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

Santana-Garcia W, Rocha-Acevedo M, Ramirez-Navarro L, Mbouamboua Y, Thieffry D, Thomas-Chollier M, Contreras-Moreira B, van Helden J, Medina-Rivera A.

Comput Struct Biotechnol J. 2019 Nov 7;17:1415-1428. doi: 10.1016/j.csbj.2019.09.009. eCollection 2019.


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

Sánchez-Villanueva JA, Rodríguez-Jorge O, Ramírez-Pliego O, Rosas Salgado G, Abou-Jaoudé W, Hernandez C, Naldi A, Thieffry D, Santana MA.

PLoS One. 2019 Dec 16;14(12):e0226388. doi: 10.1371/journal.pone.0226388. eCollection 2019.


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

Lin QXX, Thieffry D, Jha S, Benoukraf T.

Nucleic Acids Res. 2020 Jan 24;48(2):e10. doi: 10.1093/nar/gkz1088.


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

Grandclaudon M, Perrot-Dockès M, Trichot C, Karpf L, Abouzid O, Chauvin C, Sirven P, Abou-Jaoudé W, Berger F, Hupé P, Thieffry D, Sansonnet L, Chiquet J, Lévy-Leduc C, Soumelis V.

Cell. 2019 Oct 3;179(2):432-447.e21. doi: 10.1016/j.cell.2019.09.012.


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.

Thieffry D, Kaufman M.

J Theor Biol. 2019 Aug 7;474:42-47. doi: 10.1016/j.jtbi.2019.04.021. Epub 2019 Apr 24. No abstract available.


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

Rodríguez-Jorge O, Kempis-Calanis LA, Abou-Jaoudé W, Gutiérrez-Reyna DY, Hernandez C, Ramirez-Pliego O, Thomas-Chollier M, Spicuglia S, Santana MA, Thieffry D.

Sci Signal. 2019 Apr 16;12(577). pii: eaar3641. doi: 10.1126/scisignal.aar3641.


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

Sardina JL, Collombet S, Tian TV, Gómez A, Di Stefano B, Berenguer C, Brumbaugh J, Stadhouders R, Segura-Morales C, Gut M, Gut IG, Heath S, Aranda S, Di Croce L, Hochedlinger K, Thieffry D, Graf T.

Cell Stem Cell. 2018 Dec 6;23(6):905-906. doi: 10.1016/j.stem.2018.11.001. No abstract available.


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

Xuan Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T.

Nucleic Acids Res. 2019 Jan 8;47(D1):D145-D154. doi: 10.1093/nar/gky1005.


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

Sardina JL, Collombet S, Tian TV, Gómez A, Di Stefano B, Berenguer C, Brumbaugh J, Stadhouders R, Segura-Morales C, Gut M, Gut IG, Heath S, Aranda S, Di Croce L, Hochedlinger K, Thieffry D, Graf T.

Cell Stem Cell. 2018 Nov 1;23(5):727-741.e9. doi: 10.1016/j.stem.2018.08.016. Epub 2018 Sep 13. Erratum in: Cell Stem Cell. 2018 Dec 6;23(6):905-906.


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

Levy N, Naldi A, Hernandez C, Stoll G, Thieffry D, Zinovyev A, Calzone L, Paulevé L.

Front Physiol. 2018 Jul 6;9:787. doi: 10.3389/fphys.2018.00787. eCollection 2018.


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

Naldi A, Hernandez C, Levy N, Stoll G, Monteiro PT, Chaouiya C, Helikar T, Zinovyev A, Calzone L, Cohen-Boulakia S, Thieffry D, Paulevé L.

Front Physiol. 2018 Jun 19;9:680. doi: 10.3389/fphys.2018.00680. eCollection 2018.


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

Naldi A, Hernandez C, Abou-Jaoudé W, Monteiro PT, Chaouiya C, Thieffry D.

Front Physiol. 2018 Jun 19;9:646. doi: 10.3389/fphys.2018.00646. eCollection 2018.


RSAT 2018: regulatory sequence analysis tools 20th anniversary.

Nguyen NTT, Contreras-Moreira B, Castro-Mondragon JA, Santana-Garcia W, Ossio R, Robles-Espinoza CD, Bahin M, Collombet S, Vincens P, Thieffry D, van Helden J, Medina-Rivera A, Thomas-Chollier M.

Nucleic Acids Res. 2018 Jul 2;46(W1):W209-W214. doi: 10.1093/nar/gky317.


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

Castro-Mondragon JA, Jaeger S, Thieffry D, Thomas-Chollier M, van Helden J.

Nucleic Acids Res. 2017 Jul 27;45(13):e119. doi: 10.1093/nar/gkx314.


Logical modeling of lymphoid and myeloid cell specification and transdifferentiation.

