Benoît Ballester

Exonic enhancers are a widespread class of dual-function regulatory elements

The paper identifies exonic enhancers as dual-function regulatory elements that influence gene expression and are associated with disease and evolution.

Contextualising transcription factor binding during embryogenesis using natural sequence variation

The paper identifies genetic variants affecting TF binding during Drosophila embryogenesis and uses a CNN to predict functional variants.

MUFFIN : A suite of tools for the analysis of functional sequencing data

MUFFIN is a Python package that provides tools for analyzing functional genomic data, including normalization, dimensionality reduction, and differential expression analysis across various assays.

Normal and cancer tissues are accurately characterised by intergenic transcription at RNA polymerase 2 binding sites

The paper constructs an RNAP2 ChIP-seq atlas and integrates it with RNA-seq data to identify intergenic transcription as a biomarker in normal and cancer tissues.

A map of direct TF-DNA interactions in the human genome

The paper develops a method to predict direct TF-DNA interactions from ChIP-seq data and provides a resource of these interactions and cis-regulatory modules.