CV Science

Benoit Ballester PhD - Bioinformatics & Genomics

Course and current status

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
• Enhancers is coding regions

Research interests

My research focuses on gene regulation through the exploration of non-coding regions of the genome, combining comparative genomics, multi-omics analyses, and large-scale data modeling.

Early in my career, in collaboration with Paul Flicek (EMBL-EBI) and Duncan Odom (CRUK Cambridge), I studied the evolutionary conservation of transcription factor (TF) activity across mammals. These studies highlighted the functional plasticity of gene regulation, even in the absence of strong sequence conservation.

Since then, my work has focused on the identification, mapping, and characterization of regulatory elements—particularly enhancers—in human and model genomes. To this end, I developed ReMap, an open-access resource that aggregates and harmonizes thousands of ChIP-seq datasets for hundreds of transcription factors. ReMap enables the identification of genomic regions that are potentially active as enhancers or transcriptional regulatory sites:
🔗 http://remap.univ-amu.fr

I am also interested in the transcription of intergenic regions and its relationship to regulatory activity, using RNA-seq, CAGE-seq, and other transcriptomic technologies. This work aims to better understand how unannotated intergenic loci contribute to fine-tuned gene expression control.

More recently, I have been exploring the presence of regulatory elements within coding sequences, particularly enhancers located in exons. This line of research challenges the traditional boundaries between coding and non-coding regions and raises fundamental questions about the evolution and multifunctionality of the genome.

Together, these approaches aim to re-evaluate genome complexity and improve our understanding of how its different layers—coding and non-coding—interact to regulate gene expression in diverse cellular, developmental, and pathological contexts.

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).

Links

• Google  : http://goo.gl/1V82gA
• ORCID  : http://orcid.org/0000-0002-0834-7135
• ReMaP : http://remap.univ-amu.fr/