Hub publications

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58 publications in 2018

Amraoui F, Pain A, Piorkowski G, Vazeille M, Couto-Lima D, de Lamballerie X, Lourenco-de-Oliveira R, Failloux A-B. 2018. Experimental Adaptation of the Yellow Fever Virus to the Mosquito Aedes albopictus and Potential risk of urban epidemics in Brazil, South America. Sci Rep. 8:14337. doi:10.1038/s41598-018-32198-4.
Angebault C, Ghozlane A, Volant S, Botterel F, d’Enfert C, Bougnoux M-E. 2018. Combined bacterial and fungal intestinal microbiota analyses: Impact of storage conditions and DNA extraction protocols. PLoS One. 13:e0201174. doi:10.1371/journal.pone.0201174.
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.
Barbezange C, Jones L, Blanc H, Isakov O, Celniker G, Enouf V, Shomron N, Vignuzzi M, van der Werf S. 2018. Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing. Front Microbiol. 9:2596. doi:10.3389/fmicb.2018.02596.
Barckmann B, El-Barouk M, Pelisson A, Mugat B, Li B, Franckhauser C, Fiston Lavier A-S, Mirouze M, Fablet M, Chambeyron S. 2018. The somatic piRNA pathway controls germline transposition over generations. Nucleic Acids Res. 46:9524–9536. doi:10.1093/nar/gky761.
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.
Blin M, Le Tallec B, Nähse V, Schmidt M, Brossas C, Millot GA, Prioleau M-N, Debatisse M. 2019. Transcription-dependent regulation of replication dynamics modulates genome stability. Nat Struct Mol Biol. 26:58–66. doi:10.1038/s41594-018-0170-1.
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.
Bussotti G, Gouzelou E, Cortes Boite M, Kherachi I, Harrat Z, Eddaikra N, Mottram JC, Antoniou M, Christodoulou V, Bali A, Guerfali FZ, Laouini D, Mukhtar M, Dumetz F, Dujardin J-C, 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, Spath GF. 2018. Leishmania Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification. MBio. 9. doi:10.1128/mBio.01399-18.
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.
Cordier T, Forster D, Dufresne Y, Martins CIM, Stoeck T, Pawlowski J. 2018. Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring. Mol Ecol Resour. 18:1381–1391. doi:10.1111/1755-0998.12926.
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.
Cossec J-C, Theurillat I, Chica C, Bua Aguin S, Gaume X, Andrieux A, Iturbide A, Jouvion G, Li H, Bossis G, Seeler J-S, Torres-Padilla M-E, Dejean A. 2018. SUMO Safeguards Somatic and Pluripotent Cell Identities by Enforcing Distinct Chromatin States. Cell Stem Cell. 23:742-757.e8. doi:10.1016/j.stem.2018.10.001.
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.
Coya JM, De Matteis L, Giraud-Gatineau A, Biton A, Serrano-Sevilla I, Danckaert A, Dillies M-A, Gicquel B, De la Fuente JM, Tailleux L. 2019. Tri-mannose grafting of chitosan nanocarriers remodels the macrophage response to bacterial infection. J Nanobiotechnology. 17:15. doi:10.1186/s12951-018-0439-x.
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. 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.
Dargel AA, Volant S, Saha S, Etain B, Grant R, Azorin J-M, Gard S, Bellivier F, Bougerol T, Kahn J-P, Roux P, Aubin V, Courtet P, Leboyer M, Scott J, Henry C. 2018 Oct 11. Activation Levels, Cardiovascular Risk, and Functional Impairment in Remitted Bipolar Patients: Clinical Relevance of a Dimensional Approach. Psychother Psychosom.:1–3. doi:10.1159/000493690.
Dazas M, Badell E, Carmi-Leroy A, Criscuolo A, Brisse S. 2018. Taxonomic status of Corynebacterium diphtheriae biovar Belfanti and proposal of Corynebacterium belfantii sp. nov. Int J Syst Evol Microbiol. 68:3826–3831. doi:10.1099/ijsem.0.003069.
