Morgane Thomas-Chollier

Identifiants chercheurs

IdHAL :

morgane-thomas-chollier

ORCID :

0000-0003-2608-476X

IdRef :

204769965

VIAF :

60151050206033412890

Publications

Pré-publication, Document de travail (5)

Regeneration of distinct complex structures in the annelid &lt;i&gt;Platynereis&lt;/i&gt; is partially based on common morphological, cellular, and molecular events Zoe Atzin Velasquillo Ramirez,Viktor Starunov,Louis Pare,Loeiza Baduel,Theaud Hezezet al. 2025 Pré-publication, Document de travail hal-05298578v1
A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data Ali Hamraoui,Audrey Onfroy,Catherine Sénamaud-Beaufort,Fanny Coulpier,Sophie Lemoineet al. 2025 Pré-publication, Document de travail hal-05190995v1
Representing Transcription Factor Dimer Binding Sites Using Forked-Position Weight Matrices and Forked-Sequence Logos Matthew Dyer,Roberto Tirado-Magallanes,Aida Ghayour-Khiavi,Xiao Xuan Lin Quy,Walter Santanaet al. 2024 Pré-publication, Document de travail hal-04706707v1
A low CDKN1c/p57kip2 expression in spinal progenitors drives the transition from proliferative to neurogenic modes of division Baptiste Mida,Nathalie Lehman,Fanny Coulpier,Kamal Bouhali,Rosette Goiameet al. 2024 Pré-publication, Document de travail hal-04752929v1
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 Deshaieset al. 2021 Pré-publication, Document de travail hal-03784195v1

Article dans une revue (39)

