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Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28130-0
By:
- Claireaux, Mathieu;
- Robinot, Rémy;
- Kervevan, Jérôme;
- Patgaonkar, Mandar;
- Staropoli, Isabelle;
- Brelot, Anne;
- Nouël, Alexandre;
- Gellenoncourt, Stacy;
- Tang, Xian;
- Héry, Mélanie;
- Volant, Stevenn;
- Perthame, Emeline;
- Avettand-Fenoël, Véronique;
- Buchrieser, Julian;
- Cokelaer, Thomas;
- Bouchier, Christiane;
- Ma, Laurence;
- Boufassa, Faroudy;
- Hendou, Samia;
- Libri, Valentina
Publication type:
Article
SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31287-3
By:
- Vincendeau, Estelle;
- Wei, Wenming;
- Zhang, Xuefei;
- Planchais, Cyril;
- Yu, Wei;
- Lenden-Hasse, Hélène;
- Cokelaer, Thomas;
- Pipoli da Fonseca, Juliana;
- Mouquet, Hugo;
- Adams, David J.;
- Alt, Frederick W.;
- Jackson, Stephen P.;
- Balmus, Gabriel;
- Lescale, Chloé;
- Deriano, Ludovic
Publication type:
Article
Attenuation of clinical and immunological outcomes during SARS‐CoV‐2 infection by ivermectin.
Published in:
EMBO Molecular Medicine, 2021, v. 13, n. 8, p. 1, doi. 10.15252/emmm.202114122
By:
- de Melo, Guilherme Dias;
- Lazarini, Françoise;
- Larrous, Florence;
- Feige, Lena;
- Kornobis, Etienne;
- Levallois, Sylvain;
- Marchio, Agnès;
- Kergoat, Lauriane;
- Hardy, David;
- Cokelaer, Thomas;
- Pineau, Pascal;
- Lecuit, Marc;
- Lledo, Pierre‐Marie;
- Changeux, Jean‐Pierre;
- Bourhy, Hervé
Publication type:
Article
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
Published in:
BMC Systems Biology, 2014, v. 8, n. 1, p. 1, doi. 10.1186/1752-0509-8-13
By:
- Meyer, Pablo;
- Cokelaer, Thomas;
- Chandran, Deepak;
- Kyung Hyuk Kim;
- Po-Ru Loh;
- Tucker, George;
- Lipson, Mark;
- Berger, Bonnie;
- Kreutz, Clemens;
- Raue, Andreas;
- Steiert, Bernhard;
- Timmer, Jens;
- Bilal, Erhan;
- Sauro, Herbert M.;
- Stolovitzky, Gustavo;
- Saez-Rodriguez, Julio
Publication type:
Article
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Published in:
BMC Systems Biology, 2013, v. 7, n. 1, p. 3, doi. 10.1186/1752-0509-7-135
By:
- Chaouiya, Claudine;
- Berenguier, Duncan;
- Keating, Sarah M.;
- Naldi, Aurelien;
- Van Iersel, Martijn P.;
- Rodriguez, Nicolas;
- Dräger, Andreas;
- Büchel, Finja;
- Cokelaer, Thomas;
- Kowal, Bryan;
- Wicks, Benjamin;
- Gonçalves, Emanuel;
- Dorier, Julien;
- Page, Michel;
- Monteiro, Pedro T.;
- Kamp, Axel von;
- Xenarios, Ioannis;
- Jong, Hidde de;
- Hucka, Michael;
- Klamt, Steffen
Publication type:
Article
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.
Published in:
BMC Systems Biology, 2012, v. 6, n. 1, p. 1, doi. 10.1186/1752-0509-6-133
By:
- Terfve, Camille;
- Cokelaer, Thomas;
- Henriques, David;
- MacNamara, Aidan;
- Goncalves, Emanuel;
- Morris, Melody K.;
- van Iersel, Martijn;
- Lauffenburger, Douglas A.;
- Saez-Rodriguez, Julio
Publication type:
Article
Core genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing.
Published in:
BMC Infectious Diseases, 2023, v. 23, n. 1, p. 1, doi. 10.1186/s12879-023-08126-x
By:
- Grillova, Linda;
- Cokelaer, Thomas;
- Mariet, Jean-François;
- da Fonseca, Juliana Pipoli;
- Picardeau, Mathieu
Publication type:
Article
Efficient randomization of biological networks while preserving functional characterization of individual nodes.
