61 publications in 2018
Abdollahi N, Albani A, Anthony E, Baud A, Cardon M, Clerc R, Czernecki D, Conte R, David L, Delaune A, Djerroud S, Fourgoux P, Guiglielmoni N, Laurentie J, Lehmann N, Lochard C, Montagne R, Myrodia V, Opuu V, Parey E, Polit L, Privé S, Quignot C, Ruiz-Cuevas M, Sissoko M, Sompairac N, Vallerix A, Verrecchia V, Delarue M, Guérois R, Ponty Y, Sacquin-Mora S, Carbone A, Froidevaux C, Le Crom S, Lespinet O, Weigt M, Abboud S, Bernardes J, Bouvier G, Dequeker C, Ferré A, Fuchs P, Lelandais G, Poulain P, Richard H, Schweke H, Laine E, Lopes A. 2018. Meet-U: Educating through research immersion. PLoS Comput Biol. 14:e1005992. doi:
10.1371/journal.pcbi.1005992.
Ali ST, Wu P, Cauchemez S, He D, Fang VJ, Cowling BJ, Tian L. 2018. Ambient ozone and influenza transmissibility in Hong Kong. Eur Respir J. 51. doi:
10.1183/13993003.00369-2018.
Aristov A, Lelandais B, Rensen E, Zimmer C. 2018. ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range. Nat Commun. 9:2409. doi:
10.1038/s41467-018-04709-4.
Aschard H, Spiegelman D, Laville V, Kraft P, Wang M. 2018. A test for gene-environment interaction in the presence of measurement error in the environmental variable. Genetic Epidemiology. 42:250–264. doi:
10.1002/gepi.22113.
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 H-R, 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, Galaxy Training Network, Taylor J, Backofen R, Nekrutenko A, Grüning B. 2018. Community-Driven Data Analysis Training for Biology. Cell Syst. 6:752-758.e1. doi:
10.1016/j.cels.2018.05.012.
Bernal-Bayard J, Gomez-Valero L, Wessel A, Khanna V, Bouchier C, Ghigo J-M. 2018. Short genome report of cellulose-producing commensal Escherichia coli 1094. Stand Genomic Sci. 13:13. doi:
10.1186/s40793-018-0316-0.
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. 2018. Dual gene activation and knockout screen reveals directional dependencies in genetic networks. Nature Biotechnology. 36:170–178. doi:
10.1038/nbt.4062.
Bouchez V, Guglielmini J, Dazas M, Landier A, Toubiana J, Guillot S, Criscuolo A, Brisse S. 2018. Genomic Sequencing of Bordetella pertussis for Epidemiology and Global Surveillance of Whooping Cough. Emerging Infect Dis. 24:988–994. doi:
10.3201/eid2406.171464.
Carissimo G, Pain A, Belda E, Vernick KD. 2018. Highly focused transcriptional response of Anopheles coluzzii to O’nyong nyong arbovirus during the primary midgut infection. BMC Genomics. 19. doi:
10.1186/s12864-018-4918-0. [accessed 2018 Jul 11].
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4918-0.
Chatzou M, Floden EW, Di Tommaso P, Gascuel O, Notredame C, Halanych K. Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty. Syst Biol. doi:
10.1093/sysbio/syx096. [accessed 2018 May 31].
https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syx096/4948750.
Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ. 2018. GDSCTools for mining pharmacogenomic interactions in cancer. Bioinformatics. 34:1226–1228. doi:
10.1093/bioinformatics/btx744.
Cortes MC, Cauchemez S, Lefrancq N, Luby SP, Jahangir Hossain M, Sazzad HMS, Rahman M, Daszak P, Salje H, Gurley ES. 2018. Characterization of the Spatial and Temporal Distribution of Nipah Virus Spillover Events in Bangladesh, 2007-2013. J Infect Dis. 217:1390–1394. doi:
10.1093/infdis/jiy015.
Cossé MM, Barta ML, Fisher DJ, Oesterlin LK, Niragire B, Perrinet S, Millot GA, Hefty PS, Subtil A. 2018. The Loss of Expression of a Single Type 3 Effector (CT622) Strongly Reduces Chlamydia trachomatis Infectivity and Growth. Front Cell Infect Microbiol. 8:145. doi:
10.3389/fcimb.2018.00145.
Courtejoie N, Salje H, Durand B, Zanella G, Cauchemez S. 2018 May 17. Using serological studies to reconstruct the history of bluetongue epidemic in French cattle under successive vaccination campaigns. Epidemics. doi:
10.1016/j.epidem.2018.05.005.
Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, C. Rocha EP, Vergnaud G, Gautheret D, Pourcel C. 2018 May 22. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Research. doi:
10.1093/nar/gky425. [accessed 2018 May 29].
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky425/5001162.
Criscuolo A, Chesneau O, Clermont D, Bizet C. 2018. Draft Genome Sequence of the Fish Pathogen
Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753). Genome Announcements. 6:e00222-18. doi:
10.1128/genomeA.00222-18.
Cui L, Vigouroux A, Rousset F, Varet H, Khanna V, Bikard D. 2018. A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9. Nat Commun. 9:1912. doi:
10.1038/s41467-018-04209-5.
Dargél AA, Roussel F, Volant S, Etain B, Grant R, Azorin J-M, M’Bailara K, Bellivier F, Bougerol T, Kahn J-P, Roux P, Aubin V, Courtet P, Leboyer M, FACE-BD Collaborators, Kapczinski F, Henry C. 2018 May 15. Emotional hyper-reactivity and cardiometabolic risk in remitted bipolar patients: a machine learning approach. Acta Psychiatr Scand. doi:
10.1111/acps.12901.
Desvillechabrol D, Legendre R, Rioualen C, Bouchier C, van Helden J, Kennedy S, Cokelaer T. 2018. Sequanix: a dynamic graphical interface for Snakemake workflows. Bioinformatics. 34:1934–1936. doi:
10.1093/bioinformatics/bty034.
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. 2018. Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome. Parasit Vectors. 11:207. doi:
10.1186/s13071-018-2780-1.
Dobay, Maria Pamela, Pietrosemoli, Natalia. 2018. Optimized Protein–Protein Interaction Network Usage with Context Filtering. In: COMPUTATIONAL CELL BIOLOGY: methods and protocols. Vol. 1819. Louise von Stechow and Alberto Santos Delgado. S.l.: Springer Nature. (Methods in Molecular Biology).
Duval A, Obadia T, Martinet L, Boëlle P-Y, Fleury E, Guillemot D, Opatowski L, Temime L, I-Bird study group. 2018. Measuring dynamic social contacts in a rehabilitation hospital: effect of wards, patient and staff characteristics. Sci Rep. 8:1686. doi:
10.1038/s41598-018-20008-w.
Fabre E, Zimmer C. 2018. From dynamic chromatin architecture to DNA damage repair and back. Nucleus. 9:161–170. doi:
10.1080/19491034.2017.1419847.
Feitosa MF, Kraja AT, Chasman DI, Sung YJ, Winkler TW, Ntalla I, Guo X, Franceschini N, Cheng C-Y, Sim X, Vojinovic D, Marten J, Musani SK, Li C, Bentley AR, Brown MR, Schwander K, Richard MA, Noordam R, Aschard H, Bartz TM, Bielak LF, Dorajoo R, Fisher V, Hartwig FP, Horimoto ARVR, Lohman KK, Manning AK, Rankinen T, Smith AV, Tajuddin SM, Wojczynski MK, Alver M, Boissel M, Cai Q, Campbell A, Chai JF, Chen X, Divers J, Gao C, Goel A, Hagemeijer Y, Harris SE, He M, Hsu F-C, Jackson AU, Kähönen M, Kasturiratne A, Komulainen P, Kühnel B, Laguzzi F, Luan J, Matoba N, Nolte IM, Padmanabhan S, Riaz M, Rueedi R, Robino A, Said MA, Scott RA, Sofer T, Stančáková A, Takeuchi F, Tayo BO, van der Most PJ, Varga TV, Vitart V, Wang Y, Ware EB, Warren HR, Weiss S, Wen W, Yanek LR, Zhang W, Zhao JH, Afaq S, Amin N, Amini M, Arking DE, Aung T, Boerwinkle E, Borecki I, Broeckel U, Brown M, Brumat M, Burke GL, Canouil M, Chakravarti A, Charumathi S, Ida Chen Y-D, Connell JM, Correa A, de Las Fuentes L, de Mutsert R, de Silva HJ, Deng X, Ding J, Duan Q, Eaton CB, Ehret G, et al. 2018. Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries. PLoS ONE. 13:e0198166. doi:
10.1371/journal.pone.0198166.
