Denis Thieffry

According to our database1, Denis Thieffry authored at least 42 papers between 1996 and 2019.

Collaborative distances:
  • Dijkstra number2 of five.
  • Erdős number3 of four.



In proceedings 
PhD thesis 





MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.
Nucleic Acids Research, 2019

RSAT 2018: regulatory sequence analysis tools 20th anniversary.
Nucleic Acids Research, 2018

Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes.
PLoS Computational Biology, 2016

Formal derivation of qualitative dynamical models from biochemical networks.
Biosystems, 2016

Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation.
Bioinformatics, 2016

Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling.
PLoS Computational Biology, 2015

RSAT 2015: Regulatory Sequence Analysis Tools.
Nucleic Acids Research, 2015

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.
J. Integrative Bioinformatics, 2015

Cooperative development of logical modelling standards and tools with CoLoMoTo.
Bioinformatics, 2015

Derivation of Qualitative Dynamical Models from Biochemical Networks.
Proceedings of the Computational Methods in Systems Biology, 2015

Model Checking Logical Regulatory Networks.
Proceedings of the 12th International Workshop on Discrete Event Systems, 2014

Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision.
PLoS Computational Biology, 2013

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Systems Biology, 2013

Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data.
Proceedings of the Information Processign in Cells and Tissues, 2012

Dynamically consistent reduction of logical regulatory graphs.
Theor. Comput. Sci., 2011

Petri net representation of multi-valued logical regulatory graphs.
Natural Computing, 2011

RSAT 2011: regulatory sequence analysis tools.
Nucleic Acids Research, 2011

Logical modelling of haematopoietic cell fate reprogramming.
Proceedings of the Computational Methods in Systems Biology, 9th International Conference, 2011

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling.
PLoS Computational Biology, 2010

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement.
PLoS Computational Biology, 2010

Reduction of Logical Models of Regulatory Networks Yields Insight into Dynamical properties.
Proceedings of the IEEE International Conference on Control Applications, 2010

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance.
BMC Systems Biology, 2009

Logical modelling of regulatory networks with GINsim 2.3.
Biosystems, 2009

CoCAS: a ChIP-on-chip analysis suite.
Bioinformatics, 2009

Analyzing various models of Circadian Clock and Cell Cycle coupling.
Proceedings of the Formal Methods in Molecular Biology, 22.02. - 27.02.2009, 2009

A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties.
Proceedings of the Computational Methods in Systems Biology, 7th International Conference, 2009

Petri net modelling of biological regulatory networks.
J. Discrete Algorithms, 2008

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc.
Proceedings of the ECCB'08 Proceedings, 2008

Logical modelling and analysis of the budding yeast cell cycle.
BMC Bioinformatics, 2007

Dynamical roles of biological regulatory circuits.
Briefings in Bioinformatics, 2007

Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks.
Proceedings of the Computational Methods in Systems Biology, International Conference, 2007

From Logical Regulatory Graphs to Standard Petri Nets: Dynamical Roles and Functionality of Feedback Circuits.
, 2006

Qualitative Petri Net Modelling of Genetic Networks.
, 2006

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets.
Proceedings of the Applications and Theory of Petri Nets 2004, 2004

Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework.
Proceedings of the Positive Systems, 2003

A description of dynamical graphs associated to elementary regulatory circuits.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis.
Bioinformatics, 1999

RegulonDB: a database on transcriptional regulation in Escherichia coli.
Nucleic Acids Research, 1998

Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12.
Bioinformatics, 1998

Syntactic recognition of regulatory regions in Escherichia coli.
Computer Applications in the Biosciences, 1996