Morgane Thomas-Chollier

Walter Santana-Garcia, Jaime Castro-Mondragon, Mónica Padilla-Gálvez, Nga Nguyen, Ana Elizondo-Salas, et al.. RSAT 2022: regulatory sequence analysis tools. Nucleic Acids Research, Oxford University Press, 2022, ⟨10.1093/nar/gkac312⟩. ⟨hal-03669930⟩

Karen J Nuñez-Reza, Aurélien Naldi, Arantza Sánchez-Jiménez, Ana V Leon-Apodaca, M. Angélica Angélica Santana, et al.. Logical modelling of in vitro differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions. Interface Focus, Royal Society publishing, 2021, 11 (4), pp.20200061. ⟨10.1098/rsfs.2020.0061⟩. ⟨hal-03352078⟩

Swann Floc'Hlay, Emily S Wong, Bingqing Zhao, Rebecca R Viales, Morgane Thomas-Chollier, et al.. Cis-acting variation is common across regulatory layers but is often buffered during embryonic development. Genome Research, Cold Spring Harbor Laboratory Press, 2021, 31, pp.211 - 224. ⟨10.1101/gr.266338.120⟩. ⟨hal-03352083⟩

Darely Gutiérrez-Reyna, Alejandra Cedillo-Baños, Linda Kempis-Calanis, Oscar Ramírez-Pliego, Lisa Bargier, et al.. IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8+ T Cells. Frontiers in Immunology, Frontiers, 2020, 11, ⟨10.3389/fimmu.2020.01089⟩. ⟨hal-02935693⟩

Céline Hernandez, Morgane Thomas-Chollier, Aurélien Naldi, Denis Thieffry. Computational Verification of Large Logical Models—Application to the Prediction of T Cell Response to Checkpoint Inhibitors. Frontiers in Physiology, Frontiers, 2020, 11, ⟨10.3389/fphys.2020.558606⟩. ⟨hal-03352080⟩

Swann Floc'Hlay, Maria Dolores Molina, Céline Hernandez, Emmanuel Haillot, Morgane Thomas-Chollier, et al.. Deciphering and modelling the TGF-β signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo. Development (Cambridge, England), Company of Biologists, 2020, ⟨10.1242/dev.189944⟩. ⟨hal-03352081⟩

Abdenour Abbas, Thien-Phong Vu Manh, Michael Valente, Nils Collinet, Noudjoud Attaf, et al.. The activation trajectory of plasmacytoid dendritic cells in vivo during a viral infection. Nature Immunology, Nature Publishing Group, 2020, 21 (9), pp.983-997. ⟨10.1038/s41590-020-0731-4⟩. ⟨hal-02980944⟩

Walter Santana-Garcia, Maria Rocha-Acevedo, Lucia Ramirez-Navarro, yvon Mbouamboua, Denis Thieffry, et al.. RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding. Computational and Structural Biotechnology Journal, Elsevier, 2019, ⟨10.1016/j.csbj.2019.09.009⟩. ⟨hal-02458940⟩

Hervé Philippe, Albert J Poustka, Marta Chiodin, Katharina J Hoff, Christophe Dessimoz, et al.. Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria. Current Biology - CB, Elsevier, 2019, 29 (11), pp.1818-1826.e6. ⟨10.1016/j.cub.2019.04.009⟩. ⟨hal-02392672⟩

Otoniel Rodríguez-Jorge, Linda Kempis-Calanis, Wassim Abou-Jaoudé, Darely Gutiérrez-Reyna, Céline Hernandez, et al.. Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4 + T cell activation. Science Signaling, American Association for the Advancement of Science (AAAS), 2019, 12 (577), pp.eaar3641. ⟨10.1126/scisignal.aar3641⟩. ⟨hal-02154906⟩

Stefanie Schöne, Melissa Bothe, Edda Einfeldt, Marina Borschiwer, Philipp Benner, et al.. Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise. PLoS Genetics, Public Library of Science, 2018, 14 (11), pp.e1007793. ⟨10.1371/journal.pgen.1007793⟩. ⟨inserm-02155974⟩

