Benoit Ballester PhD - Bioinformatics & Genomics

Course and current status


Researcher (CRCN HDR)
INSERM | French Institute of Health and Medical Research
October 2011 – Present
Marseille, France

Postdoctoral Researcher
EMBL-European Bioinformatics Institute (EMBL-EBI)
May 2006 – September 2011 (5 years 5 months)
Cambridge, United Kingdom

PhD student in Bioinformatics
November 2002 – October 2006 (4 years)
Marseille, France
Thesis title : Bioinformatics analysis of microarray data : Application to lymphomas.

Scientific summary

Current topics

  • 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. 

Research interests

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, 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 2014Science 2010).



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