• 2022
  Mateo M, Hortion J, Perthame E, Picard C, Reynard S, Journeaux A, Germain C, Carnec X, Baillet N, Borges-Cardoso V, Pietrosemoli N, Vallve A, Barron S, Jourjon O, Lacroix O, Duthey A, Dirheimer M, Daniau M, Legras-Lachuer C, Jouvion G, Carbonnelle C, Raoul H, Baize S, , Pathogenesis of recent Lassa virus isolates from lineages II and VII in cynomolgus monkeys., Virulence 2022 Dec; 13(1): 654-669.
• 2022
  Griego A, Douché T, Gianetto QG, Matondo M, Manina G, , RNase E and HupB dynamics foster mycobacterial cell homeostasis and fitness., iScience 2022 May; 25(5): 104233.
• 2022
  Legrand V, Kergrohen T, Joly N, Criscuolo A, ROCK: digital normalization of whole genome sequencing data, JOSS 2022 May;7(73):3790.
• 2022
  Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR, , BioSimulators: a central registry of simulation engines and services for recommending specific tools., Nucleic Acids Res 2022 May; (): .
• 2022
  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.
• 2022
  Canales-Herrerias P, Crickx E, Broketa M, Sokal A, Chenon G, Azzaoui I, Vandenberghe A, Perima A, Iannascoli B, Richard-Le Goff O, Castrillon C, Mottet G, Sterlin D, Robbins A, Michel M, England P, Millot GA, Eyer K, Baudry J, Mahevas M, Bruhns P, , High-affinity autoreactive plasma cells disseminate through multiple organs in patients with immune thrombocytopenic purpura., J Clin Invest 2022 May; (): .
• 2022
  Kämpfer P, Glaeser SP, Busse HJ, McInroy JA, Clermont D, Criscuolo A, Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., isolated from maize root rhizosphere., Int J Syst Evol Microbiol 2022 May; 72(5): .
• 2022
  Laurent F, Verdier H, Duval M, Serov A, Vestergaard CL, Masson JB, , TRamWAy: Mapping physical properties of individual biomolecule random motion in large scale single-particle tracking experiments., Bioinformatics 2022 Apr; (): .
• 2022
  Mercier A, Obadia T, Carraretto D, Velo E, Gabiane G, Bino S, Vazeille M, Gasperi G, Dauga C, Malacrida AR, Reiter P, Failloux AB, , Impact of temperature on dengue and chikungunya transmission by the mosquito Aedes albopictus., Sci Rep 2022 Apr; 12(1): 6973.
• 2022
  Freyer L, Lallemand Y, Dardenne P, Sommer A, Biton A, Gomez Perdiguero E, , Erythro-myeloid progenitor origin of Hofbauer cells in the early mouse placenta., Development 2022 Apr; 149(8): .
• 2022
  Lourenço M, Chaffringeon L, Lamy-Besnier Q, Titécat M, Pédron T, Sismeiro O, Legendre R, Varet H, Coppée JY, Bérard M, De Sordi L, Debarbieux L, , The gut environment regulates bacterial gene expression which modulates susceptibility to bacteriophage infection., Cell Host Microbe 2022 Apr; 30(4): 556-569.e5.
• 2022
  Traut N, Heuer K, Lemaître G, Beggiato A, Germanaud D, Elmaleh M, Bethegnies A, Bonnasse-Gahot L, Cai W, Chambon S, Cliquet F, Ghriss A, Guigui N, de Pierrefeu A, Wang M, Zantedeschi V, Boucaud A, van den Bossche J, Kegl B, Delorme R, Bourgeron T, Toro R, Varoquaux G, , Insights from an autism imaging biomarker challenge: Promises and threats to biomarker discovery., Neuroimage 2022 Apr; 255(): 119171.
• 2022
  Palma F, Mangone I, Janowicz A, Moura A, Chiaverini A, Torresi M, Garofolo G, Criscuolo A, Brisse S, Di Pasquale A, Cammà C, Radomski N, , In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes., BMC Genomics 2022 Mar; 23(1): 235.
• 2022
  Cantoni D, Osborne A, Taib N, Thompson G, Martín-Escolano R, Kazana E, Edrich E, Brown IR, Gribaldo S, Gourlay CW, Tsaousis AD, , Localization and Functional Characterization of the Alternative Oxidase in Naegleria., J Eukaryot Microbiol 2022 Mar; (): e12908.
• 2022
  Merabet O, Pietrosemoli N, Perthame E, Armengaud J, Gaillard JC, Borges-Cardoso V, Daniau M, Legras-Lachuer C, Carnec X, Baize S, , Infection of Human Endothelial Cells with Lassa Virus Induces Early but Transient Activation and Low Type I IFN Response Compared to the Closely-Related Nonpathogenic Mopeia Virus., Viruses 2022 Mar; 14(3): .
• 2022
  Obadia T, Nekkab N, Robinson LJ, Drakeley C, Mueller I, White MT, , Developing sero-diagnostic tests to facilitate Plasmodium vivax Serological Test-and-Treat approaches: modeling the balance between public health impact and overtreatment., BMC Med 2022 03; 20(1): 98.
• 2022
  Davidović A, Chait R, Batt G, Ruess J, Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level, PLoS Comput Biol 2022 Mar; 18(3): e1009950.
• 2022
  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.
• 2022
  Witwinowski J, Sartori-Rupp A, Taib N, Pende N, Tham TN, Poppleton D, Ghigo JM, Beloin C, Gribaldo S, , An ancient divide in outer membrane tethering systems in bacteria suggests a mechanism for the diderm-to-monoderm transition., Nat Microbiol 2022 Mar; 7(3): 411-422.
• 2022
  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.
• 2022
  Temmam S, Vongphayloth K, Salazar EB, Munier S, Bonomi M, Regnault B, Douangboubpha B, Karami Y, Chrétien D, Sanamxay D, Xayaphet V, Paphaphanh P, Lacoste V, Somlor S, Lakeomany K, Phommavanh N, Pérot P, Dehan O, Amara F, Donati F, Bigot T, Nilges M, Rey FA, van der Werf S, Brey PT, Eloit M, , Bat coronaviruses related to SARS-CoV-2 and infectious for human cells., Nature 2022 604, 330–336.
• 2022
  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 02; 602(7898): 671-675.
• 2022
  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.
• 2022
  Domenger A, Choisy C, Baron L, Mayau V, Perthame E, Deriano L, Arnulf B, Bories JC, Dadaglio G, Demangel C, , The Sec61 translocon is a therapeutic vulnerability in multiple myeloma., EMBO Mol Med 2022 Jan; (): e14740.
• 2022
  Seabra SG, Libin PJK, Theys K, Zhukova A, Potter BI, Nebenzahl-Guimaraes H, Gorbalenya AE, Sidorov IA, Pimentel V, Pingarilho M, de Vasconcelos ATR, Dellicour S, Khouri R, Gascuel O, Vandamme AM, Baele G, Cuypers L, Abecasis AB, , Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal., Virus Evol 2022 ; 8(1): veac029.
• 2022
  Pepey A, Obadia T, Kim S, Sovannaroth S, Mueller I, Witkowski B, Vantaux A, Souris M, , Mobility evaluation by GPS tracking in a rural, low-income population in Cambodia., PLoS One 2022 ; 17(5): e0266460.
• 2021
  Di Gioacchino A, Legendre R, Rahou Y, Najburg V, Charneau P, Greenbaum BD, Tangy F, van der Werf S, Cocco S, Komarova AV, , sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs., RNA 2021 Dec; (): .
• 2021
  Bussotti G, Piel L, Pescher P, Domagalska MA, Rajan KS, Cohen-Chalamish S, Doniger T, Hiregange DG, Myler PJ, Unger R, Michaeli S, Späth GF, , Genome instability drives epistatic adaptation in the human pathogen Leishmania., Proc Natl Acad Sci U S A 2021 12; 118(51): .
• 2021
  Späth GF, Bussotti G, , GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells., Nucleic Acids Res 2021 Dec; (): .
• 2021
  Singh M, Chazal M, Quarato P, Bourdon L, Malabat C, Vallet T, Vignuzzi M, van der Werf S, Behillil S, Donati F, Sauvonnet N, Nigro G, Bourgine M, Jouvenet N, Cecere G, , A virus-derived microRNA targets immune response genes during SARS-CoV-2 infection., EMBO Rep 2021 Dec; (): e54341.
• 2021
  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 2021 Dec; (): .
• 2021
  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.
• 2021
  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.
• 2021
  Jagla B, Libri V, Chica C, Rouilly V, Mella S, Puceat M, Hasan M, , SCHNAPPs – Single Cell sHiNy APPlication(s)., J Immunol Methods 2021 12; 499(): 113176.
• 2021
  Kämpfer P, McInroy JA, Clermont D, Neumann-Schaal M, Criscuolo A, Busse HJ, Glaeser SP, , Leucobacter soli sp. nov., from soil amended with humic acid., Int J Syst Evol Microbiol 2021 Dec; 71(12): .
• 2021
  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 11; 224(9): 1489-1499.
• 2021
  Monel B, Planas D, Grzelak L, Smith N, Robillard N, Staropoli I, Goncalves P, Porrot F, Guivel-Benhassine F, Guinet ND, Rodary J, Puech J, Euzen V, Bélec L, Orvoen G, Nunes L, Moulin V, Fourgeaud J, Wack M, Imbeaud S, Campagne P, Duffy D, Santo JPD, Bruel T, Péré H, Veyer D, Schwartz O, , Release of infectious virus and cytokines in nasopharyngeal swabs from individuals infected with non-alpha or alpha SARS-CoV-2 variants: an observational retrospective study., EBioMedicine 2021 Nov; 73(): 103637.
• 2021
  Kämpfer P, Busse HJ, Clermont D, Criscuolo A, Glaeser SP, , Devosia equisanguinis sp. nov., isolated from horse blood., Int J Syst Evol Microbiol 2021 Nov; 71(11): .
• 2021
  Tekpinar M, Neron B, Delarue M, , Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus., J Chem Inf Model 2021 Oct; 61(10): 4832-4838.
• 2021
  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.
• 2021
  Surace L, Doisne JM, Croft CA, Thaller A, Escoll P, Marie S, Petrosemoli N, Guillemot V, Dardalhon V, Topazio D, Cama A, Buchrieser C, Taylor N, Amit I, Musumeci O, Di Santo JP, , Dichotomous metabolic networks govern human ILC2 proliferation and function., Nat Immunol 2021 Oct; 22(11):1367-1374.
• 2021
  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; (): .
• 2021
  Fillâtre P, Dufour MJ, Behillil S, Vatan R, Reusse P, Gabellec A, Velmans N, Montagne C, Du Coudret SG, Droumaguet E, Merour V, Enouf V, Buzele R, Valence M, Guillotel E, Gagniere B, Baidaliuk A, Zhukova A, Tourdjman M, Thibault V, Grolhier C, Pronier C, Lescure FX, Simon-Loriere E, Costagliola D, Van Der Werf S, Tattevin P, Massart N, , A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality: an observational study., Clin Microbiol Infect 2021 Oct; (): .
• 2021
  Guignon V, Breton C, Mariette J, Sabot F, Fumey J, Lefort V, Fiston-Lavier AS, , Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions., PLoS Comput Biol 2021 Oct; 17(10): e1009321.
• 2021
  Kämpfer P, Busse HJ, McInroy JA, Clermont D, Criscuolo A, Glaeser SP, , Paenibacillus allorhizosphaerae sp. nov., from soil of the rhizosphere of Zea mays., Int J Syst Evol Microbiol 2021 Oct; 71(10): .
• 2021
  Guglielmini J, Hennart M, Badell E, Toubiana J, Criscuolo A, Brisse S, , Genomic epidemiology and strain taxonomy of Corynebacterium diphtheriae., J Clin Microbiol 2021 Sep; (): JCM0158121.
• 2021
  Decourty L, Malabat C, Frachon E, Jacquier A, Saveanu C., Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast., Nucleic Acids Res 2021 09; 49(15): 8535-8555.
• 2021
  Lemoine F, Gascuel O, , Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows., NAR Genom Bioinform 2021 Sep; 3(3): lqab075.
• 2021
  Smith N, Goncalves P, Charbit B, Grzelak L, Beretta M, Planchais C, Bruel T, Rouilly V, Bondet V, Hadjadj J, Yatim N, Pere H, Merkling SH, Ghozlane A, Kernéis S, Rieux-Laucat F, Terrier B, Schwartz O, Mouquet H, Duffy D, Di Santo JP, , Distinct systemic and mucosal immune responses during acute SARS-CoV-2 infection., Nat Immunol 2021 Sep; 22(11):1428-1439.
• 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.
• 2021
  Tenenhaus A, Guillemot V, Gidrol X, Frouin V, , Gene association networks from microarray data using a regularized estimation of partial correlation based on PLS regression., IEEE/ACM Trans Comput Biol Bioinform ; 7(2): 251-62.
• 2021
  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 08; 13(8): e14122.
• 2021
  Julienne H, Laville V, McCaw ZR, He Z, Guillemot V, Lasry C, Ziyatdinov A, Nerin C, Vaysse A, Lechat P, Ménager H, Le Goff W, Dube MP, Kraft P, Ionita-Laza I, Vilhjálmsson BJ, Aschard H, , Multitrait GWAS to connect disease variants and biological mechanisms., PLoS Genet 2021 08; 17(8): e1009713.
• 2021
  Koepfli C, Nguitragool W, de Almeida ACG, Kuehn A, Waltmann A, Kattenberg E, Ome-Kaius M, Rarau P, Obadia T, Kazura J, Monteiro W, Darcy AW, Wini L, Bassat Q, Felger I, Sattabongkot J, Robinson LJ, Lacerda M, Mueller I, , Identification of the asymptomatic Plasmodium falciparum and Plasmodium vivax gametocyte reservoir under different transmission intensities., PLoS Negl Trop Dis 2021 08; 15(8): e0009672.
• 2021
  Badell E, Alharazi A, Criscuolo A, Almoayed KAA, Lefrancq N, Bouchez V, Guglielmini J, Hennart M, Carmi-Leroy A, Zidane N, Pascal-Perrigault M, Lebreton M, Martini H, Salje H, Toubiana J, Dureab F, Dhabaan G, Brisse S, , , Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study., Lancet Microbe 2021 Aug; 2(8): e386-e396.
• 2021
  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.
• 2021
  Aujoulat F, Mazuet C, Criscuolo A, Popoff MR, Enault C, Diancourt L, Jumas-Bilak E, Lavigne JP, Marchandin H, Peptoniphilus nemausensis sp. nov. A new Gram-positive anaerobic coccus isolated from human clinical samples, an emendated description of the genus Peptoniphilus and an evaluation of the taxonomic status of Peptoniphilus species with not validly published names., Syst Appl Microbiol 2021 Jul; 44(5): 126235.
• 2021
  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): .
• 2021
  Tatfi M, Perthame E, Hillion KH, Dillies MA, Menager H, Hermine O, Suarez F, , Gene expression analysis in EBV-infected ataxia-telangiectasia cell lines by RNA-sequencing reveals protein synthesis defect and immune abnormalities., Orphanet J Rare Dis 2021 06; 16(1): 288.
• 2021
  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.
• 2021
  Singh M, Cornes E, Li B, Quarato P, Bourdon L, Dingli F, Loew D, Proccacia S, Cecere G, , Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis., Nat Commun 2021 06; 12(1): 3492.
• 2021
  Bennedbæk M, Zhukova A, Tang M-HE, Bennet J, Munderi P, Ruxrungtham K, Gisslen M, Worobey M, Lundgren JD, Marvig RL, for the INSIGHT START study group, Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions, Virus Evolution, 2021, veab055.
• 2021
  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 06; 13(596): .
• 2021
  Uwimana A, Legrand E, Stokes BH, Ndikumana JM, Warsame M, Umulisa N, Ngamije D, Munyaneza T, Mazarati JB, Munguti K, Campagne P, Criscuolo A, Ariey F, Murindahabi M, Ringwald P, Fidock DA, Mbituyumuremyi A, Menard D, , Author Correction: Emergence and clonal expansion of in vitro artemisinin-resistant Plasmodium falciparum kelch13 R561H mutant parasites in Rwanda., Nat Med 2021 Jun; 27(6): 1113-1115.
• 2021
  Valon L, Davidović A, Levillayer F, Villars A, Chouly M, Cerqueira-Campos F, Levayer R, , Robustness of epithelial sealing is an emerging property of local ERK feedback driven by cell elimination., Dev Cell 2021 06; 56(12): 1700-1711.e8.
• 2021
  Iturri L, Freyer L, Biton A, Dardenne P, Lallemand Y, Gomez Perdiguero E, , Megakaryocyte production is sustained by direct differentiation from erythromyeloid progenitors in the yolk sac until midgestation., Immunity 2021 May; (): .
• 2021
  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): .
• 2021
  Garcia-Garcia T, Poncet S, Cuenot E, Douché T, Giai Gianetto Q, Peltier J, Courtin P, Chapot-Chartier MP, Matondo M, Dupuy B, Candela T, Martin-Verstraete I, , Ser/Thr Kinase-Dependent Phosphorylation of the Peptidoglycan Hydrolase CwlA Controls Its Export and Modulates Cell Division in Clostridioides difficile., mBio 2021 May; 12(3): .
• 2021
  Sleiman D, Garcia PS, Lagune M, Loc'h J, Haouz A, Taib N, Röthlisberger P, Gribaldo S, Marlière P, Kaminski PA, A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes., Science 2021 04; 372(6541): 516-520.
• 2021
  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.
• 2021
  Bratuleanu BE, Temmam S, Chrétien D, Regnault B, Pérot P, Bouchier C, Bigot T, Savuța G, Eloit M, , The virome of Rhipicephalus, Dermacentor and Haemaphysalis ticks from Eastern Romania includes novel viruses with potential relevance for public health., Transbound Emerg Dis 2021 Apr; (): .
• 2021
  Injarabian L, Skerniskyte J, Giai Gianetto Q, Witko-Sarsat V, Marteyn BS, Reducing neutrophil exposure to oxygen allows their basal state maintenance, Immunol Cell Biol. 2021 Apr 3. .
• 2021
  Sermet-Gaudelus I, Temmam S, Huon C, Behillil S, Gajdos V, Bigot T, Lurier T, Chrétien D, Backovic M, Delaunay-Moisan A, Donati F, Albert M, Foucaud E, Mesplées B, Benoist G, Faye A, Duval-Arnould M, Cretolle C, Charbit M, Aubart M, Auriau J, Lorrot M, Kariyawasam D, Fertitta L, Orliaguet G, Pigneur B, Bader-Meunier B, Briand C, Enouf V, Toubiana J, Guilleminot T, van der Werf S, Leruez-Ville M, Eloit M, , Prior infection by seasonal coronaviruses, as assessed by serology, does not prevent SARS-CoV-2 infection and disease in children, France, April to June 2020., Euro Surveill 2021 04; 26(13): .
• 2021
  Kämpfer P, Glaeser SP, McInroy JA, Clermont D, Criscuolo A, Busse HJ, , Pseudomonas carbonaria sp. nov., isolated from charcoal., Int J Syst Evol Microbiol 2021 Apr; 71(4): .
• 2021
  Schumann P, Kalensee F, Cao J, Criscuolo A, Clermont D, Köhler JM, Meier-Kolthoff JP, Neumann-Schaal M, Tindall BJ, Pukall R, , Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., of Haloactinobacterium album as Ruania alba comb. nov, with an emended description of the genus Ruania, recognition that the genus names Haloactinobacterium and Ruania are heterotypic synonyms and description of Occultella aeris sp. nov., a halotolerant isolate from surface soil sampled at an ancient copper smelter., Int J Syst Evol Microbiol 2021 Apr; 71(4): .