Nga thi thuy Nguyen, Bruno Contreras-Moreira, Jaime Castro-Mondragon, Walter Santana-Garcia, Raul Ossio, et al.. RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Research, Oxford University Press, 2018, 46 (W1), pp.W209 - W214. ⟨10.1093/nar/gky317⟩. ⟨hal-01874932⟩

Samuel Collombet, Chris van Oevelen, Jose Luis Sardina Ortega, Wassim Abou-Jaoudé, Bruno Di Stefano, et al.. Logical modeling of lymphoid and myeloid cell specification and transdifferentiation. Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2017, 114 (23), pp.5792-5799. ⟨10.1073/pnas.1610622114⟩. ⟨hal-03352074⟩

Michael I Love, Matthew R Huska, Marcel Jurk, Robert Schöpflin, Stephan R Starick, et al.. Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation. Nucleic Acids Research, Oxford University Press, 2017, 45 (4), pp.1805 - 1819. ⟨10.1093/nar/gkw1163⟩. ⟨hal-03352072⟩

Jaime Abraham Castro-Mondragon, Sébastien Jaeger, Denis Thieffry, Morgane Thomas-Chollier, Jacques Van helden. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. Nucleic Acids Research, Oxford University Press, 2017, 45 (13), pp.e119--e119. ⟨10.1093/nar/gkx314⟩. ⟨hal-01624366⟩

Elodie Thierion, Johan Le Men, Samuel Collombet, Céline Hernandez, Fanny Coulpier, et al.. Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements. PLoS Genetics, Public Library of Science, 2017, 13 (7), pp.e1006903. ⟨10.1371/journal.pgen.1006903⟩. ⟨inserm-02158641⟩

Jonas Telorac, Sergey V Prykhozhij, Stefanie Schöne, David Meierhofer, Sascha Sauer, et al.. Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements. Nucleic Acids Research, Oxford University Press, 2016, 44 (13), pp.6142 - 6156. ⟨10.1093/nar/gkw203⟩. ⟨hal-03352070⟩

Tareq Hossan, Sankari Nagarajan, Simon J Baumgart, Wanhua Xie, Roberto Tirado Magallanes, et al.. Histone Chaperone SSRP1 is Essential for Wnt Signaling Pathway Activity During Osteoblast Differentiation. STEM CELLS, AlphaMed Press, 2016, 34 (5), pp.1369 - 1376. ⟨10.1002/stem.2287⟩. ⟨hal-03352065⟩

Stefanie Schöne, Marcel Jurk, Mahdi Bagherpoor Helabad, Iris Dror, Isabelle Lebars, et al.. Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity. Nature Communications, Nature Publishing Group, 2016, 7 (1), ⟨10.1038/ncomms12621⟩. ⟨hal-03352071⟩

Alejandra Medina-Rivera, Matthieu Defrance, Olivier Sand, Carl Herrmann, Jaime A. Castro-Mondragon, et al.. RSAT 2015: Regulatory Sequence Analysis Tools. Nucleic Acids Research, Oxford University Press, 2015, 43 (W1), pp.W50--W56. ⟨10.1093/nar/gkv362⟩. ⟨hal-01624369⟩

Stephan R Starick, Jonas Ibn-Salem, Marcel Jurk, Céline Hernandez, Michael I Love, et al.. ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors. Genome Research, Cold Spring Harbor Laboratory Press, 2015, 25 (6), pp.825 - 835. ⟨10.1101/gr.185157.114⟩. ⟨hal-03352059⟩

Bruno Hudry, Morgane Thomas-Chollier, yael Volovik, Marilyne Duffraisse, Amélie Dard, et al.. Molecular insights into the origin of the Hox-TALE patterning system. eLife, eLife Sciences Publication, 2014, 3, ⟨10.7554/elife.01939⟩. ⟨hal-03352057⟩

Morgane Thomas-Chollier, Lisa C Watson, Samantha B Cooper, Miles A Pufall, Jennifer S Liu, et al.. A naturally occuring insertion of a single amino acid rewires transcriptional regulation by glucocorticoid receptor isoforms. Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2013, 110 (44), pp.17826 - 17831. ⟨10.1073/pnas.1316235110⟩. ⟨hal-03352056⟩

