol. Chem. 2008 May;283(22):15201-8.

Zalloua PA, Xue Y, Khalife J, Makhoul N, Debiane L, Platt DE, Royyuru AK, Herrera RJ, Hernanz DF, Blue-Smith J, Wells RS, Comas D, Bertranpetit J, Tyler-Smith C, , Y-chromosomal diversity in Lebanon is structured by recent historical events, Am. J. Hum. Genet. 2008 Apr;82(4):873-82.

Tuikue Ndam N, Bischoff E, Proux C, Lavstsen T, Salanti A, Guitard J, Nielsen MA, Coppée JY, Gaye A, Theander T, David PH, Deloron P, Plasmodium falciparum transcriptome analysis reveals pregnancy malaria associated gene expression, PLoS ONE 2008;3(3):e1855.

Treangen TJ, Ambur OH, Tonjum T, Rocha EP, The impact of the neisserial DNA uptake sequences on genome evolution and stability, Genome Biol. 2008;9(3):R60.

Reynaud Y, Saulnier D, Mazel D, Goarant C, Le Roux F, Correlation between detection of a plasmid and high-level virulence of Vibrio nigripulchritudo, a pathogen of the shrimp Litopenaeus stylirostris, Appl. Environ. Microbiol. 2008 May;74(10):3038-47.

Soler Bistué AJ, Birshan D, Tomaras AP, Dandekar M, Tran T, Newmark J, Bui D, Gupta N, Hernandez K, Sarno R, Zorreguieta A, Actis LA, Tolmasky ME, Klebsiella pneumoniae multiresistance plasmid pMET1: similarity with the Yersinia pestis plasmid pCRY and integrative conjugative elements, PLoS ONE 2008;3(3):e1800.

Baharoglu Z, Bradley AS, Le Masson M, Tsaneva I, Michel B, ruvA Mutants that resolve Holliday junctions but do not reverse replication forks, PLoS Genet. 2008 Mar;4(3):e1000012.

Barnadas C, Tichit M, Bouchier C, Ratsimbasoa A, Randrianasolo L, Raherinjafy R, Jahevitra M, Picot S, Ménard D, Plasmodium vivax dhfr and dhps mutations in isolates from Madagascar and therapeutic response to sulphadoxine-pyrimethamine, Malar. J. 2008 Feb;7:35.

Wilde C, Mazel D, Hochhut B, Middendorf B, Le Roux F, Carniel E, Dobrindt U, Hacker J, Delineation of the recombination sites necessary for integration of pathogenicity islands II and III into the Escherichia coli 536 chromosome, Mol. Microbiol. 2008 Apr;68(1):139-51.

Zilliges Y, Kehr JC, Mikkat S, Bouchier C, de Marsac NT, Börner T, Dittmann E, An extracellular glycoprotein is implicated in cell-cell contacts in the toxic cyanobacterium Microcystis aeruginosa PCC 7806, J. Bacteriol. 2008 Apr;190(8):2871-9.

Dupaigne P, Le Breton C, Fabre F, Gangloff S, Le Cam E, Veaute X, The Srs2 helicase activity is stimulated by Rad51 filaments on dsDNA: implications for crossover incidence during mitotic recombination, Mol. Cell 2008 Feb;29(2):243-54.

Picardeau M, Bulach DM, Bouchier C, Zuerner RL, Zidane N, Wilson PJ, Creno S, Kuczek ES, Bommezzadri S, Davis JC, McGrath A, Johnson MJ, Boursaux-Eude C, Seemann T, Rouy Z, Coppel RL, Rood JI, Lajus A, Davies JK, Médigue C, Adler B, Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis, PLoS ONE 2008;3(2):e1607.

Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L, Natural selection has driven population differentiation in modern humans, Nat. Genet. 2008 Mar;40(3):340-5.

Ziemert N, Ishida K, Quillardet P, Bouchier C, Hertweck C, de Marsac NT, Dittmann E, Microcyclamide biosynthesis in two strains of Microcystis aeruginosa: from structure to genes and vice versa, Appl. Environ. Microbiol. 2008 Mar;74(6):1791-7.

Quintana-Murci L, Quach H, Harmant C, Luca F, Massonnet B, Patin E, Sica L, Mouguiama-Daouda P, Comas D, Tzur S, Balanovsky O, Kidd KK, Kidd JR, van der Veen L, Hombert JM, Gessain A, Verdu P, Froment A, Bahuchet S, Heyer E, Dausset J, Salas A, Behar DM, Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers, Proc. Natl. Acad. Sci. U.S.A. 2008 Feb;105(5):1596-601.

Patin E, Quintana-Murci L, Demeter’s legacy: rapid changes to our genome imposed by diet, Trends Ecol. Evol. (Amst.) 2008 Feb;23(2):56-9.

Fang G, Rocha EP, Danchin A, Persistence drives gene clustering in bacterial genomes, BMC Genomics 2008;9:4.

Bousquet-Dubouch MP, Uttenweiler-Joseph S, Ducoux-Petit M, Matondo M, Monsarrat B, Burlet-Schiltz O, Purification and proteomic analysis of 20S proteasomes from human cells, Methods Mol. Biol. 2008;432:301-20.

Rocha EP, The organization of the bacterial genome, Annu. Rev. Genet. 2008;42:211-33.

L'Hôte D, Serres C, Veitia RA, Montagutelli X, Oulmouden A, Vaiman D, , Gene expression regulation in the context of mouse interspecific mosaic genomes., Genome Biol. 2008 ; 9(8): R133.

Tayeb LA, Lefevre M, Passet V, Diancourt L, Brisse S, Grimont PA, Comparative phylogenies of Burkholderia, Ralstonia, Comamonas, Brevundimonas and related organisms derived from rpoB, gyrB and rrs gene sequences, Res. Microbiol. 2008 Apr;159(3):169-77.

Ekala MT, Khim N, Legrand E, Randrianarivelojosia M, Jambou R, Fandeur T, Menard D, Assi SB, Henry MC, Rogier C, Bouchier C, Mercereau-Puijalon O, Sequence analysis of Plasmodium falciparum cytochrome b in multiple geographic sites, Malar. J. 2007 Dec;6:164.

Maloisel L, Fabre F, Gangloff S, DNA polymerase delta is preferentially recruited during homologous recombination to promote heteroduplex DNA extension, Mol. Cell. Biol. 2008 Feb;28(4):1373-82.

Dardalhon D, Angelin AR, Baldacci G, Sage E, Francesconi S, Unconventional effects of UVA radiation on cell cycle progression in S. pombe, Cell Cycle 2008 Mar;7(5):611-22.

Magalon H, Patin E, Austerlitz F, Hegay T, Aldashev A, Quintana-Murci L, Heyer E, Population genetic diversity of the NAT2 gene supports a role of acetylation in human adaptation to farming in Central Asia, Eur. J. Hum. Genet. 2008 Feb;16(2):243-51.

Quintana-Murci L, Alcaïs A, Abel L, Casanova JL, Immunology in natura: clinical, epidemiological and evolutionary genetics of infectious diseases, Nat. Immunol. 2007 Nov;8(11):1165-71.

Siau A, Toure FS, Ouwe-Missi-Oukem-Boyer O, Ciceron L, Mahmoudi N, Vaquero C, Froissard P, Bisvigou U, Bisser S, Coppee JY, Bischoff E, David PH, Mazier D, Whole-transcriptome analysis of Plasmodium falciparum field isolates: identification of new pathogenicity factors, J. Infect. Dis. 2007 Dec;196(11):1603-12.

Bougnoux ME, Pujol C, Diogo D, Bouchier C, Soll DR, d'Enfert C, Mating is rare within as well as between clades of the human pathogen Candida albicans, Fungal Genet. Biol. 2008 Mar;45(3):221-31.

Quiroga MP, Andres P, Petroni A, Soler Bistué AJ, Guerriero L, Vargas LJ, Zorreguieta A, Tokumoto M, Quiroga C, Tolmasky ME, Galas M, Centrón D, Complex class 1 integrons with diverse variable regions, including aac(6′)-Ib-cr, and a novel allele, qnrB10, associated with ISCR1 in clinical enterobacterial isolates from Argentina, Antimicrob. Agents Chemother. 2007 Dec;51(12):4466-70.

Ben-Ali M, Barreiro LB, Chabbou A, Haltiti R, Braham E, Neyrolles O, Dellagi K, Gicquel B, Quintana-Murci L, Barbouche MR, Promoter and neck region length variation of DC-SIGN is not associated with susceptibility to tuberculosis in Tunisian patients, Hum. Immunol. 2007 Nov;68(11):908-12.

Jacquelin B, Mayau V, Brysbaert G, Regnault B, Diop OM, Arenzana-Seisdedos F, Rogge L, Coppée JY, Barré-Sinoussi F, Benecke A, Müller-Trutwin MC, , Long oligonucleotide microarrays for African green monkey gene expression profile analysis., FASEB J 2007 Oct; 21(12): 3262-71.

van Belkum A, Tassios PT, Dijkshoorn L, Haeggman S, Cookson B, Fry NK, Fussing V, Green J, Feil E, Gerner-Smidt P, Brisse S, Struelens M, , Guidelines for the validation and application of typing methods for use in bacterial epidemiology, Clin. Microbiol. Infect. 2007 Oct;13 Suppl 3:1-46.

Touchon M, Rocha EP, From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data, Biochimie 2008 Apr;90(4):648-59.

Demarre G, Frumerie C, Gopaul DN, Mazel D, Identification of key structural determinants of the IntI1 integron integrase that influence attC x attI1 recombination efficiency, Nucleic Acids Res. 2007;35(19):6475-89.

Le Guyader D, Redd MJ, Colucci-Guyon E, Murayama E, Kissa K, Briolat V, Mordelet E, Zapata A, Shinomiya H, Herbomel P, , Origins and unconventional behavior of neutrophils in developing zebrafish., Blood 2008 Jan; 111(1): 132-41.

Zhang SY, Jouanguy E, Ugolini S, Smahi A, Elain G, Romero P, Segal D, Sancho-Shimizu V, Lorenzo L, Puel A, Picard C, Chapgier A, Plancoulaine S, Titeux M, Cognet C, von Bernuth H, Ku CL, Casrouge A, Zhang XX, Barreiro L, Leonard J, Hamilton C, Lebon P, Héron B, Vallée L, Quintana-Murci L, Hovnanian A, Rozenberg F, Vivier E, Geissmann F, Tardieu M, Abel L, Casanova JL, TLR3 deficiency in patients with herpes simplex encephalitis, Science 2007 Sep;317(5844):1522-7.

Crameri A, Marfurt J, Mugittu K, Maire N, Regös A, Coppee JY, Sismeiro O, Burki R, Huber E, Laubscher D, Puijalon O, Genton B, Felger I, Beck HP, Rapid microarray-based method for monitoring of all currently known single-nucleotide polymorphisms associated with parasite resistance to antimalaria drugs, J. Clin. Microbiol. 2007 Nov;45(11):3685-91.

Bailly-Bechet M, Vergassola M, Rocha E, Causes for the intriguing presence of tRNAs in phages, Genome Res. 2007 Oct;17(10):1486-95.

Guljamow A, Jenke-Kodama H, Saumweber H, Quillardet P, Frangeul L, Castets AM, Bouchier C, Tandeau de Marsac N, Dittmann E, Horizontal gene transfer of two cytoskeletal elements from a eukaryote to a cyanobacterium, Curr. Biol. 2007 Sep;17(17):R757-9.

Chauvaux S, Rosso ML, Frangeul L, Lacroix C, Labarre L, Schiavo A, Marceau M, Dillies MA, Foulon J, Coppée JY, Médigue C, Simonet M, Carniel E, , Transcriptome analysis of Yersinia pestis in human plasma: an approach for discovering bacterial genes involved in septicaemic plague., Microbiology (Reading, Engl.) 2007 Sep; 153(Pt 9): 3112-3124.

Schmidt-Ott KM, Masckauchan TN, Chen X, Hirsh BJ, Sarkar A, Yang J, Paragas N, Wallace VA, Dufort D, Pavlidis P, Jagla B, Kitajewski J, Barasch J, beta-catenin/TCF/Lef controls a differentiation-associated transcriptional program in renal epithelial progenitors, Development 2007 Sep;134(17):3177-90.

Haruta N, Akamatsu Y, Tsutsui Y, Kurokawa Y, Murayama Y, Arcangioli B, Iwasaki H, Fission yeast Swi5 protein, a novel DNA recombination mediator, DNA Repair (Amst.) 2008 Jan;7(1):1-9.

Santi-Rocca J, Weber C, Guigon G, Sismeiro O, Coppée JY, Guillén N, The lysine- and glutamic acid-rich protein KERP1 plays a role in Entamoeba histolytica liver abscess pathogenesis, Cell. Microbiol. 2008 Jan;10(1):202-17.

Diancourt L, Passet V, Chervaux C, Garault P, Smokvina T, Brisse S, Multilocus sequence typing of Lactobacillus casei reveals a clonal population structure with low levels of homologous recombination, Appl. Environ. Microbiol. 2007 Oct;73(20):6601-11.

Salerno A, Delétoile A, Lefevre M, Ciznar I, Krovacek K, Grimont P, Brisse S, Recombining population structure of Plesiomonas shigelloides (Enterobacteriaceae) revealed by multilocus sequence typing, J. Bacteriol. 2007 Nov;189(21):7808-18.

Hamon MA, Batsché E, Régnault B, Tham TN, Seveau S, Muchardt C, Cossart P, Histone modifications induced by a family of bacterial toxins, Proc. Natl. Acad. Sci. U.S.A. 2007 Aug;104(33):13467-72.

Demoinet E, Jacquier A, Lutfalla G, Fromont-Racine M, The Hsp40 chaperone Jjj1 is required for the nucleo-cytoplasmic recycling of preribosomal factors in Saccharomyces cerevisiae, RNA 2007 Sep;13(9):1570-81.

Pertschy B, Saveanu C, Zisser G, Lebreton A, Tengg M, Jacquier A, Liebminger E, Nobis B, Kappel L, van der Klei I, Högenauer G, Fromont-Racine M, Bergler H, Cytoplasmic recycling of 60S preribosomal factors depends on the AAA protein Drg1, Mol. Cell. Biol. 2007 Oct;27(19):6581-92.

Gómez-Valero L, Rocha EP, Latorre A, Silva FJ, Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction., Genome Res 2007 Aug; 17(8): 1178-85.

