Denis Thieffry

发表

Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2007, CMSB.

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc

Denis Thieffry, Claudine Chaouiya, Aitor González, 2008, ECCB.

Logical modelling of regulatory networks with GINsim 2.3

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2009, Biosyst..

Feedback loops analysis for chaotic dynamics with an application to Lorenz system

Denis Thieffry, Bourama Toni, Radmila Bulajich, 1999 .

Logical modelling of cell cycle control in eukaryotes: a comparative study.

Denis Thieffry, Adrien Fauré, D. Thieffry, 2009, Molecular bioSystems.

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2015, J. Integr. Bioinform..

Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes

Denis Thieffry, Aitor González, Abibatou Mbodj, 2016, PLoS Comput. Biol..

RegulonDB: a database on transcriptional regulation in Escherichia coli

Denis Thieffry, Julio Collado-Vides, Heladia Salgado, 1998, Nucleic Acids Res..

Model checking to assess T-helper cell plasticity

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2014 .

Logical modeling of the mammalian cell cycle

Denis Thieffry, François Fages, Pauline Traynard, 2015 .

Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12

Denis Thieffry, Julio Collado-Vides, Heladia Salgado, 1998, Bioinform..

Logical Modeling of Genetic Networks

Denis Thieffry, 2014 .

Dynamical roles of biological regulatory circuits

Denis Thieffry, D. Thieffry, 2007, Briefings Bioinform..

RSAT 2011: regulatory sequence analysis tools

Denis Thieffry, Jacques van Helden, Carl Herrmann, 2011, Nucleic Acids Res..

Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets

Denis Thieffry, Claudine Chaouiya, Elisabeth Remy, 2004, ICATPN.

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles

Denis Thieffry, Quy Xiao Xuan Lin, Stephanie Sian, 2018, Nucleic Acids Res..

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2018, bioRxiv.

Bacterial Molecular Networks

Denis Thieffry, Jacques van Helden, Ariane Toussaint, 2012, Methods in Molecular Biology.

Logical modelling of gene regulatory networks with GINsim.

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2012, Methods in molecular biology.

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement

Denis Thieffry, Emmanuel Barillot, Laurence Calzone, 2010, PLoS Comput. Biol..

Logical modelling and analysis of the budding yeast cell cycle

Denis Thieffry, Claudine Chaouiya, Andrea Ciliberto, 2007, BMC Bioinformatics.

Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling

Denis Thieffry, Martin Kuiper, Anaïs Baudot, 2015, PLoS Comput. Biol..

Syntactic recognition of regulatory regions in Escherichia coli

Denis Thieffry, Julio Collado-Vides, David A. Rosenblueth, 1996, Comput. Appl. Biosci..

Model Checking to Assess T-Helper Cell Plasticity

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2014, bioRxiv.

Cooperative development of logical modelling standards and tools with CoLoMoTo

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2014, bioRxiv.

Logical modelling of haematopoietic cell fate reprogramming

Denis Thieffry, 2011, CMSB.

Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data

Laurent Trilling, Denis Thieffry, Claudine Chaouiya, 2012, IPCAT.

Logical modelling of biological regulatory networks

Denis Thieffry, 2008 .

RSAT 2015: Regulatory Sequence Analysis Tools

Denis Thieffry, Christophe Blanchet, Jacques van Helden, 2015, Nucleic Acids Res..

RSAT peak-motifs: fast extraction of transcription factor binding motifs from full-size ChIP-seq datasets

Denis Thieffry, Jacques van Helden, Carl Herrmann, 2012 .

A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2009, CMSB.

Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework

Denis Thieffry, Paul Ruet, Elisabeth Remy, 2008, Adv. Appl. Math..

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2018 .

Dynamical modeling of biological regulatory networks.

Denis Thieffry, Claudine Chaouiya, Hidde de Jong, 2006, Bio Systems.

Logical Modeling and Dynamical Analysis of Cellular Networks

Denis Thieffry, Claudine Chaouiya, Julio Saez-Rodriguez, 2016, Front. Genet..

A description of dynamical graphs associated to elementary regulatory circuits

Denis Thieffry, Claudine Chaouiya, Elisabeth Remy, 2003, ECCB.

Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2018, Front. Physiol..

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

Steffen Klamt, Aurélien Naldi, Denis Thieffry, 2013, BMC Systems Biology.

Reduction of logical models of regulatory networks yields insight into dynamical properties

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2010, 2010 IEEE International Conference on Control Applications.

Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli

Denis Thieffry, Claudine Chaouiya, Elisabeth Remy, 2005, ECCB/JBI.

Formal derivation of qualitative dynamical models from biochemical networks

Denis Thieffry, Jérôme Feret, Wassim Abou-Jaoudé, 2016, Biosyst..

Qualitative Petri Net Modelling of Genetic Networks

Denis Thieffry, Claudine Chaouiya, Elisabeth Remy, 2006, Trans. Comp. Sys. Biology.

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2006, ISMB.

Dynamically consistent reduction of logical regulatory graphs

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2011, Theor. Comput. Sci..

Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis

Denis Thieffry, Luis Mendoza, Elena R. Álvarez-Buylla, 1999, Bioinform..

CoCAS: a ChIP-on-chip analysis suite

Denis Thieffry, Salvatore Spicuglia, Jean Imbert, 2009, Bioinform..

Derivation of Qualitative Dynamical Models from Biochemical Networks

Denis Thieffry, Jérôme Feret, Wassim Abou-Jaoudé, 2015, CMSB.

