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.
46, rue d'Ulm
F-75230 Paris cedex 05
Postdoc Fellow • May 2009 - August 2012• Germany
Research team : Department of Computational Molecular Biology (Gene Regulation Group) headed by Martin Vingron.
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.
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.
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"
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.
My 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.
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.
Medina-Rivera A*, Defrance M*, Sand O* et al, NAR, 2015
Thomas-Chollier M et al, Nature Protocols, 2012
Thomas-Chollier M et al, NAR, 2012
Thomas-Chollier M et al, NAR, 2011
Thomas-Chollier M*, Sand O* et al, NAR, 2008
Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M et al, NAR, 2011
Sand O, Thomas-Chollier M, van Helden J.Bioinformatics, 2009
Sand O, Thomas-Chollier M et al. Nature Protocols, 2008
Thomas-Chollier M*, Turatsinze J-V* et al. Nature Protocols, 2008
Thomas-Chollier M et al, BMC Evol Biol, 2010
Thomas-Chollier M et Ledent V, BMC Genomics, 2008
Thomas-Chollier M et al, BMC Bioinformatics, 2007
is a suite of programs dedicated to the analysis of regulatory elements in genome sequences. It has been initiated by Jacques van Helden in 1998, thus running for more than 15 years ! My involvement in the development of RSAT was focused on the matrix-related programs, and helping with the SOAP Web Services access, the new design of the website (especially with the difficult choice of the colors...) and user support. Since 2010, I have been involved in the developpement of the ChIP-seq motif finding.Analysis of cis-regulatory regions
Automated procedure to classify Hox proteins in their groups of homology. The project to develop a bioinformatics tool able to automatically perform the classification of Hox proteins was born from a close collaboration between the Belgian EMBnet Node (BEN) and the Developmental and stem cell biology laboratory of Prof Luc Leyns at the Vrije Universiteit Brussel. Hox gene classification
predicting the affinity of a given transcription factor for a given sequence. This work, initiated by Helge Roider and Thomas Manke, has been continued and enhanced towards new questions: detection of regulatory SNPs, fast detection of over-represented transcription factors in a dataset of DNA sequences... My involvement in this project was focused on making the programs more usable, adding functionnalities and providing an integrated Web portal for non-bioinformaticians. I am also introducing its usage in the context of ChIP-seq datasets.Analysis of cis-regulatory regions
Computational pipeline based on DNA binding motifs. When applied to our GR and the few available public ChIP-exo datasets, we find that ChIP-exo footprints are protein- and recognition sequence-specific signatures of genomic TF association. Furthermore, we show that ChIP-exo captures information about TFs other than the one directly targeted by the antibody in the ChIP-procedure.ChIP-exo signal analysis
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.