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Morgane Thomas-Chollier

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Alternative splicing induced by bacterial pore-forming toxins sharpens CIRBP-mediated cell response to Listeria infection

Morgane Corre , Volker Boehm , Vinko Besic , Anna Kurowska , Anouk Viry
Nucleic Acids Research, 2023, 51 (22), pp.12459-12475. ⟨10.1093/nar/gkad1033⟩
Journal articles hal-04342449v1
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RSAT 2022: regulatory sequence analysis tools

Walter Santana-Garcia , Jaime Castro-Mondragon , Mónica Padilla-Gálvez , Nga Nguyen , Ana Elizondo-Salas
Nucleic Acids Research, 2022, ⟨10.1093/nar/gkac312⟩
Journal articles hal-03669930v1
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Logical modelling of in vitro differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions

Karen J Nuñez-Reza , Aurélien Naldi , Arantza Sánchez-Jiménez , Ana V Leon-Apodaca , M. Angélica Angélica Santana
Interface Focus, 2021, 11 (4), pp.20200061. ⟨10.1098/rsfs.2020.0061⟩
Journal articles hal-03352078v1
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Cis-acting variation is common across regulatory layers but is often buffered during embryonic development

Swann Floc'Hlay , Emily S Wong , Bingqing Zhao , Rebecca R Viales , Morgane Thomas-Chollier
Genome Research, 2021, 31, pp.211 - 224. ⟨10.1101/gr.266338.120⟩
Journal articles hal-03352083v1
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Computational Verification of Large Logical Models—Application to the Prediction of T Cell Response to Checkpoint Inhibitors

Céline Hernandez , Morgane Thomas-Chollier , Aurélien Naldi , Denis Thieffry
Frontiers in Physiology, 2020, 11, ⟨10.3389/fphys.2020.558606⟩
Journal articles hal-03352080v1
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IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8+ T Cells

Darely Gutiérrez-Reyna , Alejandra Cedillo-Baños , Linda Kempis-Calanis , Oscar Ramírez-Pliego , Lisa Bargier
Frontiers in Immunology, 2020, 11, ⟨10.3389/fimmu.2020.01089⟩
Journal articles hal-02935693v1
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Deciphering and modelling the TGF-β signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo

Swann Floc'Hlay , Maria Dolores Molina , Céline Hernandez , Emmanuel Haillot , Morgane Thomas-Chollier
Development (Cambridge, England), 2020, ⟨10.1242/dev.189944⟩
Journal articles hal-03352081v1
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The activation trajectory of plasmacytoid dendritic cells in vivo during a viral infection

Abdenour Abbas , Thien-Phong Vu Manh , Michael Valente , Nils Collinet , Noudjoud Attaf
Nature Immunology, 2020, 21 (9), pp.983-997. ⟨10.1038/s41590-020-0731-4⟩
Journal articles hal-02980944v1
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Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria

Hervé Philippe , Albert J Poustka , Marta Chiodin , Katharina J Hoff , Christophe Dessimoz
Current Biology - CB, 2019, 29 (11), pp.1818-1826.e6. ⟨10.1016/j.cub.2019.04.009⟩
Journal articles hal-02392672v1
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RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding

Walter Santana-Garcia , Maria Rocha-Acevedo , Lucia Ramirez-Navarro , Yvon Mbouamboua , Denis Thieffry
Computational and Structural Biotechnology Journal, 2019, ⟨10.1016/j.csbj.2019.09.009⟩
Journal articles hal-02458940v1
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Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4 + T cell activation

Otoniel Rodríguez-Jorge , Linda Kempis-Calanis , Wassim Abou-Jaoudé , Darely Gutiérrez-Reyna , Céline Hernandez
Science Signaling, 2019, 12 (577), pp.eaar3641. ⟨10.1126/scisignal.aar3641⟩
Journal articles hal-02154906v1
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Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise

Stefanie Schöne , Melissa Bothe , Edda Einfeldt , Marina Borschiwer , Philipp Benner
PLoS Genetics, 2018, 14 (11), pp.e1007793. ⟨10.1371/journal.pgen.1007793⟩
Journal articles inserm-02155974v1
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RSAT 2018: regulatory sequence analysis tools 20th anniversary