Garcia-Hermoso D, Criscuolo A, Lee SC, Legrand M, Chaouat M, Denis B, Lafaurie M, Rouveau M, Soler C, Schaal J-V, Mimoun M, Mebazaa A, Heitman J, Dromer F, Brisse S, Bretagne S, Alanio A. 2018. Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of
Mucor circinelloides f.
circinelloides Resolved by Whole-Genome Sequencing. Chowdhary A, editor. mBio. 9:e00573-18. doi:
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Gruening B, Sallou O, Moreno P, da Veiga Leprevost F, Ménager H, Søndergaard D, Röst H, Sachsenberg T, O’Connor B, Madeira F, Dominguez Del Angel V, Crusoe MR, Varma S, Blankenberg D, Jimenez RC, Perez-Riverol Y. 2018. Recommendations for the packaging and containerizing of bioinformatics software. F1000Res. 7:742. doi:
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Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J. 2018. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods. 15:475–476. doi:
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Guérin A, Kerner G, Marr N, Markle JG, Fenollar F, Wong N, Boughorbel S, Avery DT, Ma CS, Bougarn S, Bouaziz M, Béziat V, Della Mina E, Oleaga-Quintas C, Lazarov T, Worley L, Nguyen T, Patin E, Deswarte C, Martinez-Barricarte R, Boucherit S, Ayral X, Edouard S, Boisson-Dupuis S, Rattina V, Bigio B, Vogt G, Geissmann F, Quintana-Murci L, Chaussabel D, Tangye SG, Raoult D, Abel L, Bustamante J, Casanova J-L. 2018. IRF4 haploinsufficiency in a family with Whipple’s disease. Elife. 7. doi:
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I-Bird study group, Duval A, Obadia T, Martinet L, Boëlle P-Y, Fleury E, Guillemot D, Opatowski L, Temime L. 2018. Measuring dynamic social contacts in a rehabilitation hospital: effect of wards, patient and staff characteristics. Scientific Reports. 8. doi:
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Impens F, Rolhion N, Radoshevich L, Bécavin C, Duval M, Mellin J, García Del Portillo F, Pucciarelli MG, Williams AH, Cossart P. 2018 Jun 25. Author Correction: N-terminomics identifies Prli42 as a membrane miniprotein conserved in Firmicutes and critical for stressosome activation in Listeria monocytogenes. Nat Microbiol. doi:
10.1038/s41564-018-0197-4.
Jeannin P, Chaze T, Giai Gianetto Q, Matondo M, Gout O, Gessain A, Afonso PV. 2018. Proteomic analysis of plasma extracellular vesicles reveals mitochondrial stress upon HTLV-1 infection. Sci Rep. 8:5170. doi:
10.1038/s41598-018-23505-0.
Jiang X, O’Reilly PF, Aschard H, Hsu Y-H, Richards JB, Dupuis J, Ingelsson E, Karasik D, Pilz S, Berry D, Kestenbaum B, Zheng J, Luan J, Sofianopoulou E, Streeten EA, Albanes D, Lutsey PL, Yao L, Tang W, Econs MJ, Wallaschofski H, Völzke H, Zhou A, Power C, McCarthy MI, Michos ED, Boerwinkle E, Weinstein SJ, Freedman ND, Huang W-Y, Schoor NMV, Velde N van der, Groot LCPGM de, Enneman A, Cupples LA, Booth SL, Vasan RS, Liu C-T, Zhou Y, Ripatti S, Ohlsson C, Vandenput L, Lorentzon M, Eriksson JG, Shea MK, Houston DK, Kritchevsky SB, Liu Y, Lohman KK, Ferrucci L, Peacock M, Gieger C, Beekman M, Slagboom E, Deelen J, Heemst D van, Kleber ME, März W, Boer IH de, Wood AC, Rotter JI, Rich SS, Robinson-Cohen C, Heijer M den, Jarvelin M-R, Cavadino A, Joshi PK, Wilson JF, Hayward C, Lind L, Michaëlsson K, Trompet S, Zillikens MC, Uitterlinden AG, Rivadeneira F, Broer L, Zgaga L, Campbell H, Theodoratou E, Farrington SM, Timofeeva M, Dunlop MG, Valdes AM, Tikkanen E, Lehtimäki T, Lyytikäinen L-P, Kähönen M, Raitakari OT, Mikkilä V, Ikram MA, Sattar N, Jukema JW, Wareham NJ, Langenberg C, Forouhi NG, Gundersen TE, Khaw K-T, Butterworth AS, Danesh J, Spector T, et al. 2018. Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels. Nature Communications. 9:260. doi:
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Kim Y-M, Poline J-B, Dumas G. 2018 Jun 28. Experimenting with Reproducibility: a case study of Robustness in Bioinformatics. Gigascience. doi:
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King BR, Samacoits A, Eisenhauer PL, Ziegler CM, Bruce EA, Zenklusen D, Zimmer C, Mueller F, Botten J. 2018. Visualization of Arenavirus RNA Species in Individual Cells by Single-Molecule Fluorescence In Situ Hybridization Suggests a Model of Cyclical Infection and Clearance during Persistence. J Virol. 92. doi:
