All Stories

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

    Article • PLoS ONE, December 2019, PLOS

    Professor Denis Thieffry

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

    Article • Mutagenesis, February 2015, Oxford University Press (OUP)

    Professor Denis Thieffry

  3. Model Checking to Assess T-Helper Cell Plasticity

    Article • Frontiers in Bioengineering and Biotechnology, January 2015, Frontiers

    Professor Denis Thieffry

  4. Cooperative development of logical modelling standards and tools with CoLoMoTo

    Article • Bioinformatics, January 2015, Oxford University Press (OUP)

    Professor Denis Thieffry, Professor Julio Saez-Rodriguez, Jun.-Prof. Dr. Andreas Dräger

  5. Model checking to assess T-helper cell plasticity

    Article • December 2014, Cold Spring Harbor Laboratory Press

    Professor Denis Thieffry

  6. Cooperative development of logical modelling standards and tools with CoLoMoTo

    Article • October 2014, Cold Spring Harbor Laboratory Press

    Professor Denis Thieffry

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

    Article • Molecular & Cellular Proteomics, January 2014, American Society for Biochemistry & Molecular Biology (ASBMB)

    Professor Denis Thieffry

  8. Computational Modeling of the Main Signaling Pathways Involved in Mast Cell Activation

    Article • January 2014, Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • Nature, December 2013, Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • PLoS Computational Biology, November 2013, PLOS

    Professor Denis Thieffry

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

    Article • PLoS Computational Biology, October 2013, PLOS

    Professor Denis Thieffry

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

    Article • Molecular & Cellular Proteomics, July 2013, American Society for Biochemistry & Molecular Biology (ASBMB)

    Professor Denis Thieffry

  13. Dynamical modeling and analysis of large cellular regulatory networks

    Article • Chaos An Interdisciplinary Journal of Nonlinear Science, June 2013, American Institute of Physics

    Professor Denis Thieffry

  14. RSAT peak-motifs: Efficient prediction of transcription factor motifs and binding sites from genome-wide sequencing peak sets

    Article • EMBnet journal, April 2013, EMBnet Stichting

    Professor Denis Thieffry

  15. On Circuit Functionality in Boolean Networks

    Article • The Bulletin of Mathematical Biophysics, March 2013, Springer Science + Business Media

    Professor Denis Thieffry

  16. Logical modelling of Drosophila signalling pathways

    Article • Molecular BioSystems, January 2013, Royal Society of Chemistry

    Professor Denis Thieffry

  17. Cell Cycle Modeling Using Logical Rules

    Article • January 2013, Springer Science + Business Media

    Professor Denis Thieffry

  18. Transcriptional and epigenetic signatures of zygotic genome activation during early drosophila embryogenesis

    Article • BMC Genomics, January 2013, Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • BMC Systems Biology, January 2013, Springer Science + Business Media

    Professor Denis Thieffry, Professor Julio Saez-Rodriguez, Jun.-Prof. Dr. Andreas Dräger

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

    Article • Nature Protocols, July 2012, Springer Science + Business Media

    Dr Morgane Thomas-Chollier, Professor Denis Thieffry

  21. miR-9 Controls the Timing of Neurogenesis through the Direct Inhibition of Antagonistic Factors

    Article • Developmental Cell, May 2012, Elsevier

    Professor Denis Thieffry

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

    Article • EMBnet journal, February 2012, EMBnet Stichting

    Dr Morgane Thomas-Chollier, Professor Denis Thieffry

  23. Bacterial Molecular Networks

    Article • January 2012

    Professor Denis Thieffry

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

    Article • January 2012, Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • Nucleic Acids Research, December 2011, Oxford University Press (OUP)

    Dr Morgane Thomas-Chollier, Professor Denis Thieffry

  26. Bacterial Molecular Networks: Bridging the Gap Between Functional Genomics and Dynamical Modelling

    Article • October 2011, Springer Science + Business Media

    Professor Denis Thieffry

  27. Logical Modelling of Gene Regulatory Networks with GINsim

    Article • October 2011, Springer Science + Business Media

    Professor Denis Thieffry

  28. RSAT 2011: regulatory sequence analysis tools

    Article • Nucleic Acids Research, June 2011, Oxford University Press (OUP)

    Dr Morgane Thomas-Chollier, Professor Denis Thieffry

  29. Dynamically consistent reduction of logical regulatory graphs

    Article • Theoretical Computer Science, May 2011, Elsevier

    Professor Denis Thieffry

  30. Logical modelling of haematopoietic cell fate reprogramming

    Article • January 2011, ACM (Association for Computing Machinery)

    Professor Denis Thieffry

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

    Article • PLoS Computational Biology, September 2010, PLOS

    Professor Denis Thieffry

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

    Article • September 2010, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Denis Thieffry