L'Hôte D, Serres C, Laissue P, Oulmouden A, Rogel-Gaillard C, Montagutelli X, Vaiman D, , Centimorgan-range one-step mapping of fertility traits using interspecific recombinant congenic mice., Genetics 2007 Jul; 176(3): 1907-21.

Brisse S, Iteman I, Schuffenecker I, Chikungunya outbreaks, N. Engl. J. Med. 2007 Jun;356(25):2650-2; author reply 2650-2.

Baroud CN, de Saint Vincent MR, Delville JP, An optical toolbox for total control of droplet microfluidics, Lab Chip 2007 Aug;7(8):1029-33.

Behar DM, Rosset S, Blue-Smith J, Balanovsky O, Tzur S, Comas D, Mitchell RJ, Quintana-Murci L, Tyler-Smith C, Wells RS, , The Genographic Project public participation mitochondrial DNA database, PLoS Genet. 2007 Jun;3(6):e104.

Roumagnac P, Brisse S, Weill FX, [Evolutionary history of Salmonella Typhi illustrates a new pattern of epidemiologic dynamics], Med Sci (Paris) 2007 May;23(5):455-6.

Cattoir V, Poirel L, Mazel D, Soussy CJ, Nordmann P, Vibrio splendidus as the source of plasmid-mediated QnrS-like quinolone resistance determinants, Antimicrob. Agents Chemother. 2007 Jul;51(7):2650-1.

Legrand E, Demar M, Volney B, Ekala MT, Quinternet M, Bouchier C, Fandeur T, Rogier C, Carme B, Puijalon OM, Esterre P, First case of emergence of atovaquone resistance in Plasmodium falciparum during second-line atovaquone-proguanil treatment in South America, Antimicrob. Agents Chemother. 2007 Jun;51(6):2280-1.

San Millan A, Escudero JA, Catalan A, Nieto S, Farelo F, Gibert M, Moreno MA, Dominguez L, Gonzalez-Zorn B, Beta-lactam resistance in Haemophilus parasuis Is mediated by plasmid pB1000 bearing blaROB-1, Antimicrob. Agents Chemother. 2007 Jun;51(6):2260-4.

Py C, Reverdy P, Doppler L, Bico J, Roman B, Baroud CN, Capillary origami: spontaneous wrapping of a droplet with an elastic sheet, Phys. Rev. Lett. 2007 Apr;98(15):156103.

Baroud CN, Delville JP, Gallaire F, Wunenburger R, Thermocapillary valve for droplet production and sorting, Phys Rev E Stat Nonlin Soft Matter Phys 2007 Apr;75(4 Pt 2):046302.

Cohen-Salmon M, Regnault B, Cayet N, Caille D, Demuth K, Hardelin JP, Janel N, Meda P, Petit C, Connexin30 deficiency causes instrastrial fluid-blood barrier disruption within the cochlear stria vascularis, Proc. Natl. Acad. Sci. U.S.A. 2007 Apr;104(15):6229-34.

Michel B, Boubakri H, Baharoglu Z, LeMasson M, Lestini R, Recombination proteins and rescue of arrested replication forks, DNA Repair (Amst.) 2007 Jul;6(7):967-80.

Soler Bistué AJ, Ha H, Sarno R, Don M, Zorreguieta A, Tolmasky ME, External guide sequences targeting the aac(6′)-Ib mRNA induce inhibition of amikacin resistance, Antimicrob. Agents Chemother. 2007 Jun;51(6):1918-25.

Xhemalce B, Miller KM, Driscoll R, Masumoto H, Jackson SP, Kouzarides T, Verreault A, Arcangioli B, Regulation of histone H3 lysine 56 acetylation in Schizosaccharomyces pombe, J. Biol. Chem. 2007 May;282(20):15040-7.

Szekeres S, Dauti M, Wilde C, Mazel D, Rowe-Magnus DA, Chromosomal toxin-antitoxin loci can diminish large-scale genome reductions in the absence of selection, Mol. Microbiol. 2007 Mar;63(6):1588-605.

Rousseau P, Loot C, Guynet C, Ah-Seng Y, Ton-Hoang B, Chandler M, Control of IS911 target selection: how OrfA may ensure IS dispersion, Mol. Microbiol. 2007 Mar;63(6):1701-9.

Saveanu C, Rousselle JC, Lenormand P, Namane A, Jacquier A, Fromont-Racine M, The p21-activated protein kinase inhibitor Skb15 and its budding yeast homologue are 60S ribosome assembly factors, Mol. Cell. Biol. 2007 Apr;27(8):2897-909.

Akamatsu Y, Tsutsui Y, Morishita T, Siddique MS, Kurokawa Y, Ikeguchi M, Yamao F, Arcangioli B, Iwasaki H, Fission yeast Swi5/Sfr1 and Rhp55/Rhp57 differentially regulate Rhp51-dependent recombination outcomes, EMBO J. 2007 Mar;26(5):1352-62.

Hardouin J, Lasserre JP, Canelle L, Duchateau M, Vlieghe C, Choquet-Kastylevsky G, Joubert-Caron R, Caron M, Usefulness of autoantigens depletion to detect autoantibody signatures by multiple affinity protein profiling, J Sep Sci 2007 Feb;30(3):352-8.

Wilbaux M, Mine N, Guérout AM, Mazel D, Van Melderen L, Functional interactions between coexisting toxin-antitoxin systems of the ccd family in Escherichia coli O157:H7, J. Bacteriol. 2007 Apr;189(7):2712-9.

Touchon M, Rocha EP, Causes of insertion sequences abundance in prokaryotic genomes, Mol. Biol. Evol. 2007 Apr;24(4):969-81.

Ochman H, Liu R, Rocha EP, Erosion of interaction networks in reduced and degraded genomes, J. Exp. Zool. B Mol. Dev. Evol. 2007 Jan;308(1):97-103.

Lyoumi S, Abitbol M, Andrieu V, Henin D, Robert E, Schmitt C, Gouya L, de Verneuil H, Deybach JC, Montagutelli X, Beaumont C, Puy H, , Increased plasma transferrin, altered body iron distribution, and microcytic hypochromic anemia in ferrochelatase-deficient mice., Blood 2007 Jan; 109(2): 811-8.

Stinear TP, Seemann T, Pidot S, Frigui W, Reysset G, Garnier T, Meurice G, Simon D, Bouchier C, Ma L, Tichit M, Porter JL, Ryan J, Johnson PD, Davies JK, Jenkin GA, Small PL, Jones LM, Tekaia F, Laval F, Daffé M, Parkhill J, Cole ST, Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer, Genome Res. 2007 Feb;17(2):192-200.

Xhemalce B, Riising EM, Baumann P, Dejean A, Arcangioli B, Seeler JS, Role of SUMO in the dynamics of telomere maintenance in fission yeast, Proc. Natl. Acad. Sci. U.S.A. 2007 Jan;104(3):893-8.

Noranate N, Durand R, Tall A, Marrama L, Spiegel A, Sokhna C, Pradines B, Cojean S, Guillotte M, Bischoff E, Ekala MT, Bouchier C, Fandeur T, Ariey F, Patarapotikul J, Le Bras J, Trape JF, Rogier C, Mercereau-Puijalon O, Rapid dissemination of Plasmodium falciparum drug resistance despite strictly controlled antimalarial use, PLoS ONE 2007;2(1):e139.

Chaix R, Quintana-Murci L, Hegay T, Hammer MF, Mobasher Z, Austerlitz F, Heyer E, From social to genetic structures in central Asia, Curr. Biol. 2007 Jan;17(1):43-8.

Ody CP, Baroud CN, de Langre E, Transport of wetting liquid plugs in bifurcating microfluidic channels, J Colloid Interface Sci 2007 Apr;308(1):231-8.

Murayama E, Kissa K, Zapata A, Mordelet E, Briolat V, Lin HF, Handin RI, Herbomel P, , Tracing hematopoietic precursor migration to successive hematopoietic organs during zebrafish development., Immunity 2006 Dec; 25(6): 963-75.

Barreiro LB, Neyrolles O, Babb CL, van Helden PD, Gicquel B, Hoal EG, Quintana-Murci L, Length variation of DC-SIGN and L-SIGN neck-region has no impact on tuberculosis susceptibility, Hum. Immunol. 2007 Feb;68(2):106-12.

Vilasco M, Larrea E, Vitour D, Dabo S, Breiman A, Regnault B, Riezu JI, Eid P, Prieto J, Meurs EF, The protein kinase IKKepsilon can inhibit HCV expression independently of IFN and its own expression is downregulated in HCV-infected livers, Hepatology 2006 Dec;44(6):1635-47.

Garcia O, Saveanu C, Cline M, Fromont-Racine M, Jacquier A, Schwikowski B, Aittokallio T, GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring, Bioinformatics 2007 Feb;23(3):394-6.

Roumagnac P, Weill FX, Dolecek C, Baker S, Brisse S, Chinh NT, Le TA, Acosta CJ, Farrar J, Dougan G, Achtman M, Evolutionary history of Salmonella typhi, Science 2006 Nov;314(5803):1301-4.

Le Roux F, Binesse J, Saulnier D, Mazel D, Construction of a Vibrio splendidus mutant lacking the metalloprotease gene vsm by use of a novel counterselectable suicide vector, Appl. Environ. Microbiol. 2007 Feb;73(3):777-84.

Escudero JA, San Millan A, Catalan A, de la Campa AG, Rivero E, Lopez G, Dominguez L, Moreno MA, Gonzalez-Zorn B, First characterization of fluoroquinolone resistance in Streptococcus suis, Antimicrob. Agents Chemother. 2007 Feb;51(2):777-82.

Rocha EP, Touchon M, Feil EJ, Similar compositional biases are caused by very different mutational effects, Genome Res. 2006 Dec;16(12):1537-47.

Barreiro LB, Quintana-Murci L, DC-SIGNR neck-region polymorphisms and HIV-1 susceptibility: From population stratification to a possible advantage of the 7/5 heterozygous genotype, J. Infect. Dis. 2006 Oct;194(8):1184-5; author reply 1185-7.

Achaz G, Boyer F, Rocha EP, Viari A, Coissac E, Repseek, a tool to retrieve approximate repeats from large DNA sequences, Bioinformatics 2007 Jan;23(1):119-21.

Loot C, Santiago N, Sanz A, Casacuberta JM, The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE: consequences for the transposition mechanism of MITEs, Nucleic Acids Res. 2006;34(18):5238-46.

Louvel H, Bommezzadri S, Zidane N, Boursaux-Eude C, Creno S, Magnier A, Rouy Z, Médigue C, Saint Girons I, Bouchier C, Picardeau M, Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp, J. Bacteriol. 2006 Nov;188(22):7893-904.

Hardouin J, Duchateau M, Canelle L, Vlieghe C, Joubert-Caron R, Caron M, Thiophilic adsorption revisited, J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2007 Jan;845(2):226-31.

Brisse S, Supply P, Brosch R, Vincent V, Gutierrez MC, “A re-evaluation of M. prototuberculosis”: continuing the debate, PLoS Pathog. 2006 Sep;2(9):e95.

Hurst LD, Feil EJ, Rocha EP, Protein evolution: causes of trends in amino-acid gain and loss, Nature 2006 Aug;442(7105):E11-2; discussion E12.

Verdu P, Barreiro LB, Patin E, Gessain A, Cassar O, Kidd JR, Kidd KK, Behar DM, Froment A, Heyer E, Sica L, Casanova JL, Abel L, Quintana-Murci L, Evolutionary insights into the high worldwide prevalence of MBL2 deficiency alleles, Hum. Mol. Genet. 2006 Sep;15(17):2650-8.

Mazel D, Integrons: agents of bacterial evolution, Nat. Rev. Microbiol. 2006 Aug;4(8):608-20.

Brüggemann H, Hagman A, Jules M, Sismeiro O, Dillies MA, Gouyette C, Kunst F, Steinert M, Heuner K, Coppée JY, Buchrieser C, Virulence strategies for infecting phagocytes deduced from the in vivo transcriptional program of Legionella pneumophila, Cell. Microbiol. 2006 Aug;8(8):1228-40.

Ecker JA, Massire C, Hall TA, Ranken R, Pennella TT, Agasino Ivy C, Blyn LB, Hofstadler SA, Endy TP, Scott PT, Lindler L, Hamilton T, Gaddy C, Snow K, Pe M, Fishbain J, Craft D, Deye G, Riddell S, Milstrey E, Petruccelli B, Brisse S, Harpin V, Schink A, Ecker DJ, Sampath R, Eshoo MW, Identification of Acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry, J. Clin. Microbiol. 2006 Aug;44(8):2921-32.

Neyrolles O, Gicquel B, Quintana-Murci L, Towards a crucial role for DC-SIGN in tuberculosis and beyond, Trends Microbiol. 2006 Sep;14(9):383-7.

Lebreton A, Saveanu C, Decourty L, Jacquier A, Fromont-Racine M, Nsa2 is an unstable, conserved factor required for the maturation of 27 SB pre-rRNAs, J. Biol. Chem. 2006 Sep;281(37):27099-108.

Patin E, Harmant C, Kidd KK, Kidd J, Froment A, Mehdi SQ, Sica L, Heyer E, Quintana-Murci L, Sub-Saharan African coding sequence variation and haplotype diversity at the NAT2 gene, Hum. Mutat. 2006 Jul;27(7):720.

Iverson-Cabral SL, Astete SG, Cohen CR, Rocha EP, Totten PA, Intrastrain heterogeneity of the mgpB gene in Mycoplasma genitalium is extensive in vitro and in vivo and suggests that variation is generated via recombination with repetitive chromosomal sequences, Infect. Immun. 2006 Jul;74(7):3715-26.

Rocha EP, The quest for the universals of protein evolution, Trends Genet. 2006 Aug;22(8):412-6.

Carré-Mlouka A, Méjean A, Quillardet P, Ashida H, Saito Y, Yokota A, Callebaut I, Sekowska A, Dittmann E, Bouchier C, de Marsac NT, A new rubisco-like protein coexists with a photosynthetic rubisco in the planktonic cyanobacteria Microcystis, J. Biol. Chem. 2006 Aug;281(34):24462-71.

Robert T, Dervins D, Fabre F, Gangloff S, Mrc1 and Srs2 are major actors in the regulation of spontaneous crossover, EMBO J. 2006 Jun;25(12):2837-46.