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Krin E, Pierlé SA, Sismeiro O, Jagla B, Dillies M-A, Varet H, Irazoki O, Campoy S, Rouy Z, Cruveiller S, Médigue C, Coppée J-Y, Mazel D. 2018. Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation. BMC Genomics. 19. doi:
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Lanza VF, Baquero F, Martínez JL, Ramos-Ruíz R, González-Zorn B, Andremont A, Sánchez-Valenzuela A, Ehrlich SD, Kennedy S, Ruppé E, van Schaik W, Willems RJ, de la Cruz F, Coque TM. 2018. In-depth resistome analysis by targeted metagenomics. Microbiome. 6. doi:
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Laville V, Bentley AR, Privé F, Zhu X, Gauderman J, Winkler TW, Province M, Rao DC, Aschard H, CHARGE Gene-Lifestyle Interactions Working Group. 2018 May 3. VarExp: estimating variance explained by genome-wide GxE summary statistics. Stegle O, editor. Bioinformatics. doi:
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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, Dijck PV, Munro CA, d’Enfert C. 2018 Jul 6. Generating genomic platforms to study Candida albicans pathogenesis. Nucleic Acids Res. doi:
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Lemoine F, Domelevo Entfellner J-B, Wilkinson E, Correia D, Dávila Felipe M, De Oliveira T, Gascuel O. 2018. Renewing Felsenstein’s phylogenetic bootstrap in the era of big data. Nature. 556:452–456. doi:
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Lopez M, Kousathanas A, Quach H, Harmant C, Mouguiama-Daouda P, Hombert J-M, Froment A, Perry GH, Barreiro LB, Verdu P, Patin E, Quintana-Murci L. 2018. The demographic history and mutational load of African hunter-gatherers and farmers. Nat Ecol Evol. 2:721–730. doi:
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Menichelli C, Gascuel O, Bréhélin L. 2018. Improving pairwise comparison of protein sequences with domain co-occurrence. Markel S, editor. PLOS Computational Biology. 14:e1005889. doi:
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Morel J-D, Paatero AO, Wei J, Yewdell JW, Guenin-Macé L, Van Haver D, Impens F, Pietrosemoli N, Paavilainen VO, Demangel C. 2018 Jun 18. Proteomics reveals scope of mycolactone-mediated Sec61 blockade and distinctive stress signature. Mol Cell Proteomics. doi:
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Nevers A, Doyen A, Malabat C, Néron B, Kergrohen T, Jacquier A, Badis G. 2018 May 18. Antisense transcriptional interference mediates condition-specific gene repression in budding yeast. Nucleic Acids Research. doi:
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Nikolayeva I, Bost P, Casademont I, Duong V, Koeth F, Prot M, Czerwinska U, Ly S, Bleakley K, Cantaert T, Dussart P, Buchy P, Simon-Lorière E, Sakuntabhai A, Schwikowski B. 2018. A Blood RNA Signature Detecting Severe Disease in Young Dengue Patients at Hospital Arrival. The Journal of Infectious Diseases. 217:1690–1698. doi:
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Ouyang W, Aristov A, Lelek M, Hao X, Zimmer C. 2018. Deep learning massively accelerates super-resolution localization microscopy. Nature Biotechnology. 36:460–468. doi:
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Varet H, Shaulov Y, Sismeiro O, Trebicz-Geffen M, Legendre R, Coppée J-Y, Ankri S, Guillen N. 2018. Enteric bacteria boost defences against oxidative stress in Entamoeba histolytica. Sci Rep. 8:9042. doi:
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Vestergaard CL, Blainey PC, Flyvbjerg H. 2018. Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA. Nucleic Acids Research. 46:2446–2458. doi:
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Wang Y, Gao X, Ghozlane A, Hu H, Li X, Xiao Y, Li D, Yu G, Zhang T. 2018. Characteristics of Faecal Microbiota in Paediatric Crohn’s Disease and Their Dynamic Changes During Infliximab Therapy. J Crohns Colitis. 12:337–346. doi:
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Zimmer C, Fabre E. 2018 Jun 8. Chromatin mobility upon DNA damage: state of the art and remaining questions. Curr Genet. doi:
