• 2024
  Rai LS, Chauvel M, Sanchez H, van Wijlick L, Maufrais C, Cokelaer T, Sertour N, Legrand M, Sanyal K, Andes DR, Bachellier-Bassi S, d'Enfert C, Metabolic reprogramming during Candida albicans planktonic-biofilm transition is modulated by the transcription factors Zcf15 and Zcf26., PLoS Biol 2024 Jun; 22(6): e3002693.
• 2024
  Lopes A-A, Vendrell-Fernández S, Deschamps J, Georgeault S, Cokelaer T, Briandet R, Ghigo J-M, Bile-induced biofilm formation in Bacteroides thetaiotaomicron requires magnesium efflux by an RND pump., mBio 2024 May 8;15(5): e0348823.
• 2023
  Patitucci C, Hernández-Camacho JD, Vimont E, Yde S, Cokelaer T, Chaze T, Giai Gianetto Q, Matondo M, Gazi A, Nemazanyy I, Stroud DA, Hock DH, Donnarumma E, Wai T, Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis., Nat Commun 2023 Dec; 14(1): 8474.
• 2023
  Cokelaer T, Cohen-Boulakia S, Lemoine F, Reprohackathons: promoting reproducibility in bioinformatics through training., Bioinformatics 2023 Jun; 39(39 Suppl 1): i11-i20.
• 2023
  Sarah Temmam, Xavier Montagutelli, Cécile Herate, Flora Donati, Béatrice Regnault, Mikael Attia, Eduard Baquero Salazar, Delphine Chretien, Laurine Conquet, Grégory Jouvion, Juliana Pipoli da Fonseca, Thomas Cokelaer, Faustine Amara, Francis Relouzat, Thibaut Naninck, Julien Lemaitre, Nathalie Derreudre-Bosquet, Quentin Pascal, Massimiliano Bonomi, Thomas Bigot, Sandie Munier, Felix Rey, Roger Le Grand, Sylvie van der Werf, Marc Eloit, SARS‐CoV‐2‐related bat virus behavior in human‐relevant models sheds light on the origin of COVID‐19, EMBO Reports, 2023, 24 (4), pp.e56055. ⟨10.15252/embr.202256055⟩.
• 2023
  Proutière A, du Merle L, Garcia-Lopez M, Léger C, Voegele A, Chenal A, Harrington A, Tal-Gan Y, Cokelaer T, Trieu-Cuot P, Dramsi S, , Gallocin A, an Atypical Two-Peptide Bacteriocin with Intramolecular Disulfide Bonds Required for Activity., Microbiol Spectr 2023 Mar; (): e0508522.
• 2022
  Juliana Pipoli da Fonseca,Etienne Kornobis,Elodie Turc,Vincent Enouf2,Laure Lemée, Thomas Cokelaer,Marc Monot, Capturing SARS-CoV-2 from patient samples with low viral abundance: a comparative analysis, 2022 12:19274.
• 2022
  Vincendeau E, Wei W, Zhang X, Planchais C, Yu W, Lenden-Hasse H, Cokelaer T, Pipoli da Fonseca J, Mouquet H, Adams DJ, Alt FW, Jackson SP, Balmus G, Lescale C, Deriano L, , SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination., Nat Commun 2022 Jun; 13(1): 3707.
• 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
  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
  Anne-Sophie L'Honneur, Juliana Pipoli Da Fonseca, Thomas Cokelaer, Flore Rozenberg, JC Polyomavirus whole genome sequencing at the single molecule level reveals emerging neurotropic populations in Progressive Multifocal Leucoencephalopathy, J. Infect. Dis..
• 2021
  Phoka T, Fule L, Da Fonseca JP, Cokelaer T, Picardeau M, Patarakul K., Investigating the role of the carbon storage regulator A (CsrA) Leptospira spp., PLoS One . 2021 Dec 13;16(12):e0260981.
• 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 Aug; 13(8): e14122.
• 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
  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 Jun; 13(596): .
• 2021
  Sabrina Kalia, Corinne Jallet, Saliha Azebi, Thomas Cokelaer, Juliana Pipoli Da Fonseca, Yu Wu, Julien Barbier , Jean-Christophe Cintrat, Daniel Gillet, Noël Tordo, Broad spectrum compounds targeting early stages of RABV infection, Antiviral Res 188 (2021) 105016.
• 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.
• 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
  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
  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
  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
  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.
• 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
  Eduati F, Doldàn-Martelli V, Klinger B, Cokelaer T, Sieber A, Kogera F, Dorel M, Garnett MJ, Blüthgen N, Saez-Rodriguez J, Drug resistance mechanisms in colorectal cancer dissected with cell type-specific dynamic logic models, Cancer Res. 2017 Apr;.
• 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
  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
  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.
• 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
  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.
• 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
  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
  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
  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.
• 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
  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
  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
  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.
• 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
  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.
• 2009
  Abbott et al., An upper limit on the stochastic gravitational-wave background of cosmological origin, Nature 2009 Aug;460(7258):990-4.
• 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.
• 2008
  Abbott et al., Search for gravitational-wave bursts from soft gamma repeaters, Phys. Rev. Lett. 2008 Nov;101(21):211102.
• 2005
  Abbott et al., Upper limits on a stochastic background of gravitational waves, Phys. Rev. Lett. 2005 Nov;95(22):221101.
• 2005
  Abbott et al., Limits on gravitational-wave emission from selected pulsars using LIGO data, Phys. Rev. Lett. 2005 May;94(18):181103.