• 2021
  Fontanet A, Tondeur L, Grant R, Temmam S, Madec Y, Bigot T, Grzelak L, Cailleau I, Besombes C, Ungeheuer MN, Renaudat C, Perlaza BL, Arowas L, Jolly N, Pellerin SF, Kuhmel L, Staropoli I, Huon C, Chen KY, Crescenzo-Chaigne B, Munier S, Charneau P, Demeret C, Bruel T, Eloit M, Schwartz O, Hoen B, , SARS-CoV-2 infection in schools in a northern French city: a retrospective serological cohort study in an area of high transmission, France, January to April 2020., Euro Surveill 2021 04; 26(15): .
• 2021
  Nekkab N, Lana R, Lacerda M, Obadia T, Siqueira A, Monteiro W, Villela D, Mueller I, White M, , Estimated impact of tafenoquine for Plasmodium vivax control and elimination in Brazil: A modelling study., PLoS Med 2021 04; 18(4): e1003535.
• 2021
  Boulch M, Cazaux M, Loe-Mie Y, Thibaut R, Corre B, Lemaître F, Grandjean CL, Garcia Z, Bousso P, , A cross-talk between CAR T cell subsets and the tumor microenvironment is essential for sustained cytotoxic activity., Sci Immunol 2021 Mar; 6(57): .
• 2021
  Kämpfer P, Busse HJ, Glaeser SP, Clermont D, Criscuolo A, Mietke H, , Jeotgalicoccus meleagridis sp. nov. isolated from bioaerosol from emissions of a turkey fattening plant and reclassification of Jeotgalicoccus halophilus Liu et al. 2011 as a later heterotypic synonym of Jeotgalicoccus aerolatus Martin et al. 2011., Int J Syst Evol Microbiol 2021 Mar; 71(3): .
• 2021
  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 03; 118(10): .
• 2021
  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): .
• 2021
  Quarato P, Singh M, Cornes E, Li B, Bourdon L, Mueller F, Didier C, Cecere G, , Germline inherited small RNAs facilitate the clearance of untranslated maternal mRNAs in C. elegans embryos., Nat Commun 2021 03; 12(1): 1441.
• 2021
  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 03; 15(3): 702-719.
• 2021
  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(): .
• 2021
  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.
• 2021
  Ruberto AA, Bourke C, Merienne N, Obadia T, Amino R, Mueller I, , Single-cell RNA sequencing reveals developmental heterogeneity among Plasmodium berghei sporozoites., Sci Rep 2021 02; 11(1): 4127.
• 2021
  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; (): .
• 2021
  Velly L, Volant S, Fitting C, Ghazali DA, Salipante F, Mayaux J, Monsel G, Cavaillon JM, Hausfater P, , Optimal combination of early biomarkers for infection and sepsis diagnosis in the emergency department: The BIPS study., J Infect 2021 Feb; (): .
• 2021
  Lamy-Besnier Q, Brancotte B, Ménager H, Debarbieux L, , Viral Host Range database, an online tool for recording, analyzing and disseminating virus-host interactions., Bioinformatics 2021 Feb; (): .
• 2021
  Regnault B, Bigot T, Ma L, Pérot P, Temmam S, Eloit M, , Deep Impact of Random Amplification and Library Construction Methods on Viral Metagenomics Results., Viruses 2021 02; 13(2): .
• 2021
  Ison J, Ienasescu H, Rydza E, Chmura P, Rapacki K, Gaignard A, Schwämmle V, van Helden J, Kalaš M, Ménager H, , biotoolsSchema: a formalized schema for bioinformatics software description., Gigascience 2021 Jan; 10(1): .
• 2021
  Meignié A, Combredet C, Santolini M, Kovács IA, Douché T, Gianetto QG, Eun H, Matondo M, Jacob Y, Grailhe R, Tangy F, Komarova AV, , Proteomic Analysis Uncovers Measles Virus Protein C Interaction with p65/iASPP Protein Complex., Mol Cell Proteomics 2021 Jan; (): 100049.
• 2021
  Torchet R, Druart K, Ruano LC, Moine-Franel A, Borges H, Doppelt-Azeroual O, Brancotte B, Mareuil F, Nilges M, Ménager H, Sperandio O, , The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators., Bioinformatics 2021 Jan; (): .
• 2021
  Pinto G, Saenz-de-Santa-Maria I, Chastagner P, Perthame E, Delmas C, Toulas C, Moyal-Jonathan-Cohen E, Brou C, Zurzolo C, , Patient-derived Glioblastoma Stem cells transfer mitochondria through Tunneling Nanotubes in Tumor Organoids., Biochem J 2020 11; (): .
• 2021
  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): .
• 2021
  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): .
• 2021
  Baillet N, Reynard S, Perthame E, Hortion J, Journeaux A, Mateo M, Carnec X, Schaeffer J, Picard C, Barrot L, Barron S, Vallve A, Duthey A, Jacquot F, Boehringer C, Jouvion G, Pietrosemoli N, Legendre R, Dillies MA, Allan R, Legras-Lachuer C, Carbonnelle C, Raoul H, Baize S, , Systemic viral spreading and defective host responses are associated with fatal Lassa fever in macaques., Commun Biol 2021 Jan; 4(1): 27.
• 2021
  Epelboin Y, Wang L, Giai Gianetto Q, Choumet V, Gaborit P, Issaly J, Guidez A, Douché T, Chaze T, Matondo M, Dusfour I, , CYP450 core involvement in multiple resistance strains of Aedes aegypti from French Guiana highlighted by proteomics, molecular and biochemical studies., PLoS One 2021 ; 16(1): e0243992.
• 2021
  Devi-Marulkar P, Moraes-Cabe C, Campagne P, Corre B, Meghraoui-Kheddar A, Bondet V, Llibre A, Duffy D, Maillart E, Papeix C, Pellegrini S, Michel F, , Altered Immune Phenotypes and HLA-DQB1 Gene Variation in Multiple Sclerosis Patients Failing Interferon β Treatment., Front Immunol 2021 ; 12(): 628375.
• 2021
  Dellière S, Duchateau M, Wong SSW, Giai Gianetto Q, Guegan H, Matondo M, Gangneux JP, Aimanianda V, , Proteomic Analysis of Humoral Immune Components in Bronchoalveolar Lavage of Patients Infected or Colonized by Aspergillus fumigatus., Front Immunol 2021 ; 12(): 677798.
• 2021
  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.
• 2021
  Saint-André V, , Computational biology approaches for mapping transcriptional regulatory networks., Comput Struct Biotechnol J 2021 ; 19(): 4884-4895.
• 2021
  Lamprecht AL, Palmblad M, Ison J, Schwämmle V, Al Manir MS, Altintas I, Baker CJO, Ben Hadj Amor A, Capella-Gutierrez S, Charonyktakis P, Crusoe MR, Gil Y, Goble C, Griffin TJ, Groth P, Ienasescu H, Jagtap P, Kalaš M, Kasalica V, Khanteymoori A, Kuhn T, Mei H, Ménager H, Möller S, Richardson RA, Robert V, Soiland-Reyes S, Stevens R, Szaniszlo S, Verberne S, Verhoeven A, Wolstencroft K, , Perspectives on automated composition of workflows in the life sciences., F1000Res 2021 ; 10(): 897.
• 2021
  Paul-Gilloteaux P, Tosi S, Hériché JK, Gaignard A, Ménager H, Marée R, Baecker V, Klemm A, Kalaš M, Zhang C, Miura K, Colombelli J, , Bioimage analysis workflows: community resources to navigate through a complex ecosystem., F1000Res 2021 ; 10(): 320.
• 2020
  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.
• 2020
  Menegatti S, Guillemot V, Latis E, Yahia-Cherbal H, Mittermüller D, Rouilly V, Mascia E, Rosine N, Koturan S, Millot GA, Leloup C, Duffy D, Gleizes A, Hacein-Bey-Abina S, , Sellam J, Berenbaum F, Miceli-Richard C, Dougados M, Bianchi E, Rogge L, , Immune response profiling of patients with spondyloarthritis reveals signalling networks mediating TNF-blocker function in vivo., Ann Rheum Dis 2020 Dec; (): .
• 2020
  Kämpfer P, Irgang R, Glaeser SP, Busse HJ, Criscuolo A, Clermont D, Avendaño-Herrera R, , Flavobacterium salmonis sp. nov. isolated from Atlantic salmon (Salmo salar) and formal proposal to reclassify Flavobacterium spartansii as a later heterotypic synonym of Flavobacterium tructae., Int J Syst Evol Microbiol 2020 Dec; 70(12): 6147-6154.
• 2020
  Mühle E, Abry C, Leclerc P, Goly GM, Criscuolo A, Busse HJ, Kämpfer P, Bernardet JF, Clermont D, Chesneau O, , Flavobacterium bizetiae sp. nov., isolated from diseased freshwater fish in Canada at the end of the 1970s., Int J Syst Evol Microbiol 2020 Nov; (): .
• 2020
  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.
• 2020
  Criscuolo A, On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference, F1000Res. 2020; 9:1309.
• 2020
  Lima DB, Dupré M, Duchateau M, Gianetto QG, Rey M, Matondo M, Chamot-Rooke J, , ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment., Bioinformatics 2020 Nov; (): .
• 2020
  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): .
• 2020
  Oprea* M, Njamkepo* E, Cristea* D, Zhukova* A, Clark CG, Kravetz AN, Monakhova E, Ciontea AS, Cojocaru R, Rauzier J, Damian M, Gascuel O, Quilici ML, Weill FX, , The seventh pandemic of cholera in Europe revisited by microbial genomics., Nat Commun 2020 10; 11(1): 5347.
• 2020
  Ramezani M, Pourmohyadini M, Nikou MM, Makzum S, Schumann P, Clermont D, Criscuolo A, Amoozegar MA, Kämpfer P, Spröer C, , Halomonas lysinitropha sp. nov., a novel halophilic bacterium isolated from a hypersaline wetland., Int J Syst Evol Microbiol 2020 Oct; (): .
• 2020
  Kazlauskas D, Krupovic M, Guglielmini J, Forterre P, Venclovas Č, Diversity and evolution of B-family DNA polymerases, Nucleic Acids Res 2020 Oct; 48(18): 10142-10156.
• 2020
  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; (): .
• 2020
  Kämpfer P, Glaeser SP, McInroy JA, Xu J, Busse HJ, Clermont D, Criscuolo A, , Flavobacterium panici sp. nov. isolated from the rhizosphere of the switchgrass Panicum virgatum., Int J Syst Evol Microbiol 2020 Oct; (): .
• 2020
  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.
• 2020
  Danès L, Tchitchek N, Bécavin C, , Bacnet: A user-friendly platform for building multi-omics websites., 2020 Sep; (): .
• 2020
  Declercq M, Biquand E, Karim M, Pietrosemoli N, Jacob Y, Demeret C, Barbezange C, van der Werf S, , Influenza A virus co-opts ERI1 exonuclease bound to histone mRNA to promote viral transcription., Nucleic Acids Res. 2020 Sep; (): .
• 2020
  Tejada-Arranz A, Galtier E, El Mortaji L, Turlin E, Ershov D, De Reuse H, , The RNase J-Based RNA Degradosome Is Compartmentalized in the Gastric Pathogen Helicobacter pylori., mBio 2020 Sep; 11(5): .
• 2020
  Coulibaly S, Cimino M, Ouattara M, Lecoutey C, Buchieri MV, Alonso-Rodriguez N, Briffotaux J, Mornico D, Gicquel B, Rochais C, Dallemagne P, , Phenanthrolinic analogs of quinolones show antibacterial activity against M. tuberculosis., Eur J Med Chem 2020 Sep; 207(): 112821.
• 2020
  Desnos-Ollivier M, Maufrais C, Pihet M, Aznar C, Dromer F, , , Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing., Mycoses 2020 Sep; 63(9): 942-951.
• 2020
  Menu E, Criscuolo A, Desnos-Ollivier M, Cassagne C, D'Incan E, Furst S, Ranque S, Berger P, Dromer F, , Saprochaete clavata Outbreak Infecting Cancer Center through Dishwasher., Emerg Infect Dis 2020 09; 26(9): 2031-2038.
• 2020
  Latis E, Michonneau D, Leloup C, Varet H, Peffault de Latour R, , Bianchi E, Socié G, Rogge L, , Cellular and molecular profiling of T-cell subsets at the onset of human acute GVHD., Blood Adv 2020 Aug; 4(16): 3927-3942.
• 2020
  More KR, Kaur I, Giai Gianetto Q, Invergo BM, Chaze T, Jain R, Huon C, Gutenbrunner P, Weisser H, Matondo M, Choudhary JS, Langsley G, Singh S, Chitnis CE, , Phosphorylation-Dependent Assembly of a 14-3-3 Mediated Signaling Complex during Red Blood Cell Invasion by Plasmodium falciparum Merozoites., mBio 2020 08; 11(4): .
• 2020
  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.
• 2020
  Uwimana A, Legrand E, Stokes BH, Ndikumana JM, Warsame M, Umulisa N, Ngamije D, Munyaneza T, Mazarati JB, Munguti K, Campagne P, Criscuolo A, Ariey F, Murindahabi M, Ringwald P, Fidock DA, Mbituyumuremyi A, Menard D, , Emergence and clonal expansion of in vitro artemisinin-resistant Plasmodium falciparum kelch13 R561H mutant parasites in Rwanda., Nat. Med. 2020 Aug; (): .
• 2020
  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.
• 2020
  Chang YY, Stévenin V, Duchateau M, Giai Gianetto Q, Hourdel V, Rodrigues CD, Matondo M, Reiling N, Enninga J, , Shigella hijacks the exocyst to cluster macropinosomes for efficient vacuolar escape., PLoS Pathog 2020 08; 16(8): e1008822.
• 2020
  Legros V, Jeannin P, Burlaud-Gaillard J, Chaze T, Gianetto QG, Butler-Browne G, Mouly V, Zoladek J, Afonso PV, Gonzàlez MN, Matondo M, Riederer I, Roingeard P, Gessain A, Choumet V, Ceccaldi PE, , Differentiation-dependent susceptibility of human muscle cells to Zika virus infection., PLoS Negl Trop Dis 2020 08; 14(8): e0008282.
• 2020
  Mikhailova A, Valle-Casuso JC, David A, Monceaux V, Volant S, Passaes C, Elfidha A, Müller-Trutwin M, Poyet JL, Sáez-Cirión A, , Antiapoptotic Clone 11-Derived Peptides Induce In Vitro Death of CD4+ T Cells Susceptible to HIV-1 Infection., J Virol 2020 07; 94(14): .
• 2020
  Lourenço M, Chaffringeon L, Lamy-Besnier Q, Pédron T, Campagne P, Eberl C, Bérard M, Stecher B, Debarbieux L, De Sordi L, , The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages., Cell Host Microbe 2020 Jun; (): .
• 2020
  Pérot P, Bielle F, Bigot T, Foulongne V, Bolloré K, Chrétien D, Gil P, Gutiérrez S, L'Ambert G, Mokhtari K, Hellert J, Flamand M, Tamietti C, Coulpier M, Huard de Verneuil A, Temmam S, Couderc T, De Sousa Cunha E, Boluda S, Plu I, Delisle MB, Bonneville F, Brassat D, Fieschi C, Malphettes M, Duyckaerts C, Mathon B, Demeret S, Seilhean D, Eloit M, , Identification of Umbre Orthobunyavirus as a Novel Zoonotic Virus Responsible for Lethal Encephalitis in 2 French Patients with Hypogammaglobulinemia., Clin Infect Dis 2021 May; 72(10): 1701-1708.
• 2020
  Silvia Castellanos-Castro, Arturo Aguilar-Rojas, Mariette Matondo, Quentin Gian Gianetto, Hugo Varet, Odile Sismeiro, Rachel Legendre, Julien Fernandes, David Hardy, Jean Yves Coppée, Jean Christophe Olivo-Marin, Nancy Guillen, Human Immune Response Triggered by Entamoeba histolytica in a 3D-Intestinal Model, Eukaryome Impact on Human Intestine Homeostasis and Mucosal Immunology. Springer, Cham.
• 2020
  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.
• 2020
  Dickson LB, Merkling SH, Gautier M, Ghozlane A, Jiolle D, Paupy C, Ayala D, Moltini-Conclois I, Fontaine A, Lambrechts L, , Exome-wide association study reveals largely distinct gene sets underlying specific resistance to dengue virus types 1 and 3 in Aedes aegypti., PLoS Genet 2020 05; 16(5): e1008794.
• 2020
  Dargél AA, Volant S, Brietzke E, Etain B, Olié E, Azorin JM, Gard S, Bellivier F, Bougerol T, Kahn JP, Roux P, Aubin V, Courtet P, Leboyer M, Henry C, , Allostatic load, emotional hyper-reactivity, and functioning in individuals with bipolar disorder, Bipolar Disord 2020 May;.
• 2020
  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.
• 2020
  Allain F, Mareuil F, Ménager H, Nilges M, Bardiaux B, , ARIAweb: a server for automated NMR structure calculation., Nucleic Acids Res. 2020 May; (): .
• 2020
  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.
• 2020
  Giraud-Gatineau A, Coya JM, Maure A, Biton A, Thomson M, Bernard EM, Marrec J, Gutierrez MG, Larrouy-Maumus G, Brosch R, Gicquel B, Tailleux L, The antibiotic bedaquiline activates host macrophage innate immune resistance to bacterial infection, Elife 2020 May;9.
• 2020
  Ziyatdinov A, Parker MM, Vaysse A, Beaty TH, Kraft P, Cho MH, Aschard H, , Mixed-model admixture mapping identifies smoking-dependent loci of lung function in African Americans., Eur J Hum Genet 2020 05; 28(5): 656-668.
• 2020
  Emilie Devijver, Emeline Perthame, Prediction regions through Inverse Regression, Journal of Machine Learning Research 21(113) (2020) 1-24.
• 2020
  Calvo-Villamañán A, Ng JW, Planel R, Ménager H, Chen A, Cui L, Bikard D, On-target activity predictions enable improved CRISPR-dCas9 screens in bacteria, Nucleic Acids Res. 2020 Apr;.
• 2020
  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 04; 18(1): 43.
• 2020
  Addi C, Presle A, Frémont S, Cuvelier F, Rocancourt M, Milin F, Schmutz S, Chamot-Rooke J, Douché T, Duchateau M, Giai Gianetto Q, Salles A, Ménager H, Matondo M, Zimmermann P, Gupta-Rossi N, Echard A, , The Flemmingsome reveals an ESCRT-to-membrane coupling via ALIX/syntenin/syndecan-4 required for completion of cytokinesis., Nat Commun 2020 04; 11(1): 1941.
• 2020
  Zhukova A, Gascuel O, Duchene S, Ayres D, Lemey P & Baele G, Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics, In Phylogenetics in the Genomic Era, Scornavacca C Delsuc F & Galtier N (eds). 2020; 5.3:1--5.3:43.
• 2020
  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.
• 2020
  Sitterlé E, Coste AT, Obadia T, Maufrais C, Chauvel M, Sertour N, Sanglard D, Puel A, D'Enfert C, Bougnoux ME, , Large-scale genome mining allows identification of neutral polymorphisms and novel resistance mutations in genes involved in Candida albicans resistance to azoles and echinocandins., J Antimicrob Chemother 2020 04; 75(4): 835-848.