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Amato A, Dell’Aquila G, Musacchia F, Annunziata R, Ugarte A, Maillet N, Carbone A, Ribera d’Alcalà M, Sanges R, Iudicone D, Ferrante MI. 2017. Marine diatoms change their gene expression profile when exposed to microscale turbulence under nutrient replete conditions. Scientific Reports. 7. doi:
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Arbona J-M, Herbert S, Fabre E, Zimmer C. 2017. Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations. Genome Biology. 18. doi:
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Aschard H, Guillemot V, Vilhjalmsson B, Patel CJ, Skurnik D, Ye CJ, Wolpin B, Kraft P, Zaitlen N. 2017. Covariate selection for association screening in multiphenotype genetic studies. Nature Genetics. 49:1789–1795. doi:
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Becavin C, Koutero M, Tchitchek N, Cerutti F, Lechat P, Maillet N, Hoede C, Chiapello H, Gaspin C, Cossart P. 2017. Listeriomics: an Interactive Web Platform for Systems Biology of
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Benabou M, Rolland T, Leblond CS, Millot GA, Huguet G, Delorme R, Leboyer M, Pagan C, Callebert J, Maronde E, Bourgeron T. 2017. Heritability of the melatonin synthesis variability in autism spectrum disorders. Sci Rep. 7:17746. doi:
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Bryant D, Gascuel O. 2017. Special Issue: Mathematical and Computational Evolutionary Biology—2015. Systematic Biology. 66:1–2. doi:
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Cassan É, Arigon-Chifolleau A-M, Mesnard J-M, Gros A, Gascuel O. 2017. Le dixième gène du VIH. médecine/sciences. 33:484–485. doi:
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Castaldi PJ, Cho MH, Liang L, Silverman EK, Hersh CP, Rice K, Aschard H. 2017. Screening for interaction effects in gene expression data. Brody JP, editor. PLOS ONE. 12:e0173847. doi:
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Cerutti F, Mallet L, Painset A, Hoede C, Moisan A, Bécavin C, Duval M, Dussurget O, Cossart P, Gaspin C, Chiapello H. 2017. Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria. BMC Genomics. 18:882. doi:
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Chait R, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial population behavior through computer-interfaced control of individual cells. Nat Commun. 8:1535. doi:
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Chica C, Louis A, Roest Crollius H, Colot V, Roudier F. 2017. Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation. Genome Biol. 18:207. doi:
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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. 2017. 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. 40:401–410. doi:
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Cohen-Boulakia S, Belhajjame K, Collin O, Chopard J, Froidevaux C, Gaignard A, Hinsen K, Larmande P, Bras YL, Lemoine F, Mareuil F, Ménager H, Pradal C, Blanchet C. 2017. Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities. Future Generation Computer Systems. 75:284–298. doi:
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Cokelaer T, Desvillechabrol D, Legendre R, Cardon M. 2017. “Sequana”: a Set of Snakemake NGS pipelines. The Journal of Open Source Software. 2:352. doi:
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Cubi R, Vembar SS, Biton A, Franetich J-F, Bordessoulles M, Sossau D, Zanghi G, Bosson-Vanga H, Benard M, Moreno A, Dereuddre-Bosquet N, Le Grand R, Scherf A, Mazier D. 2017. Laser capture microdissection enables transcriptomic analysis of dividing and quiescent liver stages of
Plasmodium relapsing species. Cellular Microbiology. 19:e12735. doi:
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Dahan J, Levillayer F, Xia T, Nouët Y, Werts C, Fanton d’Andon M, Adib-Conquy M, Cassard-Doulcier A-M, Khanna V, Chen J, Tordjmann T, Buendia M-A, Jouvion G, Wei Y. 2017. LIM-Only Protein FHL2 Is a Negative Regulator of Transforming Growth Factor β1 Expression. Molecular and Cellular Biology. 37:e00636-16. doi:
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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. 2017. Transposon‐driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution. EMBO reports. 18:1231–1247. doi:
