Benoit Ballester - CV - PhD - Bioinformatics & Genomics

E-mail :[email]
Phone : +33 4 91 82 87 28
Location : Marseille, France

Scientific topics

Molecular Biology & Genetics
Computer Science

Keywords

Bioinformatics
Genomics

ITMO

Last update 2021-02-11 15:14:11.537

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

INSERM ERM206 - TAGC

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, 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).

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