In summary

In 2012, I joined the team Computational Systems Biology headed by Denis Thieffry at the Institut de Biologie de l'Ecole normale superieure. In 2014, I became a member of the committee of the Société française de Bioinformatique (SFBI). I obtained the Habilitation à Diriger des recherches in 2016.

Contact Details

Morgane Thomas-Chollier
IBENS
46, rue d'Ulm
F-75230 Paris cedex 05
France

Research positions

Ecole Normale Supérieure

Associate Professor (Maitre de Conference) September 2012 - Present France

Research team : Computational Systems Biology headed by Denis Thieffry, within IBENS .

Max Planck Institute for Molecular Genetics

Postdoc Fellow May 2009 - August 2012 Germany

Research team : Department of Computational Molecular Biology (Gene Regulation Group) headed by Martin Vingron.
Humboldt fellowship

Universite Libre de Bruxelles

Postdoc July 2008- March 2009 Belgium

Research team : Laboratoire de Bioinformatique des Génomes et Réseaux (BiGRe) - (Genomes and Networks Bioinformatics) headed by Jacques van Helden.

Education

PhD in Bioinformatics

2004 - 2008 Belgium

Joint PhD between Université Libre de Bruxelles (ULB) and Vrije Universiteit Brussels (VUB) , Bruxelles, Belgium. Supervisors : Luc Leyns (CEGE, VUB) & Jacques van Helden (BiGRe, ULB), and Valérie Ledent (formerly in Belgian EMBnet Node).
"Evolutionary study of the Hox gene family with matrix-based bioinformatics approaches" (1) Identification and Classification of Hox proteins in vertebrates. (2) Regulatory elements identification in Hox clusters with pattern-matching techniques.

Master2 in Bioinformatics and Applied Genomics

2003 France

Ecole Supérieure de Biotechnologie de Strasbourg (European School of the Higher Rhine Universities), Louis Pasteur University, Strasbourg, France. Courses taken included: Bioinformatics, Genomics, Proteomics, Pharmacology, Neurology, programming, databases, molecular modelling, drug design. Master thesis at CNRS (French National Centre for Scientific Research) in the Laboratoire de Microbiologie et de Génétique in Strasbourg. Supervisor: Stéphane Vuillemier "Research of the putative role of glutathione S-transferases in rhizobacterial genomes"

Master1 in Cellular Biology and Physiology

2002 France

University of Orléans, France. Courses taken included: Advanced Molecular Biology, Advanced Cellular Biology, Advanced Human Physiology, Physiopathology, Expression and regulation of the eukaryotic genome, Cellular pathways, Immunology, Animal development genetics, Genomics. 3 months training period at CNRS in the Centre de Biophysique moléculaire in Orléans. Supervisor: Sylvain Bourgerie. Research aiming at creating S.cerevisiae strains able to produce mucin-type O-glycans. Laboratory work (Microbiology) and Bioinformatics.

Research

  • sample-imageMy projects often involve predictions of binding regions for transcription factors (motif detection, de-novo motif discovery, ChIP-seq, ChIP-exo) and I am an active developper of RSAT.

  • sample-imageI also have a strong interest for the evo-devo field, in particular the evolution of Hox and ParaHox protein sequences accross metazoans. My PhD thesis was focused on the Hox genes.

  • sample-image

    Among other competences, I analyze next-generation sequencing data. Programs to analyze these data are changing in parallel with the fast improvements of sequencing technologies, making the work of a bioinformatician very dynamic !
    On a technical level, I am interested by the technology of Web services, and the development of bioinformatic workflows that take advantage of the SOAP standard. I have contributed to the development of the Web Service access of RSAT.

Scientific Expertise

2013-2015: Program Chairs of the Regulatory Genomics Special Interest Group (RegGenSiG) meeting.