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance

Holger Fröhlich, Denis Thieffry, Claudine Chaouiya, 2009, BMC Systems Biology.

SBML Level 3 package: Qualitative Models, Version 1, Release 1

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2015, Journal of integrative bioinformatics.

Petri net representation of multi-valued logical regulatory graphs

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2010, Natural Computing.

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

Denis Thieffry, Claudine Chaouiya, Elisabeth Remy, 2006, Trans. Comp. Sys. Biology.

RSAT 2018: regulatory sequence analysis tools 20th anniversary

Denis Thieffry, Nga Thi Thuy Nguyen, Jacques van Helden, 2018, Nucleic Acids Res..

Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework

Denis Thieffry, Claudine Chaouiya, Elisabeth Remy, 2003, POSTA.

Model Checking Logical Regulatory Networks

Denis Thieffry, Claudine Chaouiya, Pedro T. Monteiro, 2014, WODES.

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

Denis Thieffry, François Fages, Pauline Traynard, 2016, Bioinform..

Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision

Denis Thieffry, Laurence Calzone, Luca Grieco, 2013, PLoS Comput. Biol..

Petri net modelling of biological regulatory networks

Denis Thieffry, Claudine Chaouiya, Elisabeth Remy, 2008, J. Discrete Algorithms.

Cooperative development of logical modelling standards and tools with CoLoMoTo

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2014, bioRxiv.

Prologue to the special issue of JTB dedicated to the memory of René Thomas (1928-2017): A journey through biological circuits, logical puzzles and complex dynamics.

Denis Thieffry, Marcelle Kaufman, D. Thieffry, 2019, Journal of theoretical biology.

Bacterial Molecular Networks: Methods and Protocols, 804

Denis Thieffry, Jacques van Helden, Ariane Toussaint, 2012 .

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2010, PLoS Comput. Biol..

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

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2020, Briefings Bioinform..

Alternative Epigenetic States Understood in Terms of Specific Regulatory Structures

Denis Thieffry, Lucas Sanchez, 2002, Annals of the New York Academy of Sciences.

Positive or negative regulatory circuit inference from multilevel dynamics

Denis Thieffry, Elisabeth Remy, Paul Ruet, 2006 .

Proteomic Analysis of the SH2 Domain-containing Leukocyte Protein of 76 kDa (SLP76) Interactome in Resting and Activated Primary Mast Cells

Denis Thieffry, Anna Niarakis, Yohann Couté, 2014, Molecular & Cellular Proteomics.

On Circuit Functionality in Boolean Networks

Adrien Richard, Aurélien Naldi, Denis Thieffry, 2013, Bulletin of mathematical biology.

From Gradients to Stripes: A Logical Analysis of Drosophila Segmentation Genetic Network

Denis Thieffry, Claudine Chaouiya, Lucas Sánchez, 2006 .

miR-9 controls the timing of neurogenesis through the direct inhibition of antagonistic factors.

Denis Thieffry, Laure Bally-Cuif, D. Thieffry, 2012, Developmental cell.

RegulonDB: A database on transcriptional regulation

Denis Thieffry, Julio Collado-Vides, Heladia Salgado, 1998 .

Logical modeling of lymphoid and myeloid cell specification and transdifferentiation

Denis Thieffry, Morgane Thomas-Chollier, Wassim Abou-Jaoudé, 2017, Proceedings of the National Academy of Sciences.

Formalisation of regulatory networks: a logical method and its automatization

Denis Thieffry, René Thomas, Denis Thieffry, 1993 .

SBML Level 3: an extensible format for the exchange and reuse of biological models

Hiroaki Kitano, Aurélien Naldi, Denis Thieffry, 2020, Molecular systems biology.

Dynamical behaviour of biological regulatory networks—II. Immunity control in bacteriophage lambda

Denis Thieffry, D. Thieffry, René Thomas, 1995 .

C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells

Denis Thieffry, Miguel Beato, Samuel Collombet, 2013, Nature.

POSITIVE LOOPS AND DIFFERENTIATION

Denis Thieffry, Jean Richelle, El Houssine Snoussi, 1995 .

Dynamical modeling of syncytial mitotic cycles in Drosophila embryos

Denis Thieffry, Laurence Calzone, John J Tyson, 2007, Molecular systems biology.

Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

Aurélien Naldi, Denis Thieffry, Andrei Zinovyev, 2018, Front. Physiol..

Proteomic Analysis of the SH2Domain-containing Leukocyte Protein of 76 kDa (SLP76) Interactome*

Denis Thieffry, Anna Niarakis, Yohann Couté, 2013, Molecular & Cellular Proteomics.

Automatic Inference of Regulatory and Dynamical Properties from Incomplete Gene Interaction and Expression Data

Laurent Trilling, Denis Thieffry, Claudine Chaouiya, 2012, International Conference on Information Processign in Cells and Tissues.

Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module.

Denis Thieffry, Lucas Sánchez, D. Thieffry, 2003, Journal of theoretical biology.

Contribution of ROS and metabolic status to neonatal and adult CD8+ T cell activation

Aurélien Naldi, Denis Thieffry, Céline Hernandez, 2019, PloS one.

C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis

Denis Thieffry, Yang Shi, Miguel Beato, 2015, Stem cell reports.

Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4+ T cell activation

Denis Thieffry, Salvatore Spicuglia, Morgane Thomas-Chollier, 2019, Science Signaling.

Dynamical modelling of pattern formation during embryonic development.

Denis Thieffry, D. Thieffry, L. Sánchez, 2003, Current opinion in genetics & development.