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Publications

Books

  1. van Helden J, Toussaint A, Thieffry D (eds.) (2012). Bacterial Molecular Networks. Methods in Molecular Biology Series. Humana Press, 546 pages.


Articles

    2018

  1. 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* (accepted). Synergy between T cell receptor and Toll-like receptor 5 signaling for CD4+ T cell activation. Science Signaling, accepted.
  2. Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T (2018). MethMotif : An integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. Nucleic Acids Research, in press.
  3. Schöne S, Bothe M, Einfeldt E, Borschiwer M, Benner P, Vingron M, Thomas-Chollier M, Meijsing SH (2018). Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise. PLoS Genetics 14 : e1007793.
  4. 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 and Graf T (2018). Transcription factors drive Tet2-mediated enhancer demethylation to reprogram cell fate. Cell Stem Cell 23 : 727-41.
  5. Naldi A*, Hernandez C, Abou-Jaoudé W, Monteiro PT, Chaouiya C*, Thieffry D*. (2018). Logical modelling and analysis of cellular regulatory networks with GINsim 3.0. Frontiers in Physiology 9 : 646.
  6. Naldi A, Hernandez C, Levy N, Stoll G, Monteiro PT, Chaouiya C, Helikar T, Zinovyev A, Calzone L, Cohen-Boulakia S, Thieffry D* and Paulevé L* (2018). The CoLoMoTo Interactive Notebook : Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. Frontiers in Physiology 9 : 680.
  7. Levy N, Naldi A, Hernandez C, Stoll G, Thieffry D, Zinovyev A, Calzone L*, Paulevé L* (2018). Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial). Frontiers in Physiology 9 : 787.
  8. Nga Thi Thuy Nguyen NT, 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* (2018). RSAT 2018 : Regulatory Sequence Analysis Tools 20th Anniversary. Nucleic Acids Research 46 : W209-14.


  9. 2017

  10. Collombet S, van Oevelen C, Sardina Ortega JL, Abou-Jaoudé W, Di Stefano B, Thomas-Chollier M, Graf T, Thieffry D (2017). Logical modeling of lymphoid and myeloid cell specification and transdifferentiation. PNAS 14:23 : 5792–5799.
  11. Castro-Mondragon JA, Jaeger S, Thieffry D, Thomas-Chollier M#, van Helden J# (2017). RSAT matrix-clustering : dynamic exploration and redundancy reduction of transcription factor binding motif collections. Nucleic Acid Research 45:13 e119.
  12. Iberg-Badeaux A, Collombet S, Laurent B, van Oevelen C, Chin K-K, Thieffry D, Graf T, Yang S (2017). A transcription factor pulse can prime chromatin for heritable transcriptional memory. Molecular and Cellular Biology 37 : e00372-16.
  13. Love MI, Huska MR, Jurk M, Schöpflin R, Starick SR, Schwahn K, Cooper SB, Yamamoto KR, Thomas-Chollier M, Vingron M, Meijsing SH (2017). Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation. Nucleic Acids Research 45:1805-19.
  14. Thierion E, Le Men J, Collombet S, Hernandez C, Coulpier F, Torbey P, Thomas-Chollier M, Noordermeer D, Charnay P, Gilardi-Hebenstreit P (2017). Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements. PLoS Genetics 13 : e1006903.


