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Author Details

Denis Thieffry
Institut de Biologie de l'Ecole Normale Superieure, Inserm, CNRS, Universite PSL
1995
114
42
Dexter Pratt (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
35309516UPMaBoSS: A Novel Framework for Dynamic Cell Population Modeling.Front Mol Biosci2022
35544234RSAT 2022: regulatory sequence analysis tools.Nucleic Acids Res2022
32313939Setting 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.Brief Bioinform2021
33828580Evaluating the Reproducibility of Single-Cell Gene Regulatory Network Inference Algorithms.Front Genet2021
35006414Interplay between SMAD2 and STAT5A is a critical determinant of IL-17A/IL-17F differential expression.Mol Biomed2021
34123352Logical modelling of <i>in vitro</i> differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions.Interface Focus2021
33402734Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer.Nat Commun2021
33310749<i>Cis</i>-acting variation is common across regulatory layers but is often buffered during embryonic development.Genome Res2021
33298464Deciphering and modelling the TGF-β signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo.Development2021
32637990The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).Bioinformatics2021
32450961Logical modeling of cell fate specification-Application to T cell commitment.Curr Top Dev Biol2020
31754708TFregulomeR reveals transcription factors' context-specific features and functions.Nucleic Acids Res2020
33281620Dynamical Boolean Modeling of Immunogenic Cell Death.Front Physiol2020
33101049Computational Verification of Large Logical Models-Application to the Prediction of T Cell Response to Checkpoint Inhibitors.Front Physiol2020
32690951The activation trajectory of plasmacytoid dendritic cells in vivo during a viral infection.Nat Immunol2020
32845085SBML Level 3: an extensible format for the exchange and reuse of biological models.Mol Syst Biol2020
32582178IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8<sup>+</sup> T Cells.Front Immunol2020
30380113MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.Nucleic Acids Res2019
31871587RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding.Comput Struct Biotechnol J2019
31841528Contribution of ROS and metabolic status to neonatal and adult CD8+ T cell activation.PLoS One2019
31585082A Quantitative Multivariate Model of Human Dendritic Cell-T Helper Cell Communication.Cell2019
31028774Prologue 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.J Theor Biol2019
30992399Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4<sup>+</sup> T cell activation.Sci Signal2019
29722874RSAT 2018: regulatory sequence analysis tools 20th anniversary.Nucleic Acids Res2018
29971009The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.Front Physiol2018
29971008Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0.Front Physiol2018
30034343Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial).Front Physiol2018
30220521Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate.Cell Stem Cell2018
30526885Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate.Cell Stem Cell2018
27920256A Transcription Factor Pulse Can Prime Chromatin for Heritable Transcriptional Memory.Mol Cell Biol2017
28591841RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.Nucleic Acids Res2017
28584084Logical modeling of lymphoid and myeloid cell specification and transdifferentiation.Proc Natl Acad Sci U S A2017
26974661C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4.Nat Cell Biol2016
27587700Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation.Bioinformatics2016
27599298Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes.PLoS Comput Biol2016
27619217Formal derivation of qualitative dynamical models from biochemical networks.Biosystems2016
27303434Logical Modeling and Dynamical Analysis of Cellular Networks.Front Genet2016
27146025Histone Chaperone SSRP1 is Essential for Wnt Signaling Pathway Activity During Osteoblast Differentiation.Stem Cells2016
25688112The shortest path is not the one you know: application of biological network resources in precision oncology research.Mutagenesis2015
26247731Syncytial apoptosis signaling network induced by the HIV-1 envelope glycoprotein complex: an overview.Cell Death Dis2015
26317215Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling.PLoS Comput Biol2015
26528568The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.J Integr Bioinform2015
26235892C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis.Stem Cell Reports2015
25904632RSAT 2015: Regulatory Sequence Analysis Tools.Nucleic Acids Res2015
25674559Model checking to assess T-helper cell plasticity.Front Bioeng Biotechnol2015
25619997Cooperative development of logical modelling standards and tools with CoLoMoTo.Bioinformatics2015
24336202C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells.Nature2014
33498147Proteomic Analysis of the SH2 Domain-containing Leukocyte Protein of 76 kDa (SLP76) Interactome in Resting and Activated Primary Mast Cells.Mol Cell Proteomics2014
25116096Computational modeling of the main signaling pathways involved in mast cell activation.Curr Top Microbiol Immunol2014
23560912Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis.BMC Genomics2013
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Collaborators

Claudine Chaouiya
Aix Marseille University CNRS
Co-authored papers 24
Aur??lien Naldi
Institut de Biologie de l'Ecole Normale Superieure, Inserm, CNRS, Universite PSL
Co-authored papers 24
Jacques van Helden
Co-authored papers 11
Laurence Calzone
Institut Curie, Universite PSL
Co-authored papers 9
Julio Saez-Rodriguez
Institute of Computational Biomedicine, Heidelberg University
Co-authored papers 5
Emmanuel Barillot
Institut Curie, Universite PSL
Co-authored papers 4
Andrei Zinovyev
INSERM U, Institut Curie, PSL Research University
Co-authored papers 4
Ioannis Xenarios
University of Lausanne
Co-authored papers 3
Martin Kuiper
Norwegian University of Science and Technology
Co-authored papers 3
Simon Heath
Barcelona Institute of Science and Technology (BIST)
Co-authored papers 2
Ivo Gut
Spain Universitat de Barcelona (UB)
Co-authored papers 2
Cristina Casals
Universidad Complutense
Co-authored papers 2
??smund Flobak
Norwegian University of Science and Technology
Co-authored papers 2
Astrid Laegreid
Norwegian University of Science and Technology
Co-authored papers 2
Henning Hermjakob
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 2
Nicolas Le Nov??re
Babraham Institute
Co-authored papers 2
Paul D Thomas
University of Southern California
Co-authored papers 2
Marta Gut
Universitat de Barcelona (UB)
Co-authored papers 2
Vasundra Tour??
Norwegian University of Science and Technology (NTNU)
Co-authored papers 2
Laura Cantini
Institut Pasteur, Universite Paris Cite, CNRS UMR 3738
Co-authored papers 2
Konrad Hochedlinger
Co-authored papers 2
Stefan Wiemann
Co-authored papers 1
Sandra Orchard
EMBL's European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 1
Bernhard O Palsson
University of California San Diego
Co-authored papers 1
Neil Swainston
Institute of Systems, University of Liverpool
Co-authored papers 1
Glyn Bradley
Co-authored papers 1
Romain Fenouil
Universite de Toulon, CNRS
Co-authored papers 1
David A Garfield
Humboldt Universitat Berlin
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Kimberly Begley
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Release 1.2