Syntactic recognition of regulatory regions in Escherichia coli. - David A. Rosenblueth; Denis Thieffry; Araceli M. Huerta; Heladia Salgado; Julio Collado-Vides (Comput. Appl. Biosci., 1996)

Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. - Denis Thieffry; Heladia Salgado; Araceli M. Huerta; Julio Collado-Vides (Bioinform., 1998)

RegulonDB: a database on transcriptional regulation in Escherichia coli. - Araceli M. Huerta; Heladia Salgado; Denis Thieffry; Julio Collado-Vides (Nucleic Acids Res., 1998)

Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis. - Luis Mendoza; Denis Thieffry; Elena R. Álvarez-Buylla (Bioinform., 1999)

A description of dynamical graphs associated to elementary regulatory circuits. - Elisabeth Remy; Brigitte Mossé; Claudine Chaouiya; Denis Thieffry (ECCB, 2003)

Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework. - Claudine Chaouiya; Elisabeth Remy; Brigitte Mossé; Denis Thieffry (POSTA, 2003)

Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets. - Claudine Chaouiya; Elisabeth Remy; Paul Ruet; Denis Thieffry (ICATPN, 2004)

Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli. - E. Simão; Elisabeth Remy; Denis Thieffry; Claudine Chaouiya (ECCB/JBI, 2005)

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. - Adrien Fauré; Aurélien Naldi; Claudine Chaouiya; Denis Thieffry (ISMB (Supplement of Bioinformatics), 2006)

Positive or Negative Regulatory Circuit Inference from Multilevel Dynamics. - Elisabeth Remy; Paul Ruet; Denis Thieffry (POSTA, 2006)

Qualitative Petri Net Modelling of Genetic Networks. - Claudine Chaouiya; Elisabeth Remy; Denis Thieffry (Trans. Comp. Sys. Biology, 2006)

From Logical Regulatory Graphs to Standard Petri Nets: Dynamical Roles and Functionality of Feedback Circuits. - Elisabeth Remy; Paul Ruet; Luis Eduardo Mendoza; Denis Thieffry; Claudine Chaouiya (Trans. Comp. Sys. Biology, 2006)

Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks. - Aurélien Naldi; Denis Thieffry; Claudine Chaouiya (CMSB, 2007)

Dynamical roles of biological regulatory circuits. - Denis Thieffry (Briefings Bioinform., 2007)

Logical modelling and analysis of the budding yeast cell cycle. - Adrien Fauré; Claudine Chaouiya; Andrea Ciliberto; Denis Thieffry (BMC Bioinform., 2007)

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc. - Aitor González; Claudine Chaouiya; Denis Thieffry (ECCB, 2008)

Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework. - Elisabeth Remy; Paul Ruet; Denis Thieffry (Adv. Appl. Math., 2008)

Petri net modelling of biological regulatory networks. - Claudine Chaouiya; Elisabeth Remy; Denis Thieffry (J. Discrete Algorithms, 2008)

A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties. - Aurélien Naldi; Elisabeth Remy; Denis Thieffry; Claudine Chaouiya (CMSB, 2009)

Analyzing various models of Circadian Clock and Cell Cycle coupling. - Attila Csikász-Nagy; Adrien Fauré; Roberto Larcher; Paola Lecca; Ivan Mura; Ferenc Jordán; Alida Palmisano; Alessandro Romanel; Sean Sedwards; Heike Siebert; Sylvain Soliman; Denis Thieffry; et al. (Formal Methods in Molecular Biology, 2009)

CoCAS: a ChIP-on-chip analysis suite. - Touati Benoukraf; Pierre Cauchy; Romain Fenouil; Adrien Jeanniard; Frederic Koch; Sébastien Jaeger; Denis Thieffry; Jean Imbert; Jean-Christophe Andrau; Salvatore Spicuglia; Pierre Ferrier (Bioinform., 2009)

Logical modelling of regulatory networks with GINsim 2.3. - Aurélien Naldi; Duncan Bérenguier; Adrien Fauré; F. Lopez; Denis Thieffry; Claudine Chaouiya (Biosyst., 2009)

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. - Özgür Sahin; Holger Fröhlich; Christian Löbke; Ulrike Korf; Sara Burmester; Meher Majety; Jens Mattern; Ingo Schupp; Claudine Chaouiya; Denis Thieffry; Annemarie Poustka; Stefan Wiemann; et al. (BMC Syst. Biol., 2009)

Reduction of Logical Models of Regulatory Networks Yields Insight into Dynamical properties. - Claudine Chaouiya; Aurélien Naldi; Elisabeth Remy; Denis Thieffry (CCA, 2010)

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement. - Laurence Calzone; Laurent Tournier; Simon Fourquet; Denis Thieffry; Boris Zhivotovsky; Emmanuel Barillot; Andrei Yu. Zinovyev (PLoS Comput. Biol., 2010)

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling. - Aurélien Naldi; Jorge Carneiro; Claudine Chaouiya; Denis Thieffry (PLoS Comput. Biol., 2010)

Logical modelling of haematopoietic cell fate reprogramming. - Denis Thieffry (CMSB, 2011)

RSAT 2011: regulatory sequence analysis tools. - Morgane Thomas-Chollier; Matthieu Defrance; Alejandra Medina-Rivera; Olivier Sand; Carl Herrmann; Denis Thieffry; Jacques van Helden (Nucleic Acids Res., 2011)