Schuffenecker I, Iteman I, Michault A, Murri S, Frangeul L, Vaney MC, Lavenir R, Pardigon N, Reynes JM, Pettinelli F, Biscornet L, Diancourt L, Michel S, Duquerroy S, Guigon G, Frenkiel MP, Bréhin AC, Cubito N, Desprès P, Kunst F, Rey FA, Zeller H, Brisse S, Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak, PLoS Med. 2006 Jul;3(7):e263.

Swidan F, Rocha EP, Shmoish M, Pinter RY, An integrative method for accurate comparative genome mapping, PLoS Comput. Biol. 2006 Aug;2(8):e75.

Weber C, Guigon G, Bouchier C, Frangeul L, Moreira S, Sismeiro O, Gouyette C, Mirelman D, Coppee JY, Guillén N, Stress by heat shock induces massive down regulation of genes and allows differential allelic expression of the Gal/GalNAc lectin in Entamoeba histolytica, Eukaryotic Cell 2006 May;5(5):871-5.

Bougnoux ME, Diogo D, François N, Sendid B, Veirmeire S, Colombel JF, Bouchier C, Van Kruiningen H, d'Enfert C, Poulain D, Multilocus sequence typing reveals intrafamilial transmission and microevolutions of Candida albicans isolates from the human digestive tract, J. Clin. Microbiol. 2006 May;44(5):1810-20.

Lebreton A, Saveanu C, Decourty L, Rain JC, Jacquier A, Fromont-Racine M, A functional network involved in the recycling of nucleocytoplasmic pre-60S factors, J. Cell Biol. 2006 May;173(3):349-60.

Soler Bistué AJ, Martín FA, Petroni A, Faccone D, Galas M, Tolmasky ME, Zorreguieta A, Vibrio cholerae InV117, a class 1 integron harboring aac(6′)-Ib and blaCTX-M-2, is linked to transposition genes, Antimicrob. Agents Chemother. 2006 May;50(5):1903-7.

MacDonald D, Demarre G, Bouvier M, Mazel D, Gopaul DN, Structural basis for broad DNA-specificity in integron recombination, Nature 2006 Apr;440(7088):1157-62.

Ariey F, Fandeur T, Durand R, Randrianarivelojosia M, Jambou R, Legrand E, Ekala MT, Bouchier C, Cojean S, Duchemin JB, Robert V, Le Bras J, Mercereau-Puijalon O, Invasion of Africa by a single pfcrt allele of South East Asian type, Malar. J. 2006;5:34.

Barreiro LB, Quach H, Krahenbuhl J, Khaliq S, Mohyuddin A, Mehdi SQ, Gicquel B, Neyrolles O, Quintana-Murci L, DC-SIGN interacts with Mycobacterium leprae but sequence variation in this lectin is not associated with leprosy in the Pakistani population, Hum. Immunol. 2006 Jan-Feb;67(1-2):102-7.

Oliveira PH, Batagov A, Ward J, Baganz F, Krabben P, Identification of erythrobactin, a hydroxamate-type siderophore produced by Saccharopolyspora erythraea, Lett. Appl. Microbiol. 2006 Apr;42(4):375-80.

Chaze T, Bouley J, Chambon C, Barboiron C, Picard B, Mapping of alkaline proteins in bovine skeletal muscle, Proteomics 2006 Apr;6(8):2571-5.

Fischer G, Rocha EP, Brunet F, Vergassola M, Dujon B, Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages, PLoS Genet. 2006 Mar;2(3):e32.

Rosas-Magallanes V, Deschavanne P, Quintana-Murci L, Brosch R, Gicquel B, Neyrolles O, Horizontal transfer of a virulence operon to the ancestor of Mycobacterium tuberculosis, Mol. Biol. Evol. 2006 Jun;23(6):1129-35.

Couturier E, Rocha EP, Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes, Mol. Microbiol. 2006 Mar;59(5):1506-18.

Koszul R, Dujon B, Fischer G, Stability of large segmental duplications in the yeast genome, Genetics 2006 Apr;172(4):2211-22.

Kehr JC, Zilliges Y, Springer A, Disney MD, Ratner DD, Bouchier C, Seeberger PH, de Marsac NT, Dittmann E, A mannan binding lectin is involved in cell-cell attachment in a toxic strain of Microcystis aeruginosa, Mol. Microbiol. 2006 Feb;59(3):893-906.

Baharoglu Z, Petranovic M, Flores MJ, Michel B, RuvAB is essential for replication forks reversal in certain replication mutants, EMBO J. 2006 Feb;25(3):596-604.

Tien MT, Girardin SE, Regnault B, Le Bourhis L, Dillies MA, Coppée JY, Bourdet-Sicard R, Sansonetti PJ, Pédron T, Anti-inflammatory effect of Lactobacillus casei on Shigella-infected human intestinal epithelial cells, J. Immunol. 2006 Jan;176(2):1228-37.

Patin E, Barreiro LB, Sabeti PC, Austerlitz F, Luca F, Sajantila A, Behar DM, Semino O, Sakuntabhai A, Guiso N, Gicquel B, McElreavey K, Harding RM, Heyer E, Quintana-Murci L, Deciphering the ancient and complex evolutionary history of human arylamine N-acetyltransferase genes, Am. J. Hum. Genet. 2006 Mar;78(3):423-36.

Behar DM, Metspalu E, Kivisild T, Achilli A, Hadid Y, Tzur S, Pereira L, Amorim A, Quintana-Murci L, Majamaa K, Herrnstadt C, Howell N, Balanovsky O, Kutuev I, Pshenichnov A, Gurwitz D, Bonne-Tamir B, Torroni A, Villems R, Skorecki K, The matrilineal ancestry of Ashkenazi Jewry: portrait of a recent founder event, Am. J. Hum. Genet. 2006 Mar;78(3):487-97.

Barreiro LB, Neyrolles O, Babb CL, Tailleux L, Quach H, McElreavey K, Helden PD, Hoal EG, Gicquel B, Quintana-Murci L, Promoter variation in the DC-SIGN-encoding gene CD209 is associated with tuberculosis, PLoS Med. 2006 Feb;3(2):e20.

Mayer T, Jagla B, Wyler MR, Kelly PD, Aulner N, Beard M, Barger G, Többen U, Smith DH, Brandén L, Rothman JE, Cell-based assays using primary endothelial cells to study multiple steps in inflammation, Meth. Enzymol. 2006;414:266-83.

Hardouin J, Duchateau M, Joubert-Caron R, Caron M, Usefulness of an integrated microfluidic device (HPLC-Chip-MS) to enhance confidence in protein identification by proteomics, Rapid Commun. Mass Spectrom. 2006;20(21):3236-44.

Quintana-Murci L, [Natural selection of DC-SIGN and its homologues L-SIGN and mSIGNR1 in pathogen recognition and innate immunity], Med Sci (Paris) 2006 Jan;22(1):29-32.

Abitbol M, Puy H, Sabaté JM, Guénet JL, Deybach JC, Montagutelli X, , Ursodesoxycholic acid and heme-arginate are unable to improve hematopoiesis and liver injury in an erythropoietic protoporphyria mouse model., Physiol Res 2006 ; 55 Suppl 2(): S93-101.

Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Baştürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D'Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Peñalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW, Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae, Nature 2005 Dec;438(7071):1105-15.

Bouvier M, Demarre G, Mazel D, Integron cassette insertion: a recombination process involving a folded single strand substrate, EMBO J. 2005 Dec;24(24):4356-67.

Jambou R, Legrand E, Niang M, Khim N, Lim P, Volney B, Ekala MT, Bouchier C, Esterre P, Fandeur T, Mercereau-Puijalon O, Resistance of Plasmodium falciparum field isolates to in-vitro artemether and point mutations of the SERCA-type PfATPase6, Lancet 2005 Dec;366(9501):1960-3.

Fevre C, Passet V, Weill FX, Grimont PA, Brisse S, Variants of the Klebsiella pneumoniae OKP chromosomal beta-lactamase are divided into two main groups, OKP-A and OKP-B, Antimicrob. Agents Chemother. 2005 Dec;49(12):5149-52.

Francesconi S, [Repair of and checkpoint response to topoisomerase I-mediated DNA damage in Schizosaccharomyces pombe], Med Sci (Paris) 2005 Dec;21(12):1031-3.

Rocha EP, Inference and analysis of the relative stability of bacterial chromosomes, Mol. Biol. Evol. 2006 Mar;23(3):513-22.

De Champs C, Vellin JF, Diancourt L, Brisse S, Kemeny JL, Gilain L, Mom T, Laryngeal scleroma associated with Klebsiella pneumoniae subsp. ozaenae, J. Clin. Microbiol. 2005 Nov;43(11):5811-3.

Lebaron S, Froment C, Fromont-Racine M, Rain JC, Monsarrat B, Caizergues-Ferrer M, Henry Y, The splicing ATPase prp43p is a component of multiple preribosomal particles, Mol. Cell. Biol. 2005 Nov;25(21):9269-82.

Ralph SA, Bischoff E, Mattei D, Sismeiro O, Dillies MA, Guigon G, Coppee JY, David PH, Scherf A, Transcriptome analysis of antigenic variation in Plasmodium falciparum–var silencing is not dependent on antisense RNA, Genome Biol. 2005;6(11):R93.

Patel PK, Arcangioli B, Baker SP, Bensimon A, Rhind N, DNA replication origins fire stochastically in fission yeast, Mol. Biol. Cell 2006 Jan;17(1):308-16.

Rocha EP, Smith JM, Hurst LD, Holden MT, Cooper JE, Smith NH, Feil EJ, Comparisons of dN/dS are time dependent for closely related bacterial genomes, J. Theor. Biol. 2006 Mar;239(2):226-35.

Barreiro LB, Patin E, Neyrolles O, Cann HM, Gicquel B, Quintana-Murci L, The heritage of pathogen pressures and ancient demography in the human innate-immunity CD209/CD209L region, Am. J. Hum. Genet. 2005 Nov;77(5):869-86.

Médigue C, Krin E, Pascal G, Barbe V, Bernsel A, Bertin PN, Cheung F, Cruveiller S, D'Amico S, Duilio A, Fang G, Feller G, Ho C, Mangenot S, Marino G, Nilsson J, Parrilli E, Rocha EP, Rouy Z, Sekowska A, Tutino ML, Vallenet D, von Heijne G, Danchin A, Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125, Genome Res. 2005 Oct;15(10):1325-35.

Marqué S, Poirel L, Héritier C, Brisse S, Blasco MD, Filip R, Coman G, Naas T, Nordmann P, Regional occurrence of plasmid-mediated carbapenem-hydrolyzing oxacillinase OXA-58 in Acinetobacter spp. in Europe, J. Clin. Microbiol. 2005 Sep;43(9):4885-8.

Huys G, Cnockaert M, Nemec A, Dijkshoorn L, Brisse S, Vaneechoutte M, Swings J, Repetitive-DNA-element PCR fingerprinting and antibiotic resistance of pan-European multi-resistant Acinetobacter baumannii clone III strains, J. Med. Microbiol. 2005 Sep;54(Pt 9):851-6.

Collura A, Blaisonneau J, Baldacci G, Francesconi S, The fission yeast Crb2/Chk1 pathway coordinates the DNA damage and spindle checkpoint in response to replication stress induced by topoisomerase I inhibitor, Mol. Cell. Biol. 2005 Sep;25(17):7889-99.

Rocha EP, Cornet E, Michel B, Comparative and evolutionary analysis of the bacterial homologous recombination systems, PLoS Genet. 2005 Aug;1(2):e15.

Val ME, Bouvier M, Campos J, Sherratt D, Cornet F, Mazel D, Barre FX, The single-stranded genome of phage CTX is the form used for integration into the genome of Vibrio cholerae., Mol Cell 2005 Aug; 19(4): 559-66.

Gutierrez MC, Brisse S, Brosch R, Fabre M, Omaïs B, Marmiesse M, Supply P, Vincent V, Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis, PLoS Pathog. 2005 Sep;1(1):e5.

Grüner AC, Hez-Deroubaix S, Snounou G, Hall N, Bouchier C, Letourneur F, Landau I, Druilhe P, Insights into the P. y. yoelii hepatic stage transcriptome reveal complex transcriptional patterns, Mol. Biochem. Parasitol. 2005 Aug;142(2):184-92.

Khim N, Bouchier C, Ekala MT, Incardona S, Lim P, Legrand E, Jambou R, Doung S, Puijalon OM, Fandeur T, Countrywide survey shows very high prevalence of Plasmodium falciparum multilocus resistance genotypes in Cambodia, Antimicrob. Agents Chemother. 2005 Aug;49(8):3147-52.

Diancourt L, Passet V, Verhoef J, Grimont PA, Brisse S, Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates, J. Clin. Microbiol. 2005 Aug;43(8):4178-82.

Fevre C, Jbel M, Passet V, Weill FX, Grimont PA, Brisse S, Six groups of the OXY beta-Lactamase evolved over millions of years in Klebsiella oxytoca, Antimicrob. Agents Chemother. 2005 Aug;49(8):3453-62.

González-Zorn B, Catalan A, Escudero JA, Domínguez L, Teshager T, Porrero C, Moreno MA, Genetic basis for dissemination of armA, J. Antimicrob. Chemother. 2005 Sep;56(3):583-5.

Fang G, Rocha E, Danchin A, How essential are nonessential genes?, Mol. Biol. Evol. 2005 Nov;22(11):2147-56.

Pain A, Renauld H, Berriman M, Murphy L, Yeats CA, Weir W, Kerhornou A, Aslett M, Bishop R, Bouchier C, Cochet M, Coulson RM, Cronin A, de Villiers EP, Fraser A, Fosker N, Gardner M, Goble A, Griffiths-Jones S, Harris DE, Katzer F, Larke N, Lord A, Maser P, McKellar S, Mooney P, Morton F, Nene V, O'Neil S, Price C, Quail MA, Rabbinowitsch E, Rawlings ND, Rutter S, Saunders D, Seeger K, Shah T, Squares R, Squares S, Tivey A, Walker AR, Woodward J, Dobbelaere DA, Langsley G, Rajandream MA, McKeever D, Shiels B, Tait A, Barrell B, Hall N, Genome of the host-cell transforming parasite Theileria annulata compared with T. parva, Science 2005 Jul;309(5731):131-3.