Publications

Peer-reviewed international journals

* = equal contributions
# = co-corresponding authors

  1. Telorac J, Prykhozhij SV, Schöne S, Meierhofer D, Sauer S, Thomas-Chollier M#, Meijsing SH#. "Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements",
    Nucleic Acid Research, in press (2016) [Pubmed][Full text]
  2. 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. "The Histone Chaperone SSRP1 is Essential for Wnt Signaling Pathway Activity During Osteoblast Differentiation",
    Stem Cells, in press (2016) [Full text]
  3. Thomas-Chollier M, Martinez P. "The origin of metazoan patterning systems and the role of ANTP-class homeobox genes".
    eLS, John Wiley Sons Ltd, Chichester.(2016) [Full text]
  4. 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# "RSAT 2015 : Regulatory Sequence Analysis Tools",
    Nucleic Acid Research 43(W1):W50-W56 (2015) [Pubmed][Full text]
  5. Starick S*, Ibn-Salem J*, Jurk M*, Hernandez C, Love MI, Chung H, Vingron M, Thomas-Chollier M#, Meijsing SH#
    "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(6):825-35 (2015) [Pubmed][Full text]
  6. Hudry B, Thomas-Chollier M, Volovik Y , Duffraisse M, Dard A, Dale F, Technau U, Merabet S
    "Molecular insights into the origin of the Hox-TALE patterning System",
    eLife 3:e01939 (2014) [Pubmed][Full text]
  7. Thomas-Chollier M*, Watson L* , Cooper S, Pufall MA, Liu JS, Borzym K, Vingron M, K.R Yamamoto, SH Meijsing
    "A naturally occurring single amino acid insertion rewires transcriptional regulation by Glucocorticoid receptor isoforms",
    Proc. Natl. Acad. Sci. U. S. A. 110(44):17826-31 (2013) [Pubmed][Full text]
  8. Thomas-Chollier M, Darbo E, Herrman C, Defrance M, Thieffry D, van Helden J.
    "A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs",
    Nature Protocols 7, 1551-1568 (2012) [Pubmed][Full text]
  9. Thomas-Chollier M, Herrman C, Defrance M, Sand O, Thieffry D, van Helden J.
    "RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets",
    Nucleic Acids Research 40(4) (2012) [Pubmed][Full text]
  10. Thomas-Chollier M, Hufton A, Heining M, O'Keeffe S, El Masri N, Roider HG, Manke T, Vingron M.
    "Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs",
    Nature Protocols 6, 1860-69 (2011) [Pubmed]
  11. Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrman C, Thieffry D, van Helden J.
    "RSAT 2011: Regulatory Sequence Analysis Tools",
    Nucleic Acids Research 39(Web Server issue):W86-91 (2011)[Pubmed][Full text]

  12. Medina-Rivera A, Abreu-Goodger C,Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J.
    "Theoretical and empirical quality assessment of transcription factor-binding motifs",
    Nucleic Acids Research 39(3):808-24 (2011) [Pubmed] [Full text]

  13. Thomas-Chollier M, Ledent V, Leyns L, Vervoort M.
    "A non-tree-based comprehensive study of metazoan Hox and ParaHox genes prompts new insights into their origin and evolution",
    BMC Evol Biol 10:73 (2010)[Pubmed] [Full text] Highly accessed

  14. Sand O, Thomas-Chollier M, van Helden J.
    "Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl",
    Bioinformatics 25(20):2739-2740 (2009)[Pubmed][Full text]
  15. Thomas-Chollier M*, Turatsinze J-V*, Defrance M, van Helden J.
    "Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules",
    Nature Protocols 3(10), 1578-88 (2008) [Pubmed]
  16. Sand O, Thomas-Chollier M, Vervisch E, van Helden J.
    "Analyzing multiple datasets by interconnecting RSAT programs via SOAP Web Services - an example with ChIP-chip data",
    Nature Protocols 3(10), 1604-15 (2008)[Pubmed]
  17. Thomas-Chollier M*, Sand O*, Turatsinze J-V, Janky R, Defrance M, Vervisch E, Brohee S, van Helden J
    "RSAT: Regulatory Sequence Analysis Tools",
    Nucleic Acids Research 36 (Web Server issue):W119-W127 (2008)[Pubmed] [Full text]
  18. Thomas-Chollier M, Ledent V
    "Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni: comment",
    BMC Genomics, 9:35 (2008) [Pubmed] [Full text]
  19. Thomas-Chollier M, Leyns L, Ledent V
    "HoxPred: automated classification of Hox proteins using combinations of generalised profiles",
    BMC Bioinformatics, 8: 247 (2007) [Pubmed] [Full text]
  20. Simionato E, Ledent V, Richards G, Thomas-Chollier M, Kerner P, Coornaert D, Degnan BM, Vervoort M.
    "Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.",
    BMC Evol Biol, 7:33 (2007) [Pubmed] [Full text] Highly accessed

