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- Transcription factors binding the human genome using next generation sequencing
- Analysis of regulatory variants
- Non-coding regions analyses (origins of replications, enhancers, repeats...)
- Transcription of non-coding regions in the human genome
- Origins of replication in mammals and their dynamics.
My research focuses on the analysis of non-coding regions of the human genome using high-throughput sequencing data such as (ChIP-seq, RNA-seq, ChIA-PET, DNase-seq, MNAse-seq). I am interested in understanding how the so called non-coding genome play a central role in gene regulation. This previously "junk-dna" is currently seen as playing a key and extremely complex role in our genome.
How those yet un-annotated regulatory elements can shape the expression and the dynamics of our genomes is the main goal of my work. To address that we first created a catalogue of regulatory elements by integrating hundreds of public TF ChIP-seq experiments as well as Encode data. This allow us to observe a complex landscape of regulatory elements (Enhancers/CRMs) in the human genome.
I am also involved in the analysis of origins of replication at the genome scale with Marcel Mechali's team (IGH), Christelle Cayrou (UNICE) and Jacques van Helden (TAGC). Jacques van Helden and I are both involved in a French National Agency for Research grant (ANR ORICHOICE, http://goo.gl/BM5Enz) together with Mechali's (IGH) and Taylor's team (IGMM).
Previously I worked for the exciting Ensembl project at the European Bioinformatics Institute in Cambridge (EMBL-EBI). I was also involved in in the Rat Genome Informatics activity of the EURATools FP6 project. Then I joined Paul Flicek's group Vertebrate Genomics as a Postdoc were I worked on large scale ChIP-Seq projects to study evolutionary conservation and divergence in TF binding across vertebrates (Elife 2014, Science 2010).
Members and past members
- Benoît Ballester - Research Associate Inserm
- Aurélien Griffon - PhD student in Bioinformatics (co-supervision with Salvatore Spicuglia)
- Johanna Chesnel - Engineer student Sup Biotech Paris
- Quentin Barbier - M2 Pro BBSG, now bioinformatic engineer at the IFB
- Jordi Dalino - M1 BBSG
- Google : http://goo.gl/1V82gA
- ORCID : http://orcid.org/0000-0002-0834-7135
- ReMAP : http://tagc.univ-mrs.fr/remap/