Anaïs Bardet

Computational Biologist

Research Associate, CR CNRS, Strasbourg, France


Multicellular organisms establish and maintain different transcriptional states in disparate cell types through complex and specific regulation of gene expression. This regulation is mediated by the cooperative binding of transcription factors (TFs) to regulatory elements through the recognition of specific DNA sequence motifs. Additionally, the physical access of TFs to DNA can be modulated by epigenetic regulation, such as DNA methylation, nucleosome positioning and histone modifications. Failure to maintain this tight regulation of gene expression results in developmental defects and various diseases including cancer.

We use both computational and experimental approaches to study TF binding and its regulation in cellular systems. Specifically, we investigate:

    • The role of TFs in establishing aberrant DNA methylation patterns in cancer
    • The sensitivity of TFs to chromatin
    • The evolution of regulatory elements in diverse species

To do so, we integrate a wide variety of genomic datasets profiling:

    • Transcription factor binding using ChIP-seq, ChIP-exo and sequence motif analysis
    • DNA methylation using WGBS and RRBS
    • Gene expression using RNA-seq
    • Open-chromatin regions using DNase-seq and ATAC-seq
    • Histone marks using ChIP-seq