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Engineering and Technology

D-Index
56
Citations
13590
World Ranking
2778
National Ranking
46

Overview

Denis Thieffry is affiliated with the École Normale Supérieure in France and focuses their research within the fields of biochemistry, genetics, and molecular biology, with notable contributions also in immunology and microbiology. Their work spans multiple subfields, including molecular biology, immunology, oncology, plant science, and genetics.

Their main research topics cover a range of subjects related to genetic and cellular processes. These topics include:

  • Gene Regulatory Network Analysis
  • Bioinformatics and Genomic Networks
  • Genomics and Chromatin Dynamics
  • T-cell and B-cell Immunology
  • Single-cell and spatial transcriptomics
  • Immunotherapy and Immune Responses
  • Microbial Metabolic Engineering and Bioproduction

Thieffry has contributed to several recent scientific papers published in various journals, which include the following:

  • "<scp>SBML</scp> Level 3: an extensible format for the exchange and reuse of biological models," 2020, Molecular Systems Biology
  • "Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer," 2021, Nature Communications
  • "RSAT 2022: regulatory sequence analysis tools," 2022, Nucleic Acids Research
  • "The activation trajectory of plasmacytoid dendritic cells in vivo during a viral infection," 2020, Nature Immunology
  • "Microglia maintain structural integrity during fetal brain morphogenesis," 2024, Cell

Their frequent coauthors include Aurélien Naldi, Morgane Thomas-Chollier, Céline Hernandez, Alejandra Medina-Rivera, and Vincent Noël. These collaborations indicate active engagement in interdisciplinary and team-based research projects.

Thieffry's publication record shows considerable presence in prominent scientific journals, with multiple papers published in venues such as:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Nucleic Acids Research
  • Briefings in Bioinformatics
  • Frontiers in Physiology
  • Interface Focus

Best Publications

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

    Adrien Fauré;Aurélien Naldi;Claudine Chaouiya;Denis Thieffry

  • Modularity in development and evolution.

    Gerhard Schlosser;Denis Thieffry

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

    René Thomas;Denis Thieffry;Marcelle Kaufman

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

    Denis Thieffry;Araceli M. Huerta;Ernesto Pérez-Rueda;Julio Collado-Vides

  • GOToolBox: functional analysis of gene datasets based on Gene Ontology

    David Martin;Christine Brun;Elisabeth Remy;Pierre Mouren

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

    Luis Mendoza;Denis Thieffry;Elena E.R. Alvarez-Buylla

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

    Özgür Sahin;Holger Fröhlich;Christian Löbke;Ulrike Korf

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

    Denis Thieffry;René Thomas

  • A logical analysis of the Drosophila gap-gene system.

    Lucas Sánchez;Denis Thieffry

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

    Sarah M. Keating;Sarah M. Keating;Dagmar Waltemath;Matthias König;Fengkai Zhang

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

    Laurence Calzone;Laurence Calzone;Laurence Calzone;Laurent Tournier;Laurent Tournier;Laurent Tournier;Simon Fourquet;Simon Fourquet;Simon Fourquet;Denis Thieffry;Denis Thieffry

  • Logical Modeling and Dynamical Analysis of Cellular Networks.

    Wassim Abou-Jaoudé;Pauline Traynard;Pedro T. Monteiro;Pedro T. Monteiro;Julio Saez-Rodriguez

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

    Bruno Di Stefano;Jose Luis Sardina;Chris van Oevelen;Samuel Collombet

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

    Élisabeth Remy;Paul Ruet;Denis Thieffry

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

    A. Gonzalez Gonzalez;A. Naldi;L. Sánchez;D. Thieffry

  • Logical modelling of regulatory networks with GINsim 2.3

    Aurélien Naldi;Duncan Bérenguier;Adrien Fauré;F. Lopez

  • Diversity and plasticity of Th cell types predicted from regulatory network modelling.

    Aurélien Naldi;Jorge Carneiro;Claudine Chaouiya;Denis Thieffry

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

    Luca Grieco;Laurence Calzone;Isabelle Bernard-Pierrot;François Radvanyi

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

    Claudine Chaouiya;Duncan Bérenguier;Sarah M. Keating;Aurélien Naldi

  • Qualitative analysis of gene networks

    Denis Thieffry;René Thomas

  • Logical modelling of gene regulatory networks with GINsim.

    Claudine Chaouiya;Aurélien Naldi;Denis Thieffry

  • Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer.

    Laura Cantini;Pooya Zakeri;Pooya Zakeri;Celine Hernandez;Celine Hernandez;Aurelien Naldi;Aurelien Naldi

  • Functional organisation of Escherichia coli transcriptional regulatory network.

    Agustino Martínez-Antonio;Sarath Chandra Janga;Denis Thieffry;Denis Thieffry

Frequent Co-Authors

Claudine Chaouiya
Claudine Chaouiya Aix-Marseille University
Jacques van Helden
Jacques van Helden Aix-Marseille University
Laurence Calzone
Laurence Calzone PSL University
Andrei Zinovyev
Andrei Zinovyev Institute Curie
Julio Saez-Rodriguez
Julio Saez-Rodriguez Heidelberg University
Emmanuel Barillot
Emmanuel Barillot Institute Curie
Hidde de Jong
Hidde de Jong French Institute for Research in Computer Science and Automation - INRIA
Thomas Graf
Thomas Graf Centre for Genomic Regulation
Julio Collado-Vides
Julio Collado-Vides National Autonomous University of Mexico
Nicolas Le Novère
Nicolas Le Novère Babraham Institute

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