Morgane Thomas-Chollier, Carl Herrmann, Matthieu Defrance, Olivier Sand, Denis Thieffry, et al.. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Research, Oxford University Press, 2012, 40 (4), pp.e31-e31. ⟨10.1093/nar/gkr1104⟩. ⟨hal-01624284⟩

Morgane Thomas-Chollier, Elodie Darbo, Carl Herrmann, Matthieu Defrance, Denis Thieffry, et al.. A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nature Protocols, Nature Publishing Group, 2012, 7 (8), pp.1551-1568. ⟨10.1038/nprot.2012.088⟩. ⟨hal-01624286⟩

Morgane Thomas-Chollier, Andrew Hufton, Matthias Heinig, Sean O'Keeffe, Nassim El Masri, et al.. Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. Nature Protocols, Nature Publishing Group, 2011, 6 (12), pp.1860-1869. ⟨10.1038/nprot.2011.409⟩. ⟨hal-03352055⟩

Alejandra Medina-Rivera, Cei Abreu-Goodger, Morgane Thomas-Chollier, Heladia Salgado, Julio Collado-Vides, et al.. Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Research, Oxford University Press, 2011, 39 (3), pp.808--824. ⟨hal-01624287⟩

Morgane Thomas-Chollier, Matthieu Defrance, Alejandra Medina-Rivera, Olivier Sand, Carl Herrmann, et al.. RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Research, Oxford University Press, 2011, 39, pp.W86--W91. ⟨hal-01624291⟩

Morgane Thomas-Chollier, Valérie Ledent, Luc Leyns, Michel Vervoort. A non-tree-based comprehensive study of metazoan Hox and ParaHox genes prompts new insights into their origin and evolution.. BMC Evolutionary Biology, BioMed Central, 2010, 10, pp.73. ⟨10.1186/1471-2148-10-73⟩. ⟨hal-00486240⟩

O. Sand, M. Thomas-Chollier, J. Van Helden. Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl. Bioinformatics, Oxford University Press (OUP), 2009, 25 (20), pp.2739--2740. ⟨hal-01624297⟩

M. Thomas-Chollier, O. Sand, J. V. Turatsinze, R. Janky, M. Defrance, et al.. RSAT: regulatory sequence analysis tools. Nucleic Acids Research, Oxford University Press, 2008, 36, pp.W119--W127. ⟨hal-01624302⟩

O. Sand, M. Thomas-Chollier, E. Vervisch, J. Van Helden. Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services-an example with ChIP-chip data. Nature Protocols, Nature Publishing Group, 2008, 3 (10), pp.1604--1615. ⟨hal-01624309⟩

Morgane Thomas-Chollier, Valérie Ledent. Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni: comment. BMC Genomics, BioMed Central, 2008, 9 (1), pp.35. ⟨10.1186/1471-2164-9-35⟩. ⟨hal-03352045⟩

Jean-Valery Turatsinze, Morgane Thomas-Chollier, Matthieu Defrance, Jacques Van Helden. Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nature Protocols, Nature Publishing Group, 2008, 3 (10), pp.1578--1588. ⟨hal-01624305⟩

Elena Simionato, Valérie Ledent, Gemma Richards, Morgane Thomas-Chollier, Pierre Kerner, et al.. Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.. BMC Evolutionary Biology, BioMed Central, 2007, 7, pp.33. ⟨10.1186/1471-2148-7-33⟩. ⟨hal-00167529⟩

Morgane Thomas-Chollier, Luc Leyns, Valérie Ledent. HoxPred: automated classification of Hox proteins using combinations of generalised profiles. BMC Bioinformatics, BioMed Central, 2007, 8 (1), ⟨10.1186/1471-2105-8-247⟩. ⟨hal-03352015⟩

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

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

Hélène Chiapello, Samuel Mondy, Morgane Thomas-Chollier. Groupe de travail sur les Métiers de la Bioinformatique (MetBIF). JOBIM 2018, Jul 2018, Marseille, France. ⟨hal-03287534⟩