• 2020
  Gérard A, Woolfe A, Mottet G, Reichen M, Castrillon C, Menrath V, Ellouze S, Poitou A, Doineau R, Briseno-Roa L, Canales-Herrerias P, Mary P, Rose G, Ortega C, Delincé M, Essono S, Jia B, Iannascoli B, Richard-Le Goff O, Kumar R, Stewart SN, Pousse Y, Shen B, Grosselin K, Saudemont B, Sautel-Caillé A, Godina A, McNamara S, Eyer K, Millot GA, Baudry J, England P, Nizak C, Jensen A, Griffiths AD, Bruhns P, Brenan C, High-throughput single-cell activity-based screening and sequencing of antibodies using droplet microfluidics, Nat. Biotechnol. 2020 Mar;.
• 2020
  Wallace EWJ, Maufrais C, Sales-Lee J, Tuck LR, de Oliveira L, Feuerbach F, Moyrand F, Natarajan P, Madhani HD, Janbon G, , Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom., Nucleic Acids Res 2020 03; 48(5): 2312-2331.
• 2020
  Jabs S, Biton A, Bécavin C, Nahori MA, Ghozlane A, Pagliuso A, Spanò G, Guérineau V, Touboul D, Giai Gianetto Q, Chaze T, Matondo M, Dillies MA, Cossart P, , Impact of the gut microbiota on the m6A epitranscriptome of mouse cecum and liver., Nat Commun 2020 03; 11(1): 1344.
• 2020
  Monteiro AN, Bouwman P, Kousholt AN, Eccles DM, Millot GA, Masson JY, Schmidt MK, Sharan SK, Scully R, Wiesmüller L, Couch F, Vreeswijk MPG, Variants of uncertain clinical significance in hereditary breast and ovarian cancer genes: best practices in functional analysis for clinical annotation, J. Med. Genet. 2020 Mar;.
• 2020
  Balbino B, Herviou P, Godon O, Stackowicz J, Goff OR, Iannascoli B, Sterlin D, Brûlé S, Millot GA, Harris FM, Voronina VA, Nadeau KC, Macdonald LE, Murphy AJ, Bruhns P, Reber LL, The anti-IgE mAb omalizumab induces adverse reactions by engaging Fcγ receptors, J. Clin. Invest. 2020 Mar;130(3):1330-1335.
• 2020
  Temmam S, Hul V, Bigot T, Bessaud M, Chrétien D, Hoem T, Gorman C, Duong V, Dussart P, Cappelle J, Eloit M, , Whole genome sequencing and phylogenetic characterization of a novel bat-associated picornavirus-like virus with an unusual genome organization., Infect Genet Evol 2020 03; 78(): 104130.
• 2020
  García-Fraile P, Spröer C, Chesneau O, Criscuolo A, Lang E, Clermont D, , Serratia vespertilionis (García-Fraile et al. 2015) is a later heterotypic synonym of Serratia ficaria (Grimont et al. 1981)., Int J Syst Evol Microbiol 2020 Mar; 70(3): 1961-1962.
• 2020
  Julienne H, Lechat P, Guillemot V, Lasry C, Yao C, Araud R, Laville V, Vilhjalmsson B, Ménager H, Aschard H, , JASS: command line and web interface for the joint analysis of GWAS results., NAR Genom Bioinform 2020 Mar; 2(1): lqaa003.
• 2020
  Kämpfer P, Busse HJ, Schumann P, Criscuolo A, Clermont D, Irgang R, Poblete-Morales M, Glaeser SP, Avendaño-Herrera R, , Arthrobacter ulcerisalmonis sp. nov., isolated from an ulcer of a farmed Atlantic salmon (Salmo salar), and emended description of the genus Arthrobacter sensu lato., Int J Syst Evol Microbiol 2020 Mar; 70(3): 1963-1968.
• 2020
  Birnberg L, Temmam S, Aranda C, Correa-Fiz F, Talavera S, Bigot T, Eloit M, Busquets N, , Viromics on Honey-Baited FTA Cards as a New Tool for the Detection of Circulating Viruses in Mosquitoes., Viruses 2020 02; 12(3): .
• 2020
  Mitri C, Bischoff E, Belda Cuesta E, Volant S, Ghozlane A, Eiglmeier K, Holm I, Dieme C, Brito-Fravallo E, Guelbeogo WM, Sagnon N, Riehle MM, Vernick KD, Leucine-Rich Immune Factor APL1 Is Associated With Specific Modulation of Enteric Microbiome Taxa in the Asian Malaria Mosquito, Front Microbiol 2020;11:306.
• 2020
  Davidović A, Coudière Y, Bourgault Y, , Modelling the action potential propagation in a heart with structural heterogeneities: From high-resolution MRI to numerical simulations., Int J Numer Method Biomed Eng 2021 11; 37(11): e3322.
• 2020
  Lecoeur H, Prina E, Rosazza T, Kokou K, N'Diaye P, Aulner N, Varet H, Bussotti G, Xing Y, Milon G, Weil R, Meng G, Späth GF, , Targeting Macrophage Histone H3 Modification as a Leishmania Strategy to Dampen the NF-κB/NLRP3-Mediated Inflammatory Response., Cell Rep 2020 02; 30(6): 1870-1882.e4.
• 2020
  Merkling SH, Raquin V, Dabo S, Henrion-Lacritick A, Blanc H, Moltini-Conclois I, Frangeul L, Varet H, Saleh MC, Lambrechts L, , Tudor-SN Promotes Early Replication of Dengue Virus in the Aedes aegypti Midgut., iScience 2020 Feb; 23(2): 100870.
• 2020
  Dieme C, Zmarlak NM, Brito-Fravallo E, Travaillé C, Pain A, Cherrier F, Genève C, Calvo-Alvarez E, Riehle MM, Vernick KD, Rotureau B, Mitri C, Exposure of Anopheles mosquitoes to trypanosomes reduces reproductive fitness and enhances susceptibility to Plasmodium, PLoS Negl Trop Dis 2020 Feb;14(2):e0008059.
• 2020
  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.
• 2020
  Derbise A, Echenique-Rivera H, Garcia-Lopez M, Beau R, Mattei M, Varet H, Dersch P, Pizarro-Cerdá J, Bread feeding is a robust and more physiological enteropathogen administration method compared to oral gavage, Infect. Immun. 2020 Feb;.
• 2020
  Barucci G, Cornes E, Singh M, Li B, Ugolini M, Samolygo A, Didier C, Dingli F, Loew D, Quarato P, Cecere G, , Small-RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants., Nat Cell Biol 2020 02; 22(2): 235-245.
• 2020
  Guglielmini J, Woo AC, Krupovic M, Forterre P, Gaia M, Reply to Ku and Sun: Ancestors of modern giant and large eukaryotic dsDNA viruses infected proto-eukaryotes, Proc. Natl. Acad. Sci. U.S.A. 2020 Feb;117(6):2749-2750.
• 2020
  Gondard M, Temmam S, Devillers E, Pinarello V, Bigot T, Chrétien D, Aprelon R, Vayssier-Taussat M, Albina E, Eloit M, Moutailler S, , RNA Viruses of Amblyomma variegatum and Rhipicephalus microplus and Cattle Susceptibility in the French Antilles., Viruses 2020 Jan; 12(2): .
• 2020
  Baidaliuk A, Lequime S, Moltini-Conclois I, Dabo S, Dickson LB, Prot M, Duong V, Dussart P, Boyer S, Shi C, Matthijnssens J, Guglielmini J, Gloria-Soria A, Simon-Lorière E, Lambrechts L, , Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of Aedes aegypti populations., Virus Evol 2020 Jan; 6(1): veaa018.
• 2020
  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.
• 2020
  Bastaraud A, Perthame E, Rakotondramanga JM, Mahazosaotra J, Ravaonindrina N, Jambou R, , The impact of rainfall on drinking water quality in Antananarivo, Madagascar., PLoS One 2020 ; 15(6): e0218698.
• 2019
  Boité MC, Späth GF, Bussotti G, Porrozzi R, Morgado FN, Llewellyn M, Schwabl P, Cupolillo E, , Trans-Atlantic Spill Over: Deconstructing the Ecological Adaptation of Leishmania infantum in the Americas., Genes (Basel) 2019 12; 11(1): .
• 2019
  Gouin E, Balestrino D, Rasid O, Nahori MA, Villiers V, Impens F, Volant S, Vogl T, Jacob Y, Dussurget O, Cossart P, , Ubiquitination of Listeria Virulence Factor InlC Contributes to the Host Response to Infection., mBio 2019 12; 10(6): .
• 2019
  Temmam S, Vongphayloth K, Hertz JC, Sutherland I, Douangboubpha B, Grandadam M, Bigot T, Brey PT, Eloit M, , Six Nearly Complete Genome Segments of a Novel Reovirus Identified in Laotian Batflies., Microbiol Resour Announc 2019 Nov; 8(46): .
• 2019
  Temmam S, Bigot T, Chrétien D, Gondard M, Pérot P, Pommelet V, Dufour E, Petres S, Devillers E, Hoem T, Pinarello V, Hul V, Vongphayloth K, Hertz JC, Loiseau I, Dumarest M, Duong V, Vayssier-Taussat M, Grandadam M, Albina E, Dussart P, Moutailler S, Cappelle J, Brey PT, Eloit M, , Insights into the Host Range, Genetic Diversity, and Geographical Distribution of Jingmenviruses., mSphere 2019 11; 4(6): .
• 2019
  Nardini L, Holm I, Pain A, Bischoff E, Gohl DM, Zongo S, Guelbeogo WM, Sagnon N, Vernick KD, Riehle MM, Influence of genetic polymorphism on transcriptional enhancer activity in the malaria vector Anopheles coluzzii, Sci Rep 2019 Oct;9(1):15275.
• 2019
  Gallois A, Mefford J, Ko A, Vaysse A, Julienne H, Ala-Korpela M, Laakso M, Zaitlen N, Pajukanta P, Aschard H, , A comprehensive study of metabolite genetics reveals strong pleiotropy and heterogeneity across time and context., Nat Commun 2019 10; 10(1): 4788.
• 2019
  Ison J, Ménager H, Brancotte B, Jaaniso E, Salumets A, Raček T, Lamprecht AL, Palmblad M, Kalaš M, Chmura P, Hancock JM, Schwämmle V, Ienasescu HI, Community curation of bioinformatics software and data resources, Brief. Bioinformatics 2019 Oct;.
• 2019
  Leman R, Harter V, Atkinson A, Davy G, Rousselin A, Muller E, Castéra L, Lemoine F, de la Grange P, Guillaud-Bataille M, Vaur D, Krieger S, SpliceLauncher: a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data, Bioinformatics 2019 Oct;.
• 2019
  Rodrigues C, Passet V, Rakotondrasoa A, Diallo TA, Criscuolo A, Brisse S, , Erratum to “Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov.” [Res Microbiol 170 (3) (2019) 165-170]., Res Microbiol ; 170(6-7): 300.
• 2019
  Savin C, Criscuolo A, Guglielmini J, Le Guern AS, Carniel E, Pizarro-Cerdá J, Brisse S, Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization, Microb Genom 2019 Oct;.
• 2019
  Mateo M, Reynard S, Carnec X, Journeaux A, Baillet N, Schaeffer J, Picard C, Legras-Lachuer C, Allan R, Perthame E, Hillion KH, Pietrosemoli N, Dillies MA, Barrot L, Vallve A, Barron S, Fellmann L, Gaillard JC, Armengaud J, Carbonnelle C, Raoul H, Tangy F, Baize S, , Vaccines inducing immunity to Lassa virus glycoprotein and nucleoprotein protect macaques after a single shot., Sci Transl Med 2019 10; 11(512): .
• 2019
  Sanchez David RY, Combredet C, Najburg V, Millot GA, Beauclair G, Schwikowski B, Léger T, Camadro JM, Jacob Y, Bellalou J, Jouvenet N, Tangy F, Komarova AV, , LGP2 binds to PACT to regulate RIG-I- and MDA5-mediated antiviral responses., Sci Signal 2019 10; 12(601): .
• 2019
  Guglielmini J, Woo AC, Krupovic M, Forterre P, Gaia M, Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes, Proc. Natl. Acad. Sci. U.S.A. 2019 Sep;116(39):19585-19592.
• 2019
  Singh P, Alaganan A, More KR, Lorthiois A, Thiberge S, Gorgette O, Guillotte Blisnick M, Guglielmini J, Aguilera SS, Touqui L, Singh S, Chitnis CE, , Role of a patatin-like phospholipase in Plasmodium falciparum gametogenesis and malaria transmission., 2019 08; 116(35): 17498-17508.
• 2019
  Dacheux L, Dommergues L, Chouanibou Y, Doméon L, Schuler C, Bonas S, Luo D, Maufrais C, Cetre-Sossah C, Cardinale E, Bourhy H, Métras R, Co-circulation and characterization of novel African arboviruses (genus Ephemerovirus) in cattle, Mayotte island, Indian Ocean, 2017, Transbound Emerg Dis 2019 Nov;66(6):2601-2604.
• 2019
  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.
• 2019
  Ison J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, Schwämmle V, Grüning B, Beard N, Lopez R, Duvaud S, Stockinger H, Persson B, Vařeková RS, Raček T, Vondrášek J, Peterson H, Salumets A, Jonassen I, Hooft R, Nyrönen T, Valencia A, Capella S, Gelpí J, Zambelli F, Savakis B, Leskošek B, Rapacki K, Blanchet C, Jimenez R, Oliveira A, Vriend G, Collin O, van Helden J, Løngreen P, Brunak S, The bio.tools registry of software tools and data resources for the life sciences, Genome Biol. 2019 08;20(1):164.
• 2019
  Chapeton-Montes D, Plourde L, Bouchier C, Ma L, Diancourt L, Criscuolo A, Popoff MR, Brüggemann H, The population structure of Clostridium tetani deduced from its pan-genome, Sci Rep 2019 Aug;9(1):11220.
• 2019
  Criscuolo A, Issenhuth-Jeanjean S, Didelot X, Thorell K, Hale J, Parkhill J, Thomson NR, Weill FX, Falush D, Brisse S, , The speciation and hybridization history of the genus Salmonella., Microb Genom 2019 08; 5(8): .
• 2019
  Quadrana L, Etcheverry M, Gilly A, Caillieux E, Madoui MA, Guy J, Bortolini Silveira A, Engelen S, Baillet V, Wincker P, Aury JM, Colot V, , Transposition favors the generation of large effect mutations that may facilitate rapid adaption., Nat Commun 2019 07; 10(1): 3421.
• 2019
  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 07; 365(6449): 176-180.
• 2019
  Wieczorek S, Giai Gianetto Q, Burger T, Five simple yet essential steps to correctly estimate the rate of false differentially abundant proteins in mass spectrometry analyses, Journal of Proteomics, 2019, 103441, ISSN 1874-3919..
• 2019
  Bigot T, Guglielmini J, Criscuolo A, Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences, Data Brief 25:104212.
• 2019
  Lemoine F, Correia D, Lefort V, Doppelt-Azeroual O, Mareuil F, Cohen-Boulakia S, Gascuel O, NGPhylogeny.fr: new generation phylogenetic services for non-specialists, Nucleic Acids Res. 2019 Jul;47(W1):W260-W265.
• 2019
  Kämpfer P, Busse HJ, McInroy JA, Criscuolo A, Clermont D, Glaeser SP, , Xinfangfangia humi sp. nov., isolated from soil amended with humic acid., Int J Syst Evol Microbiol 2019 Jul; 69(7): 2070-2075.
• 2019
  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 07; 15(7): e1007945.
• 2019
  Alexis Criscuolo, A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies, Research Ideas and Outcomes, 2019, 5:e36178.
• 2019
  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.
• 2019
  Kämpfer P, Busse HJ, Galatis H, Criscuolo A, Clermont D, Bizet C, Glaeser SP, , Paracoccus haematequi sp. nov., isolated from horse blood., Int J Syst Evol Microbiol 2019 Jun; 69(6): 1682-1688.
• 2019
  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.
• 2019
  Bastos RW, Freitas GJC, Carneiro HCS, Oliveira LVN, Gouveia-Eufrasio L, Santos APN, Moyrand F, Maufrais C, Janbon G, Santos DA, From the environment to the host: How non-azole agrochemical exposure affects the antifungal susceptibility and virulence of Cryptococcus gattii, Sci. Total Environ. 2019 Sep;681:516-523.
• 2019
  Kämpfer P, Bizet C, Clermont D, Criscuolo A, Kloepper LN, Duncan MB, McInroy JA, Kloepper JW, Schumann P, Glaeser SP, , Filibacter tadaridae sp. nov., isolated from within a guano pile from a colony of Mexican free-tailed bats Tadarida brasiliensis., Int J Syst Evol Microbiol 2019 May; 69(5): 1438-1442.
• 2019
  Pivot D, Fanton A, Badell-Ocando E, Benouachkou M, Astruc K, Huet F, Amoureux L, Neuwirth C, Criscuolo A, Aho S, Toubiana J, Brisse S, Carriage of a Single Strain of Nontoxigenic Corynebacterium diphtheriae bv. Belfanti (Corynebacterium belfantii) in Four Patients with Cystic Fibrosis, J. Clin. Microbiol. 2019 May;57(5).
• 2019
  Temmam S, Hul V, Bigot T, Hoem T, Gorman C, Duong V, Dussart P, Cappelle J, Eloit M, , A Novel Polycipiviridae Virus Identified in Pteropus lylei Stools., Microbiol Resour Announc 2019 Apr; 8(15): .
• 2019
  Kämpfer P, Busse HJ, Criscuolo A, Bizet C, Clermont D, McInroy JA, Glaeser SP, Pigmentiphaga humi sp. nov., isolated from soil amended with humic acid, Int. J. Syst. Evol. Microbiol. 2019 Apr;.
• 2019
  Borrel G, Adam PS, McKay LJ, Chen LX, Sierra-García IN, Sieber CMK, Letourneur Q, Ghozlane A, Andersen GL, Li WJ, Hallam SJ, Muyzer G, de Oliveira VM, Inskeep WP, Banfield JF, Gribaldo S, , Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea., Nat Microbiol 2019 04; 4(4): 603-613.
• 2019
  Dahl A, Guillemot V, Mefford J, Aschard H, Zaitlen N, , Adjusting for Principal Components of Molecular Phenotypes Induces Replicating False Positives., Genetics 2019 04; 211(4): 1179-1189.
• 2019
  Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M, , Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance., PLoS Negl Trop Dis 2019 04; 13(4): e0007374.
• 2019
  Liégard B, Baillet V, Etcheverry M, Joseph E, Lariagon C, Lemoine J, Evrard A, Colot V, Gravot A, Manzanares-Dauleux MJ, Jubault M, , Quantitative resistance to clubroot infection mediated by transgenerational epigenetic variation in Arabidopsis., New Phytol 2019 04; 222(1): 468-479.
• 2019
  Aujoulat F, Popoff MR, Diancourt L, Criscuolo A, Jean-Pierre H, Jumas-Bilak E, Marchandin H, Whole-Genome Sequences of a Cluster of 14 Unidentified Related sp. Strains from Human Clinical Samples and Type Strains of 3 Validated Species, Microbiol Resour Announc 2019 Mar;8(12).
• 2019
  Heurtier V, Owens N, Gonzalez I, Mueller F, Proux C, Mornico D, Clerc P, Dubois A, Navarro P, The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells, Nat Commun 2019 03;10(1):1109.
