Arnaud Regis Krebs

The paper introduces SMFNet and PRISM to analyze how transcription factor assemblies influence chromatin accessibility and identifies sequence-encoded principles of combinatorial TF assembly.

The paper quantifies co-accessibility between cis-regulatory elements in Drosophila using single-molecule footprinting and long-read sequencing, revealing coordinated regulation across genomic distances.

The paper quantifies enhancer activation frequency in response to TF perturbations and identifies H3K27Ac as a chromatin mark required for enhancer activation.

ChromSMF integrates histone modifications, protein-DNA interactions, and DNA methylation on multi-kilobase DNA molecules to study epigenetic regulation.

The paper uses SMF and live imaging to study promoter dynamics, showing Tat influences nucleosome removal and polymerase activity.

The paper shows that the promoter-proximal region is necessary for cell-type specific promoter responsiveness to distal enhancers in mouse embryonic stem cells and neural progenitor cells.

FootprintCharter detects and quantifies footprints in single molecule footprinting data without prior assumptions on genomic locations.

The paper measures RNA Polymerase II occupancy at promoters in mouse and Drosophila, finding lower occupancy and higher turnover in mammals.

COBIND identifies TF co-binding patterns using NMF on TFBS data, revealing both known and novel co-binding configurations across species.

The paper uses single molecule multi-omics to show DNA methylation can block transcription factor binding at cell-type-specific enhancers, but not all enhancers.

The paper uses single molecule footprinting to study transcription factor co-occupancy and cooperativity in mouse cis-regulatory elements, finding that high DNA co-occupancy can occur without direct physical interaction.

The paper develops synthetic promoter AAVs for cell-type-specific gene delivery in mice, non-human primates, and humans, showing 11% of AAVs target neuronal and glial cell types in multiple species.