Published in:
BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-1402-1
By:
- Iorio, Francesco;
- Bernardo-Faura, Marti;
- Gobbi, Andrea;
- Cokelaer, Thomas;
- Jurman, Giuseppe;
- Saez-Rodriguez, Julio
Publication type:
Article
BioConvert: a comprehensive format converter for life sciences.
Published in:
NAR Genomics & Bioinformatics, 2023, v. 5, n. 3, p. 1, doi. 10.1093/nargab/lqad074
By:
- Caro, Hugo;
- Dollin, Sulyvan;
- Biton, Anne;
- Brancotte, Bryan;
- Desvillechabrol, Dimitri;
- Dufresne, Yoann;
- Li, Blaise;
- Kornobis, Etienne;
- Lemoine, Frédéric;
- Maillet, Nicolas;
- Perrin, Amandine;
- Traut, Nicolas;
- Néron, Bertrand;
- Cokelaer, Thomas
Publication type:
Article
Capturing SARS-CoV-2 from patient samples with low viral abundance: a comparative analysis.
Published in:
Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-23422-3
By:
- Pipoli da Fonseca, Juliana;
- Kornobis, Etienne;
- Turc, Elodie;
- Enouf, Vincent;
- Lemée, Laure;
- Cokelaer, Thomas;
- Monot, Marc
Publication type:
Article
Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28130-0
By:
- Claireaux, Mathieu;
- Robinot, Rémy;
- Kervevan, Jérôme;
- Patgaonkar, Mandar;
- Staropoli, Isabelle;
- Brelot, Anne;
- Nouël, Alexandre;
- Gellenoncourt, Stacy;
- Tang, Xian;
- Héry, Mélanie;
- Volant, Stevenn;
- Perthame, Emeline;
- Avettand-Fenoël, Véronique;
- Buchrieser, Julian;
- Cokelaer, Thomas;
- Bouchier, Christiane;
- Ma, Laurence;
- Boufassa, Faroudy;
- Hendou, Samia;
- Libri, Valentina
Publication type:
Article
Evaluation of methods for modeling transcription factor sequence specificity.
Published in:
Nature Biotechnology, 2013, v. 31, n. 2, p. 126, doi. 10.1038/nbt.2486
By:
- Weirauch, Matthew T;
- Cote, Atina;
- Norel, Raquel;
- Annala, Matti;
- Zhao, Yue;
- Riley, Todd R;
- Saez-Rodriguez, Julio;
- Cokelaer, Thomas;
- Vedenko, Anastasia;
- Talukder, Shaheynoor;
- Agius, Phaedra;
- Arvey, Aaron;
- Bucher, Philipp;
- Callan, Curtis G;
- Chang, Cheng Wei;
- Chen, Chien-Yu;
- Chen, Yong-Syuan;
- Chu, Yu-Wei;
- Grau, Jan;
- Grosse, Ivo
Publication type:
Article
Reprohackathons: promoting reproducibility in bioinformatics through training.
Published in:
Bioinformatics, 2023, v. 39, p. i11, doi. 10.1093/bioinformatics/btad227
By:
- Cokelaer, Thomas;
- Cohen-Boulakia, Sarah;
- Lemoine, Frédéric
Publication type:
Article
Sequana coverage: detection and characterization of genomic variations using running median and mixture models.
Published in:
GigaScience, 2018, v. 7, n. 12, p. N.PAG, doi. 10.1093/gigascience/giy110
By:
- Desvillechabrol, Dimitri;
- Bouchier, Christiane;
- Kennedy, Sean;
- Cokelaer, Thomas
Publication type:
Article
Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-44143-9
By:
- Patitucci, Cecilia;
- Hernández-Camacho, Juan Diego;
- Vimont, Elodie;
- Yde, Sonny;
- Cokelaer, Thomas;
- Chaze, Thibault;
- Giai Gianetto, Quentin;
- Matondo, Mariette;
- Gazi, Anastasia;
- Nemazanyy, Ivan;
- Stroud, David A.;
- Hock, Daniella H.;
- Donnarumma, Erminia;
- Wai, Timothy
Publication type:
Article
Experimental evolution links post-transcriptional regulation to Leishmania fitness gain.