• 2019
  Valsecchi I, Lai J, Stephen-Victor E, Pillé A, Beaussart A, Lo V, Pham C, Aimanianda V, Kwan A, Duchateau M, Giai Gianetto Q, Matondo M, Lehoux M, Sheppard D, Dufrene Y, Bayry J, Iñaki Guijarro J, Sunde M, Latgé J-P, Assembly and disassembly of Aspergillus fumigatus conidial rodlets, The Cell Surface (2019).
• 2019
  Gouignard N, Cherrier F, Brito-Fravallo E, Pain A, Zmarlak NM, Cailliau K, Genève C, Vernick KD, Dissous C, Mitri C, Dual role of the Anopheles coluzzii Venus Kinase Receptor in both larval growth and immunity, Sci Rep 2019 Mar;9(1):3615.
• 2019
  Chaussade A, Millot G, Wells C, Brisse H, Laé M, Savignoni A, Desjardins L, Dendale R, Doz F, Aerts I, Jimenez I, Cassoux N, Stoppa Lyonnet D, Gauthier Villars M, Houdayer C, Correlation between RB1germline mutations and second primary malignancies in hereditary retinoblastoma patients treated with external beam radiotherapy, Eur J Med Genet 2019 Mar;62(3):217-223.
• 2019
  Diancourt L, Sautereau J, Criscuolo A, Popoff MR, Two Clostridium perfringens Type E Isolates in France, Toxins 2019 Mar;11(3):E138.
• 2019
  Rodrigues C, Passet V, Rakotondrasoa A, Diallo TA, Criscuolo A, Brisse S, , Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov., Res Microbiol ; 170(3): 165-170.
• 2019
  Sitterlé E, Maufrais C, Sertour N, Palayret M, d'Enfert C, Bougnoux ME, Within-Host Genomic Diversity of Candida albicans in Healthy Carriers, Sci Rep 2019 Feb;9(1):2563.
• 2019
  Torres-Sánchez M, Creevey CJ, Kornobis E, Gower DJ, Wilkinson M, San Mauro D, Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families, DNA Res. 2019;26(1):13-20.
• 2019
  Alves Feliciano C, Douché T, Giai Gianetto Q, Matondo M, Martin-Verstraete I, Dupuy B, , CotL, a new morphogenetic spore coat protein of Clostridium difficile., Environ Microbiol 2019 03; 21(3): 984-1003.
• 2019
  Dufresne Y, Lejzerowicz F, Perret-Gentil LA, Pawlowski J, Cordier T, SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data, BMC Bioinformatics 2019 Feb;20(1):88.
• 2019
  Marton T, Feri A, Commere PH, Maufrais C, d'Enfert C, Legrand M, Identification of Recessive Lethal Alleles in the Diploid Genome of a Candida albicans Laboratory Strain Unveils a Potential Role of Repetitive Sequences in Buffering Their Deleterious Impact, mSphere 2019 02;4(1).
• 2019
  Boettcher M, Covarrubias S, Biton A, Blau J, Wang H, Zaitlen N, McManus MT, Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding, BMC Genomics 2019 Feb;20(1):107.
• 2019
  Nadimpalli M, Vuthy Y, de Lauzanne A, Fabre L, Criscuolo A, Gouali M, Huynh BT, Naas T, Phe T, Borand L, Jacobs J, Kerléguer A, Piola P, Guillemot D, Le Hello S, Delarocque-Astagneau E, Meat and Fish as Sources of Extended-Spectrum β-Lactamase-Producing Escherichia coli, Cambodia, Emerg Infect Dis 2019 01; 25(1):126-31.
• 2019
  Coya JM, De Matteis L, Giraud-Gatineau A, Biton A, Serrano-Sevilla I, Danckaert A, Dillies MA, Gicquel B, De la Fuente JM, Tailleux L, Tri-mannose grafting of chitosan nanocarriers remodels the macrophage response to bacterial infection, J Nanobiotechnology 2019 Jan;17(1):15.
• 2019
  Gouder L, Vitrac A, Goubran-Botros H, Danckaert A, Tinevez JY, André-Leroux G, Atanasova E, Lemière N, Biton A, Leblond CS, Poulet A, Boland A, Deleuze JF, Benchoua A, Delorme R, Bourgeron T, Cloëz-Tayarani I, , Altered spinogenesis in iPSC-derived cortical neurons from patients with autism carrying de novo SHANK3 mutations., Sci Rep 2019 01; 9(1): 94.
• 2019
  Reynard S, Journeaux A, Gloaguen E, Schaeffer J, Varet H, Pietrosemoli N, Mateo M, Baillet N, Laouenan C, Raoul H, Mullaert J, Baize S, Immune parameters and outcomes during Ebola virus disease, JCI Insight 2019 Jan;4(1).
• 2019
  Furci L, Jain R, Stassen J, Berkowitz O, Whelan J, Roquis D, Baillet V, Colot V, Johannes F, Ton J, , Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis., Elife 2019 01; 8(): .
• 2019
  Blin M, Le Tallec B, Nähse V, Schmidt M, Brossas C, Millot GA, Prioleau MN, Debatisse M, Transcription-dependent regulation of replication dynamics modulates genome stability, Nat. Struct. Mol. Biol. 2019 01;26(1):58-66.
• 2019
  Temmam S, Chrétien D, Bigot T, Dufour E, Petres S, Desquesnes M, Devillers E, Dumarest M, Yousfi L, Jittapalapong S, Karnchanabanthoeng A, Chaisiri K, Gagnieur L, Cosson JF, Vayssier-Taussat M, Morand S, Moutailler S, Eloit M, , Monitoring Silent Spillovers Before Emergence: A Pilot Study at the Tick/Human Interface in Thailand., Front Microbiol 2019 ; 10(): 2315.
• 2019
  Bigot T, Temmam S, Pérot P, Eloit M, , RVDB-prot, a reference viral protein database and its HMM profiles., F1000Res 2019 ; 8(): 530.
• 2019
  Guillemot V, Beaton D, Gloaguen A, Löfstedt T, Levine B, Raymond N, Tenenhaus A, Abdi H, , A constrained singular value decomposition method that integrates sparsity and orthogonality., PLoS One 2019 ; 14(3): e0211463.
• 2019
  Batrancourt B, Lecouturier K, Ferrand-Verdejo J, Guillemot V, Azuar C, Bendetowicz D, Migliaccio R, Rametti-Lacroux A, Dubois B, Levy R, , Exploration Deficits Under Ecological Conditions as a Marker of Apathy in Frontotemporal Dementia., Front Neurol 2019 ; 10(): 941.
• 2018
  Garali I, Adanyeguh IM, Ichou F, Perlbarg V, Seyer A, Colsch B, Moszer I, Guillemot V, Durr A, Mochel F, Tenenhaus A, , A strategy for multimodal data integration: application to biomarkers identification in spinocerebellar ataxia., Brief Bioinform 2018 11; 19(6): 1356-1369.
• 2018
  François Rousset, Lun Cui, Elise Siouve, Christophe Becavin, Florence Depardieu, David Bikard, Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors, PLOS Genetics 14(11): e1007749..
• 2018
  Bussotti G, Gouzelou E, Côrtes Boité M, Kherachi I, Harrat Z, Eddaikra N, Mottram JC, Antoniou M, Christodoulou V, Bali A, Guerfali FZ, Laouini D, Mukhtar M, Dumetz F, Dujardin JC, Smirlis D, Lechat P, Pescher P, El Hamouchi A, Lemrani M, Chicharro C, Llanes-Acevedo IP, Botana L, Cruz I, Moreno J, Jeddi F, Aoun K, Bouratbine A, Cupolillo E, Späth GF, , Leishmania Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification., mBio 2018 11; 9(6): .
• 2018
  Schor IE, Bussotti G, Maleš M, Forneris M, Viales RR, Enright AJ, Furlong EEM, Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis, Curr. Biol. 2018 11;28(22):3547-3561.e9.
• 2018
  Hadj-Selem F, Lofstedt T, Dohmatob E, Frouin V, Dubois M, Guillemot V, Duchesnay E, , Continuation of Nesterov’s Smoothing for Regression With Structured Sparsity in High-Dimensional Neuroimaging., IEEE Trans Med Imaging 2018 11; 37(11): 2403-2413.
• 2018
  Dazas M, Badell E, Carmi-Leroy A, Criscuolo A, Brisse S, Taxonomic status of Corynebacterium diphtheriae biovar Belfanti and proposal of Corynebacterium belfantii sp. nov, Int. J. Syst. Evol. Microbiol. 2018 Dec;68(12):3826-3831.
• 2018
  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.
• 2018
  Dargél AA, Volant S, Saha S, Etain B, Grant R, Azorin JM, Gard S, Bellivier F, Bougerol T, Kahn JP, Roux P, Aubin V, Courtet P, Leboyer M, , Scott J, Henry C, Activation Levels, Cardiovascular Risk, and Functional Impairment in Remitted Bipolar Patients: Clinical Relevance of a Dimensional Approach, Psychother Psychosom 2019;88(1):45-47.
• 2018
  Amraoui F, Pain A, Piorkowski G, Vazeille M, Couto-Lima D, de Lamballerie X, Lourenço-de-Oliveira R, Failloux AB, Experimental Adaptation of the Yellow Fever Virus to the Mosquito Aedes albopictus and Potential risk of urban epidemics in Brazil, South America, Sci Rep 2018 Sep;8(1):14337.
• 2018
  Abolins-Abols M, Kornobis E, Ribeca P, Wakamatsu K, Peterson MP, Ketterson ED, Milá B, Differential gene regulation underlies variation in melanic plumage coloration in the dark-eyed junco (Junco hyemalis), Mol. Ecol. 2018 Sep;.
• 2018
  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.
• 2018
  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.
• 2018
  Hugo Varet, Jean-Yves Coppée, checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes, Bioinformatics, 2018.
• 2018
  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.
• 2018
  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.
• 2018
  Schiettekatte O, Vincent AT, Malosse C, Lechat P, Chamot-Rooke J, Veyrier FJ, Picardeau M, Bourhy P, , Characterization of LE3 and LE4, the only lytic phages known to infect the spirochete Leptospira., Sci Rep 2018 08; 8(1): 11781.
• 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.
• 2018
  Cordier T, Forster D, Dufresne Y, Martins CI, Stoeck T, Pawlowski J, Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring, Mol Ecol Resour 2018 Jul;.
• 2018
  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.
• 2018
  Carissimo G, Pain A, Belda E, Vernick KD, Highly focused transcriptional response of Anopheles coluzzii to O’nyong nyong arbovirus during the primary midgut infection, BMC Genomics 2018 Jul;19(1):526.
• 2018
  Rochat T, Bohn C, Morvan C, Le Lam TN, Razvi F, Pain A, Toffano-Nioche C, Ponien P, Jacq A, Jacquet E, Fey PD, Gautheret D, Bouloc P, The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus, Nucleic Acids Res. 2018 Jul;.
• 2018
  Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Johannes Köster and The Bioconda Team, Bioconda: sustainable and comprehensive software distribution for the life sciences, Nature Methods 2018; 15(7):475-6.
• 2018
  Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C, CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins, Nucleic Acids Res. 2018 Jul;46(W1):W246-W251.
• 2018
  Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D, , Taylor J, Backofen R, Nekrutenko A, Grüning B, Community-Driven Data Analysis Training for Biology, Cell Syst 2018 Jun;6(6):752-758.e1.
• 2018
  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.
• 2018
  Bourneuf E, Estellé J, Blin A, Créchet F, Schneider MDP, Gilbert H, Brossard M, Vaysse A, Lathrop M, Vincent-Naulleau S, Demenais F, New susceptibility loci for cutaneous melanoma risk and progression revealed using a porcine model, Oncotarget 2018 Jun;9(45):27682-27697.
• 2018
  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.
• 2018
  Bouchez V, Guglielmini J, Dazas M, Landier A, Toubiana J, Guillot S, Criscuolo A, Brisse S, Genomic Sequencing of Bordetella pertussis for Epidemiology and Global Surveillance of Whooping Cough, Emerging Infect. Dis. 2018 Jun;24(6):988-994.
• 2018
  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.
• 2018
  Nevers A, Doyen A, Malabat C, Néron B, Kergrohen T, Jacquier A, Badis G, Antisense transcriptional interference mediates condition-specific gene repression in budding yeast, Nucleic Acids Res. 2018 May;.
• 2018
  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.
• 2018
  Dargél AA, Roussel F, Volant S, Etain B, Grant R, Azorin JM, M'Bailara K, Bellivier F, Bougerol T, Kahn JP, Roux P, Aubin V, Courtet P, Leboyer M, , Kapczinski F, Henry C, Emotional hyper-reactivity and cardiometabolic risk in remitted bipolar patients: a machine learning approach, Acta Psychiatr Scand 2018 10;138(4):348-359.
• 2018
  Cossé MM, Barta ML, Fisher DJ, Oesterlin LK, Niragire B, Perrinet S, Millot GA, Hefty PS, Subtil A, The Loss of Expression of a Single Type 3 Effector (CT622) Strongly Reduces Infectivity and Growth, Front Cell Infect Microbiol 2018;8:145.
• 2018
  Cubi R, Vembar SS, Biton A, Franetich JF, Bordessoulles M, Sossau D, Zanghi G, Bosson-Vanga H, Benard M, Moreno A, Dereuddre-Bosquet N, Le Grand R, Scherf A, Mazier D, Laser capture microdissection enables transcriptomic analysis of dividing and quiescent liver stages of Plasmodium relapsing species, Cell. Microbiol. 2017 08;19(8).
• 2018
  Bernal-Bayard J, Gomez-Valero L, Wessel A, Khanna V, Bouchier C, Ghigo JM, Short genome report of cellulose-producing commensal 1094, Stand Genomic Sci 2018;13:13.
• 2018
  Garcia-Hermoso D, Criscuolo A, Lee SC, Legrand M, Chaouat M, Denis B, Lafaurie M, Rouveau M, Soler C, Schaal JV, Mimoun M, Mebazaa A, Heitman J, Dromer F, Brisse S, Bretagne S, Alanio A, , Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole-Genome Sequencing., mBio 2018 04; 9(2): .
• 2018
  Pereira JM, Chevalier C, Chaze T, Gianetto Q, Impens F, Matondo M, Cossart P, Hamon MA, , Infection Reveals a Modification of SIRT2 Critical for Chromatin Association., Cell Rep 2018 04; 23(4): 1124-1137.
• 2018
  Lemoine F, Domelevo Entfellner JB, Wilkinson E, Correia D, Dávila Felipe M, De Oliveira T, Gascuel O, Renewing Felsenstein’s phylogenetic bootstrap in the era of big data, Nature 2018 Apr;.
• 2018
  Criscuolo A, Chesneau O, Clermont D, Bizet C, , Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753)., Genome Announc 2018 Apr; 6(14): .
• 2018
  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.
• 2018
  Jeannin P, Chaze T, Giai Gianetto Q, Matondo M, Gout O, Gessain A, Afonso PV, , Proteomic analysis of plasma extracellular vesicles reveals mitochondrial stress upon HTLV-1 infection., Sci Rep 2018 03; 8(1): 5170.
• 2018
  Pericard P, Dufresne Y, Couderc L, Blanquart S, Touzet H, MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes, Bioinformatics 2018 02;34(4):585-591.
• 2018
  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.
• 2018
  Boettcher M, Tian R, Blau JA, Markegard E, Wagner RT, Wu D, Mo X, Biton A, Zaitlen N, Fu H, McCormick F, Kampmann M, McManus MT, Dual gene activation and knockout screen reveals directional dependencies in genetic networks, Nat. Biotechnol. 2018 02;36(2):170-178.
• 2018
  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.
• 2017
  Demenais F, Margaritte-Jeannin P, Barnes KC, Cookson WOC, Altmüller J, Ang W, Barr RG, Beaty TH, Becker AB, Beilby J, Bisgaard H, Bjornsdottir US, Bleecker E, Bønnelykke K, Boomsma DI, Bouzigon E, Brightling CE, Brossard M, Brusselle GG, Burchard E, Burkart KM, Bush A, Chan-Yeung M, Chung KF, Couto Alves A, Curtin JA, Custovic A, Daley D, de Jongste JC, Del-Rio-Navarro BE, Donohue KM, Duijts L, Eng C, Eriksson JG, Farrall M, Fedorova Y, Feenstra B, Ferreira MA, , Freidin MB, Gajdos Z, Gauderman J, Gehring U, Geller F, Genuneit J, Gharib SA, Gilliland F, Granell R, Graves PE, Gudbjartsson DF, Haahtela T, Heckbert SR, Heederik D, Heinrich J, Heliövaara M, Henderson J, Himes BE, Hirose H, Hirschhorn JN, Hofman A, Holt P, Hottenga J, Hudson TJ, Hui J, Imboden M, Ivanov V, Jaddoe VWV, James A, Janson C, Jarvelin MR, Jarvis D, Jones G, Jonsdottir I, Jousilahti P, Kabesch M, Kähönen M, Kantor DB, Karunas AS, Khusnutdinova E, Koppelman GH, Kozyrskyj AL, Kreiner E, Kubo M, Kumar R, Kumar A, Kuokkanen M, Lahousse L, Laitinen T, Laprise C, Lathrop M, Lau S, Lee YA, Lehtimäki T, Letort S, Levin AM, Li G, Liang L, Loehr LR, London SJ, Loth DW, Manichaikul A, Marenholz I, Martinez FJ, Matheson MC, Mathias RA, Matsumoto K, Mbarek H, McArdle WL, Melbye M, Melén E, Meyers D, Michel S, Mohamdi H, Musk AW, Myers RA, Nieuwenhuis MAE, Noguchi E, O'Connor GT, Ogorodova LM, Palmer CD, Palotie A, Park JE, Pennell CE, Pershagen G, Polonikov A, Postma DS, Probst-Hensch N, Puzyrev VP, Raby BA, Raitakari OT, Ramasamy A, Rich SS, Robertson CF, Romieu I, Salam MT, Salomaa V, Schlünssen V, Scott R, Selivanova PA, Sigsgaard T, Simpson A, Siroux V, Smith LJ, Solodilova M, Standl M, Stefansson K, Strachan DP, Stricker BH, Takahashi A, Thompson PJ, Thorleifsson G, Thorsteinsdottir U, Tiesler CMT, Torgerson DG, Tsunoda T, Uitterlinden AG, van der Valk RJP, Vaysse A, Vedantam S, von Berg A, von Mutius E, Vonk JM, Waage J, Wareham NJ, Weiss ST, White WB, Wickman M, Widén E, Willemsen G, Williams LK, Wouters IM, Yang JJ, Zhao JH, Moffatt MF, Ober C, Nicolae DL, Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks, Nat. Genet. 2018 Jan;50(1):42-53.
• 2017
  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.
• 2017
  Benabou M, Rolland T, Leblond CS, Millot GA, Huguet G, Delorme R, Leboyer M, Pagan C, Callebert J, Maronde E, Bourgeron T, Heritability of the melatonin synthesis variability in autism spectrum disorders, Sci Rep 2017 12;7(1):17746.
• 2017
  Aschard H, Guillemot V, Vilhjalmsson B, Patel CJ, Skurnik D, Ye CJ, Wolpin B, Kraft P, Zaitlen N, , Covariate selection for association screening in multiphenotype genetic studies., Nat Genet 2017 Dec; 49(12): 1789-1795.
