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List of works by Denis Thieffry

<i>Cis</i>-acting variation is common across regulatory layers but is often buffered during embryonic development

scientific article published on 11 December 2020

A Quantitative Multivariate Model of Human Dendritic Cell-T Helper Cell Communication

scientific article published on 01 October 2019

A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties

article

A Transcription Factor Pulse Can Prime Chromatin for Heritable Transcriptional Memory

scientific article published on 5 December 2016

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.

scientific article

A description of dynamical graphs associated to elementary regulatory circuits

scientific article published on 01 October 2003

A logical analysis of the Drosophila gap-gene system

scientific article

Abstracts from the 3rd International Society for Computational Biology (ISCB) Student Council Symposium at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria, 21 July 2007

scholarly article by Adrien Fauré published in January 2007

Alternative epigenetic states understood in terms of specific regulatory structures.

scientific article

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

article

Bacterial molecular networks: bridging the gap between functional genomics and dynamical modelling

scientific article published on January 2012

Bioinformatics in Siberia. First International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Siberia, Russia, 24-27 August 1998.

scientific article published in January 1999

Biologie des systèmes : des réseaux d’interactions moléculaires à la médecine personnalisée

scientific article published on 01 June 2009

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

scientific article

C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4.

scientific article

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

scientific article

CoCAS: a ChIP-on-chip analysis suite

scientific article published on 04 February 2009

Computational Verification of Large Logical Models-Application to the Prediction of T Cell Response to Checkpoint Inhibitors

scientific article published on 30 September 2020

Computational modeling of the main signaling pathways involved in mast cell activation

scientific article published on January 2014

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

scientific article published on 16 December 2019

Contributions of the 'Rouge-Cloître group' to the notion of 'messenger RNA'

scientific article published on January 1, 1997

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

scientific article published on 16 April 2019

Cooperative development of logical modelling standards and tools with CoLoMoTo

scientific article published on 25 January 2015

Cooperative development of logical modelling standards and tools with CoLoMoTo

article

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

scientific article published on 18 November 2013

Course 10Modeling, analysis, and simulation of genetic regulatory networks: From differential equations to logical models

article

Deciphering and modelling the TGF-β signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo

scientific article published on 09 December 2020

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

article

Definite-clause grammars for the analysis of cis-regulatory regions in E. coli.

scientific article published in January 1997

Derivation of Qualitative Dynamical Models from Biochemical Networks

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

scientific article

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

scientific article published on September 2, 2010

Dynamical Boolean Modeling of Immunogenic Cell Death

scientific article published on 12 November 2020

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

scientific article published on July 2006

Dynamical analysis of the regulatory network defining the dorsal-ventral boundary of the Drosophila wing imaginal disc

scientific article published on September 2006

Dynamical behaviour of biological regulatory networks--I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state

scientific article published in March 1995

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

scientific article published in March 1995

Dynamical modeling and analysis of large cellular regulatory networks.

scientific article published on June 2013

Dynamical modeling of biological regulatory networks

scientific article published on 28 December 2005

Dynamical modeling of syncytial mitotic cycles in Drosophila embryos

scientific article

Dynamical modelling of pattern formation during embryonic development.

scientific article

Dynamical roles of biological regulatory circuits

scientific article published on 11 July 2007

Dynamically consistent reduction of logical regulatory graphs

article

Epigenomics: Large scale analysis of chromatin modifications and transcription factors/genome interactions

scientific article published on 01 November 2005

Escherichia coli as a model system with which to study cell differentiation.

scientific article

Establishment of the dorso-ventral pattern during embryonic development of drosophila melanogasater: a logical analysis

scientific article published in December 1997

Formal derivation of qualitative dynamical models from biochemical networks.

scientific article published on 9 September 2016

Forty years under the central dogma

scientific article published on 01 August 1998

From experimental imaging techniques to virtual embryology.

scientific article

From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli ⬇️

scientific article published on May 1, 1998

Functional organisation of Escherichia coli transcriptional regulatory network

scientific article published on 29 May 2008

GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks

scientific article published on 24 January 2006

GOToolBox: functional analysis of gene datasets based on Gene Ontology

scientific article

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

scientific article published in July 1999

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

article published in 2008

Graphing genes, cells and embryos

article

Histone Chaperone SSRP1 is Essential for Wnt Signaling Pathway Activity During Osteoblast Differentiation

scientific article published on 13 February 2016

IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8+ T Cells

scientific article published on 05 June 2020

Integrative modelling of the influence of MAPK network on cancer cell fate decision

scientific article (publication date: October 2013)

Interplay between SMAD2 and STAT5A is a critical determinant of IL-17A/IL-17F differential expression

scientific article published on 01 April 2021

Introduction to 'picturing eggs, embryos and cells'.

