Home Research Network Bioinformatics B. Ballester

Benoît Ballester

 

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 +33 (0)4 91 82 87 28

 

Research interests

  • 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

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