• 2017
  Ratet G, Santecchia I, Fanton d'Andon M, Vernel-Pauillac F, Wheeler R, Lenormand P, Fischer F, Lechat P, Haake DA, Picardeau M, Boneca IG, Werts C, , LipL21 lipoprotein binding to peptidoglycan enables Leptospira interrogans to escape NOD1 and NOD2 recognition., PLoS Pathog 2017 12; 13(12): e1006725.
• 2017
  Lassalle F, Planel R, Penel S, Chapulliot D, Barbe V, Dubost A, Calteau A, Vallenet D, Mornico D, Bigot T, Guéguen L, Vial L, Muller D, Daubin V, Nesme X, Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium, Genome Biol Evol 2017 12;9(12):3413-3431.
• 2017
  Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Eric Rasche, Michael Crusoe, Hedi Peterson, Jon Ison, Hervé Ménager, Using bio.tools to generate and annotate workbench tool descriptions, F1000Research 2017, 6(ELIXIR):2074.
• 2017
  Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ, GDSCTools for Mining Pharmacogenomic Interactions in Cancer., Bioinformatics. 2017 Nov 24. doi: 10.1093/bioinformatics/btx744..
• 2017
  De Sordi L, Khanna V, Debarbieux L, The Gut Microbiota Facilitates Drifts in the Genetic Diversity and Infectivity of Bacterial Viruses, Cell Host Microbe 2017 Nov;.
• 2017
  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.
• 2017
  Golmard L, Castéra L, Krieger S, Moncoutier V, Abidallah K, Tenreiro H, Laugé A, Tarabeux J, Millot GA, Nicolas A, Laé M, Abadie C, Berthet P, Polycarpe F, Frébourg T, Elan C, de Pauw A, Gauthier-Villars M, Buecher B, Stern MH, Stoppa-Lyonnet D, Vaur D, Houdayer C, Contribution of germline deleterious variants in the RAD51 paralogs to breast and ovarian cancers, Eur. J. Hum. Genet. 2017 12;25(12):1345-1353.
• 2017
  Prieto Barja P, Pescher P, Bussotti G, Dumetz F, Imamura H, Kedra D, Domagalska M, Chaumeau V, Himmelbauer H, Pages M, Sterkers Y, Dujardin JC, Notredame C, Späth GF, Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani, Nat Ecol Evol 2017 Dec;1(12):1961-1969.
• 2017
  Zhao W, Siegel D, Biton A, Tonqueze OL, Zaitlen N, Ahituv N, Erle DJ, CRISPR-Cas9-mediated functional dissection of 3′-UTRs, Nucleic Acids Res. 2017 Oct;45(18):10800-10810.
• 2017
  Christo-Foroux E, Vallaeys T, Loux V, Dassa E, Deutscher J, Wandersman C, Livernois A, Hot C, Criscuolo A, Dauga C, Clermont D, Chesneau O, , Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: A reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group., Syst Appl Microbiol 2017 Oct; 40(7): 401-410.
• 2017
  Sugier PE, Brossard M, Sarnowski C, Vaysse A, Morin A, Pain L, Margaritte-Jeannin P, Dizier MH, Cookson WOCM, Lathrop M, Moffatt MF, Laprise C, Demenais F, Bouzigon E, A novel role for ciliary function in atopy: ADGRV1 and DNAH5 interactions, J. Allergy Clin. Immunol. 2018 May;141(5):1659-1667.e11.
• 2017
  Ibrahim EC, Guillemot V, Comte M, Tenenhaus A, Zendjidjian XY, Cancel A, Belzeaux R, Sauvanaud F, Blin O, Frouin V, Fakra E, , Modeling a linkage between blood transcriptional expression and activity in brain regions to infer the phenotype of schizophrenia patients., NPJ Schizophr 2017 Sep; 3(1): 25.
• 2017
  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.
• 2017
  Thomas Cokelaer, Dimitri Desvillechabrol, Rachel Legendre, Mélissa Cardon, Sequana: a set of snakemake NGS pipelines, J. Open Source Softw, 2 p352.
• 2017
  Marchant A, Le Coupanec A, Joly C, Perthame E, Sertour N, Garnier M, Godard V, Ferquel E, Choumet V, Infection of Ixodes ricinus by Borrelia burgdorferi sensu lato in peri-urban forests of France, PLoS ONE 2017;12(8):e0183543.
• 2017
  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.
• 2017
  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.
• 2017
  Friedman RC, Kalkhof S, Doppelt-Azeroual O, Mueller SA, Chovancová M, von Bergen M, Schwikowski B, Common and phylogenetically widespread coding for peptides by bacterial small RNAs, BMC Genomics 2017 07;18(1):553.
• 2017
  Fabien Mareuil, Olivia-Doppelt Azeroual, Hervé Ménager, Galaxy@pasteur, Mareuil F, Doppelt-Azeroual O and Ménager H. A public Galaxy platform at Pasteur used as an execution engine for web services [version 1; not peer reviewed]. F1000Research 2017, 6:1030 (poster) (doi: 10.7490/f1000research.1114334.1) .
• 2017
  Riehle MM, Bukhari T, Gneme A, Guelbeogo WM, Coulibaly B, Fofana A, Pain A, Bischoff E, Renaud F, Beavogui AH, Traore SF, Sagnon N, Vernick KD, The Anopheles gambiae 2La chromosome inversion is associated with susceptibility to Plasmodium falciparum in Africa, Elife 2017 Jun;6.
• 2017
  Alberto Amato, Gianluca Dell’Aquila, Francesco Musacchia, Rossella Annunziata, Ari Ugarte, Nicolas Maillet, Alessandra Carbone, Maurizio Ribera d’Alcalà, Remo Sanges, Daniele Iudicone & Maria I. Ferrante, Marine diatoms change their gene expression profile when exposed to microscale turbulence under nutrient replete conditions, Sci. Rep. 7, 016303–11 (2017).
• 2017
  Doppelt-Azeroual O, Mareuil F, Deveaud E, Kalaš M, Soranzo N, van den Beek M, Grüning B, Ison J, Ménager H, ReGaTE: Registration of Galaxy Tools in Elixir, Gigascience 2017 Jun;6(6):1-4.
• 2017
  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.
• 2017
  Dumetz F, Imamura H, Sanders M, Seblova V, Myskova J, Pescher P, Vanaerschot M, Meehan CJ, Cuypers B, De Muylder G, Späth GF, Bussotti G, Vermeesch JR, Berriman M, Cotton JA, Volf P, Dujardin JC, Domagalska MA, Modulation of Aneuploidy in during Adaptation to Different and Environments and Its Impact on Gene Expression, mBio 2017 05;8(3).
• 2017
  Lago M, Monteil V, Douche T, Guglielmini J, Criscuolo A, Maufrais C, Matondo M, Norel F, , Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation., Sci Rep 2017 05; 7(1): 2127.
• 2017
  Lago M, Monteil V, Douche T, Guglielmini J, Criscuolo A, Maufrais C, Matondo M, Norel F, Proteome remodelling by the stress sigma factor RpoS/σ in Salmonella: identification of small proteins and evidence for post-transcriptional regulation, Sci Rep 2017 May;7(1):2127.
• 2017
  Dahan J, Levillayer F, Xia T, Nouët Y, Werts C, Fanton d'Andon M, Adib-Conquy M, Cassard-Doulcier AM, Khanna V, Chen J, Tordjmann T, Buendia MA, Jouvion G, Wei Y, , LIM-Only Protein FHL2 Is a Negative Regulator of Transforming Growth Factor β1 Expression., Mol Cell Biol 2017 05; 37(10): .
• 2017
  Davis MP, Carrieri C, Saini HK, van Dongen S, Leonardi T, Bussotti G, Monahan JM, Auchynnikava T, Bitetti A, Rappsilber J, Allshire RC, Shkumatava A, O'Carroll D, Enright AJ, Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution, EMBO Rep. 2017 07;18(7):1231-1247.
• 2017
  Liu Y, Brossard M, Sarnowski C, Vaysse A, Moffatt M, Margaritte-Jeannin P, Llinares-López F, Dizier MH, Lathrop M, Cookson W, Bouzigon E, Demenais F, Network-assisted analysis of GWAS data identifies a functionally-relevant gene module for childhood-onset asthma, Sci Rep 2017 04;7(1):938.
• 2017
  Yazouli LE, Criscuolo A, Hejaji H, Bouaaza M, Elmdaghri N, Alami AA, Amraoui A, Dakka N, Radouani F, Molecular characterization of Chlamydia pneumoniae associated to atherosclerosis, Pathog Dis 2017 Apr;.
• 2017
  El Behi M, Sanson C, Bachelin C, Guillot-Noël L, Fransson J, Stankoff B, Maillart E, Sarrazin N, Guillemot V, Abdi H, Cournu-Rebeix I, Fontaine B, Zujovic V, , Adaptive human immunity drives remyelination in a mouse model of demyelination., Brain 2017 Apr; 140(4): 967-980.
• 2017
  Bécavin C, Koutero M, Tchitchek N, Cerutti F, Lechat P, Maillet N, Hoede C, Chiapello H, Gaspin C, Cossart P, Listeriomics: an Interactive Web Platform for Systems Biology of Listeria, mSystems 2017 Mar-Apr;2(2).
• 2017
  Impens F, Rolhion N, Radoshevich L, Bécavin C, Duval M, Mellin J, García Del Portillo F, Pucciarelli MG, Williams AH, Cossart P, N-terminomics identifies Prli42 as a membrane miniprotein conserved in Firmicutes and critical for stressosome activation in Listeria monocytogenes, Nat Microbiol 2017 Feb;2:17005.
• 2017
  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.
• 2017
  Mazuet C, Legeay C, Sautereau J, Bouchier C, Criscuolo A, Bouvet P, Trehard H, Jourdan Da Silva N, Popoff M, Characterization of Clostridium Baratii Type F Strains Responsible for an Outbreak of Botulism Linked to Beef Meat Consumption in France, PLOS Currents Outbreaks. 2017 Feb 1 . Edition 1. doi: 10.1371/currents.outbreaks.6ed2fe754b58a5c42d0c33d586ffc606..
• 2017
  Zhukova A, Fernandes LG, Hugon P, Pappas CJ, Sismeiro O, Coppée JY, Becavin C, Malabat C, Eshghi A, Zhang JJ, Yang FX, Picardeau M, Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans, Front Cell Infect Microbiol 2017;7:10.
• 2017
  Halloum I, Viljoen A, Khanna V, Craig D, Bouchier C, Brosch R, Coxon G, Kremer L, Resistance to thiacetazone derivatives active against Mycobacterium abscessus involves mutations in the MmpL5 transcriptional repressor MAB_4384, Antimicrob. Agents Chemother. 2017 Jan;.
• 2017
  Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, Alban Gaignard, Konrad Hinsen, Pierre Larmande, Yvan Le Bras, Frédéric Lemoine, Fabien Mareuil, Hervé Ménager, Christophe Pradal, Christophe Blanchet, Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities, Future Generation Computer Systems.
• 2017
  Ribet D, Lallemand-Breitenbach V, Ferhi O, Nahori M-A, Varet H, de Thé H, Cossart P., Promyelocytic Leukemia Protein (PML) Controls Listeria monocytogenes Infection, mBio 8:e02179-16..
• 2016
  Dehainault C, Golmard L, Millot GA, Charpin A, Laugé A, Tarabeux J, Aerts I, Cassoux N, Stoppa-Lyonnet D, Gauthier-Villars M, Houdayer C, Mosaicism and prenatal diagnosis options: insights from retinoblastoma, Eur. J. Hum. Genet. 2017 02;25(3):381-383.
• 2016
  Damien Correia , Olivia Doppelt-Azeroual , Jean-Baptiste Denis , Mathias Vandenbogaert , Valérie Caro, MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data, Correia D, Doppelt-Azeroual O, Denis JB et al. MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data. F1000Research 2016, 4:86 (doi: 10.12688/f1000research.6139.3) .
• 2016
  David S, Rusniok C, Mentasti M, Gomez-Valero L, Harris SR, Lechat P, Lees J, Ginevra C, Glaser P, Ma L, Bouchier C, Underwood A, Jarraud S, Harrison TG, Parkhill J, Buchrieser C, , Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently., Genome Res 2016 11; 26(11): 1555-1564.
• 2016
  Hervé Ménager, Matúš Kalaš, Kristoffer Rapacki, Jon Ison, Using registries to integrate bioinformatics tools and services into workbench environments, International Journal on Software Tools for Technology Transfer 18 (6), 581-586.
• 2016
  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..
• 2016
  Thouvenot P, Fourrière L, Dardillac E, Ben Yamin B, Lescure A, Lejour V, Heiligenstein X, Boulé JB, Romao M, Raposo-Benedetti G, Lopez BS, Nicolas A, Millot GA, Yeast cells reveal the misfolding and the cellular mislocalization of the human BRCA1 protein, J. Cell. Sci. 2016 12;129(23):4366-4378.
• 2016
  Feri A, Loll-Krippleber R, Commere PH, Maufrais C, Sertour N, Schwartz K, Sherlock G, Bougnoux ME, d'Enfert C, Legrand M, Analysis of Repair Mechanisms following an Induced Double-Strand Break Uncovers Recessive Deleterious Alleles in the Candida albicans Diploid Genome, mBio 2016 10;7(5).
• 2016
  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.
• 2016
  Kraemmer J, Smith K, Weintraub D, Guillemot V, Nalls MA, Cormier-Dequaire F, Moszer I, Brice A, Singleton AB, Corvol JC, , Clinical-genetic model predicts incident impulse control disorders in Parkinson’s disease., J Neurol Neurosurg Psychiatry 2016 Oct; 87(10): 1106-11.
• 2016
  Berthet N, Descorps-Declère S, Nkili-Meyong AA, Nakouné E, Gessain A, Manuguerra JC, Kazanji M, Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data, Biol. Res. 2016 Sep;49(1):39.
• 2016
  Antunes LC, Poppleton D, Klingl A, Criscuolo A, Dupuy B, Brochier-Armanet C, Beloin C, Gribaldo S, Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes, Elife 2016;5.
• 2016
  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.
• 2016
  Boritsch EC, Khanna V, Pawlik A, Honoré N, Navas VH, Ma L, Bouchier C, Seemann T, Supply P, Stinear TP, Brosch R, Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria, Proc. Natl. Acad. Sci. U.S.A. 2016 Aug;.
• 2016
  Francesco Iorio, Andrea Gobbi, Marti Bernardo Faura, Thomas Cokelaer, Giuseppe Jurman, Julio Saez-Rodriguez, Efficient randomization of biological networks while preserving functional characterization of individual nodes, BMC Bioinformatics (2016) 17: 542..
• 2016
  Fang S, Vaysse A, Brossard M, Wang Y, Deng D, Liu Q, Zhang P, Xu K, Li M, Feng R, Liu H, Dang Y, Chen W, Prieto V, Gershenwald JE, Ross MI, Matejka B, Malke J, Haydu LE, Reveille JD, Sui D, Bassett RL, Koshkina N, Avril MF, Lu M, Wei Q, Demenais F, Amos CI, Lee JE, Melanoma Expression Genes Identified through Genome-Wide Association Study of Breslow Tumor Thickness, J. Invest. Dermatol. 2017 Jan;137(1):253-257.
• 2016
  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.
• 2016
  Vaysse A, Fang S, Brossard M, Wei Q, Chen WV, Mohamdi H, Vincent-Fetita L, Margaritte-Jeannin P, Lavielle N, Maubec E, Lathrop M, Avril MF, Amos CI, Lee JE, Demenais F, A comprehensive genome-wide analysis of melanoma Breslow thickness identifies interaction between CDC42 and SCIN genetic variants, Int. J. Cancer 2016 11;139(9):2012-20.
• 2016
  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;.
• 2016
  Hourdel V, Volant S, O'Brien DP, Chenal A, Chamot-Rooke J, Dillies MA, Brier S, MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets, Bioinformatics 2016 Nov;32(22):3413-3419.
• 2016
  Dufour N, Clermont O, La Combe B, Messika J, Dion S, Khanna V, Denamur E, Ricard JD, Debarbieux L,, Bacteriophage LM33_P1, a fast-acting weapon against the pandemic ST131-O25b:H4 Escherichia coli clonal complex, J. Antimicrob. Chemother. 2016 Jul;.
• 2016
  Francesco Iorio, Theo A. Knijnenburg, Daniel J. Vis, Graham R. Bignell, Michael P. Menden, Michael Schubert, Nanne Aben, Emanuel Gonçalves, Syd Barthorpe, Howard Lightfoot, Thomas Cokelaer, Patricia Greninger, Ewald van Dyk, Han Chang, Heshani de Silva, Holger Heyn, Xianming Deng, Regina K. Egan, Qingsong Liu, Tatiana Mironenko, Xeni Mitropoulos, Laura Richardson, Jinhua Wang, Tinghu Zhang, Sebastian Moran, Sergi Sayols, Maryam Soleimani, David Tamborero, Nuria Lopez-Bigas, Petra Ross-Macdonald, Manel Esteller, Nathanael S. Gray, Daniel A. Haber, Michael R. Stratton, Cyril H. Benes, Lodewyk F.A. Wessels, Julio Saez-Rodriguez, Ultan McDermott, Mathew J. Garnett, A Landscape of Pharmacogenomic Interactions in Cancer, Cell. 2016 Jul 28;166(3):740-54..
• 2016
  Drini S, Criscuolo A, Lechat P, Imamura H, Skalický T, Rachidi N, Lukeš J, Dujardin JC, Späth GF, Species- and Strain-Specific Adaptation of the HSP70 Super Family in Pathogenic Trypanosomatids, Genome Biol Evol 2016 07;8(6):1980-95.
• 2016
  Mouyna I, Aimanianda V, Hartl L, Prevost MC, Sismeiro O, Dillies MA, Jagla B, Legendre R, Coppée JY, Latgé JP, GH16 and GH81 family β-(1,3)-glucanases in Aspergillus fumigatus are essential for conidial cell wall morphogenesis, Cell Microbiol. 2016 Jun 15. doi: 10.1111/cmi.12630.
• 2016
  Waltemath D, Karr J, Bergmann F, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers C, Pir P, Alaybeyoglu B, Aranganathan N, Baghalian K, Bittig A, Burke P, Cantarelli M, Chew Y, Costa R, Cursons J, Czauderna T, Goldberg A, Gomez H, Hahn J, Hameri T, Gardiol D, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley J, Moreau B, Naderi-Meshkin H, Palaniappan S, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford N, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai T, Watanabe L, Wendland F, Wolfien M, Yurkovich J, Zhu Y, Zardilis A, Zhukova A, Schreiber F, Toward community standards and software for whole-cell modeling, IEEE Trans Biomed Eng 2016 Jun;.
• 2016
  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.
• 2016
  B. P. Abbott et al, GW150914: First results from the search for binary black hole coalescence with Advanced LIGO, Phys. Rev. D 93, 122003.
• 2016
  Thouvenot P, Ben Yamin B, Fourrière L, Lescure A, Boudier T, Del Nery E, Chauchereau A, Goldgar DE, Houdayer C, Stoppa-Lyonnet D, Nicolas A, Millot GA, Functional Assessment of Genetic Variants with Outcomes Adapted to Clinical Decision-Making, PLoS Genet. 2016 06;12(6):e1006096.
• 2016
  Pupin M, Esmaeel Q, Flissi A, Dufresne Y, Jacques P, Leclère V, Norine: A powerful resource for novel nonribosomal peptide discovery, Synth Syst Biotechnol 2016 Jun;1(2):89-94.