Published in:
PLoS Pathogens, 2022, v. 18, n. 3, p. 1, doi. 10.1371/journal.ppat.1010375
By:
- Piel, Laura;
- Rajan, K. Shanmugha;
- Bussotti, Giovanni;
- Varet, Hugo;
- Legendre, Rachel;
- Proux, Caroline;
- Douché, Thibaut;
- Giai-Gianetto, Quentin;
- Chaze, Thibault;
- Cokelaer, Thomas;
- Vojtkova, Barbora;
- Gordon-Bar, Nadav;
- Doniger, Tirza;
- Cohen-Chalamish, Smadar;
- Rengaraj, Praveenkumar;
- Besse, Céline;
- Boland, Anne;
- Sadlova, Jovana;
- Deleuze, Jean-François;
- Matondo, Mariette
Publication type:
Article
SARS‐CoV‐2‐related bat virus behavior in human‐relevant models sheds light on the origin of COVID‐19.
Published in:
EMBO Reports, 2023, v. 24, n. 4, p. 1, doi. 10.15252/embr.202256055
By:
- Temmam, Sarah;
- Montagutelli, Xavier;
- Herate, Cécile;
- Donati, Flora;
- Regnault, Béatrice;
- Attia, Mikael;
- Baquero Salazar, Eduard;
- Chretien, Delphine;
- Conquet, Laurine;
- Jouvion, Grégory;
- Pipoli Da Fonseca, Juliana;
- Cokelaer, Thomas;
- Amara, Faustine;
- Relouzat, Francis;
- Naninck, Thibaut;
- Lemaitre, Julien;
- Derreudre‐Bosquet, Nathalie;
- Pascal, Quentin;
- Bonomi, Massimiliano;
- Bigot, Thomas
Publication type:
Article
Investigating the role of the carbon storage regulator A (CsrA) in Leptospira spp.
Published in:
PLoS ONE, 2021, v. 16, n. 12, p. 1, doi. 10.1371/journal.pone.0260981
By:
- Phoka, Theerapat;
- Fule, Lenka;
- Da Fonseca, Juliana Pipoli;
- Cokelaer, Thomas;
- Picardeau, Mathieu;
- Patarakul, Kanitha
Publication type:
Article
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
Published in:
BMC Bioinformatics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2105-15-136
By:
- Egea, Jose A.;
- Henriques, David;
- Cokelaer, Thomas;
- Villaverde, Alejandro F.;
- MacNamara, Aidan;
- Danciu, Diana-Patricia;
- Banga, Julio R.;
- Saez-Rodriguez, Julio
Publication type:
Article
Metabolic reprogramming during Candida albicans planktonic-biofilm transition is modulated by the transcription factors Zcf15 and Zcf26.
Published in:
PLoS Biology, 2024, v. 22, n. 6, p. 1, doi. 10.1371/journal.pbio.3002693
By:
- Rai, Laxmi Shanker;
- Chauvel, Murielle;
- Sanchez, Hiram;
- van Wijlick, Lasse;
- Maufrais, Corinne;
- Cokelaer, Thomas;
- Sertour, Natacha;
- Legrand, Mélanie;
- Sanyal, Kaustuv;
- Andes, David R.;
- Bachellier-Bassi, Sophie;
- d'Enfert, Christophe
Publication type:
Article
Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.
Published in:
Molecular Systems Biology, 2014, v. 10, n. 12, p. 1, doi. 10.15252/msb.20145112
By:
- Vaga, Stefania;
- Bernardo‐Faura, Marti;
- Cokelaer, Thomas;
- Maiolica, Alessio;
- Barnes, Christopher A;
- Gillet, Ludovic C;
- Hegemann, Björn;
- Drogen, Frank;
- Sharifian, Hoda;
- Klipp, Edda;
- Peter, Matthias;
- Saez‐Rodriguez, Julio;
- Aebersold, Ruedi
Publication type:
Article
Belt and braces: Two escape ways to maintain the cassette reservoir of large chromosomal integrons.
Published in:
PLoS Genetics, 2024, v. 20, n. 4, p. 1, doi. 10.1371/journal.pgen.1011231
By:
- Richard, Egill;
- Darracq, Baptiste;
- Littner, Eloi;
- Millot, Gael A.;
- Conte, Valentin;
- Cokelaer, Thomas;
- Engelstädter, Jan;
- Rocha, Eduardo P. C.;
- Mazel, Didier;
- Loot, Céline
Publication type:
Article
Signal-sensing triggers the shutdown of HemKR, regulating heme and iron metabolism in the spirochete Leptospira biflexa.