International conferences

National conferences

Invited seminars

  • Abroad
    Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany. October 2015.
    Centro de Ciencias Genómicas - UNAM, Cuernavaca, Mexico. March 2015.
    Max Planck Institute for Molecular Genetics, Berlin, Germany. November 2014.
    Genome Institute of Singapore, Singapour. March 2014.
    Genetics and Genome Biology - Sick Kids, Toronto, Canada. November 2013.
  • In France
    IGFL, Lyon. December 2015.
    I2BC, Gif-sur-Yvette. June 2015.
    IGBMC, Strasbourg. May 2015.
    Journée Génome du Labex Memolife, Paris. November 2014.
    IGBMC, Strasbourg. June 2013.
    Réseau RENABI ChIP-seq, Institut Curie, Paris. June 2013.
    Réseau régional des ingénieurs en bioinformatique de Lille. May 2013.
    Ecole normale supérieure, Paris. October 2011.

Teaching

Trainings ChIP-seq, NGS data processing, analysis of cis-regulatory elements

Classes at Ecole Normale Supérieure (since 2012)

Bioinformatics courses and practicals (before 2012)

  • 2011 ChIP-seq data analysis PhD students of MPIMG Berlin
  • 2009+2010+2011 Introduction to PERL and Unix PhD students of MPIMG Berlin
  • 2009+2010 Motifs and Regulatory Sequence Analysis Licenciatura en Ciencias Genomicas, Cuernavaca, Mexico
  • 2009 Regulatory sequence analysis 9th BioSapiens European School of Bioinformatics
  • 2004+2005+2006 Introduction in Bioinformatics and Genomics Different classes/levels for ULB and VUB students (Belgium)
Disclaimer : All the information provided here is for general information only and is the expressed opinion of myself and not others. This includes (but is not limited to) my membership organisations and/or employers. Unless otherwise noted, I am the legal copyright holder of all written material on this website and it may not be used, reprinted, (partially) modified or published without my written consent. I make no warranties of any kind (expressed or implied) about the completeness, accuracy, reliability, suitability or availability of any information cited on this page.

Women in science

When I started my PhD in bioinformatics, I ordered a Mac laptop as my working machine. When I received it, a senior postdoc in the lab told me "hey, you got a Linux for Barbie !".
Probably a great joke for the guys, but that day, I painfully discovered that being a woman would make a difference. That I would need to prove my skills to be considered. That I was not necessarily welcome in "their circle". After this, I have been extremely lucky with three open-minded mentors, who supported and guided me, lowering this bad feeling that nevertheless grew back as I became "older" in research.
Ten years and many discussions with female (and male !) scientists later, I'm convinced that this feeling is shared by many young women scientists, not just in bioinformatics, within France and abroad. I wish to do something about it, at my own level. This page (in construction) aims at sharing some information I gathered for a talk on women in sciences I gave as a postdoc in Berlin. I would like to be more formally involved in the matter of equal opportunities in science, not sure yet in which form.

Why do (should) we care ?

The glass ceiling (plafond de verre)

Why do women leave academia ?

Dual careers

Motherhood and science

Efforts to promote and value women in sciences

Encourage high-school / young scholars towards science careers

Sustain women scientists

Role models

Mentoring programs

Associations and equal opportunities officers

Funding and prizes