Collombet S, van Oevelen C, Sardina Ortega JL, Abou-Jaoudé W, Di Stefano B, Thomas-Chollier M, Graf T, Thieffry D.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):5792-5799. doi: 10.1073/pnas.1610622114.


A Transcription Factor Pulse Can Prime Chromatin for Heritable Transcriptional Memory.

Iberg-Badeaux A, Collombet S, Laurent B, van Oevelen C, Chin KK, Thieffry D, Graf T, Shi Y.

Mol Cell Biol. 2017 Feb 1;37(4). pii: e00372-16. doi: 10.1128/MCB.00372-16. Print 2017 Feb 15.


Formal derivation of qualitative dynamical models from biochemical networks.

Abou-Jaoudé W, Thieffry D, Feret J.

Biosystems. 2016 Nov;149:70-112. doi: 10.1016/j.biosystems.2016.09.001. Epub 2016 Sep 9.


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

Mbodj A, Gustafson EH, Ciglar L, Junion G, Gonzalez A, Girardot C, Perrin L, Furlong EE, Thieffry D.

PLoS Comput Biol. 2016 Sep 6;12(9):e1005073. doi: 10.1371/journal.pcbi.1005073. eCollection 2016 Sep.


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

Traynard P, Fauré A, Fages F, Thieffry D.

Bioinformatics. 2016 Sep 1;32(17):i772-i780. doi: 10.1093/bioinformatics/btw457.


Logical Modeling and Dynamical Analysis of Cellular Networks.

Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C.

Front Genet. 2016 May 31;7:94. doi: 10.3389/fgene.2016.00094. eCollection 2016. Review.


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

Hossan T, Nagarajan S, Baumgart SJ, Xie W, Magallanes RT, Hernandez C, Chiaroni PM, Indenbirken D, Spitzner M, Thomas-Chollier M, Grade M, Thieffry D, Grundhoff A, Wegwitz F, Johnsen SA.

Stem Cells. 2016 May;34(5):1369-76. doi: 10.1002/stem.2287. Epub 2016 Feb 13.


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

Di Stefano B, Collombet S, Jakobsen JS, Wierer M, Sardina JL, Lackner A, Stadhouders R, Segura-Morales C, Francesconi M, Limone F, Mann M, Porse B, Thieffry D, Graf T.

Nat Cell Biol. 2016 Apr;18(4):371-81. doi: 10.1038/ncb3326. Epub 2016 Mar 14.


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

Chaouiya C, Keating SM, Berenguier D, Naldi A, Thieffry D, van Iersel MP, Le Novère N, Helikar T.

J Integr Bioinform. 2015 Sep 4;12(2):270. doi: 10.2390/biecoll-jib-2015-270.


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

Flobak Å, Baudot A, Remy E, Thommesen L, Thieffry D, Kuiper M, Lægreid A.

PLoS Comput Biol. 2015 Aug 28;11(8):e1004426. doi: 10.1371/journal.pcbi.1004426. eCollection 2015 Aug.


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

Nardacci R, Perfettini JL, Grieco L, Thieffry D, Kroemer G, Piacentini M.

Cell Death Dis. 2015 Aug 6;6:e1846. doi: 10.1038/cddis.2015.204. Review.


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

van Oevelen C, Collombet S, Vicent G, Hoogenkamp M, Lepoivre C, Badeaux A, Bussmann L, Sardina JL, Thieffry D, Beato M, Shi Y, Bonifer C, Graf T.

Stem Cell Reports. 2015 Aug 11;5(2):232-47. doi: 10.1016/j.stemcr.2015.06.007. Epub 2015 Jul 30.


RSAT 2015: Regulatory Sequence Analysis Tools.

Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M, van Helden J.

Nucleic Acids Res. 2015 Jul 1;43(W1):W50-6. doi: 10.1093/nar/gkv362. Epub 2015 Apr 22.


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

Kuperstein I, Grieco L, Cohen DP, Thieffry D, Zinovyev A, Barillot E.

Mutagenesis. 2015 Mar;30(2):191-204. doi: 10.1093/mutage/geu078. Review.


Model checking to assess T-helper cell plasticity.

Abou-Jaoudé W, Monteiro PT, Naldi A, Grandclaudon M, Soumelis V, Chaouiya C, Thieffry D.

Front Bioeng Biotechnol. 2015 Jan 28;2:86. doi: 10.3389/fbioe.2014.00086. eCollection 2014.


Cooperative development of logical modelling standards and tools with CoLoMoTo.

Naldi A, Monteiro PT, Müssel C; Consortium for Logical Models and Tools, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C.

Bioinformatics. 2015 Apr 1;31(7):1154-9. doi: 10.1093/bioinformatics/btv013. Epub 2015 Jan 25.