Skurnik D, Le Menac'h A, Zurakowski D, Mazel D, Courvalin P, Denamur E, Andremont A, Ruimy R, Integron-associated antibiotic resistance and phylogenetic grouping of Escherichia coli isolates from healthy subjects free of recent antibiotic exposure, Antimicrob. Agents Chemother. 2005 Jul;49(7):3062-5.

Jagla B, Aulner N, Kelly PD, Song D, Volchuk A, Zatorski A, Shum D, Mayer T, De Angelis DA, Ouerfelli O, Rutishauser U, Rothman JE, Sequence characteristics of functional siRNAs, RNA 2005 Jun;11(6):864-72.

Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Régnault B, Devaux F, Namane A, Séraphin B, Libri D, Jacquier A, Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase, Cell 2005 Jun;121(5):725-37.

Froment C, Uttenweiler-Joseph S, Bousquet-Dubouch MP, Matondo M, Borges JP, Esmenjaud C, Lacroix C, Monsarrat B, Burlet-Schiltz O, A quantitative proteomic approach using two-dimensional gel electrophoresis and isotope-coded affinity tag labeling for studying human 20S proteasome heterogeneity, Proteomics 2005 Jun;5(9):2351-63.

Moulédous L, Neasta J, Uttenweiler-Joseph S, Stella A, Matondo M, Corbani M, Monsarrat B, Meunier JC, Long-term morphine treatment enhances proteasome-dependent degradation of G beta in human neuroblastoma SH-SY5Y cells: correlation with onset of adenylate cyclase sensitization, Mol. Pharmacol. 2005 Aug;68(2):467-76.

Monot M, Honoré N, Garnier T, Araoz R, Coppée JY, Lacroix C, Sow S, Spencer JS, Truman RW, Williams DL, Gelber R, Virmond M, Flageul B, Cho SN, Ji B, Paniz-Mondolfi A, Convit J, Young S, Fine PE, Rasolofo V, Brennan PJ, Cole ST, On the origin of leprosy, Science 2005 May;308(5724):1040-2.

Loeillet S, Palancade B, Cartron M, Thierry A, Richard GF, Dujon B, Doye V, Nicolas A, Genetic network interactions among replication, repair and nuclear pore deficiencies in yeast, DNA Repair (Amst.) 2005 Apr;4(4):459-68.

Najjar I, Baran-Marszak F, Le Clorennec C, Laguillier C, Schischmanoff O, Youlyouz-Marfak I, Schlee M, Bornkamm GW, Raphaël M, Feuillard J, Fagard R, Latent membrane protein 1 regulates STAT1 through NF-kappaB-dependent interferon secretion in Epstein-Barr virus-immortalized B cells, J. Virol. 2005 Apr;79(8):4936-43.

Demarre G, Guérout AM, Matsumoto-Mashimo C, Rowe-Magnus DA, Marlière P, Mazel D, A new family of mobilizable suicide plasmids based on broad host range R388 plasmid (IncW) and RP4 plasmid (IncPalpha) conjugative machineries and their cognate Escherichia coli host strains, Res. Microbiol. 2005 Mar;156(2):245-55.

Biskri L, Bouvier M, Guérout AM, Boisnard S, Mazel D, Comparative study of class 1 integron and Vibrio cholerae superintegron integrase activities, J. Bacteriol. 2005 Mar;187(5):1740-50.

Carretto E, Barbarini D, Couto I, De Vitis D, Marone P, Verhoef J, De Lencastre H, Brisse S, Identification of coagulase-negative staphylococci other than Staphylococcus epidermidis by automated ribotyping, Clin. Microbiol. Infect. 2005 Mar;11(3):177-84.

Abitbol M, Bernex F, Puy H, Jouault H, Deybach JC, Guénet JL, Montagutelli X, A mouse model provides evidence that genetic background modulates anemia and liver injury in erythropoietic protoporphyria, Am. J. Physiol. Gastrointest. Liver Physiol. 2005 Jun;288(6):G1208-16.

Brisse S, Duijkeren Ev, Identification and antimicrobial susceptibility of 100 Klebsiella animal clinical isolates, Vet. Microbiol. 2005 Feb;105(3-4):307-12.

Forissier JE, Bonne G, Bouchier C, Duboscq-Bidot L, Richard P, Briault S, Moraine C, Dubourg O, Schwartz K, Komajda M, [Apical left ventricular aneurysm without atrio-ventricular block due to a lamin A/C gene mutation], Arch Mal Coeur Vaiss 2005 Jan;98(1):67-70.

Talla E, Anthouard V, Bouchier C, Frangeul L, Dujon B, The complete mitochondrial genome of the yeast Kluyveromyces thermotolerans, FEBS Lett. 2005 Jan;579(1):30-40.

Petit-Bertron AF, Pedron T, Gross U, Coppée JY, Sansonetti PJ, Cavaillon JM, Adib-Conquy M, Adherence modifies the regulation of gene expression induced by interleukin-10, Cytokine 2005 Jan;29(1):1-12.

Quintana-Murci L, Gal I, Bakhan T, Quach H, Sayar SH, Shiri-Sverdlov R, Baruch RG, McElreavey K, Dagan E, Narod S, Friedman E, The Tyr978X BRCA1 mutation: occurrence in non-Jewish Iranians and haplotype in French-Canadian and non-Ashkenazi Jews, Fam. Cancer 2005;4(2):85-8.

Holmes AM, Kaykov A, Arcangioli B, Molecular and cellular dissection of mating-type switching steps in Schizosaccharomyces pombe, Mol. Cell. Biol. 2005 Jan;25(1):303-11.

Figueiredo LM, Rocha EP, Mancio-Silva L, Prevost C, Hernandez-Verdun D, Scherf A, , The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus., Nucleic Acids Res 2005 ; 33(3): 1111-22.

Navarro S, Del Hoyo P, Campos Y, Abitbol M, Morán-Jiménez MJ, García-Bravo M, Ochoa P, Grau M, Montagutelli X, Frank J, Garesse R, Arenas J, de Salamanca RE, Fontanellas A, , Increased mitochondrial respiratory chain enzyme activities correlate with minor extent of liver damage in mice suffering from erythropoietic protoporphyria., Exp. Dermatol. 2005 Jan; 14(1): 26-33.

Ezraty B, Bos J, Barras F, Aussel L, , Methionine sulfoxide reduction and assimilation in Escherichia coli: new role for the biotin sulfoxide reductase BisC., J Bacteriol 2005 Jan; 187(1): 231-7.

Nemec A, Dolzani L, Brisse S, van den Broek P, Dijkshoorn L, Diversity of aminoglycoside-resistance genes and their association with class 1 integrons among strains of pan-European Acinetobacter baumannii clones, J. Med. Microbiol. 2004 Dec;53(Pt 12):1233-40.

Kaykov A, Arcangioli B, A programmed strand-specific and modified nick in S. pombe constitutes a novel type of chromosomal imprint, Curr. Biol. 2004 Nov;14(21):1924-8.

Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, Beatty J, Beavis WD, Belknap JK, Bennett B, Berrettini W, Bleich A, Bogue M, Broman KW, Buck KJ, Buckler E, Burmeister M, Chesler EJ, Cheverud JM, Clapcote S, Cook MN, Cox RD, Crabbe JC, Crusio WE, Darvasi A, Deschepper CF, Doerge RW, Farber CR, Forejt J, Gaile D, Garlow SJ, Geiger H, Gershenfeld H, Gordon T, Gu J, Gu W, de Haan G, Hayes NL, Heller C, Himmelbauer H, Hitzemann R, Hunter K, Hsu HC, Iraqi FA, Ivandic B, Jacob HJ, Jansen RC, Jepsen KJ, Johnson DK, Johnson TE, Kempermann G, Kendziorski C, Kotb M, Kooy RF, Llamas B, Lammert F, Lassalle JM, Lowenstein PR, Lu L, Lusis A, Manly KF, Marcucio R, Matthews D, Medrano JF, Miller DR, Mittleman G, Mock BA, Mogil JS, Montagutelli X, Morahan G, Morris DG, Mott R, Nadeau JH, Nagase H, Nowakowski RS, O'Hara BF, Osadchuk AV, Page GP, Paigen B, Paigen K, Palmer AA, Pan HJ, Peltonen-Palotie L, Peirce J, Pomp D, Pravenec M, Prows DR, Qi Z, Reeves RH, Roder J, Rosen GD, Schadt EE, Schalkwyk LC, Seltzer Z, Shimomura K, Shou S, Sillanpää MJ, Siracusa LD, Snoeck HW, Spearow JL, Svenson K, Tarantino LM, Threadgill D, Toth LA, Valdar W, de Villena FP, Warden C, Whatley S, Williams RW, Wiltshire T, Yi N, Zhang D, Zhang M, Zou F, , , The Collaborative Cross, a community resource for the genetic analysis of complex traits., Nat. Genet. 2004 Nov; 36(11): 1133-7.

Rocha EP, Codon usage bias from tRNA’s point of view: redundancy, specialization, and efficient decoding for translation optimization, Genome Res. 2004 Nov;14(11):2279-86.

Cazalet C, Rusniok C, Brüggemann H, Zidane N, Magnier A, Ma L, Tichit M, Jarraud S, Bouchier C, Vandenesch F, Kunst F, Etienne J, Glaser P, Buchrieser C, Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity, Nat. Genet. 2004 Nov;36(11):1165-73.

Chaix R, Austerlitz F, Khegay T, Jacquesson S, Hammer MF, Heyer E, Quintana-Murci L, The genetic or mythical ancestry of descent groups: lessons from the Y chromosome, Am. J. Hum. Genet. 2004 Dec;75(6):1113-6.

Rocha EP, Order and disorder in bacterial genomes, Curr. Opin. Microbiol. 2004 Oct;7(5):519-27.

Brisse S, Cordevant C, Vandamme P, Bidet P, Loukil C, Chabanon G, Lange M, Bingen E, Species distribution and ribotype diversity of Burkholderia cepacia complex isolates from French patients with cystic fibrosis, J. Clin. Microbiol. 2004 Oct;42(10):4824-7.

Brisse S, van Himbergen T, Kusters K, Verhoef J, Development of a rapid identification method for Klebsiella pneumoniae phylogenetic groups and analysis of 420 clinical isolates, Clin. Microbiol. Infect. 2004 Oct;10(10):942-5.

Xhemalce B, Seeler JS, Thon G, Dejean A, Arcangioli B, Role of the fission yeast SUMO E3 ligase Pli1p in centromere and telomere maintenance, EMBO J. 2004 Oct;23(19):3844-53.

Brisse S, Issenhuth-Jeanjean S, Grimont PA, Molecular serotyping of Klebsiella species isolates by restriction of the amplified capsular antigen gene cluster, J. Clin. Microbiol. 2004 Aug;42(8):3388-98.

Turlan C, Loot C, Chandler M, IS911 partial transposition products and their processing by the Escherichia coli RecG helicase, Mol. Microbiol. 2004 Aug;53(4):1021-33.

Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL, Genome evolution in yeasts, Nature 2004 Jul;430(6995):35-44.

Matsumoto-Mashimo C, Guerout AM, Mazel D, A new family of conditional replicating plasmids and their cognate Escherichia coli host strains, Res. Microbiol. 2004 Jul-Aug;155(6):455-61.

Badis G, Saveanu C, Fromont-Racine M, Jacquier A, Targeted mRNA degradation by deadenylation-independent decapping, Mol. Cell 2004 Jul;15(1):5-15.

Haeggman S, Löfdahl S, Paauw A, Verhoef J, Brisse S, Diversity and evolution of the class A chromosomal beta-lactamase gene in Klebsiella pneumoniae, Antimicrob. Agents Chemother. 2004 Jul;48(7):2400-8.

Lambert A, Fontaine JF, Legendre M, Leclerc F, Permal E, Major F, Putzer H, Delfour O, Michot B, Gautheret D, The ERPIN server: an interface to profile-based RNA motif identification, Nucleic Acids Res. 2004 Jul;32(Web Server issue):W160-5.

Kim N, Bouchier C, Ekala MT, Mercereau-Puijalon O, Fandeur T, [Chemoresistance and polymorphism in falciparum malaria in Cambodia], Med Mal Infect 2004 Jun;34 Suppl 1:S61-4.

Wang Y, Rocha EP, Leung FC, Danchin A, Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes, J. Mol. Evol. 2004 Jun;58(6):692-700.

Rocha EP, The replication-related organization of bacterial genomes, Microbiology (Reading, Engl.) 2004 Jun;150(Pt 6):1609-27.

Behar DM, Hammer MF, Garrigan D, Villems R, Bonne-Tamir B, Richards M, Gurwitz D, Rosengarten D, Kaplan M, Della Pergola S, Quintana-Murci L, Skorecki K, MtDNA evidence for a genetic bottleneck in the early history of the Ashkenazi Jewish population, Eur. J. Hum. Genet. 2004 May;12(5):355-64.

Jean D, Briolat V, Reysset G, , Oxidative stress response in Clostridium perfringens., Microbiology (Reading, Engl.) 2004 Jun; 150(Pt 6): 1649-1659.

Quintana-Murci L, Chaix R, Wells RS, Behar DM, Sayar H, Scozzari R, Rengo C, Al-Zahery N, Semino O, Santachiara-Benerecetti AS, Coppa A, Ayub Q, Mohyuddin A, Tyler-Smith C, Qasim Mehdi S, Torroni A, McElreavey K, Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor, Am. J. Hum. Genet. 2004 May;74(5):827-45.

Mlouka A, Comte K, Castets AM, Bouchier C, Tandeau de Marsac N, The gas vesicle gene cluster from Microcystis aeruginosa and DNA rearrangements that lead to loss of cell buoyancy, J. Bacteriol. 2004 Apr;186(8):2355-65.

Grimont PA, Grimont F, Efstratiou A, De Zoysa A, Mazurova I, Ruckly C, Lejay-Collin M, Martin-Delautre S, Regnault B, , International nomenclature for Corynebacterium diphtheriae ribotypes, Res. Microbiol. 2004 Apr;155(3):162-6.

van Dessel H, Dijkshoorn L, van der Reijden T, Bakker N, Paauw A, van den Broek P, Verhoef J, Brisse S, Identification of a new geographically widespread multiresistant Acinetobacter baumannii clone from European hospitals, Res. Microbiol. 2004 Mar;155(2):105-12.

Kaykov A, Holmes AM, Arcangioli B, Formation, maintenance and consequences of the imprint at the mating-type locus in fission yeast, EMBO J. 2004 Feb;23(4):930-8.

