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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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	Molecular insights into the origin of the Hox-TALE patterning system Bruno Hudry , Morgane Thomas-Chollier , Yael Volovik , Marilyne Duffraisse , Amélie Dard eLife, 2014, 3, ⟨10.7554/elife.01939⟩ Journal articles hal-03352057v1
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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

	Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses Nathalie Lehmann , Sandrine Perrin , Claire Wallon , Xavier Bauquet , Vivien Deshaies 2021 Preprints, Working Papers, ... hal-03784195v1

	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

	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

	Origin of Metazoan Patterning Systems and the Role of ANTP-Class Homeobox Genes Morgane Thomas-Chollier , Pedro Martinez eLS, 2016, ⟨10.1002/9780470015902.a0022852.pub2⟩ Book sections hal-03352064v1

	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
	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

Morgane Thomas-Chollier

Publications

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

RSAT 2022: regulatory sequence analysis tools

Logical modelling of in vitro differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions

Cis-acting variation is common across regulatory layers but is often buffered during embryonic development

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

IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8+ T Cells

The activation trajectory of plasmacytoid dendritic cells in vivo during a viral infection

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

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

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

Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria

Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise

RSAT 2018: regulatory sequence analysis tools 20th anniversary

Logical modeling of lymphoid and myeloid cell specification and transdifferentiation

Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements

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

Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation

Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements

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

Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

RSAT 2015: Regulatory Sequence Analysis Tools

ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors

Molecular insights into the origin of the Hox-TALE patterning system

A naturally occuring insertion of a single amino acid rewires transcriptional regulation by glucocorticoid receptor isoforms

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

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

Theoretical and empirical quality assessment of transcription factor-binding motifs

RSAT 2011: regulatory sequence analysis tools

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

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

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

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

RSAT: regulatory sequence analysis tools

Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni: comment

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

HoxPred: automated classification of Hox proteins using combinations of generalised profiles

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

Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses

Computational analysis of transcriptional regulation in metazoans

IFB/ELIXIR-FR, the french node of ELIXIR

Origin of Metazoan Patterning Systems and the Role of ANTP-Class Homeobox Genes

A Unix competency framework for learning bioinformatics

Groupe de travail sur les Métiers de la Bioinformatique (MetBIF)