Published in:
PLoS ONE, 2024, v. 19, n. 9, p. 1, doi. 10.1371/journal.pone.0311040
By:
- Imelio, Juan Andrés;
- Trajtenberg, Felipe;
- Mondino, Sonia;
- Zarantonelli, Leticia;
- Vitrenko, Iakov;
- Lemée, Laure;
- Cokelaer, Thomas;
- Picardeau, Mathieu;
- Buschiazzo, Alejandro
Publication type:
Article
COVID-19–related anosmia is associated with viral persistence and inflammation in human olfactory epithelium and brain infection in hamsters.
Published in:
Science Translational Medicine, 2021, v. 13, n. 596, p. 1, doi. 10.1126/scitranslmed.abf8396
By:
- de Melo, Guilherme Dias;
- Lazarini, Françoise;
- Levallois, Sylvain;
- Hautefort, Charlotte;
- Michel, Vincent;
- Larrous, Florence;
- Verillaud, Benjamin;
- Aparicio, Caroline;
- Wagner, Sebastien;
- Gheusi, Gilles;
- Kergoat, Lauriane;
- Kornobis, Etienne;
- Donati, Flora;
- Cokelaer, Thomas;
- Hervochon, Rémi;
- Madec, Yoann;
- Roze, Emmanuel;
- Salmon, Dominique;
- Bourhy, Hervé;
- Lecuit, Marc
Publication type:
Article
JC Polyomavirus Whole Genome Sequencing at the Single-Molecule Level Reveals Emerging Neurotropic Populations in Progressive Multifocal Leukoencephalopathy.
Published in:
2022
By:
- L'Honneur, Anne Sophie;
- Fonseca, Juliana Pipoli Da;
- Cokelaer, Thomas;
- Rozenberg, Flore;
- Pipoli Da Fonseca, Juliana
Publication type:
journal article
Sequanix: a dynamic graphical interface for Snakemake workflows.
Published in:
Bioinformatics, 2018, v. 34, n. 11, p. 1934, doi. 10.1093/bioinformatics/bty034
By:
- Desvillechabrol, Dimitri;
- Legendre, Rachel;
- Rioualen, Claire;
- Bouchier, Christiane;
- Helden, Jacques van;
- Kennedy, Sean;
- Cokelaer, Thomas
Publication type:
Article
GDSCTools for mining pharmacogenomic interactions in cancer.
Published in:
Bioinformatics, 2018, v. 34, n. 7, p. 1226, doi. 10.1093/bioinformatics/btx744
By:
- Cokelaer, Thomas;
- Chen, Elisabeth;
- Iorio, Francesco;
- Menden, Michael P;
- Lightfoot, Howard;
- Saez-Rodriguez, Julio;
- Garnett, Mathew J
Publication type:
Article
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Published in:
2014
By:
- Guziolowski, Carito;
- Videla, Santiago;
- Eduati, Federica;
- Thiele, Sven;
- Cokelaer, Thomas;
- Siegel, Anne;
- Saez-Rodriguez, Julio
Publication type:
Correction Notice
BioServices: a common Python package to access biological Web Services programmatically.
Published in:
Bioinformatics, 2013, v. 29, n. 24, p. 3241, doi. 10.1093/bioinformatics/btt547
By:
- Cokelaer, Thomas;
- Pultz, Dennis;
- Harder, Lea M.;
- Serra-Musach, Jordi;
- Saez-Rodriguez, Julio
Publication type:
Article
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Published in:
Bioinformatics, 2013, v. 29, n. 18, p. 2320, doi. 10.1093/bioinformatics/btt393
By:
- Guziolowski, Carito;
- Videla, Santiago;
- Eduati, Federica;
- Thiele, Sven;
- Cokelaer, Thomas;
- Siegel, Anne;
- Saez-Rodriguez, Julio
Publication type:
Article
L-Py:an L-system simulation framework for modeling plant architecture development based on a dynamic language.
Published in:
Frontiers in Plant Science, 2012, v. 3, p. 1, doi. 10.3389/fpls.2012.00076
By:
- Boudon, Frédéric;
- Christophe Pradal;
- Thomas Cokelaer;
- Prusinkiewicz, Przemyslaw;
- Godin, Christophe
Publication type:
Article

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