Desvillechabrol D, Bouchier C, Kennedy S, Cokelaer T. 2018. Sequana coverage: detection and characterization of genomic variations using running median and mixture models. Gigascience. 7. doi:10.1093/gigascience/giy110.
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-Rua 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, Alvarez AS, Baraffe A, Beiró M, Bertucci I, Cyncynatus C, Dannet F, Delaby ML, Denys P, De Cellès MD, Fraboulet A, Gaillard J-L, Herrmann J-L, Labrador B, Lasley J, Lawrence C, Legrand J, Le Minor O, Ligier C, Mignon K, Sacleux C, Salomon J, Perard M, Petit L, Remy L, Thiebaut A, Thomas D, Tronchet P, Villain I. 2018. Measuring dynamic social contacts in a rehabilitation hospital: Effect of wards, patient and staff characteristics. Scientific Reports. 8. doi:10.1038/s41598-018-20008-w.
Fogel O, Riviere E, Seror R, Nocturne G, Boudaoud S, Ly B, Gottenberg J-E, Le Guern V, Dubost J-J, Nititham J, Taylor KE, Chanson P, Dieude P, Criswell LA, Jagla B, Thai A, Mingueneau M, Mariette X, Miceli-Richard C. 2018. Role of the IL-12/IL-35 balance in patients with Sjogren syndrome. J Allergy Clin Immunol. 142:258-268.e5. doi:10.1016/j.jaci.2017.07.041.
Fourati S, Talla A, Mahmoudian M, Burkhart JG, Klén R, Henao R, Yu T, Aydın Z, Yeung KY, Ahsen ME, Almugbel R, Jahandideh S, Liang X, Nordling TEM, Shiga M, Stanescu A, Vogel R, Respiratory Viral DREAM Challenge Consortium, Pandey G, Chiu C, McClain MT, Woods CW, Ginsburg GS, Elo LL, Tsalik EL, Mangravite LM, Sieberts SK. 2018. A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection. Nat Commun. 9:4418. doi:10.1038/s41467-018-06735-8.
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. mBio. 9. doi:10.1128/mBio.00573-18.
Gouder L, Vitrac A, Goubran-Botros H, Danckaert A, Tinevez J-Y, André-Leroux G, Atanasova E, Lemière N, Biton A, Leblond CS, Poulet A, Boland A, Deleuze J-F, Benchoua A, Delorme R, Bourgeron T, Cloëz-Tayarani I. 2019. Altered spinogenesis in iPSC-derived cortical neurons from patients with autism carrying de novo SHANK3 mutations. Sci Rep. 9:94. doi:10.1038/s41598-018-36993-x.
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, BioContainers Community, Perez-Riverol Y. 2018. Recommendations for the packaging and containerizing of bioinformatics software. F1000Research. 7:742. doi:10.12688/f1000research.15140.1.
Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J, Bioconda Team. 2018. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 15:475–476. doi:10.1038/s41592-018-0046-7.
Haupt A, Ershov D, Minc N. 2018. A Positive Feedback between Growth and Polarity Provides Directional Persistency  and Flexibility to the Process of Tip Growth. Curr Biol. 28:3342-3351.e3. doi:10.1016/j.cub.2018.09.022.
Impens F, Rolhion N, Radoshevich L, Bécavin C, Duval M, Mellin J, García Del Portillo F, Pucciarelli MG, Williams AH, Cossart P. 2018. Author Correction: N-terminomics identifies Prli42 as a membrane miniprotein conserved in Firmicutes and critical for stressosome activation in Listeria monocytogenes. Nat Microbiol. 3:962. 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. Scientific Reports. 8. 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 May 29]. 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.
Maataoui N, Mayet A, Duron S, Delacour H, Mentre F, Laouenan C, Desvillechabrol D, Cokelaer T, Meynard JB, Ducher A, Andremont A, Armand-Lefevre L, Merens A. 2018 Aug 9. High acquisition rate of extended-spectrum beta-lactamase-producing Enterobacteriaceae among French military personnel on mission abroad, without evidence of inter-individual transmission. Clin Microbiol Infect. doi:10.1016/j.cmi.2018.07.030.