Quintana-Murci L, Bigham A, Rouba H, Barakat A, McElreavey K, Hammer M, Y-chromosomal STR haplotypes in Berber and Arabic-speaking populations from Morocco, Forensic Sci. Int. 2004 Feb;140(1):113-5.

Montagutelli X, de Vienne D, [The experimental populations of genetic mapping], Med Sci (Paris) 2008 Jan;24(1):77-80.

Behar DM, Garrigan D, Kaplan ME, Mobasher Z, Rosengarten D, Karafet TM, Quintana-Murci L, Ostrer H, Skorecki K, Hammer MF, Contrasting patterns of Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populations, Hum. Genet. 2004 Mar;114(4):354-65.

Galy V, Gadal O, Fromont-Racine M, Romano A, Jacquier A, Nehrbass U, Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1, Cell 2004 Jan;116(1):63-73.

Boyer J, Badis G, Fairhead C, Talla E, Hantraye F, Fabre E, Fischer G, Hennequin C, Koszul R, Lafontaine I, Ozier-Kalogeropoulos O, Ricchetti M, Richard GF, Thierry A, Dujon B, , Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae., Genome Biol 2004 ; 5(9): R72.

Hommais F, Krin E, Coppée JY, Lacroix C, Yeramian E, Danchin A, Bertin P, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli, Microbiology (Reading, Engl.) 2004 Jan;150(Pt 1):61-72.

Krausz C, Quintana-Murci L, Forti G, Y chromosome polymorphisms in medicine, Ann. Med. 2004;36(8):573-83.

Jonas D, Spitzmüller B, Daschner FD, Verhoef J, Brisse S, Discrimination of Klebsiella pneumoniae and Klebsiella oxytoca phylogenetic groups and other Klebsiella species by use of amplified fragment length polymorphism, Res. Microbiol. 2004 Jan-Feb;155(1):17-23.

Loot C, Turlan C, Chandler M, Host processing of branched DNA intermediates is involved in targeted transposition of IS911, Mol. Microbiol. 2004 Jan;51(2):385-93.

Koszul R, Caburet S, Dujon B, Fischer G, Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments, EMBO J. 2004 Jan;23(1):234-43.

Forissier JF, Bonne G, Bouchier C, Duboscq-Bidot L, Richard P, Wisnewski C, Briault S, Moraine C, Dubourg O, Schwartz K, Komajda M, Apical left ventricular aneurysm without atrio-ventricular block due to a lamin A/C gene mutation, Eur. J. Heart Fail. 2003 Dec;5(6):821-5.

Rocha EP, Danchin A, Gene essentiality determines chromosome organisation in bacteria, Nucleic Acids Res. 2003 Nov;31(22):6570-7.

Bougnoux ME, Tavanti A, Bouchier C, Gow NA, Magnier A, Davidson AD, Maiden MC, D'Enfert C, Odds FC, Collaborative consensus for optimized multilocus sequence typing of Candida albicans, J. Clin. Microbiol. 2003 Nov;41(11):5265-6.

Rocha EP, DNA repeats lead to the accelerated loss of gene order in bacteria, Trends Genet. 2003 Nov;19(11):600-3.

Onteniente L, Brisse S, Tassios PT, Vergnaud G, Evaluation of the polymorphisms associated with tandem repeats for Pseudomonas aeruginosa strain typing, J. Clin. Microbiol. 2003 Nov;41(11):4991-7.

Mashimo T, Glaser P, Lucas M, Simon-Chazottes D, Ceccaldi PE, Montagutelli X, Desprès P, Guénet JL, Structural and functional genomics and evolutionary relationships in the cluster of genes encoding murine 2′,5′-oligoadenylate synthetases, Genomics 2003 Nov;82(5):537-52.

Rocha EP, Danchin A, An analysis of determinants of amino acids substitution rates in bacterial proteins, Mol. Biol. Evol. 2004 Jan;21(1):108-16.

Biskri L, Mazel D, Erythromycin esterase gene ere(A) is located in a functional gene cassette in an unusual class 2 integron, Antimicrob. Agents Chemother. 2003 Oct;47(10):3326-31.

de Lahondès R, Ribes V, Arcangioli B, Fission yeast Sap1 protein is essential for chromosome stability, Eukaryotic Cell 2003 Oct;2(5):910-21.

Zei G, Lisa A, Fiorani O, Magri C, Quintana-Murci L, Semino O, Santachiara-Benerecetti AS, From surnames to the history of Y chromosomes: the Sardinian population as a paradigm, Eur. J. Hum. Genet. 2003 Oct;11(10):802-7.

Kovtunovych G, Lytvynenko T, Negrutska V, Lar O, Brisse S, Kozyrovska N, Identification of Klebsiella oxytoca using a specific PCR assay targeting the polygalacturonase pehX gene, Res. Microbiol. 2003 Oct;154(8):587-92.

Janvier M, Regnault B, Grimont P, Development and use of fluorescent 16S rRNA-targeted probes for the specific detection of Methylophaga species by in situ hybridization in marine sediments, Res. Microbiol. 2003 Sep;154(7):483-90.

Meister P, Poidevin M, Francesconi S, Tratner I, Zarzov P, Baldacci G, Nuclear factories for signalling and repairing DNA double strand breaks in living fission yeast, Nucleic Acids Res. 2003 Sep;31(17):5064-73.

Fromont-Racine M, Senger B, Saveanu C, Fasiolo F, Ribosome assembly in eukaryotes, Gene 2003 Aug;313:17-42.

van Westreenen M, Paauw A, Fluit AC, Brisse S, van Dijk W, Verhoef J, Occurrence and spread of SHV extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates in Curacao, J. Antimicrob. Chemother. 2003 Sep;52(3):530-2.

Sielaff H, Dittmann E, Tandeau De Marsac N, Bouchier C, Von Döhren H, Börner T, Schwecke T, The mcyF gene of the microcystin biosynthetic gene cluster from Microcystis aeruginosa encodes an aspartate racemase, Biochem. J. 2003 Aug;373(Pt 3):909-16.

Sébillon P, Bouchier C, Bidot LD, Bonne G, Ahamed K, Charron P, Drouin-Garraud V, Millaire A, Desrumeaux G, Benaïche A, Charniot JC, Schwartz K, Villard E, Komajda M, Expanding the phenotype of LMNA mutations in dilated cardiomyopathy and functional consequences of these mutations, J. Med. Genet. 2003 Aug;40(8):560-7.

Desnoues N, Lin M, Guo X, Ma L, Carreño-Lopez R, Elmerich C, Nitrogen fixation genetics and regulation in a Pseudomonas stutzeri strain associated with rice, Microbiology (Reading, Engl.) 2003 Aug;149(Pt 8):2251-62.

Achaz G, Coissac E, Netter P, Rocha EP, Associations between inverted repeats and the structural evolution of bacterial genomes, Genetics 2003 Aug;164(4):1279-89.

Rocha EP, Fralick J, Vediyappan G, Danchin A, Norris V, A strand-specific model for chromosome segregation in bacteria, Mol. Microbiol. 2003 Aug;49(4):895-903.

Rocha EP, Danchin A, Essentiality, not expressiveness, drives gene-strand bias in bacteria, Nat. Genet. 2003 Aug;34(4):377-8.

Sylvius N, Duboscq-Bidot L, Bouchier C, Charron P, Benaiche A, Sébillon P, Komajda M, Villard E, Mutational analysis of the beta- and delta-sarcoglycan genes in a large number of patients with familial and sporadic dilated cardiomyopathy, Am. J. Med. Genet. A 2003 Jul;120A(1):8-12.

Guillemin I, Bouchier C, Garrigues T, Wisner A, Choumet V, Sequences and structural organization of phospholipase A2 genes from Vipera aspis aspis, V. aspis zinnikeri and Vipera berus berus venom. Identification of the origin of a new viper population based on ammodytin I1 heterogeneity, Eur. J. Biochem. 2003 Jul;270(13):2697-706.

McElreavey K, Quintana-Murci L, Male reproductive function and the human Y chromosome: is selection acting on the Y?, Reprod. Biomed. Online 2003 Jul-Aug;7(1):17-23.

Badis G, Fromont-Racine M, Jacquier A, A snoRNA that guides the two most conserved pseudouridine modifications within rRNA confers a growth advantage in yeast, RNA 2003 Jul;9(7):771-9.

Saveanu C, Namane A, Gleizes PE, Lebreton A, Rousselle JC, Noaillac-Depeyre J, Gas N, Jacquier A, Fromont-Racine M, Sequential protein association with nascent 60S ribosomal particles, Mol. Cell. Biol. 2003 Jul;23(13):4449-60.

Smeets MF, Francesconi S, Baldacci G, High dosage Rhp51 suppression of the MMS sensitivity of DNA structure checkpoint mutants reveals a relationship between Crb2 and Rhp51, Genes Cells 2003 Jul;8(7):573-86.

Baroud CN, Okkels F, Ménétrier L, Tabeling P, Reaction-diffusion dynamics: confrontation between theory and experiment in a microfluidic reactor, Phys Rev E Stat Nonlin Soft Matter Phys 2003 Jun;67(6 Pt 1):060104.

Quintana-Murci L, Veitia R, Fellous M, Semino O, Poloni ES, Genetic structure of Mediterranean populations revealed by Y-chromosome haplotype analysis, Am. J. Phys. Anthropol. 2003 Jun;121(2):157-71.

Lucas M, Mashimo T, Frenkiel MP, Simon-Chazottes D, Montagutelli X, Ceccaldi PE, Guénet JL, Desprès P, Infection of mouse neurones by West Nile virus is modulated by the interferon-inducible 2′-5′ oligoadenylate synthetase 1b protein, Immunol. Cell Biol. 2003 Jun;81(3):230-6.

Rocha EP, An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction, Genome Res. 2003 Jun;13(6A):1123-32.

Charniot JC, Pascal C, Bouchier C, Sébillon P, Salama J, Duboscq-Bidot L, Peuchmaurd M, Desnos M, Artigou JY, Komajda M, Functional consequences of an LMNA mutation associated with a new cardiac and non-cardiac phenotype, Hum. Mutat. 2003 May;21(5):473-81.

Kljuic A, Bazzi H, Sundberg JP, Martinez-Mir A, O'Shaughnessy R, Mahoney MG, Levy M, Montagutelli X, Ahmad W, Aita VM, Gordon D, Uitto J, Whiting D, Ott J, Fischer S, Gilliam TC, Jahoda CA, Morris RJ, Panteleyev AA, Nguyen VT, Christiano AM, , Desmoglein 4 in hair follicle differentiation and epidermal adhesion: evidence from inherited hypotrichosis and acquired pemphigus vulgaris., Cell 2003 Apr; 113(2): 249-60.

Milohanic E, Glaser P, Coppée JY, Frangeul L, Vega Y, Vázquez-Boland JA, Kunst F, Cossart P, Buchrieser C, Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differently regulated by PrfA, Mol. Microbiol. 2003 Mar;47(6):1613-25.

Rowe-Magnus DA, Guerout AM, Biskri L, Bouige P, Mazel D, Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae, Genome Res. 2003 Mar;13(3):428-42.

Kanoh J, Francesconi S, Collura A, Schramke V, Ishikawa F, Baldacci G, Géli V, The fission yeast spSet1p is a histone H3-K4 methyltransferase that functions in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway, J. Mol. Biol. 2003 Feb;326(4):1081-94.

Barnabe C, Brisse S, Tibayrenc M, Phylogenetic diversity of bat trypanosomes of subgenus Schizotrypanum based on multilocus enzyme electrophoresis, random amplified polymorphic DNA, and cytochrome b nucleotide sequence analyses, Infect. Genet. Evol. 2003 Feb;2(3):201-8.

Brisse S, Henriksson J, Barnabé C, Douzery EJ, Berkvens D, Serrano M, De Carvalho MR, Buck GA, Dujardin JC, Tibayrenc M, Evidence for genetic exchange and hybridization in Trypanosoma cruzi based on nucleotide sequences and molecular karyotype, Infect. Genet. Evol. 2003 Feb;2(3):173-83.

Koszul R, Malpertuy A, Frangeul L, Bouchier C, Wincker P, Thierry A, Duthoy S, Ferris S, Hennequin C, Dujon B, The complete mitochondrial genome sequence of the pathogenic yeast Candida (Torulopsis) glabrata, FEBS Lett. 2003 Jan;534(1-3):39-48.

McElreavey K, Quintana-Murci L, Y chromosome haplogroups: a correlation with testicular dysgenesis syndrome?, APMIS 2003 Jan;111(1):106-13; discussion 114.

Fabre F, Chan A, Heyer WD, Gangloff S, Alternate pathways involving Sgs1/Top3, Mus81/ Mms4, and Srs2 prevent formation of toxic recombination intermediates from single-stranded gaps created by DNA replication, Proc. Natl. Acad. Sci. U.S.A. 2002 Dec;99(26):16887-92.

Pulkkinen L, Choi YW, Simpson A, Montagutelli X, Sundberg J, Uitto J, Mahoney MG, , Loss of cell adhesion in Dsg3bal-Pas mice with homozygous deletion mutation (2079del14) in the desmoglein 3 gene., J. Invest. Dermatol. 2002 Dec; 119(6): 1237-43.

Wielders CL, Fluit AC, Brisse S, Verhoef J, Schmitz FJ, mecA gene is widely disseminated in Staphylococcus aureus population, J. Clin. Microbiol. 2002 Nov;40(11):3970-5.

Patsalis PC, Sismani C, Quintana-Murci L, Taleb-Bekkouche F, Krausz C, McElreavey K, Effects of transmission of Y chromosome AZFc deletions, Lancet 2002 Oct;360(9341):1222-4.

Bandelt HJ, Quintana-Murci L, Salas A, Macaulay V, The fingerprint of phantom mutations in mitochondrial DNA data, Am. J. Hum. Genet. 2002 Nov;71(5):1150-60.

Rocha EP, Pradillon O, Bui H, Sayada C, Denamur E, A new family of highly variable proteins in the Chlamydophila pneumoniae genome, Nucleic Acids Res. 2002 Oct;30(20):4351-60.

Manni F, Leonardi P, Barakat A, Rouba H, Heyer E, Klintschar M, McElreavey K, Quintana-Murci L, Y-chromosome analysis in Egypt suggests a genetic regional continuity in Northeastern Africa, Hum. Biol. 2002 Oct;74(5):645-58.