  15. 2016

  16. 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 (2016). C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4. Nature Cell Biology 18 : 371-81.
  17. Schöne S, Jurk M, Helabad MB, Dror I, Lebars I, Kieffer B, Imhof B, Rohs R, Vingron M, Thomas-Chollier M#, and Meijsing SH# (2016). Sequences flanking the core binding site modulate glucocorticoid receptor structure and activity. Nature Communications, 7 : 12621.
  18. Love MI, Huska MR, Jurk M, Schöpflin R, Starick SR, Schwahn K, Cooper SB, Yamamoto KR, Thomas-Chollier M, Vingron M, Meijsing SH (2016). Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation.Nucleic Acid Research 45:1805-1819.
  19. Telorac J, Prykhozhij SV, Schöne S, Meierhofer D, Sauer S, Thomas-Chollier M#, Meijsing SH# (2016). Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements. Nucleic Acid Research, 44(13):6142-6156.
  20. Abou-Jaoudé W, Thieffry D, Feret J (2016). Formal Derivation of Qualitative Dynamical Models from Biochemical Networks. Biosystems, 149 : 70-112.
  21. Mbodj A, Gustafson H, Ciglar L, Junion G, Gonzalez A, Girardot C, Perrin L, Furlong E#, Thieffry D# (2016). Qualitative dynamical modelling can formally explain mesoderm specification and predict novel developmental phenotypes. PLoS Computational Biology, 12 : e1005073.
  22. Traynard P, Fauré A, Fages F, Thieffry D (2016). Logical model specification aided by model-checking techniques : application to the mammalian cell cycle regulation. Bioinformatics, 32 : i772-80.
  23. Abou-Jaoudé W, Traynard P, Monteiro P, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya D (2016). Logical modeling and dynamical analysis of cellular networks. Frontiers in Genetics 7 : 94.
  24. Hossan T, Nagarajan S, Baumgart SJ, Xie W, Tirado Magallanes R, Hernandez C, Chiaroni P, Indenbirken D, Spitzner M, Thomas-Chollier M, Grade M, Thieffry D, Grundhoff A, Wegwitz F, Johnsen SA (2016). The Histone Chaperone SSRP1 is Essential for Wnt Signaling Pathway Activity During Osteoblast Differentiation. Stem Cells, 34(5):1369-76.
  25. Thomas-Chollier M, Martinez P (2016). The origin of metazoan patterning systems and the role of ANTP-class homeobox genes. eLS, John Wiley Sons Ltd, Chichester.

  26. 2015

  27. Starick S*, Ibn-Salem J*, Jurk M*, Hernandez C, Love MI, Chung H, Vingron M, Thomas-Chollier M#, Meijsing SH# (2015) ChIP-exo signal associated with DNA-binding motifs provide insights into the genomic binding of the glucocorticoid receptor and cooperating transcription factors. Genome Research 25 : 825-35.
  28. Medina-Rivera A*, Defrance M*, Sand O*, Herrmann C, Castro-Mondragon J, 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# (2015) RSAT 2015 : Regulatory Sequence Analysis Tools. Nucleic Acid Research 43 : W50-6.
  29. Chaouiya C, Keating SM, Berenguier D, Naldi A, Thieffry D, van Iersel MP, Le Novère N, Helikar T (2015). The Systems Biology Markup Language (SBML) Level 3 Package : Qualitative Models, Version 1, Release 1. Journal of Integrative Bioinformatics 12 : 270.
  30. Naldi A, Monteiro PT, Müssel C, the Consortium for Logical Models and Tools, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C (2015). Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics 31 : 1154-9.
  31. Abou-Jaoudé W, Monteiro PT, Naldi A, Grandclaudon M, Soumelis V, Chaouiya C, Thieffry D (2015). Model checking to assess T-helper cell plasticity. Frontiers in Bioengineering and Biotechnology 2 : 86.
  32. Flobak Å, Baudot A, Remy E, Thommesen L, Thieffry D, Kuiper M, Lægreid A (2015). Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLoS Computational Biology 11 : e1004426.
  33. 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 (2015). C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis. Stem Cell Reports 5 : 232-47.
  34. Nardacci R, Perfettini JL, Grieco L, Thieffry D, Kroemer G, Piacentini M (2015). Syncytial apoptosis signaling network induced by the HIV-1 envelope glycoprotein complex : an overview. Cell Death Diseases 6 : e1846.
  35. Kuperstein I, Grieco L, Cohen D, Thieffry D, Zinovyev A, Barillot E (2015). The shortest path is not the one you know : application of biological network resources in precision oncology research. Mutagenesis 30 : 191–204.


  36. 2014

  37. Niarakis A, Marc Daëron M (2014). Activating and Inhibitory Receptors on Mast Cells. In : IR Mackay & NR Rose (eds.), Encyclopedia of Medical Immunology – Allergic Diseases, pp. [DOI 10.1007/ 978-1-4614-9194-1]
  38. Niarakis A, Bounab Y, Grieco L, Roncagalli R, Hesse A-M, Garin J, Malissen B, Daëron M, Thieffry D (2014). Computational modelling of the main signaling pathways involved in mast cell activation. Current Topics in Microbiology and Immunology 382 : 69-93.
  39. Hudry B, Thomas-Chollier M, Volovik Y,Duffraisse M,Dard A,Frank D, Technau U, Merabet S (2014). Molecular insights into the origin of the Hox-TALE patterning system. Elife 3:e01939.
  40. Di Stefano B, Sardina JL, van Oevelen C, Collombet S, Kallin EM, Vicent GP, Lu J, Thieffry D, Beato M , Graf T (2014). C/EBPa poises B cells for rapid reprogramming into induced pluripotent stem cells. Nature 506:235–239.