Nga thi thuy Nguyen , Bruno Contreras-Moreira , Jaime Castro-Mondragon , Walter Santana-Garcia , Raul Ossio
Nucleic Acids Research, 2018, 46 (W1), pp.W209 - W214. ⟨10.1093/nar/gky317⟩
Journal articles hal-01874932v1

Logical modeling of lymphoid and myeloid cell specification and transdifferentiation

Samuel Collombet , Chris van Oevelen , Jose Luis Sardina Ortega , Wassim Abou-Jaoudé , Bruno Di Stefano
Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (23), pp.5792-5799. ⟨10.1073/pnas.1610622114⟩
Journal articles hal-03352074v1
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RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

Jaime Abraham Castro-Mondragon , Sébastien Jaeger , Denis Thieffry , Morgane Thomas-Chollier , Jacques Van helden
Nucleic Acids Research, 2017, 45 (13), pp.e119--e119. ⟨10.1093/nar/gkx314⟩
Journal articles hal-01624366v1
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Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation

Michael I Love , Matthew R Huska , Marcel Jurk , Robert Schöpflin , Stephan R Starick
Nucleic Acids Research, 2017, 45 (4), pp.1805 - 1819. ⟨10.1093/nar/gkw1163⟩
Journal articles hal-03352072v1
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Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements

Elodie Thierion , Johan Le Men , Samuel Collombet , Céline Hernandez , Fanny Coulpier
PLoS Genetics, 2017, 13 (7), pp.e1006903. ⟨10.1371/journal.pgen.1006903⟩
Journal articles inserm-02158641v1
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Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements

Jonas Telorac , Sergey V Prykhozhij , Stefanie Schöne , David Meierhofer , Sascha Sauer
Nucleic Acids Research, 2016, 44 (13), pp.6142 - 6156. ⟨10.1093/nar/gkw203⟩
Journal articles hal-03352070v1

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

Tareq Hossan , Sankari Nagarajan , Simon J Baumgart , Wanhua Xie , Roberto Tirado Magallanes
STEM CELLS, 2016, 34 (5), pp.1369 - 1376. ⟨10.1002/stem.2287⟩
Journal articles hal-03352065v1
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Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

Stefanie Schöne , Marcel Jurk , Mahdi Bagherpoor Helabad , Iris Dror , Isabelle Lebars
Nature Communications, 2016, 7 (1), ⟨10.1038/ncomms12621⟩
Journal articles hal-03352071v1
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ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors

Stephan R Starick , Jonas Ibn-Salem , Marcel Jurk , Céline Hernandez , Michael I Love
Genome Research, 2015, 25 (6), pp.825 - 835. ⟨10.1101/gr.185157.114⟩
Journal articles hal-03352059v1
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RSAT 2015: Regulatory Sequence Analysis Tools

Alejandra Medina-Rivera , Matthieu Defrance , Olivier Sand , Carl Herrmann , Jaime A. Castro-Mondragon
Nucleic Acids Research, 2015, 43 (W1), pp.W50--W56. ⟨10.1093/nar/gkv362⟩
Journal articles hal-01624369v1
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Molecular insights into the origin of the Hox-TALE patterning system

Bruno Hudry , Morgane Thomas-Chollier , Yael Volovik , Marilyne Duffraisse , Amélie Dard
Journal articles hal-03352057v1
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A naturally occuring insertion of a single amino acid rewires transcriptional regulation by glucocorticoid receptor isoforms

Morgane Thomas-Chollier , Lisa C Watson , Samantha B Cooper , Miles A Pufall , Jennifer S Liu
Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (44), pp.17826 - 17831. ⟨10.1073/pnas.1316235110⟩
Journal articles hal-03352056v1
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A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs

Morgane Thomas-Chollier , Elodie Darbo , Carl Herrmann , Matthieu Defrance , Denis Thieffry
Nature Protocols, 2012, 7 (8), pp.1551-1568. ⟨10.1038/nprot.2012.088⟩
Journal articles hal-01624286v1
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RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

Morgane Thomas-Chollier , Carl Herrmann , Matthieu Defrance , Olivier Sand , Denis Thieffry
Nucleic Acids Research, 2012, 40 (4), pp.e31-e31. ⟨10.1093/nar/gkr1104⟩
Journal articles hal-01624284v1
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RSAT 2011: regulatory sequence analysis tools