Leverstein-van Hall MA, Fluit AC, Paauw A, Box AT, Brisse S, Verhoef J, Evaluation of the Etest ESBL and the BD Phoenix, VITEK 1, and VITEK 2 automated instruments for detection of extended-spectrum beta-lactamases in multiresistant Escherichia coli and Klebsiella spp, J. Clin. Microbiol. 2002 Oct;40(10):3703-11.

Rocha E, Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?, Trends Microbiol. 2002 Sep;10(9):393-5.

Mashimo T, Lucas M, Simon-Chazottes D, Frenkiel MP, Montagutelli X, Ceccaldi PE, Deubel V, Guenet JL, Despres P, A nonsense mutation in the gene encoding 2′-5′-oligoadenylate synthetase/L1 isoform is associated with West Nile virus susceptibility in laboratory mice, Proc. Natl. Acad. Sci. U.S.A. 2002 Aug;99(17):11311-6.

Loot C, Turlan C, Rousseau P, Ton-Hoang B, Chandler M, A target specificity switch in IS911 transposition: the role of the OrfA protein, EMBO J. 2002 Aug;21(15):4172-82.

Shor E, Gangloff S, Wagner M, Weinstein J, Price G, Rothstein R, Mutations in homologous recombination genes rescue top3 slow growth in Saccharomyces cerevisiae, Genetics 2002 Oct;162(2):647-62.

Rowe-Magnus DA, Mazel D, The role of integrons in antibiotic resistance gene capture, Int. J. Med. Microbiol. 2002 Jul;292(2):115-25.

Achaz G, Rocha EP, Netter P, Coissac E, Origin and fate of repeats in bacteria, Nucleic Acids Res. 2002 Jul;30(13):2987-94.

Francesconi S, Smeets M, Grenon M, Tillit J, Blaisonneau J, Baldacci G, Fission yeast chk1 mutants show distinct responses to different types of DNA damaging treatments, Genes Cells 2002 Jul;7(7):663-73.

Rocha EP, Danchin A, Base composition bias might result from competition for metabolic resources, Trends Genet. 2002 Jun;18(6):291-4.

van Dessel H, Kamp-Hopmans TE, Fluit AC, Brisse S, de Smet AM, Dijkshoorn L, Troelstra A, Verhoef J, Mascini EM, Outbreak of a susceptible strain of Acinetobacter species 13 (sensu Tjernberg and Ursing) in an adult neurosurgical intensive care unit, J. Hosp. Infect. 2002 Jun;51(2):89-95.

Brisse S, Fussing V, Ridwan B, Verhoef J, Willems RJ, Automated ribotyping of vancomycin-resistant Enterococcus faecium isolates, J. Clin. Microbiol. 2002 Jun;40(6):1977-84.

Rocha EP, Blanchard A, Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution, Nucleic Acids Res. 2002 May;30(9):2031-42.

Rocha EP, Matic I, Taddei F, Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?, Nucleic Acids Res. 2002 May;30(9):1886-94.

Brisse S, Stefani S, Verhoef J, Van Belkum A, Vandamme P, Goessens W, Comparative evaluation of the BD Phoenix and VITEK 2 automated instruments for identification of isolates of the Burkholderia cepacia complex, J. Clin. Microbiol. 2002 May;40(5):1743-8.

Amrani YM, Voegtlé D, Montagutelli X, Cazenave PA, Six A, The Ig light chain restricted B6.kappa(-)lambda(SEG) mouse strain suggests that the IGL locus genomic organization is subject to constant evolution, Immunogenetics 2002 May;54(2):106-19.

Feuerbach F, Galy V, Trelles-Sticken E, Fromont-Racine M, Jacquier A, Gilson E, Olivo-Marin JC, Scherthan H, Nehrbass U, Nuclear architecture and spatial positioning help establish transcriptional states of telomeres in yeast, Nat. Cell Biol. 2002 Mar;4(3):214-21.

Rowe-Magnus DA, Guerout AM, Mazel D, Bacterial resistance evolution by recruitment of super-integron gene cassettes, Mol. Microbiol. 2002 Mar;43(6):1657-69.

Le Masson I, Saveanu C, Chevalier A, Namane A, Gobin R, Fromont-Racine M, Jacquier A, Mann C, Spc24 interacts with Mps2 and is required for chromosome segregation, but is not implicated in spindle pole body duplication, Mol. Microbiol. 2002 Mar;43(6):1431-43.

Henriksson J, Dujardin JC, Barnabé C, Brisse S, Timperman G, Venegas J, Pettersson U, Tibayrenc M, Solari A, Chromosomal size variation in Trypanosoma cruzi is mainly progressive and is evolutionarily informative, Parasitology 2002 Mar;124(Pt 3):277-86.

Baroud CN, Plapp BB, She ZS, Swinney HL, Anomalous self-similarity in a turbulent rapidly rotating fluid, Phys. Rev. Lett. 2002 Mar;88(11):114501.

Fromont-Racine M, Rain JC, Legrain P, Building protein-protein networks by two-hybrid mating strategy, Meth. Enzymol. 2002;350:513-24.

Hetet G, Grandchamp B, Bouchier C, Nicaud V, Tiret L, Roizès G, Desnos M, Schwartz K, Dorent R, Komajda M, , Idiopathic dilated cardiomyopathy: lack of association with haemochromatosis gene in the CARDIGENE study, Heart 2001 Dec;86(6):702-3.

Schaper S, Fromont-Racine M, Linder P, de la Cruz J, Namane A, Yaniv M, A yeast homolog of chromatin assembly factor 1 is involved in early ribosome assembly, Curr. Biol. 2001 Nov;11(23):1885-90.

Saveanu C, Bienvenu D, Namane A, Gleizes PE, Gas N, Jacquier A, Fromont-Racine M, Nog2p, a putative GTPase associated with pre-60S subunits and required for late 60S maturation steps, EMBO J. 2001 Nov;20(22):6475-84.

Rocha EP, Danchin A, Ongoing evolution of strand composition in bacterial genomes, Mol. Biol. Evol. 2001 Sep;18(9):1789-99.

Brisse S, Verhoef J, Tibayrenc M, Characterisation of large and small subunit rRNA and mini-exon genes further supports the distinction of six Trypanosoma cruzi lineages, Int. J. Parasitol. 2001 Sep;31(11):1218-26.

Fitch W, Brisse S, Stevens J, Tibayrenc M, Infectious diseases and the golden age of phylogenetics: an E-debate, Infect. Genet. Evol. 2001 Jul;1(1):69-74.

Rocha EP, Danchin A, Viari A, Evolutionary role of restriction/modification systems as revealed by comparative genome analysis, Genome Res. 2001 Jun;11(6):946-58.

Wielders CL, Vriens MR, Brisse S, de Graaf-Miltenburg LA, Troelstra A, Fleer A, Schmitz FJ, Verhoef J, Fluit AC, In-vivo transfer of mecA DNA to Staphylococcus aureus [corrected], Lancet 2001 May;357(9269):1674-5.

Chambaud I, Heilig R, Ferris S, Barbe V, Samson D, Galisson F, Moszer I, Dybvig K, Wróblewski H, Viari A, Rocha EP, Blanchard A, The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis, Nucleic Acids Res. 2001 May;29(10):2145-53.

Brisse S, Verhoef J, Phylogenetic diversity of Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates revealed by randomly amplified polymorphic DNA, gyrA and parC genes sequencing and automated ribotyping, Int. J. Syst. Evol. Microbiol. 2001 May;51(Pt 3):915-24.

Garapin A, Ma L, Pescher P, Lagranderie M, Marchal G, Mixed immune response induced in rodents by two naked DNA genes coding for mycobacterial glycosylated proteins, Vaccine 2001 Apr;19(20-22):2830-41.

Lefort J, Motreff L, Vargaftig BB, , Airway administration of Escherichia coli endotoxin to mice induces glucocorticosteroid-resistant bronchoconstriction and vasopermeation., Am J Respir Cell Mol Biol 2001 Mar; 24(3): 345-51.

Saveanu C, Fromont-Racine M, Harington A, Ricard F, Namane A, Jacquier A, Identification of 12 new yeast mitochondrial ribosomal proteins including 6 that have no prokaryotic homologues, J. Biol. Chem. 2001 May;276(19):15861-7.

Hennequin C, Thierry A, Richard GF, Lecointre G, Nguyen HV, Gaillardin C, Dujon B, Microsatellite typing as a new tool for identification of Saccharomyces cerevisiae strains, J. Clin. Microbiol. 2001 Feb;39(2):551-9.

Urdaci MC, Regnault B, Grimont PA, Identification by in situ hybridization of segmented filamentous bacteria in the intestine of diarrheic rainbow trout (Oncorhynchus mykiss), Res. Microbiol. 2001 Jan-Feb;152(1):67-73.

Quintana-Murci L, Fellous M, The Human Y Chromosome: The Biological Role of a “Functional Wasteland”, J. Biomed. Biotechnol. 2001;1(1):18-24.

Sylvius N, Tesson F, Gayet C, Charron P, Bénaïche A, Peuchmaurd M, Duboscq-Bidot L, Feingold J, Beckmann JS, Bouchier C, Komajda M, A new locus for autosomal dominant dilated cardiomyopathy identified on chromosome 6q12-q16, Am. J. Hum. Genet. 2001 Jan;68(1):241-6.

Tesson F, Sylvius N, Pilotto A, Dubosq-Bidot L, Peuchmaurd M, Bouchier C, Benaiche A, Mangin L, Charron P, Gavazzi A, Tavazzi L, Arbustini E, Komajda M, Epidemiology of desmin and cardiac actin gene mutations in a european population of dilated cardiomyopathy, Eur. Heart J. 2000 Nov;21(22):1872-6.

Villarino A, Bouvet OM, Regnault B, Martin-Delautre S, Grimont PAD , Exploring the frontier between life and death in Escherichia coli: evaluation of different viability markers in live and heat- or UV-killed cells, Res. Microbiol. 2000 Nov;151(9):755-68.

Brisse S, Dujardin JC, Tibayrenc M, Identification of six Trypanosoma cruzi lineages by sequence-characterised amplified region markers, Mol. Biochem. Parasitol. 2000 Nov;111(1):95-105.

Wolf B, Rey LC, Brisse S, Moreira LB, Milatovic D, Fleer A, Roord JJ, Verhoef J, Molecular epidemiology of penicillin-resistant Streptococcus pneumoniae colonizing children with community-acquired pneumonia and children attending day-care centres in Fortaleza, Brazil, J. Antimicrob. Chemother. 2000 Nov;46(5):757-65.

Montagutelli X, , Effect of the genetic background on the phenotype of mouse mutations., J. Am. Soc. Nephrol. 2000 Nov; 11 Suppl 16(): S101-5.

Brisse S, Milatovic D, Fluit AC, Kusters K, Toelstra A, Verhoef J, Schmitz FJ, Molecular surveillance of European quinolone-resistant clinical isolates of Pseudomonas aeruginosa and Acinetobacter spp. using automated ribotyping, J. Clin. Microbiol. 2000 Oct;38(10):3636-45.

Regnault B, Martin-Delautre S, Lejay-Collin M, Lefèvre M, Grimont PA, Oligonucleotide probe for the visualization of Escherichia coli/Escherichia fergusonii cells by in situ hybridization: specificity and potential applications, Res. Microbiol. 2000 Sep;151(7):521-33.

Schlegel L, Grimont F, Collins MD, Régnault B, Grimont PA, Bouvet A, Streptococcus infantarius sp. nov., Streptococcus infantarius subsp. infantarius subsp. nov. and Streptococcus infantarius subsp. coli subsp. nov., isolated from humans and food, Int. J. Syst. Evol. Microbiol. 2000 Jul;50 Pt 4:1425-34.

Rocha EP, Danchin A, Viari A, The DB case: pattern matching evidence is not significant, Mol. Microbiol. 2000 Jul;37(1):216-8.

Dujardin JC, Henriksson J, Victoir K, Brisse S, Gamboa D, Arevalo J, Le Ray D, Genomic rearrangements in trypanosomatids: an alternative to the “one gene” evolutionary hypotheses?, Mem. Inst. Oswaldo Cruz 2000 Jul-Aug;95(4):527-34.

Schmitz FJ, Fluit AC, Milatovic D, Verhoef J, Heinz HP, Brisse S, In vitro potency of moxifloxacin, clinafloxacin and sitafloxacin against 248 genetically defined clinical isolates of Staphylococcus aureus, J. Antimicrob. Chemother. 2000 Jul;46(1):109-13.

Fontanellas A, Mazurier F, Landry M, Taine L, Morel C, Larou M, Daniel JY, Montagutelli X, de Salamanca RE, de Verneuil H, , Reversion of hepatobiliary alterations By bone marrow transplantation in a murine model of erythropoietic protoporphyria., Hepatology 2000 Jul; 32(1): 73-81.

Rocha EP, Sekowska A, Danchin A, Sulphur islands in the Escherichia coli genome: markers of the cell’s architecture?, FEBS Lett. 2000 Jun;476(1-2):8-11.

Gangloff S, Soustelle C, Fabre F, Homologous recombination is responsible for cell death in the absence of the Sgs1 and Srs2 helicases, Nat. Genet. 2000 Jun;25(2):192-4.

Sundberg JP, Boggess D, Bascom C, Limberg BJ, Shultz LD, Sundberg BA, King LE, Montagutelli X, , Lanceolate hair-J (lahJ): a mouse model for human hair disorders., Exp. Dermatol. 2000 Jun; 9(3): 206-18.

Barnabé C, Brisse S, Tibayrenc M, Population structure and genetic typing of Trypanosoma cruzi, the agent of Chagas disease: a multilocus enzyme electrophoresis approach, Parasitology 2000 May;120 ( Pt 5):513-26.

Brisse S, Verduin CM, Milatovic D, Fluit A, Verhoef J, Laevens S, Vandamme P, Tümmler B, Verbrugh HA, van Belkum A, Distinguishing species of the Burkholderia cepacia complex and Burkholderia gladioli by automated ribotyping, J. Clin. Microbiol. 2000 May;38(5):1876-84.

Regnault B, Martin-Delautre S, Grimont PA, Problems associated with the direct viable count procedure applied to gram-positive bacteria, Int. J. Food Microbiol. 2000 Apr;55(1-3):281-4.

Villarino A, Bouvet O, Regnault B, Delautre S, Grimont PA, Cellular activities in ultra-violet killed Escherichia coli, Int. J. Food Microbiol. 2000 Apr;55(1-3):245-7.