  41. 2013

  42. Chaouiya C, Berenguier D, Keating SK, 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. (2013) SBML Qualitative Models : a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology 7:135.
  43. Grieco L, Calzone L, Bernard-Pierrot I, Radvanyi F, Kahn-Perlès B, Thieffry D (2013). Integrative modelling of the influence of MAPK network on cancer cell fate decision. PLoS Computational Biology 9 : e1003286.
  44. Thomas-Chollier M, Watson L, Cooper S, Pufall MA, Liu JS, Borzym K, Vingron M, Yamamoto K.R, Meijsing SH (2013). A naturally occurring single amino acid insertion rewires transcriptional regulation by Glucocorticoid receptor isoforms. Proceedings of National Academy of Sciences of U. S. A. 110(44):17826-31.
  45. 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 (2013). Proteomic Analysis of the SH2Domain-containing Leukocyte Protein of 76 kDa (SLP76) Interactome. Molecular Cell Proteomics 12 : 2874-89.
  46. Mbodj A, Junion G, Brun C, Furlong E, Thieffry D (2013). Logical modelling of drosophila signalling pathways. Molecular Biosystems 9 : 2248-2258.
  47. Bérenguier D, Chaouiya C, Monteiro PT, Naldi A, Remy E, Thieffry D, Tichit L (2013). Dynamical modeling and analysis of large cellular regulatory networks. Chaos 23 : 025114.
  48. Comet JP, Noual M, Richard A, Aracena J, Calzone L, Demongeot J, Kaufman M, Naldi An Snoussi EH, Thieffry D (2013). On circuit functionality in Boolean networks. Bulletin of Mathematical Biology 75 : 906–19.
  49. Darbo E, Herrmann C, Lecuit T, Thieffry D, van Helden J (2013). Transcriptional and epigenetic signatures of zygotic genome activation during early drosophila embryogenesis. BMC Genomics 14 : 226.
  50. Abou-Jaoudé W, Chaves M, Gouzé JL. (2013) Links between topology of the transition graph and limit cycles in a two-dimensional piecewise affine biological model. Journal of Mathematical Biology doi : 10.1007/s00285-013-0735-x
  51. Gonze D and Abou-Jaoudé W (2013) The Goodwin model : behind the Hill function. PLoS ONE 8(8) : e69573.


  52. 2012

  53. Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J (2012). From peaks to motifs : a complete workflow for full-sized ChIP-seq (and similar) datasets. Nature Protocols 7 : 1551-68.
  54. Coolen M, Thieffry D, Drivenes Ø, Becker TS, Bally-Cuif L (2012). miR-9 controls the timing of neurogenesis through the direct inhibition of antagonistic factors. Developmental Cell 22:1052-64.
  55. Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J (2012). RSAT peak-motifs : motif analysis in full-size ChIP-seq datasets. Nucleic Acid Research 40 : e31.
  56. Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, van Helden J (2011). RSAT 2011 : Regulatory Sequence Analysis Tools. Nucleic Acid Research 39 : W86-91.


  57. 2011

  58. Chaouiya C, Naldi A, Remy E, Thieffry D (2011). Petri net representation of multi-valued logical regulatory graphs. Natural Computing 10 : 727-50.
  59. Naldi A, Remy E, Thieffry D, Chaouiya C (2011). Dynamically consistent reduction of logical regulatory graphs. Theoretical Computer Science 412 : 2207-18.


  60. 2010

  61. Naldi A, Carneiro J, Chaouiya C, Thieffry D (2010). Diversity and plasticity of Th cell types predicted from regulatory network modelling. PLoS Computational Biology 6 : e1000912.
  62. Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, Zinovyev A (2010). Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement. PLoS Computational Biology 6 : e1000702.