Denis Thieffry

49 papers C 3Journal 33Unranked 13

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Predictive modelling of acute Promyelocytic leukaemia resistance to retinoic acid therapy. Briefings Bioinform. José A. Sánchez-Villanueva, Lia N'guyen, Mathilde Poplineau, Estelle Duprez, Elisabeth Remy, Denis Thieffry
2025	—	`conf`	Twelve Tips for Reproducible Analysis of Single-Cell Transcriptomics Data. ACM REP Audrey Onfroy, Piotr Topilko, Sophie Hüe, Denis Thieffry
2022	J	`jnl`	RSAT 2022: regulatory sequence analysis tools. Nucleic Acids Res. 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
2021	J	`jnl`	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. 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
2021	J	`jnl`	The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinform. 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
2019	J	`jnl`	MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. Nucleic Acids Res. Quy Xiao Xuan Lin, Stephanie Sian, Omer An, Denis Thieffry, Sudhakar Jha, Touati Benoukraf
2018	J	`jnl`	RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Res. 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
2016	J	`jnl`	Formal derivation of qualitative dynamical models from biochemical networks. Biosyst. Wassim Abou-Jaoudé, Denis Thieffry, Jérôme Feret
2016	J	`jnl`	Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation. Bioinform. Pauline Traynard, Adrien Fauré, François Fages, Denis Thieffry
2016	J	`jnl`	Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes. PLoS Comput. Biol. Abibatou Mbodj, Eleanor Hilary Gustafson, Lucia Ciglar, Guillaume Junion, Aitor González, Charles Girardot, Laurent Perrin, Eileen E. M. Furlong, Denis Thieffry
2015	J	`jnl`	Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinform. Aurélien Naldi, Pedro T. Monteiro, Christoph Müssel, Hans A. Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomás Helikar, Claudine Chaouiya
2015	—	`conf`	Derivation of Qualitative Dynamical Models from Biochemical Networks. CMSB Wassim Abou-Jaoudé, Jérôme Feret, Denis Thieffry
2015	J	`jnl`	Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLoS Comput. Biol. Åsmund Flobak, Anaïs Baudot, Elisabeth Remy, Liv Thommesen, Denis Thieffry, Martin Kuiper, Astrid Lægreid
2015	J	`jnl`	RSAT 2015: Regulatory Sequence Analysis Tools. Nucleic Acids Res. 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
2015	J	`jnl`	The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. J. Integr. Bioinform. Claudine Chaouiya, Sarah M. Keating, Duncan Bérenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel, Nicolas Le Novère, Tomás Helikar
2014	—	`conf`	Model Checking Logical Regulatory Networks. WODES Pedro T. Monteiro, Wassim Abou-Jaoudé, Denis Thieffry, Claudine Chaouiya
2013	J	`jnl`	Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision. PLoS Comput. Biol. Luca Grieco, Laurence Calzone, Isabelle Bernard-Pierrot, François Radvanyi, Brigitte Kahn-Perlès, Denis Thieffry
2013	J	`jnl`	SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 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
2012	—	`conf`	Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data. IPCAT Fabien Corblin, Eric Fanchon, Laurent Trilling, Claudine Chaouiya, Denis Thieffry
2011	J	`jnl`	Dynamically consistent reduction of logical regulatory graphs. Theor. Comput. Sci. Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
2011	—	`conf`	Logical modelling of haematopoietic cell fate reprogramming. CMSB Denis Thieffry
2011	J	`jnl`	Petri net representation of multi-valued logical regulatory graphs. Nat. Comput. Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry
2011	J	`jnl`	RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res. Morgane Thomas-Chollier, Matthieu Defrance, Alejandra Medina-Rivera, Olivier Sand, Carl Herrmann, Denis Thieffry, Jacques van Helden
2010	J	`jnl`	Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling. PLoS Comput. Biol. Aurélien Naldi, Jorge Carneiro, Claudine Chaouiya, Denis Thieffry
