Denis Thieffry

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Citations	13046	5228
h-index	59	42
i10-index	116	91

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Claudine ChaouiyaI2M UMR 7373, Aix Marseille University (France)Verified email at univ-amu.fr
Aurélien NaldiInria, FranceVerified email at inria.fr
Elisabeth RemyDirectrice de Recherche, CNRS, Aix-Marseille UniversitéVerified email at univ-amu.fr
THOMAS-CHOLLIER Morganeassociate professor, Ecole Normale Supérieure ParisVerified email at biologie.ens.fr
Jacques van HeldenAix-Marseille UniversitéVerified email at univ-amu.fr
Pedro T. MonteiroINESC-ID / IST - Universidade de LisboaVerified email at tecnico.ulisboa.pt
Céline HernandezI2BC / CNRSVerified email at i2bc.paris-saclay.fr
Wassim Abou-JaoudéCo-founder at GencoveryVerified email at gencovery.com
Samuel CollombetEMBLVerified email at embl.de
Alejandra Medina-RiveraLaboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma deVerified email at liigh.unam.mx
Adrien FauréYamaguchi UniversityVerified email at yamaguchi-u.ac.jp
Julio Collado-VidesProfessor of Computational Genomics, CCG, UNAMVerified email at ccg.unam.mx
Laurence CalzoneInstitut CurieVerified email at curie.fr
Carl HerrmannProfessor of Bioinformatics - IPMB - Heidelberg UniversityVerified email at uni-heidelberg.de
Thomas GrafCenter for Genomic Regulation, CRGVerified email at crg.eu
Tomas HelikarSusan J Rosowski Professor, Department of Biochemistry, University of Nebraska - LincolnVerified email at unl.edu
Matthieu DefranceAssociate Professor, Université Libre de BruxellesVerified email at ulb.be
José Luis Sardina OrtegaJosep Carreras Leukaemia Research InstituteVerified email at carrerasresearch.org
Hidde de JongINRIAVerified email at inria.fr
Kaufman MarcelleUniversité libre de BruxellesVerified email at ulb.ac.be

Denis Thieffry

Professor of Systems Biology, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris

Verified email at ens.fr

computational systems biology bioinformatics gene regulatory networks Boolean networks history of biology


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Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle A Fauré, A Naldi, C Chaouiya, D Thieffry Bioinformatics 22 (14), e124-e131, 2006	738	2006
Dynamical behaviour of biological regulatory networks—I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state R Thomas, D Thieffry, M Kaufman Bulletin of mathematical biology 57, 247-276, 1995	697	1995
From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli D Thieffry, AM Huerta, E Pérez‐Rueda, J Collado‐Vides Bioessays 20 (5), 433-440, 1998	647	1998
GOToolBox: functional analysis of gene datasets based on Gene Ontology D Martin, C Brun, E Remy, P Mouren, D Thieffry, B Jacq Genome biology 5 (12), 1-8, 2004	462	2004
Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis. L Mendoza, D Thieffry, ER Alvarez-Buylla Bioinformatics (Oxford, England) 15 (7), 593-606, 1999	406	1999
Dynamical behaviour of biological regulatory networks—II. Immunity control in bacteriophage lambda D Thieffry, R Thomas Bulletin of mathematical biology 57, 277-297, 1995	332	1995
RSAT 2011: regulatory sequence analysis tools M Thomas-Chollier, M Defrance, A Medina-Rivera, O Sand, C Herrmann, ... Nucleic acids research 39 (suppl_2), W86-W91, 2011	292	2011
A logical analysis of the Drosophila gap-gene system L Sánchez, D Thieffry Journal of theoretical Biology 211 (2), 115-141, 2001	287	2001
RSAT 2015: regulatory sequence analysis tools A Medina-Rivera, M Defrance, O Sand, C Herrmann, ... Nucleic acids research 43 (W1), W50-W56, 2015	269	2015
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets M Thomas-Chollier, C Herrmann, M Defrance, O Sand, D Thieffry, ... Nucleic acids research 40 (4), e31-e31, 2012	258	2012
RegulonDB: A database on transcriptional regulation in Escherichia coli AM Huerta, H Salgado, D Thieffry, J Collado-Vides Nucleic acids research 26 (1), 55-59, 1998	246	1998
Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework É Remy, P Ruet, D Thieffry Advances in Applied Mathematics 41 (3), 335-350, 2008	241	2008
Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance Ö Sahin, H Fröhlich, C Löbke, U Korf, S Burmester, M Majety, J Mattern, ... BMC systems biology 3 (1), 1-20, 2009	240	2009
C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells B Di Stefano, JL Sardina, C van Oevelen, S Collombet, EM Kallin, ... Nature 506 (7487), 235-239, 2014	237	2014
Logical modeling and dynamical analysis of cellular networks W Abou-Jaoudé, P Traynard, PT Monteiro, J Saez-Rodriguez, T Helikar, ... Frontiers in genetics 7, 94, 2016	227	2016
Mathematical modelling of cell-fate decision in response to death receptor engagement L Calzone, L Tournier, S Fourquet, D Thieffry, B Zhivotovsky, E Barillot, ... PLoS computational biology 6 (3), e1000702, 2010	226	2010
GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks AG Gonzalez, A Naldi, L Sanchez, D Thieffry, C Chaouiya Biosystems 84 (2), 91-100, 2006	215	2006
Logical modelling of regulatory networks with GINsim 2.3 A Naldi, D Berenguier, A Fauré, F Lopez, D Thieffry, C Chaouiya Biosystems 97 (2), 134-139, 2009	211	2009
Qualitative analysis of gene networks D Thieffry, R Thomas World Scientific, 1997	209	1997
Transcription factors drive Tet2-mediated enhancer demethylation to reprogram cell fate JL Sardina, S Collombet, TV Tian, A Gómez, B Di Stefano, C Berenguer, ... Cell stem cell 23 (5), 727-741. e9, 2018	200	2018

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