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De Sordi L, Khanna V, Debarbieux L. 2017. The Gut Microbiota Facilitates Drifts in the Genetic Diversity and Infectivity of Bacterial Viruses. Cell Host Microbe. 22:801-808.e3. doi:
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Dickson LB, Jiolle D, Minard G, Moltini-Conclois I, Volant S, Ghozlane A, Bouchier C, Ayala D, Paupy C, Moro CV, Lambrechts L. 2017. Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector. Sci Adv. 3:e1700585. doi:
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Doppelt-Azeroual O, Mareuil F, Deveaud E, Kalaš M, Soranzo N, van den Beek M, Grüning B, Ison J, Ménager H. 2017. ReGaTE: Registration of Galaxy Tools in Elixir. GigaScience. 6:1–4. doi:
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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. 2017. Modulation of Aneuploidy in
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El Yazouli L, Criscuolo A, Hejaji H, Bouazza M, Elmdaghri N, Aroussi Alami A, Amraoui A, Dakka N, Radouani F. 2017. Molecular characterisation of Chlamydia pneumoniae associated to atherosclerosis. Pathogens and Disease. 75. doi:
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d’Enfert C, Bougnoux M-E, Feri A, Legrand M, Loll-Krippleber R, Marton T, Maufrais C, Ropars J, Sertour N, Sitterlé E. 2017. Genome Diversity and Dynamics in Candida albicans. In: Candida albicans: Cellular and Molecular Biology. Springer, Cham. p. 205–232. [accessed 2018 Jul 10].
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Farasin J, Koechler S, Varet H, Deschamps J, Dillies M-A, Proux C, Erhardt M, Huber A, Jagla B, Briandet R, Coppée J-Y, Arsène-Ploetze F. 2017. Comparison of biofilm formation and motility processes in arsenic-resistant Thiomonas spp. strains revealed divergent response to arsenite. Microb Biotechnol. 10:789–803. doi:
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Fogel O, Rivière E, Seror R, Nocturne G, Boudaoud S, Ly B, Gottenberg J-E, Le Guern V, Dubost J-J, Nititham J, Taylor KE, Chanson P, Dieudé P, Criswell LA, Jagla B, Thai A, Mingueneau M, Mariette X, Miceli-Richard C. 2017 Sep. Role of the IL-12/IL-35 balance in patients with Sjögren syndrome. Journal of Allergy and Clinical Immunology. doi:
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Gopalan S, Carja O, Fagny M, Patin E, Myrick JW, McEwen LM, Mah SM, Kobor MS, Froment A, Feldman MW, Quintana-Murci L, Henn BM. 2017. Trends in DNA Methylation with Age Replicate Across Diverse Human Populations. Genetics. 206:1659–1674. doi:
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Grotzke JE, Kozik P, Morel J-D, Impens F, Pietrosemoli N, Cresswell P, Amigorena S, Demangel C. 2017. Sec61 blockade by mycolactone inhibits antigen cross-presentation independently of endosome-to-cytosol export. Proc Natl Acad Sci USA. 114:E5910–E5919. doi:
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Halloum I, Viljoen A, Khanna V, Craig D, Bouchier C, Brosch R, Coxon G, Kremer L. 2017. Resistance to Thiacetazone Derivatives Active against Mycobacterium abscessus Involves Mutations in the MmpL5 Transcriptional Repressor MAB_4384. Antimicrob Agents Chemother. 61. doi:
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Herbert S, Brion A, Arbona J, Lelek M, Veillet A, Lelandais B, Parmar J, Fernández FG, Almayrac E, Khalil Y, Birgy E, Fabre E, Zimmer C. 2017. Chromatin stiffening underlies enhanced locus mobility after DNA damage in budding yeast. The EMBO Journal. 36:2595–2608. doi:
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Hillion K-H, Kuzmin I, Khodak A, Rasche E, Crusoe M, Peterson H, Ison J, Ménager H. 2017. Using bio.tools to generate and annotate workbench tool descriptions. F1000Research. 6:2074. doi:
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Hurtado-Ortiz R, Nazimoudine A, Criscuolo A, Hugon P, Mornico D, Brisse S, Bizet C, Clermont D. 2017. Psychrobacter pasteurii and Psychrobacter piechaudii sp. nov., two novel species within the genus Psychrobacter. Int J Syst Evol Microbiol. 67:3192–3197. doi:
