Eric S. Davis

This study investigates how NUP98-HOXA9 drives aberrant chromatin looping in AML by interacting with CTCF and cohesin, revealing a non-canonical mechanism involving phase separation and loop extrusion.

The paper introduces tidyomics, an ecosystem bridging Bioconductor and tidy R to streamline omic analysis using data from the Human Cell Atlas.

The paper identifies differential chromatin loops during megakaryocyte differentiation and shows their association with gene expression changes and histone modifications.

The paper uses ultra-deep Hi-C and a new computational method to fine-map nuclear compartments, revealing that active promoters and enhancers localize in the A compartment even when adjacent sequences are inactive.

The paper introduces matchRanges, a tool for generating covariate-matched null genomic ranges to facilitate comparative genomic analyses.

bootRanges generates null genomic ranges for hypothesis testing, improving reliability by preserving genomic correlation structure through block bootstrap methods.

This paper evaluates statistical power in Hi-C experiments to detect differential loops and provides guidelines for experimental design using a web tool.

The paper shows that the lncRNA Airn recruits Polycomb Repressive Complexes to silence genes during mouse embryogenesis through chromatin contacts and regulatory elements.

The paper provides exclusion region sets for T2T-CHM13, GRCm39, and other genomes through an R/Bioconductor package and API, offering unified access to curated genomic ranges.

The paper analyzes temporal changes in chromatin structure and gene expression during macrophage activation, finding a reciprocal relationship between loops and transcription.

The paper identifies 56 putative OA risk genes by integrating GWAS, chromatin structure, and RNA-seq data in chondrocytes, with SOCS2 as a novel target gene.

Plotgardener enables precise, programmatic creation of multi-panel figures in R by offering coordinate-based control over plot placement and aesthetics.

CoralP provides an interactive web tool for visualizing human phosphatome data with customizable attributes, offering a unique resource for phosphatase analysis.