Morgane Thomas-Chollier , Olivier Sand , Jean-Valery Turatsinze , Rekin'S Janky , Matthieu Defrance
Nucleic Acids Research, 2011, 39, pp.W86--W91. ⟨10.1093/nar/gkr377⟩
Journal articles hal-01624291v1

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

Morgane Thomas-Chollier , Andrew Hufton , Matthias Heinig , Sean O'Keeffe , Nassim El Masri
Nature Protocols, 2011, 6 (12), pp.1860-1869. ⟨10.1038/nprot.2011.409⟩
Journal articles hal-03352055v1
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Theoretical and empirical quality assessment of transcription factor-binding motifs

Alejandra Medina-Rivera , Cei Abreu-Goodger , Morgane Thomas-Chollier , Heladia Salgado , Julio Collado-Vides
Nucleic Acids Research, 2011, 39 (3), pp.808--824. ⟨10.1093/nar/gkq710⟩
Journal articles hal-01624287v1

A non-tree-based comprehensive study of metazoan Hox and ParaHox genes prompts new insights into their origin and evolution.

Morgane Thomas-Chollier , Valérie Ledent , Luc Leyns , Michel Vervoort
BMC Evolutionary Biology, 2010, 10, pp.73. ⟨10.1186/1471-2148-10-73⟩
Journal articles hal-00486240v1

Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl

O. Sand , M. Thomas-Chollier , J. Van Helden
Bioinformatics, 2009, 25 (20), pp.2739--2740
Journal articles hal-01624297v1
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RSAT: regulatory sequence analysis tools

M. Thomas-Chollier , Olivier Sand , J. V. Turatsinze , R. Janky , M. Defrance
Nucleic Acids Research, 2008, 36, pp.W119--W127. ⟨10.1093/nar/gkn304⟩
Journal articles hal-01624302v1

Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services-an example with ChIP-chip data

O. Sand , M. Thomas-Chollier , E. Vervisch , J. Van Helden
Nature Protocols, 2008, 3 (10), pp.1604--1615
Journal articles hal-01624309v1
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Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni: comment

Morgane Thomas-Chollier , Valérie Ledent
BMC Genomics, 2008, 9 (1), pp.35. ⟨10.1186/1471-2164-9-35⟩
Journal articles hal-03352045v1

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

Jean-Valery Turatsinze , Morgane Thomas-Chollier , Matthieu Defrance , Jacques Van Helden
Nature Protocols, 2008, 3 (10), pp.1578--1588
Journal articles hal-01624305v1

Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.

Elena Simionato , Valérie Ledent , Gemma Richards , Morgane Thomas-Chollier , Pierre Kerner
BMC Evolutionary Biology, 2007, 7, pp.33. ⟨10.1186/1471-2148-7-33⟩
Journal articles hal-00167529v1
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HoxPred: automated classification of Hox proteins using combinations of generalised profiles

Morgane Thomas-Chollier , Luc Leyns , Valérie Ledent
BMC Bioinformatics, 2007, 8 (1), ⟨10.1186/1471-2105-8-247⟩
Journal articles hal-03352015v1
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Computational analysis of transcriptional regulation in metazoans

Morgane Thomas-Chollier
Quantitative Methods [q-bio.QM]. Ecole normale supérieure - ENS PARIS, 2016
Habilitation à diriger des recherches tel-01362020v1
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IFB/ELIXIR-FR, the french node of ELIXIR

Anne-Françoise Adam-Blondon , Jacques van Helden , Gildas Le Corguillé , Christophe Blanchet , Hélène Chiapello
ISMB ECCB 2023, International Society for Computational Biology, Jul 2023, Lyon, France
Conference papers hal-04503051v1
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A Unix competency framework for learning bioinformatics

Hélène Chiapello , Thomas Denecker , Lucie Khamvongsa Charbonnier , Pierre Poulain , Denis Puthier
JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques 2024, Jun 2024, Toulouse, France.
Conference poster hal-04619317v1
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Groupe de travail sur les Métiers de la Bioinformatique (MetBIF)

Hélène Chiapello , Samuel Mondy , Morgane Thomas-Chollier
JOBIM 2018, Jul 2018, Marseille, France
Conference poster hal-03287534v1