François Serra

This study shows translocations can drive widespread gene expression changes across entire chromosome arms in MCL by altering chromatin organization and regulatory loops.

This study shows p53 rapidly changes 3D chromatin structure to regulate gene transcription, identifying 340 new direct target genes.

The paper introduces liCHi-C, a low-input Hi-C method, to map promoter-enhancer interactions in clinical samples and identify disease-relevant regulatory elements and structural variants.

The paper introduces LOOPbit, a method to detect chromatin loops from Hi-C data by classifying CTCF-CTCF interactions, achieving higher enhancer-promoter loop detection than existing tools.

This study identifies DIDO3 binding at active chromatin and topological boundaries in mouse stem cells, linking it to chromatin organization and transcriptional regulation.

The paper introduces TADdyn, a tool that simulates chromatin structural rearrangements during cell reprogramming using time-course 3C data and molecular dynamics, revealing a hit-and-stick mechanism for transcriptional stabilization.

MuGVRE provides a cloud-based infrastructure for 3D/4D genomics analysis, supporting both high-computational and high-throughput applications.

The paper predicts the first eigenvector of the Hi-C matrix from whole genome bisulfite sequencing data, showing that methylation variability better predicts chromatin compartments than methylation levels.

The paper shows transcription factors drive genome topology changes before gene expression during cell reprogramming.

The paper compares two Hi-C samples, showing how adherence to FAIR principles leads to successful sequencing projects.

The paper introduces TADbit, a computational framework for 3D chromatin modeling, and applies it to fly genomic domains to reveal structural differences linked to chromatin colors.

The paper examines how hormone-induced changes in gene regulation are coordinated by structural transitions of chromatin topological domains in breast cancer cells.