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2020 – today
- 2022
[j32]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): 670-676 (2022)- 2021
- [j31]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): 1848-1859 (2021) - [j30]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): 5712-5718 (2021)
2010 – 2019
- 2019
- [j29]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): D145-D154 (2019) - 2018
- [j28]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): W209-W214 (2018) - 2016
- [j27]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): 772-780 (2016) - [j26]Wassim Abou-Jaoudé, Denis Thieffry, Jérôme Feret:
Formal derivation of qualitative dynamical models from biochemical networks. Biosyst. 149: 70-112 (2016) - [j25]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) - 2015
- [j24]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): 1154-1159 (2015) - [j23]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) - [j22]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): W50-W56 (2015) - [j21]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) - [c14]Wassim Abou-Jaoudé, Jérôme Feret, Denis Thieffry:
Derivation of Qualitative Dynamical Models from Biochemical Networks. CMSB 2015: 195-207 - 2014
- [c13]Pedro T. Monteiro, Wassim Abou-Jaoudé, Denis Thieffry, Claudine Chaouiya:
Model Checking Logical Regulatory Networks. WODES 2014: 170-175 - 2013
- [j20]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: 135 (2013) - [j19]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) - 2012
- [c12]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: 25-30 - 2011
- [j18]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): 86-91 (2011) - [j17]Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry:
Petri net representation of multi-valued logical regulatory graphs. Nat. Comput. 10(2): 727-750 (2011) - [j16]Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya:
Dynamically consistent reduction of logical regulatory graphs. Theor. Comput. Sci. 412(21): 2207-2218 (2011) - [c11]Denis Thieffry:
Logical modelling of haematopoietic cell fate reprogramming. CMSB 2011: 7 - 2010
- [j15]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) - [j14]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) - [c10]Claudine Chaouiya, Aurélien Naldi, Elisabeth Remy, Denis Thieffry:
Reduction of Logical Models of Regulatory Networks Yields Insight into Dynamical properties. CCA 2010: 524-529
2000 – 2009
- 2009
- [j13]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): 954-955 (2009) - [j12]Aurélien Naldi, Duncan Bérenguier, Adrien Fauré, F. Lopez, Denis Thieffry, Claudine Chaouiya:
Logical modelling of regulatory networks with GINsim 2.3. Biosyst. 97(2): 134-139 (2009) - [j11]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: 1 (2009) - [c9]Aurélien Naldi, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya:
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties. CMSB 2009: 266-280 - [i1]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 - 2008
- [j10]Elisabeth Remy, Paul Ruet, Denis Thieffry:
Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework. Adv. Appl. Math. 41(3): 335-350 (2008) - [j9]Claudine Chaouiya, Elisabeth Remy, Denis Thieffry:
Petri net modelling of biological regulatory networks. J. Discrete Algorithms 6(2): 165-177 (2008) - [c8]Aitor González, Claudine Chaouiya, Denis Thieffry:
Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc. ECCB 2008: 234-240 - 2007
- [j8]Denis Thieffry:
Dynamical roles of biological regulatory circuits. Briefings Bioinform. 8(4): 220-225 (2007) - [j7]Adrien Fauré, Claudine Chaouiya, Andrea Ciliberto, Denis Thieffry:
Logical modelling and analysis of the budding yeast cell cycle. BMC Bioinform. 8(S-8) (2007) - [c7]Aurélien Naldi, Denis Thieffry, Claudine Chaouiya:
Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks. CMSB 2007: 233-247 - 2006
- [j6]Claudine Chaouiya, Elisabeth Remy, Denis Thieffry:
Qualitative Petri Net Modelling of Genetic Networks. Trans. Comp. Sys. Biology 6: 95-112 (2006) - [j5]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: 56-72 (2006) - [c6]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: 124-131 - [c5]Elisabeth Remy, Paul Ruet, Denis Thieffry:
Positive or Negative Regulatory Circuit Inference from Multilevel Dynamics. POSTA 2006: 263-270 - 2005
- [c4]E. Simão, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya:
Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli. ECCB/JBI 2005: 196 - 2004
- [c3]Claudine Chaouiya, Elisabeth Remy, Paul Ruet, Denis Thieffry:
Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets. ICATPN 2004: 137-156 - 2003
- [c2]Elisabeth Remy, Brigitte Mossé, Claudine Chaouiya, Denis Thieffry:
A description of dynamical graphs associated to elementary regulatory circuits. ECCB 2003: 172-178 - [c1]Claudine Chaouiya, Elisabeth Remy, Brigitte Mossé, Denis Thieffry:
Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework. POSTA 2003: 119-126
1990 – 1999
- 1999
- [j4]Luis Mendoza, Denis Thieffry, Elena R. Álvarez-Buylla:
Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis. Bioinform. 15(7): 593-606 (1999) - 1998
- [j3]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): 391-400 (1998) - [j2]Araceli M. Huerta, Heladia Salgado, Denis Thieffry, Julio Collado-Vides:
RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. 26(1): 55-59 (1998) - 1996
- [j1]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): 415-422 (1996)
Coauthor Index
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