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Impens F, Rolhion N, Radoshevich L, Bécavin C, Duval M, Mellin J, García Del Portillo F, Pucciarelli MG, Williams AH, Cossart P. 2017. N-terminomics identifies Prli42 as a membrane miniprotein conserved in Firmicutes and critical for stressosome activation in Listeria monocytogenes. Nat Microbiol. 2:17005. doi:
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Jacob V, Monsempès C, Rospars J-P, Masson J-B, Lucas P. 2017. Olfactory coding in the turbulent realm. Morozov AV, editor. PLOS Computational Biology. 13:e1005870. doi:
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Kiattibutr K, Roobsoong W, Sriwichai P, Saeseu T, Rachaphaew N, Suansomjit C, Buates S, Obadia T, Mueller I, Cui L, Nguitragool W, Sattabongkot J. 2017. Infectivity of symptomatic and asymptomatic Plasmodium vivax infections to a Southeast Asian vector, Anopheles dirus. Int J Parasitol. 47:163–170. doi:
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Koepfli C, Ome-Kaius M, Jally S, Malau E, Maripal S, Ginny J, Timinao L, Kattenberg JH, Obadia T, White M, Rarau P, Senn N, Barry AE, Kazura JW, Mueller I, Robinson LJ. 2017. Sustained Malaria Control Over an 8-Year Period in Papua New Guinea: The Challenge of Low-Density Asymptomatic Plasmodium Infections. J Infect Dis. 216:1434–1443. doi:
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Kraemer MUG, Faria NR, Reiner RC, Golding N, Nikolay B, Stasse S, Johansson MA, Salje H, Faye O, Wint GRW, Niedrig M, Shearer FM, Hill SC, Thompson RN, Bisanzio D, Taveira N, Nax HH, Pradelski BSR, Nsoesie EO, Murphy NR, Bogoch II, Khan K, Brownstein JS, Tatem AJ, de Oliveira T, Smith DL, Sall AA, Pybus OG, Hay SI, Cauchemez S. 2017. Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study. Lancet Infect Dis. 17:330–338. doi:
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Lago M, Monteil V, Douche T, Guglielmini J, Criscuolo A, Maufrais C, Matondo M, Norel F. 2017. Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation. Sci Rep. 7:2127. doi:
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Laso-Jadart R, Harmant C, Quach H, Zidane N, Tyler-Smith C, Mehdi Q, Ayub Q, Quintana-Murci L, Patin E. 2017. The Genetic Legacy of the Indian Ocean Slave Trade: Recent Admixture and Post-admixture Selection in the Makranis of Pakistan. Am J Hum Genet. 101:977–984. doi:
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Lazar‐Stefanita L, Scolari VF, Mercy G, Muller H, Guérin TM, Thierry A, Mozziconacci J, Koszul R. 2017. Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle. The EMBO Journal. 36:2684–2697. doi:
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Lèbre S, Gascuel O. 2017. The combinatorics of overlapping genes. Journal of Theoretical Biology. 415:90–101. doi:
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Lefort V, Longueville J-E, Gascuel O. 2017. SMS: Smart Model Selection in PhyML. Molecular Biology and Evolution. 34:2422–2424. doi:
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Lugagne J-B, Sosa Carrillo S, Kirch M, Köhler A, Batt G, Hersen P. 2017. Balancing a genetic toggle switch by real-time feedback control and periodic forcing. Nat Commun. 8:1671. doi:
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Machado L, Esteves de Lima J, Fabre O, Proux C, Legendre R, Szegedi A, Varet H, Ingerslev LR, Barrès R, Relaix F, Mourikis P. 2017. In Situ Fixation Redefines Quiescence and Early Activation of Skeletal Muscle Stem Cells. Cell Rep. 21:1982–1993. doi:
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Manry J, Nédélec Y, Fava VM, Cobat A, Orlova M, Thuc NV, Thai VH, Laval G, Barreiro LB, Schurr E. 2017. Deciphering the genetic control of gene expression following Mycobacterium leprae antigen stimulation. PLoS Genet. 13:e1006952. doi:
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Marchant A, Le Coupanec A, Joly C, Perthame E, Sertour N, Garnier M, Godard V, Ferquel E, Choumet V. 2017. Infection of Ixodes ricinus by Borrelia burgdorferi sensu lato in peri-urban forests of France. PLoS ONE. 12:e0183543. doi:
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Mazuet C, Legeay C, Sautereau J, Bouchier C, Criscuolo A, Bouvet P, Trehard H, Silva NJD, Popoff M. 2017 Feb 1. Characterization of Clostridium Baratii Type F Strains Responsible for an Outbreak of Botulism Linked to Beef Meat Consumption in France. PLoS Curr. doi:
