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Department: Genomes and Genetics

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Duitama González C, Vicedomini R, Lemane T, Rascovan N, Richard H, Chikhi R, decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods., Microbiome 2023 Nov; 11(1): 243.

Ségolène Gracias, Maxime Chazal, Alice Decombe, Yves Unterfinger, Adrià Sogues, Lauryne Pruvost, Valentine Robert, Sandrine Lacour, Manon Lemasson, Marion Sourisseau, Zhi Li, Jennifer Richardson, Sandra Pellegrini, Etienne Decroly, Vincent Caval, Nolwenn Jouvenet, Tick-borne flavivirus NS5 antagonizes interferon signaling by inhibiting the catalytic activity of TYK2., EMBO Reports, In press, pp.e57424. ⟨10.15252/embr.202357424⟩.

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 Oct; (): .

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.

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⟩.

Tom Dott, Slobodan Culina, Rene Chemali, Cedric Ait Mansour, Florian Dubois, Bernd Jagla, Jean Marc Doisne, Lars Rogge, François Huetz, Friederike Jönsson, Pierre-Henri Commere, James Di Santo, Benjamin Terrier, Lluis Quintana-Murci, Darragh Duffy, Milena Hasan, Milieu Intérieur Consortium, Standardized high-dimensional spectral cytometry protocol and panels for whole blood immune phenotyping in clinical and translational studies., Cytometry Part A, In press, ⟨10.1002/cyto.a.24801⟩.

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, Smith ESJ, Berthelot C, Villar D, Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits., Genome Res 2023 Aug; (): .

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⟩.

Etienne Villain, Aurélie Chanson, Malwina Mainka, Nadja Kampschulte, Pauline Le Faouder, Justine Bertrand-Michel, Marion Brandolini-Bunlon, Bruno Charbit, Munyaradzi Musvosvi, Nicole Bilek, Thomas Scriba, Lluis Quintana-Murci, Nils Helge Schebb, Darragh Duffy, Cécile Gladine, Laurent Abel, Andrés Alcover, Hugues Aschard, Philippe Bousso, Nollaig Bourke, Petter Brodin, Pierre Bruhns, Nadine Cerf-Bensussan, Ana Cumano, Christophe D’enfert, Ludovic Deriano, Marie-Agnès Dillies, James Di Santo, Gérard Eberl, Jost Enninga, Jacques Fellay, Ivo Gomperts-Boneca, Milena Hasan, Gunilla Karlsson Hedestam, Serge Hercberg, Molly Ingersoll, Olivier Lantz, Rose Anne Kenny, Mickaël Ménager, Hugo Mouquet, Cliona O'Farrelly, Etienne Patin, Sandra Pellegrini, Antonio Rausell, Frédéric Rieux-Laucat, Lars Rogge, Magnus Fontes, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Frédéric Tangy, Antoine Toubert, Mathilde Touvier, Marie-Noëlle Ungeheuer, Christophe Zimmer, Matthew Albert, Integrated analysis of whole blood oxylipin and cytokine responses after bacterial, viral, and T cell stimulation reveals new immune networks, iScience, 2023, 26 (8), pp.107422. ⟨10.1016/j.isci.2023.107422⟩.

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.

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.

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): .

Jack-Christophe Cossec 1 , Tatiana Traboulsi 2 , Sébastien Sart 3 , Yann Loe-Mie 4 , Manuel Guthmann 5 , Ivo A Hendriks 6 , Ilan Theurillat 7 , Michael L Nielsen 6 , Maria-Elena Torres-Padilla 8 , Charles N Baroud 3 , Anne Dejean 9, 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; (): .

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 Mar; (): e0343222.

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; (): .

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 Jan; (): .

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.

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.

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.

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): .

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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.

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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.

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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.

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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.

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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): .

Blanchet C, Jaubert J, Carniel E, Fayolle C, Milon G, Szatanik M, Panthier JJ, Montagutelli X, Mus spretus SEG/Pas mice resist virulent Yersinia pestis, under multigenic control, Genes Immun. 2011 Jan;12(1):23-30.

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.

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.

Loot C, Bikard D, Rachlin A, Mazel D, Cellular pathways controlling integron cassette site folding, EMBO J. 2010 Aug;29(15):2623-34.

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.

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.

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.

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.

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.

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.

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.

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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.

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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.

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