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

    Article • PLoS Computational Biology, March 2010, PLOS

    Professor Denis Thieffry

  34. Petri net representation of multi-valued logical regulatory graphs

    Article • Natural Computing, February 2010, Springer Science + Business Media

    Professor Denis Thieffry

  35. Logical modelling of regulatory networks with GINsim 2.3

    Article • Biosystems, August 2009, Elsevier

    Professor Denis Thieffry

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

    Article • médecine/sciences, June 2009, EDP Sciences

    Professor Denis Thieffry

  37. CoCAS: a ChIP-on-chip analysis suite

    Article • Bioinformatics, February 2009, Oxford University Press (OUP)

    Professor Denis Thieffry

  38. Modular logical modelling of the budding yeast cell cycle

    Article • Molecular BioSystems, January 2009, Royal Society of Chemistry

    Professor Denis Thieffry

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

    Article • Molecular BioSystems, January 2009, Royal Society of Chemistry

    Professor Denis Thieffry

  40. A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties

    Article • January 2009, Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • BMC Systems Biology, January 2009, Springer Science + Business Media

    Professor Denis Thieffry

  42. Metagenome Annotation Using a Distributed Grid of Undergraduate Students

    Article • PLoS Biology, November 2008, PLOS

    Professor Denis Thieffry

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

    Article • Advances in Applied Mathematics, September 2008, Elsevier

    Professor Denis Thieffry

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

    Article • Bioinformatics, August 2008, Oxford University Press (OUP)

    Professor Denis Thieffry

  45. Functional organisation of Escherichia coli transcriptional regulatory network

    Article • Journal of Molecular Biology, August 2008, Elsevier

    Professor Denis Thieffry, Dr Agustino Martínez-Antonio

  46. Petri net modelling of biological regulatory networks

    Article • Journal of Discrete Algorithms, June 2008, Elsevier

    Professor Denis Thieffry

  47. Segmenting the fly embryo: logical analysis of the role of the Segment Polarity cross-regulatory module

    Article • The International Journal of Developmental Biology, January 2008, UBC Press

    Professor Denis Thieffry

  48. Logical modelling and analysis of the budding yeast cell cycle

    Article • BMC Bioinformatics, November 2007, Springer Science + Business Media

    Professor Denis Thieffry

  49. Dynamical modeling of syncytial mitotic cycles in Drosophila embryos

    Article • Molecular Systems Biology, July 2007, EMBO

    Professor John J Tyson, Professor Denis Thieffry

  50. Dynamical roles of biological regulatory circuits

    Article • Briefings in Bioinformatics, March 2007, Oxford University Press (OUP)

    Professor Denis Thieffry

  51. Graphing genes, cells and embryos

    Article • BioEssays, January 2007, Wiley

    Professor Denis Thieffry

  52. Putting DNA on the map

    Article • Nature, October 2006, Springer Science + Business Media

    Professor Denis Thieffry

  53. Dynamical Analysis of the Regulatory Network Defining the Dorsal-Ventral Boundary of the Drosophila Wing Imaginal Disc

    Article • Genetics, September 2006, Genetics Society of America

    Professor Denis Thieffry

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

    Article • Bioinformatics, July 2006, Oxford University Press (OUP)

    Professor Denis Thieffry

  55. Dynamical modeling of biological regulatory networks

    Article • Biosystems, May 2006, Elsevier

    Professor Denis Thieffry

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

    Article • Biosystems, May 2006, Elsevier

    Professor Denis Thieffry

  57. Alternative Epigenetic States Understood in Terms of Specific Regulatory Structures

    Article • Annals of the New York Academy of Sciences, January 2006, Wiley

    Professor Denis Thieffry

  58. Qualitative Petri Net Modelling of Genetic Networks

    Article • January 2006, Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • January 2006, Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • Bioinformatics, September 2005, Oxford University Press (OUP)

    Professor Denis Thieffry

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

    Article • BioEssays, January 2005, Wiley

    Professor Denis Thieffry

  62. Preface

    Article • January 2005, Elsevier

    Professor Denis Thieffry

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

    Article • January 2005, Elsevier

    Professor Denis Thieffry

  64. Prédire la transcription à partir des séquences génomique

    Article • médecine/sciences, November 2004, EDP Sciences

    Professor Denis Thieffry

  65. Mathematical Modeling of Molecular/Metabolic/Genetic Networks

    Article • October 2004, Wiley

    Professor Denis Thieffry

  66. Network (Genetic Network, Metabolic Network, Molecular Network)

    Article • October 2004, Wiley

    Professor Denis Thieffry

  67. Genetic Network

    Article • October 2004, Wiley

    Professor Denis Thieffry

  68. Logical Modeling of Genetic Networks

    Article • October 2004, Wiley

    Professor Denis Thieffry

  69. Network (Genetic Network, Molecular Network, Metabolic Network)

    Article • October 2004, Wiley

    Professor Denis Thieffry

  70. Mathematical Modeling (of Molecular/Metabolic/Genetic Networks)

    Article • October 2004, Wiley

    Professor Denis Thieffry

  71. Regulatory Motifs in Network Biology

    Article • October 2004, Wiley

    Professor Denis Thieffry

  72. Graph Representation of Genetic, Molecular, and Metabolic Networks

    Article • October 2004, Wiley

    Professor Denis Thieffry

  73. Graph Representation of Genetic, Molecular and Metabolic Networks

    Article • October 2004, Wiley

    Professor Denis Thieffry

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

    Article • April 2004, Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • January 2004, Springer Science + Business Media