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Moratorio G, Henningsson R, Barbezange C, Carrau L, Bordería AV, Blanc H, Beaucourt S, Poirier EZ, Vallet T, Boussier J, Mounce BC, Fontes M, Vignuzzi M. 2017. Attenuation of RNA viruses by redirecting their evolution in sequence space. Nature Microbiology. 2:17088. doi:
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Moura A, Tourdjman M, Leclercq A, Hamelin E, Laurent E, Fredriksen N, Van Cauteren D, Bracq-Dieye H, Thouvenot P, Vales G, Tessaud-Rita N, Maury MM, Alexandru A, Criscuolo A, Quevillon E, Donguy M-P, Enouf V, de Valk H, Brisse S, Lecuit M. 2017. Real-Time Whole-Genome Sequencing for Surveillance of Listeria monocytogenes, France. Emerging Infect Dis. 23:1462–1470. doi:
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Nikolay B, Salje H, Sturm-Ramirez K, Azziz-Baumgartner E, Homaira N, Ahmed M, Iuliano AD, Paul RC, Rahman M, Hossain MJ, Luby SP, Cauchemez S, Gurley ES. 2017. Evaluating Hospital-Based Surveillance for Outbreak Detection in Bangladesh: Analysis of Healthcare Utilization Data. PLoS Med. 14:e1002218. doi:
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Paladino S, Lebreton S, Lelek M, Riccio P, De Nicola S, Zimmer C, Zurzolo C. 2017. GPI-anchored proteins are confined in subdiffraction clusters at the apical surface of polarized epithelial cells. Biochemical Journal. 474:4075–4090. doi:
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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. 2017. Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. Nature Communications. 8:15483. doi:
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Pietrosemoli N, Mella S, Yennek S, Baghdadi MB, Sakai H, Sambasivan R, Pala F, Di Girolamo D, Tajbakhsh S. 2017. Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells. Skelet Muscle. 7:28. doi:
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Poirson J, Biquand E, Straub M-L, Cassonnet P, Nominé Y, Jones L, van der Werf S, Travé G, Zanier K, Jacob Y, Demeret C, Masson M. 2017. Mapping the interactome of HPV E6 and E7 oncoproteins with the ubiquitin-proteasome system. The FEBS Journal. 284:3171–3201. doi:
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Prieto Barja P, Pescher P, Bussotti G, Dumetz F, Imamura H, Kedra D, Domagalska M, Chaumeau V, Himmelbauer H, Pages M, Sterkers Y, Dujardin J-C, Notredame C, Späth GF. 2017. Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani. Nat Ecol Evol. 1:1961–1969. doi:
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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. 2017. LipL21 lipoprotein binding to peptidoglycan enables Leptospira interrogans to escape NOD1 and NOD2 recognition. PLoS Pathog. 13:e1006725. doi:
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Remorino A, De Beco S, Cayrac F, Di Federico F, Cornilleau G, Gautreau A, Parrini MC, Masson J-B, Dahan M, Coppey M. 2017. Gradients of Rac1 Nanoclusters Support Spatial Patterns of Rac1 Signaling. Cell Rep. 21:1922–1935. doi:
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Ribet D, Lallemand-Breitenbach V, Ferhi O, Nahori M-A, Varet H, de Thé H, Cossart P. 2017. Promyelocytic Leukemia Protein (PML) Controls
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Zellweger RM, Cano J, Mangeas M, Taglioni F, Mercier A, Despinoy M, Menkès CE, Dupont-Rouzeyrol M, Nikolay B, Teurlai M. 2017. Socioeconomic and environmental determinants of dengue transmission in an urban setting: An ecological study in Nouméa, New Caledonia. PLoS Negl Trop Dis. 11:e0005471. doi:
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Zhao W, Siegel D, Biton A, Tonqueze OL, Zaitlen N, Ahituv N, Erle DJ. 2017. CRISPR–Cas9-mediated functional dissection of 3′-UTRs. Nucleic Acids Research. 45:10800–10810. doi:
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41 publications in 2016
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Antunes LC, Poppleton D, Klingl A, Criscuolo A, Dupuy B, Brochier-Armanet C, Beloin C, Gribaldo S. 2016. Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes. Elife. 5. doi:
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