A low-level Cdkn1c/p57kip2 expression in spinal progenitors drives the transition from proliferative to neurogenic modes of division Baptiste Mida,Nathalie Lehmann,Rosette Goïame,Fanny Coulpier,Kamal Bouhaliet al. EMBO Reports, 2025, ⟨10.1038/s44319-025-00653-9⟩ Article dans une revue hal-05426812v1
AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow Ali Hamraoui,Laurent Jourdren,Morgane Thomas-Chollier Bioinformatics, 2025, Volume 41 (Issue 3), pp.March 2025, btaf087. ⟨10.1093/bioinformatics/btaf087⟩ Article dans une revue hal-04708885v2
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 Viryet al. Nucleic Acids Research, 2023, 51 (22), pp.12459-12475. ⟨10.1093/nar/gkad1033⟩ Article dans une revue hal-04342449v1
RSAT 2022: regulatory sequence analysis tools Walter Santana-Garcia,Jaime Castro-Mondragon,Mónica Padilla-Gálvez,Nga Nguyen,Ana Elizondo-Salaset al. Nucleic Acids Research, 2022, ⟨10.1093/nar/gkac312⟩ Article dans une revue 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 Santanaet al. Interface Focus, 2021, 11 (4), pp.20200061. ⟨10.1098/rsfs.2020.0061⟩ Article dans une revue 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-Chollieret al. Genome Research, 2021, 31, pp.211 - 224. ⟨10.1101/gr.266338.120⟩ Article dans une revue hal-03352083v1
The activation trajectory of plasmacytoid dendritic cells in vivo during a viral infection Abdenour Abbas,Thien-Phong Vu Manh,Michael Valente,Nils Collinet,Noudjoud Attafet al. Nature Immunology, 2020, 21 (9), pp.983-997. ⟨10.1038/s41590-020-0731-4⟩ Article dans une revue hal-02980944v1
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 Bargieret al. Frontiers in Immunology, 2020, 11, ⟨10.3389/fimmu.2020.01089⟩ Article dans une revue hal-02935693v1
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⟩ Article dans une revue hal-03352080v1
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-Chollieret al. Development (Cambridge, England), 2020, ⟨10.1242/dev.189944⟩ Article dans une revue hal-03352081v1
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 Dessimozet al. Current Biology, 2019, 29 (11), pp.1818-1826.e6. ⟨10.1016/j.cub.2019.04.009⟩ Article dans une revue hal-02392672v1
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 Thieffryet al. Computational and Structural Biotechnology Journal, 2019, ⟨10.1016/j.csbj.2019.09.009⟩ Article dans une revue hal-02458940v1
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 Hernandezet al. Science Signaling, 2019, 12 (577), pp.eaar3641. ⟨10.1126/scisignal.aar3641⟩ Article dans une revue hal-02154906v1
RSAT 2018: regulatory sequence analysis tools 20th anniversary Nga thi thuy Nguyen,Bruno Contreras-Moreira,Jaime Castro-Mondragon,Walter Santana-Garcia,Raul Ossioet al. Nucleic Acids Research, 2018, 46 (W1), pp.W209 - W214. ⟨10.1093/nar/gky317⟩ Article dans une revue hal-01874932v1
Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise Stefanie Schöne,Melissa Bothe,Edda Einfeldt,Marina Borschiwer,Philipp Benneret al. PLoS Genetics, 2018, 14 (11), pp.e1007793. ⟨10.1371/journal.pgen.1007793⟩ Article dans une revue inserm-02155974v1
Logical modeling of lymphoid and myeloid cell specification and transdifferentiation Samuel Collombet,Chris van Oevelen,Jose Luis Sardina Ortega,Wassim Abou-Jaoudé,Bruno Di Stefanoet al. Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (23), pp.5792-5799. ⟨10.1073/pnas.1610622114⟩ Article dans une revue hal-03352074v1
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⟩ Article dans une revue 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 Staricket al. Nucleic Acids Research, 2017, 45 (4), pp.1805 - 1819. ⟨10.1093/nar/gkw1163⟩ Article dans une revue hal-03352072v1
Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements Elodie Thierion,Johan Le Men,Samuel Collombet,Céline Hernandez,Fanny Coulpieret al. PLoS Genetics, 2017, 13 (7), pp.e1006903. ⟨10.1371/journal.pgen.1006903⟩ Article dans une revue inserm-02158641v1
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 Saueret al. Nucleic Acids Research, 2016, 44 (13), pp.6142 - 6156. ⟨10.1093/nar/gkw203⟩ Article dans une revue 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 Magallaneset al. STEM CELLS, 2016, 34 (5), pp.1369 - 1376. ⟨10.1002/stem.2287⟩ Article dans une revue hal-03352065v1
Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity Stefanie Schöne,Marcel Jurk,Mahdi Bagherpoor Helabad,Iris Dror,Isabelle Lebarset al. Nature Communications, 2016, 7 (1), ⟨10.1038/ncomms12621⟩ Article dans une revue hal-03352071v1
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 Loveet al. Genome Research, 2015, 25 (6), pp.825 - 835. ⟨10.1101/gr.185157.114⟩ Article dans une revue hal-03352059v1
RSAT 2015: Regulatory Sequence Analysis Tools Alejandra Medina-Rivera,Matthieu Defrance,Olivier Sand,Carl Herrmann,Jaime A. Castro-Mondragonet al. Nucleic Acids Research, 2015, 43 (W1), pp.W50--W56. ⟨10.1093/nar/gkv362⟩ Article dans une revue hal-01624369v1
Molecular insights into the origin of the Hox-TALE patterning system Bruno Hudry,Morgane Thomas-Chollier,Yael Volovik,Marilyne Duffraisse,Amélie Dardet al. eLife, 2014, 3, ⟨10.7554/elife.01939⟩ Article dans une revue 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 Liuet al. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (44), pp.17826 - 17831. ⟨10.1073/pnas.1316235110⟩ Article dans une revue hal-03352056v1
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets Morgane Thomas-Chollier,Carl Herrmann,Matthieu Defrance,Olivier Sand,Denis Thieffryet al. Nucleic Acids Research, 2012, 40 (4), pp.e31-e31. ⟨10.1093/nar/gkr1104⟩ Article dans une revue 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 Thieffryet al. Nature Protocols, 2012, 7 (8), pp.1551-1568. ⟨10.1038/nprot.2012.088⟩ Article dans une revue hal-01624286v1
RSAT 2011: regulatory sequence analysis tools Morgane Thomas-Chollier,Olivier Sand,Jean-Valery Turatsinze,Rekin'S Janky,Matthieu Defranceet al. Nucleic Acids Research, 2011, 39, pp.W86--W91. ⟨10.1093/nar/gkr377⟩ Article dans une revue 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 Masriet al. Nature Protocols, 2011, 6 (12), pp.1860-1869. ⟨10.1038/nprot.2011.409⟩ Article dans une revue hal-03352055v1
Theoretical and empirical quality assessment of transcription factor-binding motifs Alejandra Medina-Rivera,Cei Abreu-Goodger,Morgane Thomas-Chollier,Heladia Salgado,Julio Collado-Videset al. Nucleic Acids Research, 2011, 39 (3), pp.808--824. ⟨10.1093/nar/gkq710⟩ Article dans une revue 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⟩ Article dans une revue 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 Article dans une revue hal-01624297v1
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 Article dans une revue hal-01624305v1
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⟩ Article dans une revue hal-03352045v1
RSAT: regulatory sequence analysis tools M. Thomas-Chollier,Olivier Sand,J. V. Turatsinze,R. Janky,M. Defranceet al. Nucleic Acids Research, 2008, 36, pp.W119--W127. ⟨10.1093/nar/gkn304⟩ Article dans une revue 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 Article dans une revue hal-01624309v1
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 Kerneret al. BMC Evolutionary Biology, 2007, 7, pp.33. ⟨10.1186/1471-2148-7-33⟩ Article dans une revue hal-00167529v1
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⟩ Article dans une revue hal-03352015v1