• 2016
  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.
• 2016
  Quereda JJ, Dussurget O, Nahori MA, Ghozlane A, Volant S, Dillies MA, Regnault B, Kennedy S, Mondot S, Villoing B, Cossart P, Pizarro-Cerda J, , Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection., Proc Natl Acad Sci U S A 2016 May; 113(20): 5706-11.
• 2016
  Richard A, Corvol JC, Debs R, Reach P, Tahiri K, Carpentier W, Gueguen J, Guillemot V, Labeyrie C, Adams D, Viala K, Cohen Aubart F, , Transcriptome Analysis of Peripheral Blood in Chronic Inflammatory Demyelinating Polyradiculoneuropathy Patients Identifies TNFR1 and TLR Pathways in the IVIg Response., Medicine (Baltimore) 2016 May; 95(19): e3370.
• 2016
  Bussotti G, Leonardi T, Clark MB, Mercer TR, Crawford J, Malquori L, Notredame C, Dinger ME, Mattick JS, Enright AJ, Improved definition of the mouse transcriptome via targeted RNA sequencing, Genome Res. 2016 05;26(5):705-16.
• 2016
  Benati D, Galperin M, Lambotte O, Gras S, Lim A, Mukhopadhyay M, Nouël A, Campbell KA, Lemercier B, Claireaux M, Hendou S, Lechat P, de Truchis P, Boufassa F, Rossjohn J, Delfraissy JF, Arenzana-Seisdedos F, Chakrabarti LA, Public T cell receptors confer high-avidity CD4 responses to HIV controllers, J. Clin. Invest. 2016 Apr;.
• 2016
  Galtier M, De Sordi L, Maura D, Arachchi H, Volant S, Dillies MA, Debarbieux L, Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition, Environ. Microbiol. 2016 Mar;.
• 2016
  Almeida M, Pop M, Le Chatelier E, Prifti E, Pons N, Ghozlane A, Ehrlich SD, Capturing the most wanted taxa through cross-sample correlations, ISME J 2016 Mar;.
• 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.
• 2016
  Biton A, Torgerson D, Letonqueze O, Zhao W, Zaitlen N, Erle DJ, Massively Parallel Identification of Regulatory Variants in Asthma, Ann Am Thorac Soc 2016 Mar;13 Suppl 1:S104.
• 2016
  Eloy P, Dehainault C, Sefta M, Aerts I, Doz F, Cassoux N, Lumbroso le Rouic L, Stoppa-Lyonnet D, Radvanyi F, Millot GA, Gauthier-Villars M, Houdayer C, A Parent-of-Origin Effect Impacts the Phenotype in Low Penetrance Retinoblastoma Families Segregating the c.1981C>T/p.Arg661Trp Mutation of RB1, PLoS Genet. 2016 Feb;12(2):e1005888.
• 2016
  Dahmane N, Gadelle D, Delmas S, Criscuolo A, Eberhard S, Desnoues N, Collin S, Zhang H, Pommier Y, Forterre P, Sezonov G, topIb, a phylogenetic hallmark gene of Thaumarchaeota encodes a functional eukaryote-like topoisomerase IB, Nucleic Acids Res. 2016 Feb;.
• 2016
  Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ, , Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S, Inferring causal molecular networks: empirical assessment through a community-based effort, Nat. Methods 2016 Apr;13(4):310-8.
• 2016
  Bidet P, Basmaci R, Guglielmini J, Doit C, Jost C, Birgy A, Bonacorsi S, Genome Analysis of Kingella kingae Strain KWG1 Reveals How a β-Lactamase Gene Inserted in the Chromosome of This Species, Antimicrob. Agents Chemother. 2015;60(1):703-8.
• 2016
  Técher H, Koundrioukoff S, Carignon S, Wilhelm T, Millot GA, Lopez BS, Brison O, Debatisse M, Signaling from Mus81-Eme2-Dependent DNA Damage Elicited by Chk1 Deficiency Modulates Replication Fork Speed and Origin Usage, Cell Rep 2016 Feb;14(5):1114-1127.
• 2016
  De Carli F, Gaggioli V, Millot GA, Hyrien O, Single-molecule, antibody-free fluorescent visualisation of replication tracts along barcoded DNA molecules, Int. J. Dev. Biol. 2016;60(7-8-9):297-304.
• 2015
  Dufresne Y, Noé L, Leclère V, Pupin M, Smiles2Monomers: a link between chemical and biological structures for polymers, J Cheminform 2015;7:62.
• 2015
  Nava C, Rupp J, Boissel JP, Mignot C, Rastetter A, Amiet C, Jacquette A, Dupuits C, Bouteiller D, Keren B, Ruberg M, Faudet A, Doummar D, Philippe A, Périsse D, Laurent C, Lebrun N, Guillemot V, Chelly J, Cohen D, Héron D, Brice A, Closs EI, Depienne C, , Hypomorphic variants of cationic amino acid transporter 3 in males with autism spectrum disorders., Amino Acids 2015 Dec; 47(12): 2647-58.
• 2015
  Chatzou M, Magis C, Chang JM, Kemena C, Bussotti G, Erb I, Notredame C, Multiple sequence alignment modeling: methods and applications, Brief. Bioinformatics 2016 11;17(6):1009-1023.
• 2015
  Herbert F, Tchitchek N, Bansal D, Jacques J, Pathak S, Bécavin C, Fesel C, Dalko E, Cazenave PA, Preda C, Ravindran B, Sharma S, Das B, Pied S, Evidence of IL-17, IP-10, and IL-10 involvement in multiple-organ dysfunction and IL-17 pathway in acute renal failure associated to Plasmodium falciparum malaria, J Transl Med 2015 Nov;13:369.
• 2015
  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.
• 2015
  Flissi A, Dufresne Y, Michalik J, Tonon L, Janot S, Noé L, Jacques P, Leclère V, Pupin M, Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing, Nucleic Acids Res. 2016 Jan;44(D1):D1113-8.
• 2015
  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.
• 2015
  Petrini E, Baillet V, Cridge J, Hogan CJ, Guillaume C, Ke H, Brandetti E, Walker S, Koohy H, Spivakov M, Varga-Weisz P, , A new phosphate-starvation response in fission yeast requires the endocytic function of myosin I., J Cell Sci 2015 Oct; 128(20): 3707-13.
• 2015
  Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, de la Fuente A, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J, DREAMTools: a Python package for scoring collaborative challenges, F1000Res 2015;4:1030.
• 2015
  Allaïli N, Valabrègue R, Auerbach EJ, Guillemot V, Yahia-Cherif L, Bardinet E, Jabourian M, Fossati P, Lehéricy S, Marjańska M, , Single-voxel (1)H spectroscopy in the human hippocampus at 3 T using the LASER sequence: characterization of neurochemical profile and reproducibility., NMR Biomed 2015 Oct; 28(10): 1209-17.
• 2015
  Ounzain S, Micheletti R, Arnan C, Plaisance I, Cecchi D, Schroen B, Reverter F, Alexanian M, Gonzales C, Ng SY, Bussotti G, Pezzuto I, Notredame C, Heymans S, Guigó R, Johnson R, Pedrazzini T, CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis, J. Mol. Cell. Cardiol. 2015 Dec;89(Pt A):98-112.
• 2015
  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.
• 2015
  D Garcia-Hermoso, A Criscuolo, M Legrande, M Chaouat, B Denis, M Lafaurie, M Rouveau, C Soler, M Mimoun, A Mebazaa, F Dromer, S Brisse, S Bretagne, A Alanio, Épidémie de mucormycose dans un centre de traitement des brûlés : des biomarqueurs diagnostiques au séquençage complets des souches, J. Myc. Med. 2015 Sep; 25(3):219.
• 2015
  Craveur P, Joseph AP, Esque J, Narwani TJ, Noël F, Shinada N, Goguet M, Leonard S, Poulain P, Bertrand O, Faure G, Rebehmed J, Ghozlane A, Swapna LS, Bhaskara RM, Barnoud J, Téletchéa S, Jallu V, Cerny J, Schneider B, Etchebest C, Srinivasan N, Gelly JC, de Brevern AG, Protein flexibility in the light of structural alphabets, Front Mol Biosci 2015;2:20.
• 2015
  Brossard M, Fang S, Vaysse A, Wei Q, Chen WV, Mohamdi H, Maubec E, Lavielle N, Galan P, Lathrop M, Avril MF, Lee JE, Amos CI, Demenais F, Integrated pathway and epistasis analysis reveals interactive effect of genetic variants at TERF1 and AFAP1L2 loci on melanoma risk, Int. J. Cancer 2015 Oct;137(8):1901-1909.
• 2015
  Kornobis E, Cabellos L, Aguilar F, Frías-López C, Rozas J, Marco J, Zardoya R, TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing, Evol. Bioinform. Online 2015;11:97-104.
• 2015
  Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR, Zhang R, Eng C, Torgerson DG, Urbanek C, , Li JB, Rodriguez-Santana JR, Burchard EG, Seibold MA, MacArthur DG, Montgomery SB, Zaitlen NA, Lappalainen T, The landscape of genomic imprinting across diverse adult human tissues, Genome Res. 2015 Jul;25(7):927-36.
• 2015
  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.
• 2015
  Malabat C, Feuerbach F, Ma L, Saveanu C, Jacquier A, Quality control of transcription start site selection by nonsense-mediated-mRNA decay, Elife 2015;4.
• 2015
  Obadia T, Opatowski L, Temime L, Herrmann JL, Fleury É, Boëlle PY, Guillemot D, Interindividual Contacts and Carriage of Methicillin-Resistant Staphylococcus aureus: A Nested Case-Control Study, Infect Control Hosp Epidemiol 2015 Aug;36(8):922-9.
• 2015
  Bouzigon E, Nadif R, Thompson EE, Concas MP, Kuldanek S, Du G, Brossard M, Lavielle N, Sarnowski C, Vaysse A, Dessen P, van der Valk RJ, Duijts L, Henderson AJ, Jaddoe VW, de Jongste JC, , Casula S, Biino G, Dizier MH, Pin I, Matran R, Lathrop M, Pirastu M, Demenais F, Ober C, , A common variant in RAB27A gene is associated with fractional exhaled nitric oxide levels in adults, Clin. Exp. Allergy 2015 Apr;45(4):797-806.
• 2015
  Obadia T, Silhol R, Opatowski L, Temime L, Legrand J, Thiébaut AC, Herrmann JL, Fleury É, Guillemot D, Boëlle PY, , Detailed contact data and the dissemination of Staphylococcus aureus in hospitals, PLoS Comput. Biol. 2015 Mar;11(3):e1004170.
• 2015
  Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KA, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME, Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing, Nat. Methods 2015 Apr;12(4):339-42.
• 2015
  Zhukova A, Sherman DJ, Mimoza: web-based semantic zooming and navigation in metabolic networks, BMC Syst Biol 2015;9:10.
• 2015
  Willing EM, Rawat V, Mandáková T, Maumus F, James GV, Nordström KJ, Becker C, Warthmann N, Chica C, Szarzynska B, Zytnicki M, Albani MC, Kiefer C, Bergonzi S, Castaings L, Mateos JL, Berns MC, Bujdoso N, Piofczyk T, de Lorenzo L, Barrero-Sicilia C, Mateos I, Piednoël M, Hagmann J, Chen-Min-Tao R, Iglesias-Fernández R, Schuster SC, Alonso-Blanco C, Roudier F, Carbonero P, Paz-Ares J, Davis SJ, Pecinka A, Quesneville H, Colot V, Lysak MA, Weigel D, Coupland G, Schneeberger K, Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation, Nat Plants 2015;1:14023.
• 2015
  Jhuraney A, Velkova A, Johnson RC, Kessing B, Carvalho RS, Whiley P, Spurdle AB, Vreeswijk MP, Caputo SM, Millot GA, Vega A, Coquelle N, Galli A, Eccles D, Blok MJ, Pal T, van der Luijt RB, Santamariña Pena M, Neuhausen SL, Donenberg T, Machackova E, Thomas S, Vallée M, Couch FJ, Tavtigian SV, Glover JN, Carvalho MA, Brody LC, Sharan SK, Monteiro AN, , BRCA1 Circos: a visualisation resource for functional analysis of missense variants, J. Med. Genet. 2015 Apr;52(4):224-30.
• 2015
  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.
• 2015
  Naldi A, Monteiro PT, Müssel C, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C, Cooperative development of logical modelling standards and tools with CoLoMoTo, Bioinformatics 2015 Apr;31(7):1154-9.
• 2015
  Loll-Krippleber R, Feri A, Nguyen M, Maufrais C, Yansouni J, d'Enfert C, Legrand M, A FACS-optimized screen identifies regulators of genome stability in Candida albicans, Eukaryotic Cell 2015 Mar;14(3):311-22.
• 2015
  Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR, Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression, Nat Commun 2015 Jan;6:5903.
• 2015
  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.
• 2015
  Loira N, Zhukova A, Sherman DJ, Pantograph: A template-based method for genome-scale metabolic model reconstruction, J Bioinform Comput Biol 2015 Apr;13(2):1550006.
• 2015
  Vidalain PO, Jacob Y, Hagemeijer MC, Jones LM, Neveu G, Roussarie JP, Rottier PJ, Tangy F, de Haan CA, A field-proven yeast two-hybrid protocol used to identify coronavirus-host protein-protein interactions, Methods Mol. Biol. 2015;1282:213-29.
• 2014
  Plassais J, Guaguère E, Lagoutte L, Guillory AS, de Citres CD, Degorce-Rubiales F, Delverdier M, Vaysse A, Quignon P, Bleuart C, Hitte C, Fautrel A, Kaerle C, Bellaud P, Bensignor E, Queney G, Bourrat E, Thomas A, André C, A spontaneous KRT16 mutation in a dog breed: a model for human focal non-epidermolytic palmoplantar keratoderma (FNEPPK), J. Invest. Dermatol. 2015 Apr;135(4):1187-1190.
• 2014
  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): e02309-14.
• 2014
  Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R, Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast, Mol. Syst. Biol. 2014;10:767.
• 2014
  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.
• 2014
  Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B, , Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP, Principles of regulatory information conservation between mouse and human, Nature 2014 Nov;515(7527):371-375.
• 2014
  Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, , A comparative encyclopedia of DNA elements in the mouse genome, Nature 2014 Nov;515(7527):355-64.
• 2014
  Biton A, Bernard-Pierrot I, Lou Y, Krucker C, Chapeaublanc E, Rubio-Pérez C, López-Bigas N, Kamoun A, Neuzillet Y, Gestraud P, Grieco L, Rebouissou S, de Reyniès A, Benhamou S, Lebret T, Southgate J, Barillot E, Allory Y, Zinovyev A, Radvanyi F, Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes, Cell Rep 2014 Nov;9(4):1235-45.
• 2014
  Maillet N, Collet G, Vannier T, Lavenier D, Peterlongo P, COMMET: comparing and combining multiple metagenomic datasets, BIBM, IEEE 2014 Nov.
• 2014
  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.
• 2014
  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.
• 2014
  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.
• 2014
  Rebouissou S, Bernard-Pierrot I, de Reyniès A, Lepage ML, Krucker C, Chapeaublanc E, Hérault A, Kamoun A, Caillault A, Letouzé E, Elarouci N, Neuzillet Y, Denoux Y, Molinié V, Vordos D, Laplanche A, Maillé P, Soyeux P, Ofualuka K, Reyal F, Biton A, Sibony M, Paoletti X, Southgate J, Benhamou S, Lebret T, Allory Y, Radvanyi F, EGFR as a potential therapeutic target for a subset of muscle-invasive bladder cancers presenting a basal-like phenotype, Sci Transl Med 2014 Jul;6(244):244ra91.
• 2014
  Tenenhaus A, Philippe C, Guillemot V, Le Cao KA, Grill J, Frouin V, , Variable selection for generalized canonical correlation analysis., Biostatistics 2014 Jul; 15(3): 569-83.
• 2014
  Di Tommaso P, Bussotti G, Kemena C, Capriotti E, Chatzou M, Prieto P, Notredame C, SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments, Nucleic Acids Res. 2014 Jul;42(Web Server issue):W356-60.
• 2014
  Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, , Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G, A community effort to assess and improve drug sensitivity prediction algorithms, Nat. Biotechnol. 2014 Dec;32(12):1202-12.
• 2014
  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.
• 2014
  Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J, MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics, BMC Bioinformatics 2014;15:136.
• 2014
  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.
• 2014
  Sanderson-Smith M, De Oliveira DM, Guglielmini J, McMillan DJ, Vu T, Holien JK, Henningham A, Steer AC, Bessen DE, Dale JB, Curtis N, Beall BW, Walker MJ, Parker MW, Carapetis JR, Van Melderen L, Sriprakash KS, Smeesters PR, , A systematic and functional classification of Streptococcus pyogenes that serves as a new tool for molecular typing and vaccine development, J. Infect. Dis. 2014 Oct;210(8):1325-38.
• 2014
  Zhukova A, Sherman DJ, Knowledge-based generalization of metabolic models, J. Comput. Biol. 2014 Jul;21(7):534-47.
• 2014
  Richard GF, Viterbo D, Khanna V, Mosbach V, Castelain L, Dujon B, Highly specific contractions of a single CAG/CTG trinucleotide repeat by TALEN in yeast, PLoS ONE 2014;9(4):e95611.
• 2014
  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.
• 2014
  Shi J, Yang XR, Ballew B, Rotunno M, Calista D, Fargnoli MC, Ghiorzo P, Bressac-de Paillerets B, Nagore E, Avril MF, Caporaso NE, McMaster ML, Cullen M, Wang Z, Zhang X, , , , Bruno W, Pastorino L, Queirolo P, Banuls-Roca J, Garcia-Casado Z, Vaysse A, Mohamdi H, Riazalhosseini Y, Foglio M, Jouenne F, Hua X, Hyland PL, Yin J, Vallabhaneni H, Chai W, Minghetti P, Pellegrini C, Ravichandran S, Eggermont A, Lathrop M, Peris K, Scarra GB, Landi G, Savage SA, Sampson JN, He J, Yeager M, Goldin LR, Demenais F, Chanock SJ, Tucker MA, Goldstein AM, Liu Y, Landi MT, Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma, Nat. Genet. 2014 May;46(5):482-6.
• 2014
  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;5(2):e00969-14.
• 2014
  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): .
• 2014
  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.
• 2014
  Zhukova A, Sherman DJ, Knowledge-based generalization of metabolic networks: a practical study, J Bioinform Comput Biol 2014 Apr;12(2):1441001.
• 2014
  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.
• 2014
  Okada N, Lin CP, Ribeiro MC, Biton A, Lai G, He X, Bu P, Vogel H, Jablons DM, Keller AC, Wilkinson JE, He B, Speed TP, He L, A positive feedback between p53 and miR-34 miRNAs mediates tumor suppression, Genes Dev. 2014 Mar;28(5):438-50.
• 2014
  Decourty L, Doyen A, Malabat C, Frachon E, Rispal D, Séraphin B, Feuerbach F, Jacquier A, Saveanu C, Long open reading frame transcripts escape nonsense-mediated mRNA decay in yeast, Cell Rep 2014 Feb;6(4):593-8.
• 2014
  Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Dream Six and Seven Parameter Estimation Consortium , Sauro HM, Stolovitzky G, Saez-Rodriguez J, Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach, BMC Syst Biol 2014;8:13.
• 2014
  Dacheux L, Cervantes-Gonzalez M, Guigon G, Thiberge JM, Vandenbogaert M, Maufrais C, Caro V, Bourhy H, A preliminary study of viral metagenomics of French bat species in contact with humans: identification of new mammalian viruses, PLoS ONE 2014;9(1):e87194.
