Hub publications

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28 publications in 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 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.
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.
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.
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 Jun 8]. 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. Nature Communications. 9. doi:10.1038/s41467-018-04209-5. [accessed 2018 Jun 14]. http://www.nature.com/articles/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.
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:10.1128/mBio.00573-18.
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:10.12688/f1000research.15140.1.
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.
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:10.1186/s12864-018-4716-8. [accessed 2018 Jun 14]. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4716-8.
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:10.1038/s41586-018-0043-0.
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:10.1093/nar/gky342. [accessed 2018 Jun 8]. https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky342/4999236.
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. 2018. 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. 111:55–72. doi:10.1007/s10482-017-0926-3.
Poupel O, Proux C, Jagla B, Msadek T, Dubrac S. 2018. SpdC, a novel virulence factor, controls histidine kinase activity in Staphylococcus aureus. PLoS Pathog. 14:e1006917. doi:10.1371/journal.ppat.1006917.
Randrianjatovo-Gbalou I, Rosario S, Sismeiro O, Varet H, Legendre R, Coppée J-Y, Huteau V, Pochet S, Delarue M. 2018 May 21. Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries. Nucleic Acids Research. doi:10.1093/nar/gky413. [accessed 2018 Jun 14]. https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky413/5000021.
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. 2018 Jul 9. The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus. Nucleic Acids Research. doi:10.1093/nar/gky584. [accessed 2018 Jul 11]. https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky584/5050623.
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 M-E, d’Enfert C. 2018. Gene flow contributes to diversification of the major fungal pathogen Candida albicans. Nat Commun. 9:2253. doi:10.1038/s41467-018-04787-4.
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:10.1038/s41598-018-27086-w.
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:10.1093/ecco-jcc/jjx153.