Denis Thieffry

Publication Activity (10 Years)

Years Active: 1996-2022
Publications (10 Years): 8

Top Topics

Systems Biology

Biochemical Networks

Dynamical Model

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

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, Alejandra Medina-Rivera
RSAT 2022: regulatory sequence analysis tools. Nucleic Acids Res. 50 (W1) (2022)
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, Charles Tapley Hoyt, Luana Licata, Astrid Lægreid, Christopher J. Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Julio Saez-Rodriguez, Denis Thieffry, Paul D. Thomas, Dénes Türei, Martin Kuiper
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinform. 36 (24) (2021)
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, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone
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. Briefings Bioinform. 22 (2) (2021)
Quy Xiao Xuan Lin, Stephanie Sian, Omer An, Denis Thieffry, Sudhakar Jha, Touati Benoukraf
MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. Nucleic Acids Res. 47 (Database-Issue) (2019)
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, Morgane Thomas-Chollier
RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Wassim Abou-Jaoudé, Denis Thieffry, Jérôme Feret
Formal derivation of qualitative dynamical models from biochemical networks. Biosyst. 149 (2016)
Pauline Traynard, Adrien Fauré, François Fages, Denis Thieffry
Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation. Bioinform. 32 (17) (2016)
Abibatou Mbodj, Eleanor Hilary Gustafson, Lucia Ciglar, Guillaume Junion, Aitor González, Charles Girardot, Laurent Perrin, Eileen E. M. Furlong, Denis Thieffry
Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes. PLoS Comput. Biol. 12 (9) (2016)
Åsmund Flobak, Anaïs Baudot, Elisabeth Remy, Liv Thommesen, Denis Thieffry, Martin Kuiper, Astrid Lægreid
Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLoS Comput. Biol. 11 (8) (2015)
Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya
Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinform. 31 (7) (2015)
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, Marie Artufel, Lucie Charbonnier-Khamvongsa, Céline Hernandez, Denis Thieffry, Morgane Thomas-Chollier, Jacques van Helden
RSAT 2015: Regulatory Sequence Analysis Tools. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Claudine Chaouiya, Sarah M. Keating, Duncan Bérenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel, Nicolas Le Novère, Tomás Helikar
The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. J. Integr. Bioinform. 12 (2) (2015)
Wassim Abou-Jaoudé, Jérôme Feret, Denis Thieffry
Derivation of Qualitative Dynamical Models from Biochemical Networks. CMSB (2015)
Pedro T. Monteiro, Wassim Abou-Jaoudé, Denis Thieffry, Claudine Chaouiya
Model Checking Logical Regulatory Networks. WODES (2014)
Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7 (2013)
Luca Grieco, Laurence Calzone, Isabelle Bernard-Pierrot, François Radvanyi, Brigitte Kahn-Perlès, Denis Thieffry
Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision. PLoS Comput. Biol. 9 (10) (2013)
Fabien Corblin, Eric Fanchon, Laurent Trilling, Claudine Chaouiya, Denis Thieffry
Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data. IPCAT (2012)
Morgane Thomas-Chollier, Matthieu Defrance, Alejandra Medina-Rivera, Olivier Sand, Carl Herrmann, Denis Thieffry, Jacques van Helden
RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Denis Thieffry
Logical modelling of haematopoietic cell fate reprogramming. CMSB (2011)
Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
Dynamically consistent reduction of logical regulatory graphs. Theor. Comput. Sci. 412 (21) (2011)
Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry
Petri net representation of multi-valued logical regulatory graphs. Nat. Comput. 10 (2) (2011)
Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot, Andrei Yu. Zinovyev