    Professor Denis Thieffry

  76. Segmenting the fly embryo:

    Article • Journal of Theoretical Biology, October 2003, Elsevier

    Professor Denis Thieffry

  77. A description of dynamical graphs associated to elementary regulatory circuits

    Article • Bioinformatics, September 2003, Oxford University Press (OUP)

    Professor Denis Thieffry

  78. Dynamical modelling of pattern formation during embryonic development

    Article • Current Opinion in Genetics & Development, August 2003, Elsevier

    Professor Denis Thieffry

  79. Qualitative modelling and simulation of developmental regulatory networks

    Article • January 2003, Elsevier

    Professor Denis Thieffry

  80. Contributors

    Article • January 2003, Elsevier

    Professor Denis Thieffry

  81. Modélisation, analyse et simulationdes réseaux génétiques

    Article • médecine/sciences, April 2002, EDP Sciences

    Professor Denis Thieffry

  82. The genome in context: Biologists and philosophers on epigenetics

    Article • BioEssays, March 2002, Wiley

    Professor Denis Thieffry

  83. A Logical Analysis of the Drosophila Gap-gene System

    Article • Journal of Theoretical Biology, July 2001, Elsevier

    Professor Denis Thieffry

  84. Synthèse de circuits génétiquement autoréglés.

    Article • médecine/sciences, January 2001, INIST-CNRS

    Professor Denis Thieffry

  85. Modéliser les réseaux de gènes

    Article • Biofutur, December 2000, Elsevier

    Professor Denis Thieffry

  86. Modularity in development and evolution

    Article • BioEssays, October 2000, Wiley

    Professor Denis Thieffry

  87. From global expression data to gene networks

    Article • BioEssays, October 1999, Wiley

    Professor Denis Thieffry

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

    Article • Bioinformatics, July 1999, Oxford University Press (OUP)

    Professor Denis Thieffry

  89. The modularity of biological regulatory networks

    Article • Biosystems, April 1999, Elsevier

    Professor Denis Thieffry

  90. Postgenomics? A conference at the Max Planck Institute for the History of Science in Berlin

    Article • BioScience, March 1999, Oxford University Press (OUP)

    Professor Denis Thieffry

  91. Bioinformatics in Siberia

    Article • Trends in Genetics, January 1999, Elsevier

    Professor Denis Thieffry

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

    Article • BioEssays, December 1998, Wiley

    Professor Denis Thieffry

  93. Forty years under the central dogma

    Article • Trends in Biochemical Sciences, August 1998, Elsevier

    Professor Denis Thieffry

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

    Article • Bioinformatics, June 1998, Oxford University Press (OUP)

    Professor Denis Thieffry

  95. Establishement of the Dorso-ventral Pattern During Embryonic Development ofDrosophila melanogaster: a Logical Analysis

    Article • Journal of Theoretical Biology, December 1997, Elsevier

    Professor Denis Thieffry

  96. Toxicity and Neuroendocrine Regulation of the Immune Response: A Model Analysis

    Article • Journal of Theoretical Biology, December 1996, Elsevier

    Professor Denis Thieffry

  97. Jean Brachet's alternative scheme for protein synthesis

    Article • Trends in Biochemical Sciences, March 1996, Elsevier

    Professor Denis Thieffry

  98. Jean Brachet's alternative scheme for protein synthesis

    Article • Trends in Biochemical Sciences, March 1996, Elsevier

    Professor Denis Thieffry

  99. Syntactic recognition of regulatory regions in Escherichia coli

    Article • Bioinformatics, January 1996, Oxford University Press (OUP)

    Professor Denis Thieffry

  100. POSITIVE LOOPS AND DIFFERENTIATION

    Article • Journal of Biological System, June 1995, World Scientific Pub Co Pte Lt

    Professor Denis Thieffry

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

    Article • The Bulletin of Mathematical Biophysics, March 1995, Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • The Bulletin of Mathematical Biophysics, March 1995, Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • The Bulletin of Mathematical Biophysics, March 1995, Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • The Bulletin of Mathematical Biophysics, March 1995, Springer Science + Business Media

    Professor Denis Thieffry

  105. Les boucles de rétroaction, rouages des réseaux de régulation biologiques

    Article • médecine/sciences, January 1995, INIST-CNRS

    Professor Denis Thieffry

  106. Positive or Negative Regulatory Circuit Inference from Multilevel Dynamics

    Article • Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • Springer Science + Business Media

    Professor Denis Thieffry

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

    Article • Springer Science + Business Media

    Professor Denis Thieffry