Milatovic D, Schmitz FJ, Brisse S, Verhoef J, Fluit AC, In vitro activities of sitafloxacin (DU-6859a) and six other fluoroquinolones against 8,796 clinical bacterial isolates, Antimicrob. Agents Chemother. 2000 Apr;44(4):1102-7.

Rocha EP, Guerdoux-Jamet P, Moszer I, Viari A, Danchin A, Implication of gene distribution in the bacterial chromosome for the bacterial cell factory, J. Biotechnol. 2000 Mar;78(3):209-19.

Jagla B, Schuchhardt J, Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites, Bioinformatics 2000 Mar;16(3):245-50.

Brisse S, Milatovic D, Fluit AC, Verhoef J, Schmitz FJ, Epidemiology of quinolone resistance of Klebsiella pneumoniae and Klebsiella oxytoca in Europe, Eur. J. Clin. Microbiol. Infect. Dis. 2000 Jan;19(1):64-8.

Brisse S, Barnabé C, Tibayrenc M, Identification of six Trypanosoma cruzi phylogenetic lineages by random amplified polymorphic DNA and multilocus enzyme electrophoresis, Int. J. Parasitol. 2000 Jan;30(1):35-44.

Rothstein R, Michel B, Gangloff S, Replication fork pausing and recombination or “gimme a break”, Genes Dev. 2000 Jan;14(1):1-10.

Willig TN, Draptchinskaia N, Dianzani I, Ball S, Niemeyer C, Ramenghi U, Orfali K, Gustavsson P, Garelli E, Brusco A, Tiemann C, Pérignon JL, Bouchier C, Cicchiello L, Dahl N, Mohandas N, Tchernia G, Mutations in ribosomal protein S19 gene and diamond blackfan anemia: wide variations in phenotypic expression, Blood 1999 Dec;94(12):4294-306.

Schmitz FJ, Fluit AC, Brisse S, Verhoef J, Köhrer K, Milatovic D, Molecular epidemiology of quinolone resistance and comparative in vitro activities of new quinolones against European Staphylococcus aureus isolates, FEMS Immunol. Med. Microbiol. 1999 Dec;26(3-4):281-7.

Rocha EP, Danchin A, Viari A, Functional and evolutionary roles of long repeats in prokaryotes, Res. Microbiol. 1999 Nov-Dec;150(9-10):725-33.

Richard GF, Hennequin C, Thierry A, Dujon B, Trinucleotide repeats and other microsatellites in yeasts, Res. Microbiol. 1999 Nov-Dec;150(9-10):589-602.

Moszer I, Rocha EP, Danchin A, Codon usage and lateral gene transfer in Bacillus subtilis, Curr. Opin. Microbiol. 1999 Oct;2(5):524-8.

Brisse S, Fluit AC, Wagner U, Heisig P, Milatovic D, Verhoef J, Scheuring S, Köhrer K, Schmitz FJ, Association of alterations in ParC and GyrA proteins with resistance of clinical isolates of Enterococcus faecium to nine different fluoroquinolones, Antimicrob. Agents Chemother. 1999 Oct;43(10):2513-6.

Rocha EP, Danchin A, Viari A, Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes, Mol. Biol. Evol. 1999 Sep;16(9):1219-30.

Rocha EP, Danchin A, Viari A, Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis, Nucleic Acids Res. 1999 Sep;27(17):3567-76.

Rocha EP, Danchin A, Viari A, Bacterial DNA strand compositional asymmetry: response, Trends Microbiol. 1999 Aug;7(8):308.

Brisse S, Milatovic D, Fluit AC, Verhoef J, Martin N, Scheuring S, Köhrer K, Schmitz FJ, Comparative in vitro activities of ciprofloxacin, clinafloxacin, gatifloxacin, levofloxacin, moxifloxacin, and trovafloxacin against Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, and Enterobacter aerogenes clinical isolates with alterations in GyrA and ParC proteins, Antimicrob. Agents Chemother. 1999 Aug;43(8):2051-5.

Autiero M, Culerrier R, Bouchier C, Basmaciogullari S, Gaubin M, El Marhomy S, Blanchet P, Paradis V, Jardin A, Guardiola J, Piatier-Tonneau D, Abnormal restriction pattern of PIP gene associated with human primary prostate cancers, DNA Cell Biol. 1999 Jun;18(6):481-7.

Rothstein R, Gangloff S, The shuffling of a mortal coil, Nat. Genet. 1999 May;22(1):4-6.

Rocha EP, Danchin A, Viari A, Universal replication biases in bacteria, Mol. Microbiol. 1999 Apr;32(1):11-6.

Gangloff S, de Massy B, Arthur L, Rothstein R, Fabre F, The essential role of yeast topoisomerase III in meiosis depends on recombination, EMBO J. 1999 Mar;18(6):1701-11.

Bañuls AL, Brisse S, Sidibé I, Noël S, Tibayrenc M, A phylogenetic analysis by multilocus enzyme electrophoresis and multiprimer random amplified polymorphic DNA fingerprinting of the Leishmania genome project Friedlin reference strain, Folia Parasitol. 1999;46(1):10-4.

Grenon M, Tillit J, Piard K, Baldacci G, Francesconi S, The S/M checkpoint at 37 degrees C and the recovery of viability of the mutant poldeltats3 require the crb2+/rhp9+ gene in fission yeast, Mol. Gen. Genet. 1999 Jan;260(6):522-34.

Manning K, Fernández-Cañón JM, Montagutelli X, Grompe M, , Identification of the mutation in the alkaptonuria mouse model. Mutations in brief no. 216. Online., Hum. Mutat. 1999 ; 13(2): 171.

Kress W, Schmidt SR, Halliger-Keller B, Montagutelli X, Müller CR, , The genetic defect of the alkaptonuric mouse (aku)., Mamm. Genome 1999 Jan; 10(1): 68-70.

Hillebrandt S, Streffer C, Montagutelli X, Balling R, , A locus for radiation-induced gastroschisis on mouse Chromosome 7., Mamm. Genome 1998 Dec; 9(12): 995-7.

Santiago ML, Mary C, Parzy D, Jacquet C, Montagutelli X, Parkhouse RM, Lemoine R, Izui S, Reininger L, , Linkage of a major quantitative trait locus to Yaa gene-induced lupus-like nephritis in (NZW x C57BL/6)F1 mice., Eur. J. Immunol. 1998 12; 28(12): 4257-67.

Fairhead C, Thierry A, Denis F, Eck M, Dujon B, ‘Mass-murder’ of ORFs from three regions of chromosome XI from Saccharomyces cerevisiae, Gene 1998 Nov;223(1-2):33-46.

Perderiset M, Maga G, Piard K, Francesconi S, Tratner I, Hübscher U, Baldacci G, Mutant DNA polymerase delta from thermosensitive Schizosaccharomyces pombe strains display reduced stimulation by proliferating cell nuclear antigen, Biochem. J. 1998 Nov;335 ( Pt 3):581-8.

Cornélis F, Fauré S, Martinez M, Prud'homme JF, Fritz P, Dib C, Alves H, Barrera P, de Vries N, Balsa A, Pascual-Salcedo D, Maenaut K, Westhovens R, Migliorini P, Tran TH, Delaye A, Prince N, Lefevre C, Thomas G, Poirier M, Soubigou S, Alibert O, Lasbleiz S, Fouix S, Bouchier C, Lioté F, Loste MN, Lepage V, Charron D, Gyapay G, Lopes-Vaz A, Kuntz D, Bardin T, Weissenbach J, , New susceptibility locus for rheumatoid arthritis suggested by a genome-wide linkage study, Proc. Natl. Acad. Sci. U.S.A. 1998 Sep;95(18):10746-50.

Colnot C, Ripoche MA, Milon G, Montagutelli X, Crocker PR, Poirier F, , Maintenance of granulocyte numbers during acute peritonitis is defective in galectin-3-null mutant mice., Immunology 1998 Jul; 94(3): 290-6.

Rocha EP, Viari A, Danchin A, Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons, Nucleic Acids Res. 1998 Jun;26(12):2971-80.

Brisse S, Barnabé C, Tibayrenc M, Trypanosoma cruzi: How Many Relevant Phylogenetic Subdivisions are There?, Parasitol. Today (Regul. Ed.) 1998 May;14(5):178-9.

Brisse S, Barnabé C, Bañuls AL, Sidibé I, Noël S, Tibayrenc M, A phylogenetic analysis of the Trypanosoma cruzi genome project CL Brener reference strain by multilocus enzyme electrophoresis and multiprimer random amplified polymorphic DNA fingerprinting, Mol. Biochem. Parasitol. 1998 May;92(2):253-63.

Tettelin H, Thierry A, Goffeau A, Dujon B, Physical mapping of chromosomes VII and XV of Saccharomyces cerevisiae at 3.5 kb average resolution to allow their complete sequencing, Yeast 1998 May;14(7):601-16.

Rhodes M, Straw R, Fernando S, Evans A, Lacey T, Dearlove A, Greystrong J, Walker J, Watson P, Weston P, Kelly M, Taylor D, Gibson K, Mundy C, Bourgade F, Poirier C, Simon D, Brunialti AL, Montagutelli X, Gu'enet JL, Haynes A, Brown SD, , A high-resolution microsatellite map of the mouse genome., Genome Res. 1998 May; 8(5): 531-42.

Regnault B, Grimont F, Grimont PA, Universal ribotyping method using a chemically labelled oligonucleotide probe mixture, Res. Microbiol. 1997 Nov;148(8):649-59.

Montagutelli X, Lalouette A, Boulouis HJ, Guénet JL, Sundberg JP, , Vesicle formation and follicular root sheath separation in mice homozygous for deleterious alleles at the balding (bal) locus., J. Invest. Dermatol. 1997 Sep; 109(3): 324-8.

Tettelin H, Agostoni Carbone ML, Albermann K, Albers M, Arroyo J, Backes U, Barreiros T, Bertani I, Bjourson AJ, Brückner M, Bruschi CV, Carignani G, Castagnoli L, Cerdan E, Clemente ML, Coblenz A, Coglievina M, Coissac E, Defoor E, Del Bino S, Delius H, Delneri D, de Wergifosse P, Dujon B, Kleine K, The nucleotide sequence of Saccharomyces cerevisiae chromosome VII, Nature 1997 May;387(6632 Suppl):81-4.

Dujon B, Albermann K, Aldea M, Alexandraki D, Ansorge W, Arino J, Benes V, Bohn C, Bolotin-Fukuhara M, Bordonné R, Boyer J, Camasses A, Casamayor A, Casas C, Chéret G, Cziepluch C, Daignan-Fornier B, Dang DV, de Haan M, Delius H, Durand P, Fairhead C, Feldmann H, Gaillon L, Kleine K, The nucleotide sequence of Saccharomyces cerevisiae chromosome XV, Nature 1997 May;387(6632 Suppl):98-102.

Francesconi S, Grenon M, Bouvier D, Baldacci G, p56(chk1) protein kinase is required for the DNA replication checkpoint at 37 degrees C in fission yeast, EMBO J. 1997 Mar;16(6):1332-41.

Montagutelli X, Guénet JL, , [Animal models of hereditary diseases]., Rev Prat 1997 Jan; 47(2): 162-8.

Autiero M, Bouchier C, Basmaciogullari S, Zaborski P, el Marhomy S, Martin M, Guardiola J, Piatier-Tonneau D, Isolation from a human seminal vesicle library of the cDNA for gp17, a CD4 binding factor, Immunogenetics 1997;46(4):345-8.

Bouvet A, Grimont F, Collins MD, Benaoudia F, Devine C, Regnault B, Grimont PA, Streptococcus infantarius sp. nov. related to Streptococcus bovis and Streptococcus equinus, Adv. Exp. Med. Biol. 1997;418:393-5.

Lalouette A, Lablack A, Guenet JL, Montagutelli X, Segretain D, , Male sterility caused by sperm cell-specific structural abnormalities in ebouriffé, a new mutation of the house mouse., Biol. Reprod. 1996 Aug; 55(2): 355-63.

Montagutelli X, Turner R, Nadeau JH, , Epistatic control of non-Mendelian inheritance in mouse interspecific crosses., Genetics 1996 Aug; 143(4): 1739-52.

Montagutelli X, Hogan ME, Aubin G, Lalouette A, Guénet JL, King LE, Sundberg JP, , Lanceolate hair (lah): a recessive mouse mutation with alopecia and abnormal hair., J. Invest. Dermatol. 1996 Jul; 107(1): 20-5.

Gangloff S, Zou H, Rothstein R, Gene conversion plays the major role in controlling the stability of large tandem repeats in yeast, EMBO J. 1996 Apr;15(7):1715-25.

Choumet V, Bouchier C, Délot E, Faure G, Saliou B, Bon C, Structure and function relationship of crotoxin, a heterodimeric neurotoxic phospholipase A2 from the venom of a South-American rattlesnake, Adv. Exp. Med. Biol. 1996;391:197-202.

Rothstein R, Gangloff S, Hyper-recombination and Bloom’s syndrome: microbes again provide clues about cancer, Genome Res. 1995 Dec;5(5):421-6.

Sundberg JP, Boggess D, Montagutelli X, Hogan ME, King LE, , C3H/HeJ mouse model for alopecia areata., J. Invest. Dermatol. 1995 May; 104(5 Suppl): 16S-17S.

Deltour L, Montagutelli X, Guenet JL, Jami J, Páldi A, , Tissue- and developmental stage-specific imprinting of the mouse proinsulin gene, Ins2., Dev. Biol. 1995 Apr; 168(2): 686-8.

Francesconi S, De Recondo AM, Baldacci G, DNA polymerase delta is required for the replication feedback control of cell cycle progression in Schizosaccharomyces pombe, Mol. Gen. Genet. 1995 Mar;246(5):561-9.

Auffray C, Behar G, Bois F, Bouchier C, Da Silva C, Devignes MD, Duprat S, Houlgatte R, Jumeau MN, Lamy B, [IMAGE: molecular integration of the analysis of the human genome and its expression], C. R. Acad. Sci. III, Sci. Vie 1995 Feb;318(2):263-72.

Thierry A, Gaillon L, Galibert F, Dujon B, Construction of a complete genomic library of Saccharomyces cerevisiae and physical mapping of chromosome XI at 3.7 kb resolution, Yeast 1995 Feb;11(2):121-35.