• 2014
  Halbron M, Sachon C, Simon D, Obadia T, Grimaldi A, Hartemann A, Evaluation of a 5-day education programme in type 1 diabetes: achieving individual targets with a patient-centred approach, Diabet. Med. 2014 Apr;31(4):500-3.
• 2014
  Magis C, Taly JF, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Notredame C, T-Coffee: Tree-based consistency objective function for alignment evaluation, Methods Mol. Biol. 2014;1079:117-29.
• 2013
  Espaillat A, Carrasco-López C, Bernardo-García N, Pietrosemoli N, Otero LH, Álvarez L, de Pedro MA, Pazos F, Davis BM, Waldor MK, Hermoso JA, Cava F, Structural basis for the broad specificity of a new family of amino-acid racemases, Acta Crystallogr. D Biol. Crystallogr. 2014 Jan;70(Pt 1):79-90.
• 2013
  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.
• 2013
  Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T, SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools, BMC Syst Biol 2013;7:135.
• 2013
  Clavel J, Poulet N, Porcher E, Blanchet S, Grenouillet G, Pavoine S, Biton A, Seon-Massin N, Argillier C, Daufresne M, Teillac-Deschamps P, Julliard R, A new freshwater biodiversity indicator based on fish community assemblages, PLoS ONE 2013;8(11):e80968.
• 2013
  Olive V, Sabio E, Bennett MJ, De Jong CS, Biton A, McGann JC, Greaney SK, Sodir NM, Zhou AY, Balakrishnan A, Foth M, Luftig MA, Goga A, Speed TP, Xuan Z, Evan GI, Wan Y, Minella AC, He L, A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis, Elife 2013;2:e00822.
• 2013
  Dubois J, Ghozlane A, Thébault P, Dutour I, Bourqui R, Genome-wide detection of sRNA targets with rNAV, Biological Data Visualization,2013:81-88.
• 2013
  Cokelaer T, Pultz D, Harder LM, Serra-Musach J, Saez-Rodriguez J, BioServices: a common Python package to access biological Web Services programmatically, Bioinformatics 2013 Dec;29(24):3241-2.
• 2013
  Lechat P, Souche E, Moszer I, SynTView – an interactive multi-view genome browser for next-generation comparative microorganism genomics, BMC Bioinformatics 2013;14:277.
• 2013
  Pazos F, Pietrosemoli N, García-Martín JA, Solano R, Protein intrinsic disorder in plants, Front Plant Sci 2013;4:363.
• 2013
  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.
• 2013
  Le Tallec B, Millot GA, Blin ME, Brison O, Dutrillaux B, Debatisse M, Common fragile site profiling in epithelial and erythroid cells reveals that most recurrent cancer deletions lie in fragile sites hosting large genes, Cell Rep 2013 Aug;4(3):420-8.
• 2013
  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.
• 2013
  Bussotti G, Notredame C, Enright AJ, Detecting and comparing non-coding RNAs in the high-throughput era, Int J Mol Sci 2013 Jul;14(8):15423-58.
• 2013
  Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF, Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, Gigascience 2013;2(1):10.
• 2013
  Pietrosemoli N, Pancsa R, Tompa P, Structural disorder provides increased adaptability for vesicle trafficking pathways, PLoS Comput. Biol. 2013;9(7):e1003144.
• 2013
  Obadia T, Sallou O, Ouedraogo M, Guernec G, Lecerf F, The GAG database: a new resource to gather genomic annotation cross-references, Gene 2013 Sep;527(2):503-9.
• 2013
  Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, Saez-Rodriguez J, Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming, Bioinformatics 2013 Sep;29(18):2320-6.
• 2013
  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.
• 2013
  Maynaud G, Brunel B, Mornico D, Durot M, Severac D, Dubois E, Navarro E, Cleyet-Marel JC, Le Quéré A, Genome-wide transcriptional responses of two metal-tolerant symbiotic Mesorhizobium isolates to zinc and cadmium exposure, BMC Genomics 2013;14:292.
• 2013
  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.
• 2013
  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.
• 2013
  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.
• 2013
  McMillan DJ, Drèze PA, Vu T, Bessen DE, Guglielmini J, Steer AC, Carapetis JR, Van Melderen L, Sriprakash KS, Smeesters PR, Updated model of group A Streptococcus M proteins based on a comprehensive worldwide study, Clin. Microbiol. Infect. 2013 May;19(5):E222-9.
• 2013
  Kemena C, Bussotti G, Capriotti E, Marti-Renom MA, Notredame C, Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package, Bioinformatics 2013 May;29(9):1112-9.
• 2013
  Belda E, Sekowska A, Le Fèvre F, Morgat A, Mornico D, Ouzounis C, Vallenet D, Médigue C, Danchin A, An updated metabolic view of the Bacillus subtilis 168 genome, Microbiology (Reading, Engl.) 2013 Apr;159(Pt 4):757-70.
• 2013
  Pietrosemoli N, García-Martín JA, Solano R, Pazos F, Genome-wide analysis of protein disorder in Arabidopsis thaliana: implications for plant environmental adaptation, PLoS ONE 2013;8(2):e55524.
• 2013
  Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, , Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR, Evaluation of methods for modeling transcription factor sequence specificity, Nat. Biotechnol. 2013 Feb;31(2):126-34.
• 2013
  Moulin L, Mornico D, Melkonian R, Klonowska A, Draft Genome Sequence of Rhizobium mesoamericanum STM3625, a Nitrogen-Fixing Symbiont of Mimosa pudica Isolated in French Guiana (South America), Genome Announc 2013 Jan;1(1).
• 2013
  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.
• 2013
  Morales L, Noel B, Porcel B, Marcet-Houben M, Hullo MF, Sacerdot C, Tekaia F, Leh-Louis V, Despons L, Khanna V, Aury JM, Barbe V, Couloux A, Labadie K, Pelletier E, Souciet JL, Boekhout T, Gabaldon T, Wincker P, Dujon B, Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina), Genome Biol Evol 2013;5(12):2524-39.
• 2013
  Guillemot V, Bender A, Boulesteix AL, , Iterative reconstruction of high-dimensional Gaussian Graphical Models based on a new method to estimate partial correlations under constraints., PLoS One 2013 ; 8(4): e60536.
• 2012
  Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P, Compareads: comparing huge metagenomic experiments, BMC Bioinformatics 2012;13 Suppl 19:S10.
• 2012
  Obadia T, Haneef R, Boëlle PY, The R0 package: a toolbox to estimate reproduction numbers for epidemic outbreaks, BMC Med Inform Decis Mak 2012;12:147.
• 2012
  Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, Le Fèvre F, Longin C, Mornico D, Roche D, Rouy Z, Salvignol G, Scarpelli C, Thil Smith AA, Weiman M, Médigue C, MicroScope–an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data, Nucleic Acids Res. 2013 Jan;41(Database issue):D636-47.
• 2012
  Terfve C, Cokelaer T, Henriques D, MacNamara A, Goncalves E, Morris MK, van Iersel M, Lauffenburger DA, Saez-Rodriguez J, CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms, BMC Syst Biol 2012;6:133.
• 2012
  Le Floch E, Guillemot V, Frouin V, Pinel P, Lalanne C, Trinchera L, Tenenhaus A, Moreno A, Zilbovicius M, Bourgeron T, Dehaene S, Thirion B, Poline JB, Duchesnay E, , Significant correlation between a set of genetic polymorphisms and a functional brain network revealed by feature selection and sparse Partial Least Squares., Neuroimage 2012 Oct; 63(1): 11-24.
• 2012
  Ghozlane A, Bringaud F, Soueidan H, Dutour I, Jourdan F, Thébault P, Flux Analysis of the Trypanosoma brucei Glycolysis Based on a Multiobjective-Criteria Bioinformatic Approach, Adv Bioinformatics 2012;2012:159423.
• 2012
  Archambaud C, Nahori MA, Soubigou G, Bécavin C, Laval L, Lechat P, Smokvina T, Langella P, Lecuit M, Cossart P, , Impact of lactobacilli on orally acquired listeriosis., Proc Natl Acad Sci U S A 2012 Oct; 109(41): 16684-9.
• 2012
  Zhukova A, Adams R, Laibe C, Le Novère N, LibKiSAO: a Java library for Querying KiSAO, BMC Res Notes 2012;5:520.
• 2012
  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.
• 2012
  , An integrated encyclopedia of DNA elements in the human genome, Nature 2012 Sep;489(7414):57-74.
• 2012
  Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R, The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression, Genome Res. 2012 Sep;22(9):1775-89.
• 2012
  Neveu G, Cassonnet P, Vidalain PO, Rolloy C, Mendoza J, Jones L, Tangy F, Muller M, Demeret C, Tafforeau L, Lotteau V, Rabourdin-Combe C, Travé G, Dricot A, Hill DE, Vidal M, Favre M, Jacob Y, Comparative analysis of virus-host interactomes with a mammalian high-throughput protein complementation assay based on Gaussia princeps luciferase, Methods 2012 Dec;58(4):349-59.
• 2012
  Millot GA, Carvalho MA, Caputo SM, Vreeswijk MP, Brown MA, Webb M, Rouleau E, Neuhausen SL, Hansen Tv, Galli A, Brandão RD, Blok MJ, Velkova A, Couch FJ, Monteiro AN, , A guide for functional analysis of BRCA1 variants of uncertain significance, Hum. Mutat. 2012 Nov;33(11):1526-37.
• 2012
  Dubois J, Cottret L, Ghozlane A, Auber D, Bringaud F, Thébault P, Jourdan F, Bourqui R, Systrip: a visual environment for the investigation of time-series data in the context of metabolic networks, Information Visualisation, 2012. 204-213. IEEE.
• 2012
  Muller M, Jacob Y, Jones L, Weiss A, Brino L, Chantier T, Lotteau V, Favre M, Demeret C, Large scale genotype comparison of human papillomavirus E2-host interaction networks provides new insights for e2 molecular functions, PLoS Pathog. 2012;8(6):e1002761.
• 2012
  Boudon F, Pradal C, Cokelaer T, Prusinkiewicz P, Godin C, L-py: an L-system simulation framework for modeling plant architecture development based on a dynamic language, Front Plant Sci 2012;3:76.
• 2012
  Peyroche G, Saveanu C, Dauplais M, Lazard M, Beuneu F, Decourty L, Malabat C, Jacquier A, Blanquet S, Plateau P, Sodium selenide toxicity is mediated by O2-dependent DNA breaks, PLoS ONE 2012;7(5):e36343.
• 2012
  Gudipati RK, Neil H, Feuerbach F, Malabat C, Jacquier A, The yeast RPL9B gene is regulated by modulation between two modes of transcription termination, EMBO J. 2012 May;31(10):2427-37.
• 2012
  Renaut S, Maillet N, Normandeau E, Sauvage C, Derome N, Rogers SM, Bernatchez L, Genome-wide patterns of divergence during speciation: the lake whitefish case study, Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2012 Feb;367(1587):354-63.
• 2012
  Bouraï M, Lucas-Hourani M, Gad HH, Drosten C, Jacob Y, Tafforeau L, Cassonnet P, Jones LM, Judith D, Couderc T, Lecuit M, André P, Kümmerer BM, Lotteau V, Desprès P, Tangy F, Vidalain PO, , Mapping of Chikungunya virus interactions with host proteins identified nsP2 as a highly connected viral component., J Virol 2012 Mar; 86(6): 3121-34.
• 2012
  Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C, Use of ChIP-Seq data for the design of a multiple promoter-alignment method, Nucleic Acids Res. 2012 Apr;40(7):e52.
• 2012
  Permal E, Flutre T, Quesneville H, Roadmap for annotating transposable elements in eukaryote genomes, Methods Mol. Biol. 2012;859:53-68.
• 2011
  Mornico D, Miché L, Béna G, Nouwen N, Verméglio A, Vallenet D, Smith AA, Giraud E, Médigue C, Moulin L, Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia, Genes (Basel) 2011;3(1):35-61.
• 2011
  Cassonnet P, Rolloy C, Neveu G, Vidalain PO, Chantier T, Pellet J, Jones L, Muller M, Demeret C, Gaud G, Vuillier F, Lotteau V, Tangy F, Favre M, Jacob Y, Benchmarking a luciferase complementation assay for detecting protein complexes, Nat. Methods 2011 Dec;8(12):990-2.
• 2011
  Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, Jödicke L, Dammert MA, Schroeter C, Hammer M, Schmidt T, Jehl P, McGuigan C, Dymecka M, Chica C, Luck K, Via A, Chatr-Aryamontri A, Haslam N, Grebnev G, Edwards RJ, Steinmetz MO, Meiselbach H, Diella F, Gibson TJ, ELM–the database of eukaryotic linear motifs, Nucleic Acids Res. 2012 Jan;40(Database issue):D242-51.
• 2011
  Derrien T, Vaysse A, André C, Hitte C, Annotation of the domestic dog genome sequence: finding the missing genes, Mamm. Genome 2012 Feb;23(1-2):124-31.
• 2011
  Esteve-Codina A, Kofler R, Palmieri N, Bussotti G, Notredame C, Pérez-Enciso M, Exploring the gonad transcriptome of two extreme male pigs with RNA-seq, BMC Genomics 2011 Nov;12:552.
• 2011
  Le Tallec B, Dutrillaux B, Lachages AM, Millot GA, Brison O, Debatisse M, Molecular profiling of common fragile sites in human fibroblasts, Nat. Struct. Mol. Biol. 2011 Nov;18(12):1421-3.
• 2011
  Guglielmini J, Van Melderen L, Bacterial toxin-antitoxin systems: Translation inhibitors everywhere, Mob Genet Elements 2011 Nov;1(4):283-290.
• 2011
  Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C, Notredame C, Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures, Nat Protoc 2011 Nov;6(11):1669-82.
• 2011
  Courtot* M, Juty* N, Knüpfer* C, Waltemath* D, Zhukova* A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N, Controlled vocabularies and semantics in systems biology, Mol. Syst. Biol. 2011;7:543.
• 2011
  Millot GA, Berger A, Lejour V, Boulé JB, Bobo C, Cullin C, Lopes J, Stoppa-Lyonnet D, Nicolas A, Assessment of human Nter and Cter BRCA1 mutations using growth and localization assays in yeast, Hum. Mutat. 2011 Dec;32(12):1470-80.
• 2011
  Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Rosengren Pielberg G, Sigurdsson S, Fall T, Seppälä EH, Hansen MS, Lawley CT, Karlsson EK, , Bannasch D, Vilà C, Lohi H, Galibert F, Fredholm M, Häggström J, Hedhammar A, André C, Lindblad-Toh K, Hitte C, Webster MT, Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping, PLoS Genet. 2011 Oct;7(10):e1002316.
• 2011
  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.
• 2011
  Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B, Assemblathon 1: a competitive assessment of de novo short read assembly methods, Genome Res. 2011 Dec;21(12):2224-41.
• 2011
  Criscuolo A, morePhyML: improving the phylogenetic tree space exploration with PhyML 3, Mol. Phylogenet. Evol. 2011 Dec;61(3):944-8.
• 2011
  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.
• 2011
  Kornobis E, Pálsson S, Discordance in variation of the ITS region and the mitochondrial COI gene in the subterranean amphipod Crangonyx islandicus, J. Mol. Evol. 2011 Aug;73(1-2):34-44.
• 2011
  Boulesteix AL, Guillemot V, Sauerbrei W, , Use of pretransformation to cope with extreme values in important candidate features., Biom J 2011 Jul; 53(4): 673-88.
• 2011
  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.
• 2011
  Criscuolo A, Gribaldo S, Large-scale phylogenomic analyses indicate a deep origin of primary plastids within cyanobacteria, Mol. Biol. Evol. 2011 Nov;28(11):3019-32.
• 2011
  Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C, BlastR–fast and accurate database searches for non-coding RNAs, Nucleic Acids Res. 2011 Sep;39(16):6886-95.
• 2011
  Bertin PN, Heinrich-Salmeron A, Pelletier E, Goulhen-Chollet F, Arsène-Ploetze F, Gallien S, Lauga B, Casiot C, Calteau A, Vallenet D, Bonnefoy V, Bruneel O, Chane-Woon-Ming B, Cleiss-Arnold J, Duran R, Elbaz-Poulichet F, Fonknechten N, Giloteaux L, Halter D, Koechler S, Marchal M, Mornico D, Schaeffer C, Smith AA, Van Dorsselaer A, Weissenbach J, Médigue C, Le Paslier D, Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics, ISME J 2011 Nov;5(11):1735-47.
• 2011
  Leplae R, Geeraerts D, Hallez R, Guglielmini J, Drèze P, Van Melderen L, Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families, Nucleic Acids Res. 2011 Jul;39(13):5513-25.
• 2011
  Letessier A, Millot GA, Koundrioukoff S, Lachagès AM, Vogt N, Hansen RS, Malfoy B, Brison O, Debatisse M, Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site, Nature 2011 Feb;470(7332):120-3.
• 2011
  Henquell C, Guglielmini J, Verbeeck J, Mahul A, Thibault V, Lebray P, Laperche S, Trimoulet P, Foucher J, Le Guillou-Guillemette H, Fouchard-Hubert I, Legrand-Abravanel F, Métivier S, Gaudy C, D'Alteroche L, Rosenberg AR, Podevin P, Plantier JC, Riachi G, Saoudin H, Coppere H, André E, Gournay J, Feray C, Vallet S, Nousbaum JB, Baazia Y, Roulot D, Alain S, Loustaud-Ratti V, Schvoerer E, Habersetzer F, Pérez-Serra RJ, Gourari S, Mirand A, Odent-Malaure H, Garraud O, Izopet J, Bommelaer G, Peigue-Lafeuille H, van Ranst M, Abergel A, Bailly JL, Evolutionary history of hepatitis C virus genotype 5a in France, a multicenter ANRS study, Infect. Genet. Evol. 2011 Mar;11(2):496-503.
• 2011
  Vieira G, Sabarly V, Bourguignon PY, Durot M, Le Fèvre F, Mornico D, Vallenet D, Bouvet O, Denamur E, Schachter V, Médigue C, Core and panmetabolism in Escherichia coli, J. Bacteriol. 2011 Mar;193(6):1461-72.
• 2011
  Guillemot V, Tenenhaus A, Le Brusquet L, Frouin V, , Graph constrained discriminant analysis: a new method for the integration of a graph into a classification process., PLoS One 2011 ; 6(10): e26146.
• 2010
  Kornobis E, Pálsson S, Sidorov DA, Holsinger JR, Kristjánsson BK, Molecular taxonomy and phylogenetic affinities of two groundwater amphipods, Crangonyx islandicus and Crymostygius thingvallensis, endemic to Iceland, Mol. Phylogenet. Evol. 2011 Mar;58(3):527-39.
• 2010
  Heride C, Ricoul M, Kiêu K, von Hase J, Guillemot V, Cremer C, Dubrana K, Sabatier L, , Distance between homologous chromosomes results from chromosome positioning constraints., J Cell Sci 2010 Dec; 123(Pt 23): 4063-75.
• 2010
  Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F, Phospho.ELM: a database of phosphorylation sites–update 2011, Nucleic Acids Res. 2011 Jan;39(Database issue):D261-7.
• 2010
  Servant N, Gravier E, Gestraud P, Laurent C, Paccard C, Biton A, Brito I, Mandel J, Asselain B, Barillot E, Hupé P, EMA – A R package for Easy Microarray data analysis, BMC Res Notes 2010;3:277.
