Publications by authors named "Denis Thieffry"

79Publications

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

Nat Commun 2021 01 5;12(1):124. Epub 2021 Jan 5.

Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics, CNRS, Turing Center for Living Systems, Marseille, France.

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January 2021

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

Development 2021 Jan 20;148(2). Epub 2021 Jan 20.

Department of Biology, Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France

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January 2021

Dynamical Boolean Modeling of Immunogenic Cell Death.

Front Physiol 2020 12;11:590479. Epub 2020 Nov 12.

Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, INSERM U1138, Université de Paris, Sorbonne Université, Institut Universitaire de France, Paris, France.

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November 2020

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

Front Physiol 2020 30;11:558606. Epub 2020 Sep 30.

Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.

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September 2020

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

Curr Top Dev Biol 2020 19;139:205-238. Epub 2020 Mar 19.

Computational Systems Biology Team, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS, INSERM, École Normale Supérieure, Université PSL, Paris, France.; Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.. Electronic address:

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March 2020

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

Comput Struct Biotechnol J 2019 7;17:1415-1428. Epub 2019 Nov 7.

Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Blvd Juriquilla 3001, Santiago de Querétaro 76230, Mexico.

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November 2019

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

PLoS One 2019 16;14(12):e0226388. Epub 2019 Dec 16.

Centro de Investigación en Dinámica Celular (IICBA), Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, México.

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April 2020

TFregulomeR reveals transcription factors' context-specific features and functions.

Nucleic Acids Res 2020 01;48(2):e10

Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.

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January 2020

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.

J Theor Biol 2019 08 24;474:42-47. Epub 2019 Apr 24.

Université libre de Bruxelles (ULB), Service de Chimie physique et Biologie théorique, Campus Plaine ULB, CP 231, Boulevard du Triomphe, 1050, Bruxelles, Belgium. Electronic address:

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August 2019

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

Sci Signal 2019 04 16;12(577). Epub 2019 Apr 16.

Computational System Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, École Normale Supérieure, Université PSL, 75005 Paris, France.

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April 2019

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

Nucleic Acids Res 2019 01;47(D1):D145-D154

Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.

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January 2019

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

Cell Stem Cell 2018 11 13;23(5):727-741.e9. Epub 2018 Sep 13.

Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain. Electronic address:

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November 2018