HDR (1)

Computational analysis of transcriptional regulation in metazoans Morgane Thomas-Chollier Quantitative Methods [q-bio.QM]. Ecole normale supérieure - ENS PARIS, 2016 HDR tel-01362020v1

Communication dans un congrès (1)

IFB/ELIXIR-FR, the french node of ELIXIR Anne-Françoise Adam-Blondon,Jacques van Helden,Gildas Le Corguillé,Christophe Blanchet,Hélène Chiapelloet al. ISMB ECCB 2023, International Society for Computational Biology, Jul 2023, Lyon, France Communication dans un congrès hal-04503051v1

Chapitre d'ouvrage (1)

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⟩ Chapitre d'ouvrage hal-03352064v1

Poster de conférence (6)

ToulligQC: What’s new in 2024? Ali Hamraoui,Brunon Salomé,Morgane Thomas-Chollier,Laurent Jourdren jobim 2024, Jun 2024, Toulouse, France. Poster de conférence hal-05142761v1
A Unix competency framework for learning bioinformatics Hélène Chiapello,Thomas Denecker,Lucie Khamvongsa Charbonnier,Pierre Poulain,Denis Puthieret al. JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques 2024, Jun 2024, Toulouse, France. Poster de conférence hal-04619317v1
Wf-ToulligQC : A User-Friendly Solution for Quality Control of Nanopore sequencing data on EPI2ME Labs Ali Hamraoui,Karine Dias,Sophie Lemoine,Morgane Thomas-Chollier,Stéphane Le Cromet al. Assemblée générale France Génomique, Jun 2023, Paris, France. Poster de conférence hal-05142806v1
ToulligQC 2: fast and comprehensive quality control for Oxford Nanopore sequencing data Karine Dias,Sophie Lemoine,Morgane Thomas-Chollier,Stéphane Le Crom,Laurent Jourdren JOBIM 2022, Jul 2022, Rennes (Campus de Beaulieu), France. Poster de conférence hal-05144856v1
scRNA-seq with Nanopore sequencing: benchmark of approaches based on hybrid sequencing Ali Hamraoui,Catherine Sénamaud-Beaufort,Audrey Onfroy,Stéphane Le Crom,Morgane Thomas-Chollieret al. jobim 2022, Jul 2022, Rennes (Campus de Beaulieu), France. Poster de conférence hal-05144874v1
Groupe de travail sur les Métiers de la Bioinformatique (MetBIF) Hélène Chiapello,Samuel Mondy,Morgane Thomas-Chollier JOBIM 2018, Jul 2018, Marseille, France Poster de conférence hal-03287534v1

Cours (1)

Sandbox.bio tutorials – Linux basics training modules (IFB ELIXIR-FR) Lucie Khamvongsa-Charbonnier,Thomas Denecker,Claire Toffano-Nioche,Denis Puthier,Olivier Sandet al. École thématique. France. 2026 Cours hal-05506951v1