• 2010
  Lew JM, Kapopoulou A, Jones LM, Cole ST, TubercuList–10 years after, Tuberculosis (Edinb) 2011 Jan;91(1):1-7.
• 2010
  Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R, Long noncoding RNAs with enhancer-like function in human cells, Cell 2010 Oct;143(1):46-58.
• 2010
  Jelizarow M, Guillemot V, Tenenhaus A, Strimmer K, Boulesteix AL, , Over-optimism in bioinformatics: an illustration., Bioinformatics 2010 Aug; 26(16): 1990-8.
• 2010
  Gay S, Lachages AM, Millot GA, Courbet S, Letessier A, Debatisse M, Brison O, Nucleotide supply, not local histone acetylation, sets replication origin usage in transcribed regions, EMBO Rep. 2010 Sep;11(9):698-704.
• 2010
  Criscuolo A, Gribaldo S, BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evol. Biol. 2010;10:210.
• 2010
  Ranwez V, Criscuolo A, Douzery EJ, SuperTriplets: a triplet-based supertree approach to phylogenomics, Bioinformatics 2010 Jun;26(12):i115-23.
• 2010
  Remenant B, Coupat-Goutaland B, Guidot A, Cellier G, Wicker E, Allen C, Fegan M, Pruvost O, Elbaz M, Calteau A, Salvignol G, Mornico D, Mangenot S, Barbe V, Médigue C, Prior P, Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence, BMC Genomics 2010;11:379.
• 2010
  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.
• 2010
  Kornobis E, Pálsson S, Kristjánsson BK, Svavarsson J, Molecular evidence of the survival of subterranean amphipods (Arthropoda) during Ice Age underneath glaciers in Iceland, Mol. Ecol. 2010 Jun;19(12):2516-30.
• 2010
  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.
• 2010
  Debarbieux L, Leduc D, Maura D, Morello E, Criscuolo A, Grossi O, Balloy V, Touqui L, Bacteriophages can treat and prevent Pseudomonas aeruginosa lung infections, J. Infect. Dis. 2010 Apr;201(7):1096-104.
• 2010
  Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H, Modeling sample variables with an Experimental Factor Ontology, Bioinformatics 2010 Apr;26(8):1112-8.
• 2010
  , Genome sequence of the pea aphid Acyrthosiphon pisum, PLoS Biol. 2010 Feb;8(2):e1000313.
• 2010
  Coll O, Villalba A, Bussotti G, Notredame C, Gebauer F, A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis, Genes Dev. 2010 Jan;24(2):129-34.
• 2009
  Rimbault M, Robin S, Vaysse A, Galibert F, RNA profiles of rat olfactory epithelia: individual and age related variations, BMC Genomics 2009 Dec;10:572.
• 2009
  Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Médigue C, MicroScope: a platform for microbial genome annotation and comparative genomics, Database (Oxford) 2009;2009:bap021.
• 2009
  Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ, ELM: the status of the 2010 eukaryotic linear motif resource, Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80.
• 2009
  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.
• 2009
  Caignard G, Komarova AV, Bouraï M, Mourez T, Jacob Y, Jones LM, Rozenberg F, Vabret A, Freymuth F, Tangy F, Vidalain PO, Differential regulation of type I interferon and epidermal growth factor pathways by a human Respirovirus virulence factor, PLoS Pathog. 2009 Sep;5(9):e1000587.
• 2009
  Abbott et al., An upper limit on the stochastic gravitational-wave background of cosmological origin, Nature 2009 Aug;460(7258):990-4.
• 2009
  Néron B, Ménager H, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S, Tuffery P, Letondal C, Mobyle: a new full web bioinformatics framework, Bioinformatics 2009 Nov;25(22):3005-11.
• 2009
  Chica C, Diella F, Gibson TJ, Evidence for the concerted evolution between short linear protein motifs and their flanking regions, PLoS ONE 2009;4(7):e6052.
• 2009
  Abadie J, Hédan B, Cadieu E, De Brito C, Devauchelle P, Bourgain C, Parker HG, Vaysse A, Margaritte-Jeannin P, Galibert F, Ostrander EA, André C, Epidemiology, pathology, and genetics of histiocytic sarcoma in the Bernese mountain dog breed, J. Hered. 2009 Jul-Aug;100 Suppl 1:S19-27.
• 2009
  Ghozlane A, Joseph AP, Bornot A, de Brevern AG, Analysis of protein chameleon sequence characteristics, Bioinformation 2009;3(9):367-9.
• 2009
  Criscuolo A, Michel CJ, Phylogenetic inference with weighted codon evolutionary distances, J. Mol. Evol. 2009 Apr;68(4):377-92.
• 2009
  Bert A, Dmitriev I, Agliozzo S, Pietrosemoli N, Mandelkern M, Gallo T, Regge D, An automatic method for colon segmentation in CT colonography, Comput Med Imaging Graph 2009 Jun;33(4):325-31.
• 2009
  Abbott et al., All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data, Phys. Rev. Lett. 2009 Mar;102(11):111102.
• 2009
  Van Doninck K, Mandigo ML, Hur JH, Wang P, Guglielmini J, Milinkovitch MC, Lane WS, Meselson M, Phylogenomics of unusual histone H2A Variants in Bdelloid rotifers, PLoS Genet. 2009 Mar;5(3):e1000401.
• 2009
  Derrien T, Thézé J, Vaysse A, André C, Ostrander EA, Galibert F, Hitte C, Revisiting the missing protein-coding gene catalog of the domestic dog, BMC Genomics 2009 Feb;10:62.
• 2009
  Mine N, Guglielmini J, Wilbaux M, Van Melderen L, The decay of the chromosomally encoded ccdO157 toxin-antitoxin system in the Escherichia coli species, Genetics 2009 Apr;181(4):1557-66.
• 2009
  Neil H, Malabat C, d'Aubenton-Carafa Y, Xu Z, Steinmetz LM, Jacquier A, Widespread bidirectional promoters are the major source of cryptic transcripts in yeast, Nature 2009 Feb;457(7232):1038-42.
• 2009
  Robin S, Tacher S, Rimbault M, Vaysse A, Dréano S, André C, Hitte C, Galibert F, Genetic diversity of canine olfactory receptors, BMC Genomics 2009 Jan;10:21.
• 2008
  Diella F, Chabanis S, Luck K, Chica C, Ramu C, Nerlov C, Gibson TJ, KEPE–a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors, Bioinformatics 2009 Jan;25(1):1-5.
• 2008
  Abbott et al., Search for gravitational-wave bursts from soft gamma repeaters, Phys. Rev. Lett. 2008 Nov;101(21):211102.
• 2008
  Malak S, Wolf M, Millot GA, Mariotte E, Veyradier A, Meynard JL, Korach JM, Malot S, Bussel A, Azoulay E, Boulanger E, Galicier L, Devaux E, Eschwège V, Gallien S, Adrie C, Schlemmer B, Rondeau E, Coppo P, , Human immunodeficiency virus-associated thrombotic microangiopathies: clinical characteristics and outcome according to ADAMTS13 activity, Scand. J. Immunol. 2008 Sep;68(3):337-44.
• 2008
  Guglielmini J, Szpirer C, Milinkovitch MC, Automated discovery and phylogenetic analysis of new toxin-antitoxin systems, BMC Microbiol. 2008;8:104.
• 2008
  Chica C, Labarga A, Gould CM, López R, Gibson TJ, A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences, BMC Bioinformatics 2008;9:229.
• 2008
  Diella F, Haslam N, Chica C, Budd A, Michael S, Brown NP, Trave G, Gibson TJ, Understanding eukaryotic linear motifs and their role in cell signaling and regulation, Front. Biosci. 2008;13:6580-603.
• 2008
  Perrodou E, Chica C, Poch O, Gibson TJ, Thompson JD, A new protein linear motif benchmark for multiple sequence alignment software, BMC Bioinformatics 2008;9:213.
• 2008
  Criscuolo A, Gascuel O, Fast NJ-like algorithms to deal with incomplete distance matrices, BMC Bioinformatics 2008;9:166.
• 2008
  Marcatili P, Bussotti G, Tramontano A, The MoVIN server for the analysis of protein interaction networks, BMC Bioinformatics 2008 Mar;9 Suppl 2:S11.
• 2008
  Guinet F, Avé P, Jones L, Huerre M, Carniel E, Defective innate cell response and lymph node infiltration specify Yersinia pestis infection, PLoS ONE 2008;3(2):e1688.
• 2008
  Michael S, Travé G, Ramu C, Chica C, Gibson TJ, Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation, Bioinformatics 2008 Feb;24(4):453-7.
• 2008
  Gonnet F, Bouazza B, Millot GA, Ziaei S, Garcia L, Butler-Browne GS, Mouly V, Tortajada J, Danos O, Svinartchouk F, Proteome analysis of differentiating human myoblasts by dialysis-assisted two-dimensional gel electrophoresis (DAGE), Proteomics 2008 Jan;8(2):264-78.
• 2007
  Rossignol T, Lechat P, Cuomo C, Zeng Q, Moszer I, d'Enfert C, CandidaDB: a multi-genome database for Candida species and related Saccharomycotina, Nucleic Acids Res. 2008 Jan;36(Database issue):D557-61.
• 2007
  Lechat P, Hummel L, Rousseau S, Moszer I, GenoList: an integrated environment for comparative analysis of microbial genomes, Nucleic Acids Res. 2008 Jan;36(Database issue):D469-74.
• 2007
  Diella F, Gould CM, Chica C, Via A, Gibson TJ, Phospho.ELM: a database of phosphorylation sites–update 2008, Nucleic Acids Res. 2008 Jan;36(Database issue):D240-4.
• 2007
  Ranwez V, Berry V, Criscuolo A, Fabre PH, Guillemot S, Scornavacca C, Douzery EJ, PhySIC: a veto supertree method with desirable properties, Syst. Biol. 2007 Oct;56(5):798-817.
• 2007
  Caignard G, Guerbois M, Labernardière JL, Jacob Y, Jones LM, , Wild F, Tangy F, Vidalain PO, Measles virus V protein blocks Jak1-mediated phosphorylation of STAT1 to escape IFN-alpha/beta signaling, Virology 2007 Nov;368(2):351-62.
• 2007
  Pietrosemoli N, Crespo A, Fernandez A, Dehydration propensity of order-disorder intermediate regions in soluble proteins, J. Proteome Res. 2007 Sep;6(9):3519-26.
• 2007
  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.
• 2007
  Benedetto D, Caglioti E, Chica C, Compressing proteomes: the relevance of medium range correlations, EURASIP J Bioinform Syst Biol 2007;:60723.
• 2006
  Chica C, Jost C, Féthière J, Reynaud EG, Adéquation Germany, meeting the needs of scientists in the developing world, Biotechnol J 2006 Dec;1(12):1347-50.
• 2006
  Criscuolo A, Berry V, Douzery EJ, Gascuel O, SDM: a fast distance-based approach for (super) tree building in phylogenomics, Syst. Biol. 2006 Oct;55(5):740-55.
• 2006
  Coppo P, Wolf M, Veyradier A, Bussel A, Malot S, Millot GA, Daubin C, Bordessoule D, Pène F, Mira JP, Heshmati F, Maury E, Guidet B, Boulanger E, Galicier L, Parquet N, Vernant JP, Rondeau E, Azoulay E, Schlemmer B, , Prognostic value of inhibitory anti-ADAMTS13 antibodies in adult-acquired thrombotic thrombocytopenic purpura, Br. J. Haematol. 2006 Jan;132(1):66-74.
• 2005
  Abbott et al., Upper limits on a stochastic background of gravitational waves, Phys. Rev. Lett. 2005 Nov;95(22):221101.
• 2005
  Hubert JF, Duchesne L, Delamarche C, Vaysse A, Gueuné H, Raguénès-Nicol C, Pore selectivity analysis of an aquaglyceroporin by stopped-flow spectrophotometry on bacterial cell suspensions, Biol. Cell 2005 Sep;97(9):675-86.
• 2005
  Abbott et al., Limits on gravitational-wave emission from selected pulsars using LIGO data, Phys. Rev. Lett. 2005 May;94(18):181103.
• 2005
  d'Enfert C, Goyard S, Rodriguez-Arnaveilhe S, Frangeul L, Jones L, Tekaia F, Bader O, Albrecht A, Castillo L, Dominguez A, Ernst JF, Fradin C, Gaillardin C, Garcia-Sanchez S, de Groot P, Hube B, Klis FM, Krishnamurthy S, Kunze D, Lopez MC, Mavor A, Martin N, Moszer I, Onésime D, Perez Martin J, Sentandreu R, Valentin E, Brown AJ, CandidaDB: a genome database for Candida albicans pathogenomics, Nucleic Acids Res. 2005 Jan;33(Database issue):D353-7.
• 2004
  Coppo P, Bengoufa D, Veyradier A, Wolf M, Bussel A, Millot GA, Malot S, Heshmati F, Mira JP, Boulanger E, Galicier L, Durey-Dragon MA, Frémeaux-Bacchi V, Ramakers M, Pruna A, Bordessoule D, Gouilleux V, Scrobohaci ML, Vernant JP, Moreau D, Azoulay E, Schlemmer B, Guillevin L, Lassoued K, , Severe ADAMTS13 deficiency in adult idiopathic thrombotic microangiopathies defines a subset of patients characterized by various autoimmune manifestations, lower platelet count, and mild renal involvement, Medicine (Baltimore) 2004 Jul;83(4):233-44.
• 2004
  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.
• 2004
  Millot GA, Vainchenker W, Duménil D, Svinarchuk F, Differential signalling of NH2-terminal flag-labelled thrombopoietin receptor activated by TPO or anti-FLAG antibodies, Cell. Signal. 2004 Mar;16(3):355-63.
• 2003
  Maufrais C, Fazakerley GV, Cadet J, Boulard Y, Structural study of DNA duplex containing an N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide frameshift by NMR and restrained molecular dynamics, Nucleic Acids Res. 2003 Oct;31(20):5930-40.
• 2003
  Yeramian E, Jones L, GeneFizz: A web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives, Nucleic Acids Res. 2003 Jul;31(13):3843-9.
• 2003
  Coppo P, Dusanter-Fourt I, Millot G, Nogueira MM, Dugray A, Bonnet ML, Mitjavila-Garcia MT, Le Pesteur D, Guilhot F, Vainchenker W, Sainteny F, Turhan AG, Constitutive and specific activation of STAT3 by BCR-ABL in embryonic stem cells, Oncogene 2003 Jun;22(26):4102-10.
• 2002
  Maufrais C, Boulard Y, Solution structure of a DNA duplex containing a formamide-adenine base pair, Can. J. Physiol. Pharmacol. 2002 Jul;80(7):609-17.
• 2002
  Chureau C, Prissette M, Bourdet A, Barbe V, Cattolico L, Jones L, Eggen A, Avner P, Duret L, Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine, Genome Res. 2002 Jun;12(6):894-908.
• 2002
  Millot GA, Vainchenker W, Duménil D, Svinarchuk F, Distinct effects of thrombopoietin depending on a threshold level of activated Mpl in BaF-3 cells, J. Cell. Sci. 2002 Jun;115(Pt 11):2329-37.
• 2002
  Filippi MD, Porteu F, Le Pesteur F, Schiavon V, Millot GA, Vainchenker W, de Sauvage FJ, Dubart Kupperschmitt A, Sainteny F, Requirement for mitogen-activated protein kinase activation in the response of embryonic stem cell-derived hematopoietic cells to thrombopoietin in vitro, Blood 2002 Feb;99(4):1174-82.
• 2002
  Millot GA, Feger F, Garçon L, Vainchenker W, Dumenil D, Svinarchuk F, MplK, a natural variant of the thrombopoietin receptor with a truncated cytoplasmic domain, binds thrombopoietin but does not interfere with thrombopoietin-mediated cell growth, Exp. Hematol. 2002 Feb;30(2):166-75.
• 2002
  Moszer I, Jones LM, Moreira S, Fabry C, Danchin A, SubtiList: the reference database for the Bacillus subtilis genome, Nucleic Acids Res. 2002 Jan;30(1):62-5.
• 2001
  Jones L, Moszer I, Cole ST, Leproma: a Mycobacterium leprae genome browser, Lepr Rev 2001 Dec;72(4):470-7.
• 2001
  Glaser P, Frangeul L, Buchrieser C, Rusniok C, Amend A, Baquero F, Berche P, Bloecker H, Brandt P, Chakraborty T, Charbit A, Chetouani F, Couvé E, de Daruvar A, Dehoux P, Domann E, Domínguez-Bernal G, Duchaud E, Durant L, Dussurget O, Entian KD, Fsihi H, García-del Portillo F, Garrido P, Gautier L, Goebel W, Gómez-López N, Hain T, Hauf J, Jackson D, Jones LM, Kaerst U, Kreft J, Kuhn M, Kunst F, Kurapkat G, Madueno E, Maitournam A, Vicente JM, Ng E, Nedjari H, Nordsiek G, Novella S, de Pablos B, Pérez-Diaz JC, Purcell R, Remmel B, Rose M, Schlueter T, Simoes N, Tierrez A, Vázquez-Boland JA, Voss H, Wehland J, Cossart P, , Comparative genomics of Listeria species., Science 2001 Oct; 294(5543): 849-52.
• 2001
  Millot GA, Svinarchuk F, Lacout C, Vainchenker W, Dumenil D, The granulocyte colony-stimulating factor receptor supports erythroid differentiation in the absence of the erythropoietin receptor or Stat5, Br. J. Haematol. 2001 Feb;112(2):449-58.
• 2000
  Maufrais C, Fazakerley GV, Cadet J, Boulard Y, Solution structure by NMR and molecular dynamics of a duplex containing a guanine opposite a N-(2-deoxy-beta-D-erythro-pentofuranosyl)formamide lesion, Biochemistry 2000 May;39(18):5614-21.
• 2000
  Maufrais C, Fazakerley GV, Guy A, Cadet J, Boulard Y, Structure of an oligonucleotide containing a N-(2-deoxy-beta-D-erythro-pentofuranosyl)formamide residue facing a guanine, Biochimie 2000 Jan;82(1):65-9.
• 1999
  Mandard N, Sy D, Maufrais C, Bonmatin JM, Bulet P, Hetru C, Vovelle F, Androctonin, a novel antimicrobial peptide from scorpion Androctonus australis: solution structure and molecular dynamics simulations in the presence of a lipid monolayer, J. Biomol. Struct. Dyn. 1999 Oct;17(2):367-80.
• 1977
  Luine VN, McEwen BS, Black IB, , Effect of 17 beta-estradiol on hypothalamic tyrosine hydroxylase activity., Brain Res. 1977 Jan; 120(1): 188-92.
• 1976
  Davey MW, Sulkowski E, Carter WA, , Purification and characterization of mouse interferon with novel affinity sorbents., J. Virol. 1976 Feb; 17(2): 439-45.
• 1975
  Sanchez G, Alderete JF, , The effect of host adrenalectomy on the physiology of Trypanosoma rhodesiense., Comp Biochem Physiol A Comp Physiol 1975 Dec; 52(4): 623-6.
• 1975
  Wiesmann UN, DiDonato S, Herschkowitz NN, , Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and inhibition of their uptake., Biochem. Biophys. Res. Commun. 1975 Oct; 66(4): 1338-43.
• 1975
  Barthel W, Markwardt F, , Aggregation of blood platelets by adrenaline and its uptake., Biochem. Pharmacol. 1975 Oct; 24(20): 1903-4.