scientific article

Introduction to the special issue. 'From embryology to developmental biology'.

scientific article

Jean Brachet's alternative scheme for protein synthesis

scientific article

Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0.

scientific article

Logical Modeling and Dynamical Analysis of Cellular Networks

scientific article

Logical Modelling of Gene Regulatory Networks with GINsim ⬇️

scientific article published on January 1, 2012

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

scientific article

Logical modeling of cell fate specification-Application to T cell commitment

scientific article published on 19 March 2020

Logical modeling of lymphoid and myeloid cell specification and transdifferentiation.

scientific article

Logical modelling and analysis of cellular regulatory networks with GINsim 3.0

scientific article published on 27 March 2018

Logical modelling of <i>in vitro</i> differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions

scientific article published on 11 June 2021

Logical modelling of Drosophila signalling pathways

scientific article published in September 2013

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

scientific article published on 17 September 2009

Logical modelling of regulatory networks with GINsim 2.3.

scientific article

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

scientific article published on August 2008

Mathematical modelling of cell-fate decision in response to death receptor engagement

scientific article

Metagenome annotation using a distributed grid of undergraduate students

scientific article

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

scientific article published on 01 January 2019

Model Checking Logical Regulatory Networks

article

Model checking to assess T-helper cell plasticity

scientific article

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

scientific article

Modular logical modelling of the budding yeast cell cycle

scientific article published on 31 July 2009

Modularity in development and evolution

scientific article published in November 2000

On circuit functionality in Boolean networks

scientific article published on 16 March 2013

Petri net modelling of biological regulatory networks

article published in 2008

Petri net representation of multi-valued logical regulatory graphs

article

Positive or negative regulatory circuit inference from multilevel dynamics

chapter; published in Lecture Notes in Control and Information Sciences 341

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

scientific article published on 06 July 2018

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

Prediction of transcription and genomic sequences ⬇️

scientific article published in November 2004

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

scientific article published in June 1998

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

scientific article published on 24 April 2019

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

scientific article

Proteomic analysis of the SH2 domain-containing leukocyte protein of 76 kDa (SLP76) interactome in resting and activated primary mast cells [corrected].

scientific article published on 2 July 2013

Putting DNA on the map

scientific article published in Nature

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

scientific article

Qualitative analysis of gene networks

scientific article published in January 1998

Qualitative modelling and simulation of developmental regulatory networks

article published in 2003

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

scientific article

RSAT 2011: regulatory sequence analysis tools.

scientific article

RSAT 2015: Regulatory Sequence Analysis Tools.

scientific article published on 22 April 2015

RSAT 2018: regulatory sequence analysis tools 20th anniversary.

scientific article published in July 2018

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

scientific article published on 07 June 2017

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

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

scientific article published on 8 December 2011

RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding

scientific article published on 07 November 2019

Rationalizing early embryogenesis in the 1930s: Albert Dalcq on gradients and fields

scientific article published on January 1, 2001

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

article

RegulonDB: a database on transcriptional regulation in Escherichia coli ⬇️

scientific article published on January 1, 1998

René Thomas (1928-2017): From DNA denaturation to positive gene regulation, kinetic logic and complex dynamical systems

scientific article published on 25 October 2017

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

scientific article published in June 2015

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

scientific article published on 01 August 2020

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

scientific article

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

scientific article published in October 2003

Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module

scientific article published in January 2008

Selected bibliography on history of embryology and development.

scientific article published in January 2000

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

scientific article published on 21 April 2020

Syncytial apoptosis signaling network induced by the HIV-1 envelope glycoprotein complex: an overview.

scientific article

Syntactic recognition of regulatory regions in Escherichia coli.

scientific article published in October 1996

TFregulomeR reveals transcription factors' context-specific features and functions

scientific article published on 01 January 2020

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

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

scientific article

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

scientific article published on 30 June 2020

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

scientific article published on 04 September 2015

The activation trajectory of plasmacytoid dendritic cells in vivo during a viral infection

scientific article published on 20 July 2020

The genome in context: biologists and philosophers on epigenetics

scientific article published in April 2002

The modularity of biological regulatory networks

scientific article published in April 1999

The shortest path is not the one you know: application of biological network resources in precision oncology research

scientific article

Toxicity and neuroendocrine regulation of the immune response: a model analysis.

scientific article published in December 1996

Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate

scientific article published on 01 December 2018

Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate

scientific article published on 13 September 2018

Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis

scientific article

UPMaBoSS: A Novel Framework for Dynamic Cell Population Modeling

publication published on 02 March 2022

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

scientific article published in May 2012

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