2010	J	`jnl`	Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement. PLoS Comput. Biol. Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot, Andrei Yu. Zinovyev
2010	C	`conf`	Reduction of Logical Models of Regulatory Networks Yields Insight into Dynamical properties. CCA Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry
2009	—	`conf`	A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties. CMSB Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
2009	—	`conf`	Analyzing various models of Circadian Clock and Cell Cycle coupling. Formal Methods in Molecular Biology 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
2009	J	`jnl`	CoCAS: a ChIP-on-chip analysis suite. Bioinform. Touati Benoukraf, Pierre Cauchy, Romain Fenouil, Adrien Jeanniard, Frederic Koch, Sébastien Jaeger, Denis Thieffry, Jean Imbert, Jean-Christophe Andrau, Salvatore Spicuglia, Pierre Ferrier
2009	J	`jnl`	Logical modelling of regulatory networks with GINsim 2.3. Biosyst. Aurélien Naldi, Duncan Bérenguier, Adrien Fauré, Fabrice Lopez, Denis Thieffry, Claudine Chaouiya
2009	J	`jnl`	Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst. Biol. 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
2008	J	`jnl`	Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework. Adv. Appl. Math. Elisabeth Remy, Paul Ruet, Denis Thieffry
2008	C	`conf`	Logical modelling of the role of the Hh pathway in the patterning of the ECCB Aitor González, Claudine Chaouiya, Denis Thieffry
2008	J	`jnl`	Petri net modelling of biological regulatory networks. J. Discrete Algorithms Claudine Chaouiya, Elisabeth Remy, Denis Thieffry
2007	—	`conf`	Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks. CMSB Aurélien Naldi, Denis Thieffry, Claudine Chaouiya
2007	J	`jnl`	Dynamical roles of biological regulatory circuits. Briefings Bioinform. Denis Thieffry
2007	J	`jnl`	Logical modelling and analysis of the budding yeast cell cycle. BMC Bioinform. Adrien Fauré, Claudine Chaouiya, Andrea Ciliberto, Denis Thieffry
2006	—	`conf`	Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. ISMB (Supplement of Bioinformatics) Adrien Fauré, Aurélien Naldi, Claudine Chaouiya, Denis Thieffry
2006	J	`jnl`	From Logical Regulatory Graphs to Standard Petri Nets: Dynamical Roles and Functionality of Feedback Circuits. Trans. Comp. Sys. Biology Elisabeth Remy, Paul Ruet, Luis Eduardo Mendoza, Denis Thieffry, Claudine Chaouiya
2006	—	`conf`	Positive or Negative Regulatory Circuit Inference from Multilevel Dynamics. POSTA Elisabeth Remy, Paul Ruet, Denis Thieffry
2006	J	`jnl`	Qualitative Petri Net Modelling of Genetic Networks. Trans. Comp. Sys. Biology Claudine Chaouiya, Elisabeth Remy, Denis Thieffry
2005	—	`conf`	Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in ECCB/JBI E. Simão, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya
2004	—	`conf`	Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets. ICATPN Claudine Chaouiya, Elisabeth Remy, Paul Ruet, Denis Thieffry
2003	C	`conf`	A description of dynamical graphs associated to elementary regulatory circuits. ECCB Elisabeth Remy, Brigitte Mossé, Claudine Chaouiya, Denis Thieffry
2003	—	`conf`	Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework. POSTA Claudine Chaouiya, Elisabeth Remy, Brigitte Mossé, Denis Thieffry
1999	J	`jnl`	Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis. Bioinform. Luis Mendoza, Denis Thieffry, Elena R. Álvarez-Buylla
1998	J	`jnl`	Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. Bioinform. Denis Thieffry, Heladia Salgado, Araceli M. Huerta, Julio Collado-Vides
1998	J	`jnl`	RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. Araceli M. Huerta, Heladia Salgado, Denis Thieffry, Julio Collado-Vides
1996	J	`jnl`	Syntactic recognition of regulatory regions in Escherichia coli. Comput. Appl. Biosci. David A. Rosenblueth, Denis Thieffry, Araceli M. Huerta, Heladia Salgado, Julio Collado-Vides