Missri L, Smiljkovski D, Prigent G, Lesenne A, Obadia T, Joumaa M, Chelha R, Chalumeau-Lemoine L, Obadia E, Galbois A. 2018 Nov 15. Bacterial colonization of healthcare workers’ mobile phones in the ICU and effectiveness of sanitization. J Occup Environ Hyg.:1–4. doi:10.1080/15459624.2018.1546051.
Morel J-D, Paatero AO, Wei J, Yewdell JW, Guenin-Macé L, Van Haver D, Impens F, Pietrosemoli N, Paavilainen VO, Demangel C. 2018. Proteomics Reveals Scope of Mycolactone-mediated Sec61 Blockade and Distinctive Stress Signature. Mol Cell Proteomics. 17:1750–1765. doi:10.1074/mcp.RA118.000824.
Nevers A, Doyen A, Malabat C, Néron B, Kergrohen T, Jacquier A, Badis G. 2018. Antisense transcriptional interference mediates condition-specific gene repression in budding yeast. Nucleic Acids Research. 46:6009–6025. doi:10.1093/nar/gky342.
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.
Pietrosemoli N, Dobay MP. 2018. Optimized Protein-Protein Interaction Network Usage with Context Filtering. Methods Mol Biol. 1819:33–50. doi:10.1007/978-1-4939-8618-7_2.
Pietrosemoli N, Mella S, Yennek S, Baghdadi MB, Sakai H, Sambasivan R, Pala F, Di Girolamo D, Tajbakhsh S. 2018. Correction to: Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells. Skelet Muscle. 8:19. doi:10.1186/s13395-018-0165-y.
Poupel O, Proux C, Jagla B, Msadek T, Dubrac S. 2018. SpdC, a novel virulence factor, controls histidine kinase activity in Staphylococcus aureus. PLoS Pathogens. 14. 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 May 29]. 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. The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus. Nucleic Acids Res. 46:8803–8816. doi:10.1093/nar/gky584.
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.
Rousset F, Cui L, Siouve E, Becavin C, Depardieu F, Bikard D. 2018. Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. PLoS Genet. 14:e1007749. doi:10.1371/journal.pgen.1007749.
Ruppe E, Ghozlane A, Tap J, Pons N, Alvarez A-S, Maziers N, Cuesta T, Hernando-Amado S, Clares I, Martinez JL, Coque TM, Baquero F, Lanza VF, Maiz L, Goulenok T, de Lastours V, Amor N, Fantin B, Wieder I, Andremont A, van Schaik W, Rogers M, Zhang X, Willems RJL, de Brevern AG, Batto J-M, Blottiere HM, Leonard P, Lejard V, Letur A, Levenez F, Weiszer K, Haimet F, Dore J, Kennedy SP, Ehrlich SD. 2019. Prediction of the intestinal resistome by a three-dimensional structure-based method. Nat Microbiol. 4:112–123. doi:10.1038/s41564-018-0292-6.
Schaeffer J, Carnec X, Reynard S, Mateo M, Picard C, Pietrosemoli N, Dillies M-A, Baize S. 2018. Lassa virus activates myeloid dendritic cells but suppresses their ability to stimulate T cells. PLoS Pathog. 14:e1007430. doi:10.1371/journal.ppat.1007430.
Schiettekatte O, Vincent AT, Malosse C, Lechat P, Chamot-Rooke J, Veyrier FJ, Picardeau M, Bourhy P. 2018. Characterization of LE3 and LE4, the only lytic phages known to infect the spirochete Leptospira. Sci Rep. 8:11781. doi:10.1038/s41598-018-29983-6.
Torres-Sanchez M, Creevey CJ, Kornobis E, Gower DJ, Wilkinson M, San Mauro D. 2018 Oct 22. Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families. DNA Res. doi:10.1093/dnares/dsy034.
Varet H, Coppee J-Y. 2018 Aug 25. checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes. Bioinformatics. doi:10.1093/bioinformatics/bty706.
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. Scientific Reports. 8. 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. Journal of Crohn’s and Colitis. 12:337–346. doi:10.1093/ecco-jcc/jjx153.