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

Niarakis A, Bounab Y, Grieco L, Roncagalli R, Hesse AM, Garin J, Malissen B, Daëron M, Thieffry D.

Curr Top Microbiol Immunol. 2014;382:69-93. doi: 10.1007/978-3-319-07911-0_4. Review.


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

Di Stefano B, Sardina JL, van Oevelen C, Collombet S, Kallin EM, Vicent GP, Lu J, Thieffry D, Beato M, Graf T.

Nature. 2014 Feb 13;506(7487):235-9. doi: 10.1038/nature12885. Epub 2013 Dec 15.


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

Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T.

BMC Syst Biol. 2013 Dec 10;7:135. doi: 10.1186/1752-0509-7-135.


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

Grieco L, Calzone L, Bernard-Pierrot I, Radvanyi F, Kahn-Perlès B, Thieffry D.

PLoS Comput Biol. 2013 Oct;9(10):e1003286. doi: 10.1371/journal.pcbi.1003286. Epub 2013 Oct 24. Erratum in: PLoS Comput Biol. 2013 Nov;9(11). doi:10.1371/annotation/90e5e4be-952b-42b8-b56d-46baae3479ed.


Logical modelling of Drosophila signalling pathways.

Mbodj A, Junion G, Brun C, Furlong EE, Thieffry D.

Mol Biosyst. 2013 Sep;9(9):2248-58. doi: 10.1039/c3mb70187e.


Dynamical modeling and analysis of large cellular regulatory networks.

Bérenguier D, Chaouiya C, Monteiro PT, Naldi A, Remy E, Thieffry D, Tichit L.

Chaos. 2013 Jun;23(2):025114. doi: 10.1063/1.4809783.


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

Bounab Y, Hesse AM, Iannascoli B, Grieco L, Couté Y, Niarakis A, Roncagalli R, Lie E, Lam KP, Demangel C, Thieffry D, Garin J, Malissen B, Daëron M.

Mol Cell Proteomics. 2013 Oct;12(10):2874-89. doi: 10.1074/mcp.M112.025908. Epub 2013 Jul 2. Erratum in: Mol Cell Proteomics. 2013 Feb ;13(2):678.


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

Darbo E, Herrmann C, Lecuit T, Thieffry D, van Helden J.

BMC Genomics. 2013 Apr 5;14:226. doi: 10.1186/1471-2164-14-226.


On circuit functionality in Boolean networks.

Comet JP, Noual M, Richard A, Aracena J, Calzone L, Demongeot J, Kaufman M, Naldi A, Snoussi el H, Thieffry D.

Bull Math Biol. 2013 Jun;75(6):906-19. doi: 10.1007/s11538-013-9829-2. Epub 2013 Mar 16.


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

Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J.

Nat Protoc. 2012 Jul 26;7(8):1551-68. doi: 10.1038/nprot.2012.088.


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

Coolen M, Thieffry D, Drivenes Ø, Becker TS, Bally-Cuif L.

Dev Cell. 2012 May 15;22(5):1052-64. doi: 10.1016/j.devcel.2012.03.003.


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

Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J.

Nucleic Acids Res. 2012 Feb;40(4):e31. doi: 10.1093/nar/gkr1104. Epub 2011 Dec 8.


Logical modelling of gene regulatory networks with GINsim.

Chaouiya C, Naldi A, Thieffry D.

Methods Mol Biol. 2012;804:463-79. doi: 10.1007/978-1-61779-361-5_23.


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

van Helden J, Toussaint A, Thieffry D.

Methods Mol Biol. 2012;804:1-11. doi: 10.1007/978-1-61779-361-5_1. Review.


RSAT 2011: regulatory sequence analysis tools.

Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, van Helden J.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W86-91. doi: 10.1093/nar/gkr377.


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

Naldi A, Carneiro J, Chaouiya C, Thieffry D.

PLoS Comput Biol. 2010 Sep 2;6(9):e1000912. doi: 10.1371/journal.pcbi.1000912.


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

Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, Zinovyev A.

PLoS Comput Biol. 2010 Mar 5;6(3):e1000702. doi: 10.1371/journal.pcbi.1000702.


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

Fauré A, Thieffry D.

Mol Biosyst. 2009 Dec;5(12):1569-81. doi: 10.1039/B907562n. Epub 2009 Sep 17. Review.


Modular logical modelling of the budding yeast cell cycle.

Fauré A, Naldi A, Lopez F, Chaouiya C, Ciliberto A, Thieffry D.

Mol Biosyst. 2009 Dec;5(12):1787-96. doi: 10.1039/B910101m. Epub 2009 Jul 31.


[Systems biology: from molecular networks to personalized medicine].

Thieffry D.

Med Sci (Paris). 2009 Jun-Jul;25(6-7):547-8. doi: 10.1051/medsci/2009256-7547. French. No abstract available.

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