Petri net representation of multi-valued logical regulatory graphs. - Claudine Chaouiya; Aurélien Naldi; Elisabeth Remy; Denis Thieffry (Nat. Comput., 2011)

Dynamically consistent reduction of logical regulatory graphs. - Aurélien Naldi; Elisabeth Remy; Denis Thieffry; Claudine Chaouiya (Theor. Comput. Sci., 2011)

Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data. - Fabien Corblin; Eric Fanchon; Laurent Trilling; Claudine Chaouiya; Denis Thieffry (IPCAT, 2012)

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. - Claudine Chaouiya; Duncan Bérenguier; Sarah M. Keating; Aurélien Naldi; Martijn P. van Iersel; Nicolas Rodriguez 001; Andreas Dräger; Finja Büchel; Thomas Cokelaer; Bryan M. Kowal; Benjamin Wicks; Emanuel J. V. Gonçalves; et al. (BMC Syst. Biol., 2013)

Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision. - Luca Grieco; Laurence Calzone; Isabelle Bernard-Pierrot; François Radvanyi; Brigitte Kahn-Perlès; Denis Thieffry (PLoS Comput. Biol., 2013)

Model Checking Logical Regulatory Networks. - Pedro T. Monteiro 001; Wassim Abou-Jaoudé; Denis Thieffry; Claudine Chaouiya (WODES, 2014)

Derivation of Qualitative Dynamical Models from Biochemical Networks. - Wassim Abou-Jaoudé; Jérôme Feret; Denis Thieffry (CMSB, 2015)

Cooperative development of logical modelling standards and tools with CoLoMoTo. - Aurélien Naldi; Pedro T. Monteiro 001; Christoph Müssel; Hans A. Kestler; Denis Thieffry; Ioannis Xenarios; Julio Saez-Rodriguez; Tomás Helikar; Claudine Chaouiya (Bioinform., 2015)

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. - Claudine Chaouiya; Sarah M. Keating; Duncan Bérenguier; Aurélien Naldi; Denis Thieffry; Martijn P. van Iersel; Nicolas Le Novère; Tomás Helikar (J. Integr. Bioinform., 2015)

RSAT 2015: Regulatory Sequence Analysis Tools. - Alejandra Medina-Rivera; Matthieu Defrance; Olivier Sand; Carl Herrmann; Jaime Abraham Castro-Mondragón; Jeremy Delerce; Sébastien Jaeger; Christophe Blanchet; Pierre Vincens; Christophe Caron; Daniel M. Staines; Bruno Contreras-Moreira; et al. (Nucleic Acids Res., 2015)

Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. - Åsmund Flobak; Anaïs Baudot; Elisabeth Remy; Liv Thommesen; Denis Thieffry; Martin Kuiper; Astrid Lægreid (PLoS Comput. Biol., 2015)

Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation. - Pauline Traynard; Adrien Fauré; François Fages; Denis Thieffry (Bioinform., 2016)

Formal derivation of qualitative dynamical models from biochemical networks. - Wassim Abou-Jaoudé; Denis Thieffry; Jérôme Feret (Biosyst., 2016)

Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes. - Abibatou Mbodj; Eleanor Hilary Gustafson; Lucia Ciglar; Guillaume Junion; Aitor González; Charles Girardot; Laurent Perrin; Eileen E. M. Furlong; Denis Thieffry (PLoS Comput. Biol., 2016)

RSAT 2018: regulatory sequence analysis tools 20th anniversary. - Nga Thi Thuy Nguyen; Bruno Contreras-Moreira; Jaime Abraham Castro-Mondragón; Walter Santana-Garcia; Raul Ossio; Carla Daniela Robles-Espinoza; Mathieu Bahin; Samuel Collombet; Pierre Vincens; Denis Thieffry; Jacques van Helden; Alejandra Medina-Rivera; et al. (Nucleic Acids Res., 2018)

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. - Quy Xiao Xuan Lin; Stephanie Sian; Omer An; Denis Thieffry; Sudhakar Jha; Touati Benoukraf (Nucleic Acids Res., 2019)

Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. - Anna Niarakis; Martin Kuiper; Marek Ostaszewski; Rahuman S. Malik-Sheriff; Cristina Casals-Casas; Denis Thieffry; Tom C. Freeman; Paul D. Thomas; Vasundra Touré; Vincent Noël; Gautier Stoll; Julio Saez-Rodriguez; et al. (Briefings Bioinform., 2021)

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). - Vasundra Touré; Steven Vercruysse; Marcio Luis Acencio; Ruth C. Lovering; Sandra E. Orchard; Glyn Bradley; Cristina Casals-Casas; Claudine Chaouiya; Noemi del-Toro; Åsmund Flobak; Pascale Gaudet; Henning Hermjakob; et al. (Bioinform., 2021)

RSAT 2022: regulatory sequence analysis tools. - Walter Santana-Garcia; Jaime Abraham Castro-Mondragón; Mónica Padilla-Gálvez; Nga Thi Thuy Nguyen; Ana Elizondo-Salas; Najla Ksouri; François Gerbes; Denis Thieffry; Pierre Vincens; Bruno Contreras-Moreira; Jacques van Helden; Morgane Thomas-Chollier; et al. (Nucleic Acids Res., 2022)

Predictive modelling of acute Promyelocytic leukaemia resistance to retinoic acid therapy. - José A. Sánchez-Villanueva; Lia N'guyen; Mathilde Poplineau; Estelle Duprez; Elisabeth Remy; Denis Thieffry (Briefings Bioinform., 2024)