Gangloff S, McDonald JP, Bendixen C, Arthur L, Rothstein R, The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase, Mol. Cell. Biol. 1994 Dec;14(12):8391-8.

Beckers MC, Bar I, Huynh-Thu T, Dernoncourt C, Brunialti AL, Montagutelli X, Guénet JL, Goffinet AM, , A high-resolution genetic map of mouse chromosome 5 encompassing the reeler (rl) locus., Genomics 1994 Oct; 23(3): 685-90.

Faure G, Choumet V, Bouchier C, Camoin L, Guillaume JL, Monegier B, Vuilhorgne M, Bon C, The origin of the diversity of crotoxin isoforms in the venom of Crotalus durissus terrificus, Eur. J. Biochem. 1994 Jul;223(1):161-4.

Robert B, Montagutelli X, Houzelstein D, Ferland L, Cohen A, Buckingham M, Guénet JL, Msx1 is close but not allelic to either Hm or Hx on mouse chromosome 5., Mamm Genome 1994 Jul; 5(7): 446-9.

Dujon B, Alexandraki D, André B, Ansorge W, Baladron V, Ballesta JP, Banrevi A, Bolle PA, Bolotin-Fukuhara M, Bossier P, Bou G, Boyer J, Bultrago MJ, Cheret G, Colleaux L, Dalgnan-Fornler B, del Rey F, Dlon C, Domdey H, Düsterhoft A, Düsterhus S, Entlan KD, Erfle H, Esteban PF, Feldmann H, Fernandes L, Robo GM, Fritz C, Fukuhara H, Gabel C, Gaillon L, Carcia-Cantalejo JM, Garcia-Ramirez JJ, Gent NE, Ghazvini M, Goffeau A, Gonzaléz A, Grothues D, Guerreiro P, Hegemann J, Hewitt N, Hilger F, Hollenberg CP, Horaitis O, Indge KJ, Jacquier A, James CM, Jauniaux C, Jimenez A, Keuchel H, Kirchrath L, Kleine K, Kötter P, Legrain P, Liebl S, Louis EJ, Maia e Silva A, Marck C, Monnier AL, Möstl D, Müller S, Obermaier B, Oliver SG, Pallier C, Pascolo S, Pfeiffer F, Philippsen P, Planta RJ, Pohl FM, Pohl TM, Pöhlmann R, Portetelle D, Purnelle B, Puzos V, Ramezani Rad M, Rasmussen SW, Remacha M, Revuelta JL, Richard GF, Rieger M, Rodrigues-Pousada C, Rose M, Rupp T, Santos MA, Schwager C, Sensen C, Skala J, Soares H, Sor F, Stegemann J, Tettelin H, Thierry A, Tzermia M, Urrestarazu LA, van Dyck L, Van Vliet-Reedijk JC, Valens M, Vandenbo M, Vilela C, Vissers S, von Wettstein D, Voss H, Wiemann S, Xu G, Zimmermann J, Haasemann M, Becker I, Mewes HW, Complete DNA sequence of yeast chromosome XI, Nature 1994 Jun;369(6479):371-8.

Davies PO, Poirier C, Deltour L, Montagutelli X, , Genetic reassignment of the insulin-1 (Ins1) gene to distal mouse chromosome 19., Genomics 1994 Jun; 21(3): 665-7.

Bendixen C, Gangloff S, Rothstein R, A yeast mating-selection scheme for detection of protein-protein interactions, Nucleic Acids Res. 1994 May;22(9):1778-9.

Gangloff S, Lieber MR, Rothstein R, Transcription, topoisomerases and recombination, Experientia 1994 Mar;50(3):261-9.

Huang ME, Chuat JC, Thierry A, Dujon B, Galibert F, Construction of a cosmid contig and of an EcoRI restriction map of yeast chromosome X, DNA Seq. 1994;4(5):293-300.

Montagutelli X, Lalouette A, Coudé M, Kamoun P, Forest M, Guénet JL, , aku, a mutation of the mouse homologous to human alkaptonuria, maps to chromosome 16., Genomics 1994 Jan; 19(1): 9-11.

Coudé M, Montagutelli X, Guenet JL, Kamoun P, , Homogentisic acid oxidase activity in homozygous and heterozygous alkaptonuric mice., Ann. Biol. Clin. (Paris) 1994 ; 52(7-8): 569-70.

Janocha S, Wolz W, Srsen S, Srsnova K, Montagutelli X, Guénet JL, Grimm T, Kress W, Müller CR, , The human gene for alkaptonuria (AKU) maps to chromosome 3q., Genomics 1994 Jan; 19(1): 5-8.

Francesconi S, Copeland WC, Wang TS, In vivo species specificity of DNA polymerase alpha, Mol. Gen. Genet. 1993 Nov;241(3-4):457-66.

Bureau JF, Montagutelli X, Bihl F, Lefebvre S, Guénet JL, Brahic M, , Mapping loci influencing the persistence of Theiler’s virus in the murine central nervous system., Nat. Genet. 1993 Sep; 5(1): 87-91.

Francesconi S, Park H, Wang TS, Fission yeast with DNA polymerase delta temperature-sensitive alleles exhibits cell division cycle phenotype, Nucleic Acids Res. 1993 Aug;21(16):3821-8.

Scieux C, Grimont F, Regnault B, Bianchi A, Kowalski S, Grimont PA, Molecular typing of Chlamydia trachomatis by random amplification of polymorphic DNA, Res. Microbiol. 1993 Jun;144(5):395-404.

Boulechfar S, Lamoril J, Montagutelli X, Guenet JL, Deybach JC, Nordmann Y, Dailey H, Grandchamp B, de Verneuil H, , Ferrochelatase structural mutant (Fechm1Pas) in the house mouse., Genomics 1993 Jun; 16(3): 645-8.

Park H, Francesconi S, Wang TS, Cell cycle expression of two replicative DNA polymerases alpha and delta from Schizosaccharomyces pombe, Mol. Biol. Cell 1993 Feb;4(2):145-57.

Alonso S, Montagutelli X, Simon-Chazottes D, Guénet JL, Buckingham M, Re-localization of Actsk-1 to mouse chromosome 8, a new region of homology with human chromosome 1., Mamm Genome 1993 ; 4(1): 15-20.

Kondo Y, Mori M, Kuramoto T, Yamada J, Beckmann JS, Simon-Chazottes D, Montagutelli X, Guénet JL, Serikawa T, , DNA segments mapped by reciprocal use of microsatellite primers between mouse and rat., Mamm. Genome 1993 ; 4(10): 571-6.

Pascolo S, Ghazvini M, Boyer J, Colleaux L, Thierry A, Dujon B, The sequence of a 9.3 kb segment located on the left arm of the yeast chromosome XI reveals five open reading frames including the CCE1 gene and putative products related to MYO2 and to the ribosomal protein L10, Yeast 1992 Nov;8(11):987-95.

Scieux C, Grimont F, Regnault B, Grimont PA, DNA fingerprinting of Chlamydia trachomatis by use of ribosomal RNA, oligonucleotide and randomly cloned DNA probes, Res. Microbiol. 1992 Oct;143(8):755-65.

Bureau JF, Montagutelli X, Lefebvre S, Guénet JL, Pla M, Brahic M, , The interaction of two groups of murine genes determines the persistence of Theiler’s virus in the central nervous system., J. Virol. 1992 Aug; 66(8): 4698-704.

Oliver SG, van der Aart QJ, Agostoni-Carbone ML, Aigle M, Alberghina L, Alexandraki D, Antoine G, Anwar R, Ballesta JP, Benit P, The complete DNA sequence of yeast chromosome III, Nature 1992 May;357(6373):38-46.

Kamoun P, Coude M, Forest M, Montagutelli X, Guenet JL, , Ascorbic acid and alkaptonuria., Eur. J. Pediatr. 1992 Feb; 151(2): 149.

Grimont F, Verger JM, Cornelis P, Limet J, Lefèvre M, Grayon M, Régnault B, Van Broeck J, Grimont PA, Molecular typing of Brucella with cloned DNA probes, Res. Microbiol. 1992 Jan;143(1):55-65.

Serikawa T, Montagutelli X, Simon-Chazottes D, Guénet JL, , Polymorphisms revealed by PCR with single, short-sized, arbitrary primers are reliable markers for mouse and rat gene mapping., Mamm. Genome 1992 ; 3(2): 65-72.

Le Roy H, Simon-Chazottes D, Montagutelli X, Guénet JL, , A set of anonymous DNA clones as markers for mouse gene mapping., Mamm. Genome 1992 ; 3(4): 244-6.

Bouchier C, Boyot P, Tesson F, Trémeau O, Bouet F, Hodgson D, Boulain JC, Ménez A, Notechis 11’2, a non-toxic phospholipase A2 from the venom of Notechis scutatus scutatus, Eur. J. Biochem. 1991 Dec;202(2):493-500.

Tutois S, Montagutelli X, Da Silva V, Jouault H, Rouyer-Fessard P, Leroy-Viard K, Guénet JL, Nordmann Y, Beuzard Y, Deybach JC, , Erythropoietic protoporphyria in the house mouse. A recessive inherited ferrochelatase deficiency with anemia, photosensitivity, and liver disease., J. Clin. Invest. 1991 Nov; 88(5): 1730-6.

Francesconi S, Longhese MP, Piseri A, Santocanale C, Lucchini G, Plevani P, Mutations in conserved yeast DNA primase domains impair DNA replication in vivo, Proc. Natl. Acad. Sci. U.S.A. 1991 May;88(9):3877-81.

Boyer S, Montagutelli X, Gomès D, Simon-Chazottes D, Guénet JL, Dupouey P, , Recent evolutionary origin of the expression of the glial fibrillary acidic protein (GFAP) in lens epithelial cells. A molecular and genetic analysis of various mouse species., Brain Res. Mol. Brain Res. 1991 May; 10(2): 159-66.

Bouchier C, Boulain JC, Bon C, Ménez A, Analysis of cDNAs encoding the two subunits of crotoxin, a phospholipase A2 neurotoxin from rattlesnake venom: the acidic non enzymatic subunit derives from a phospholipase A2-like precursor, Biochim. Biophys. Acta 1991 Mar;1088(3):401-8.

Montagutelli X, Serikawa T, Guénet JL, , PCR-analyzed microsatellites: data concerning laboratory and wild-derived mouse inbred strains., Mamm. Genome 1991 ; 1(4): 255-9.

Sheppard RD, Montagutelli X, Jean WC, Tsai JY, Rose A, Guénet JL, Cole MD, Silver LM, , Two-dimensional gel analysis of complex DNA families: methodology and apparatus., Mamm. Genome 1991 ; 1(2): 104-11.

Montagutelli X, , GENE-LINK: a program in PASCAL for backcross genetic analysis., J. Hered. ; 81(6): 490-1.

Gangloff SP, Marguet D, Lauquin GJ, Molecular cloning of the yeast mitochondrial aconitase gene (ACO1) and evidence of a synergistic regulation of expression by glucose plus glutamate, Mol. Cell. Biol. 1990 Jul;10(7):3551-61.

Pérolat P, Grimont F, Regnault B, Grimont PA, Fournié E, Thevenet H, Baranton G, rRNA gene restriction patterns of Leptospira: a molecular typing system, Res. Microbiol. 1990 Feb;141(2):159-71.

Bon C, Bouchier C, Choumet V, Faure G, Jiang MS, Lambezat MP, Radvanyi F, Saliou B, Crotoxin, half-century of investigations on a phospholipase A2 neurotoxin, Acta Physiol Pharmacol Latinoam 1989;39(4):439-48.

Charriere-Bertrand C, Le Prince G, Bouchier C, Fages C, Tardy M, Nunez J, Expression of tubulin, GFAP and of their encoding mRNAs during the proliferation and differentiation of cultured astrocytes, Neurochem. Int. 1989;15(2):215-22.

Plevani P, Foiani M, Muzi Falconi M, Pizzagalli A, Santocanale C, Francesconi S, Valsasnini P, Comedini A, Piatti S, Lucchini G, The yeast DNA polymerase-primase complex: genes and proteins, Biochim. Biophys. Acta 1988 Dec;951(2-3):268-73.

Ducancel F, Guignery-Frelat G, Bouchier C, Ménez A, Boulain JC, Sequence analysis of a cDNA encoding a PLA2 from the sea-snake Aipysurus laevis, Nucleic Acids Res. 1988 Sep;16(18):9048.

Bouchier C, Ducancel F, Guignery-Frelat G, Bon C, Boulain JC, Ménez A, Cloning and sequencing of cDNAs encoding the two subunits of Crotoxin, Nucleic Acids Res. 1988 Sep;16(18):9050.

Ducancel F, Guignery-Frelat G, Bouchier C, Ménez A, Boulain JC, Complete amino acid sequence of a PLA2 from the tiger snake Notechis scutatus scutatus as deduced from a complementary DNA, Nucleic Acids Res. 1988 Sep;16(18):9049.

Plevani P, Francesconi S, Lucchini G, The nucleotide sequence of the PRI1 gene related to DNA primase in Saccharomyces cerevisiae, Nucleic Acids Res. 1987 Oct;15(19):7975-89.

Lucchini G, Francesconi S, Foiani M, Badaracco G, Plevani P, Yeast DNA polymerase–DNA primase complex; cloning of PRI 1, a single essential gene related to DNA primase activity, EMBO J. 1987 Mar;6(3):737-42.

Turut P, Pfaelzer I, Regnault B, [Idiopathic massive preretinal hemorrhage. Etiopathogenic hypothesis. Prognosis], Bull Soc Ophtalmol Fr 1985 Feb;85(2):229-32, 235.

Harris WS, Marai L, Myher JJ, Subbiah MT, Bile acid ethyl esters. Their infrequent formation during routine bile acid analysis and identification by gas chromatography and mass spectrometry, J. Chromatogr. 1977 Jan;131:437-41.

Nagradova NK, Asriiants RA, Ivanov MV, [Binding of 1-anilino-8-naphthalene sulfonate by glyceraldehyde-3-phosphate dehydrogenase], Biokhimiia 1972 Mar-Apr;37(2):299-304.

Deutsch V, Frankl O, Drory Y, Eliahou H, Braf ZF, Bilateral renal cortical necrosis with survival through the acute phase with a note on the value of selective nephroangiography, Am. J. Med. 1971 Jun;50(6):828-34.

, [Introduction of medical records. 3. Record of cardiology], Lyon Med 1971 Feb;225(4):325-8.