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement. PLoS Comput. Biol. 6 (3) (2010)
Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry
Reduction of Logical Models of Regulatory Networks Yields Insight into Dynamical properties. CCA (2010)
Aurélien Naldi, Jorge Carneiro, Claudine Chaouiya, Denis Thieffry
Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling. PLoS Comput. Biol. 6 (9) (2010)
Touati Benoukraf, Pierre Cauchy, Romain Fenouil, Adrien Jeanniard, Frederic Koch, Sébastien Jaeger, Denis Thieffry, Jean Imbert, Jean-Christophe Andrau, Salvatore Spicuglia, Pierre Ferrier
CoCAS: a ChIP-on-chip analysis suite. Bioinform. 25 (7) (2009)
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, Judit Zámborszky, Tommaso Mazza, Paolo Ballarini
Analyzing various models of Circadian Clock and Cell Cycle coupling. Formal Methods in Molecular Biology (2009)
Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties. CMSB (2009)
Aurélien Naldi, Duncan Bérenguier, Adrien Fauré, F. Lopez, Denis Thieffry, Claudine Chaouiya
Logical modelling of regulatory networks with GINsim 2.3. Biosyst. 97 (2) (2009)
Özgür Sahin, Holger Fröhlich, Christian Löbke, Ulrike Korf, Sara Burmester, Meher Majety, Jens Mattern, Ingo Schupp, Claudine Chaouiya, Denis Thieffry, Annemarie Poustka, Stefan Wiemann, Tim Beißbarth, Dorit Arlt
Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst. Biol. 3 (2009)
Elisabeth Remy, Paul Ruet, Denis Thieffry
Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework. Adv. Appl. Math. 41 (3) (2008)
Claudine Chaouiya, Elisabeth Remy, Denis Thieffry
Petri net modelling of biological regulatory networks. J. Discrete Algorithms 6 (2) (2008)
Aitor González, Claudine Chaouiya, Denis Thieffry
wing disc. ECCB (2008)
Adrien Fauré, Claudine Chaouiya, Andrea Ciliberto, Denis Thieffry
Logical modelling and analysis of the budding yeast cell cycle. BMC Bioinform. 8 (S-8) (2007)
Denis Thieffry
Dynamical roles of biological regulatory circuits. Briefings Bioinform. 8 (4) (2007)
Aurélien Naldi, Denis Thieffry, Claudine Chaouiya
Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks. CMSB (2007)
Claudine Chaouiya, Elisabeth Remy, Denis Thieffry
Qualitative Petri Net Modelling of Genetic Networks. Trans. Comp. Sys. Biology 6 (2006)
Adrien Fauré, Aurélien Naldi, Claudine Chaouiya, Denis Thieffry
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. ISMB (Supplement of Bioinformatics) (2006)
Elisabeth Remy, Paul Ruet, Denis Thieffry
Positive or Negative Regulatory Circuit Inference from Multilevel Dynamics. POSTA (2006)
Elisabeth Remy, Paul Ruet, Luis Eduardo Mendoza, Denis Thieffry, Claudine Chaouiya
From Logical Regulatory Graphs to Standard Petri Nets: Dynamical Roles and Functionality of Feedback Circuits. Trans. Comp. Sys. Biology 7 (2006)
E. Simão, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
. ECCB/JBI (2005)
Claudine Chaouiya, Elisabeth Remy, Paul Ruet, Denis Thieffry
Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets. ICATPN (2004)
Elisabeth Remy, Brigitte Mossé, Claudine Chaouiya, Denis Thieffry
A description of dynamical graphs associated to elementary regulatory circuits. ECCB (2003)
Claudine Chaouiya, Elisabeth Remy, Brigitte Mossé, Denis Thieffry
Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework. POSTA (2003)
Luis Mendoza, Denis Thieffry, Elena R. Álvarez-Buylla
Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis. Bioinform. 15 (7) (1999)
Araceli M. Huerta, Heladia Salgado, Denis Thieffry, Julio Collado-Vides
RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. 26 (1) (1998)
Denis Thieffry, Heladia Salgado, Araceli M. Huerta, Julio Collado-Vides
Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. Bioinform. 14 (5) (1998)
David A. Rosenblueth, Denis Thieffry, Araceli M. Huerta, Heladia Salgado, Julio Collado-Vides
Syntactic recognition of regulatory regions in Escherichia coli. Comput. Appl. Biosci. 12 (5) (1996)