Douglas H. Phanstiel

One hour of 200 mM sorbitol collapses most chromatin loops in human cells while several hundred transient, cohesin-dependent, CTCF-independent loops form at active promoters, preceding anchor-gene activation.

This study uses single-cell RNA sequencing to analyze how fibronectin fragment treatment alters chondrocyte states and transcriptional programs in primary human cells.

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.

This paper uses CRISPR/Cas9 to edit bovine satellite cells to remove the alpha-gal epitope, creating AGS-compatible cultivated meat with reduced allergenic potential.

This study shows anthracycline drugs disrupt 3D chromatin structure by interfering with CTCF binding, altering gene regulation and clinical outcomes in AML.

The paper identifies OA risk genes by integrating eQTLs, chromatin accessibility, and 3D chromatin structure in human chondrocytes, revealing 13 putative risk genes, 10 of which are novel.

The paper identifies response splicing QTLs in human chondrocytes and links them to osteoarthritis risk genes through alternative splicing analysis.

The paper identifies 47 expression-modulating variants in AD-associated loci by analyzing their impact in immune cells under different inflammatory conditions.

This study shows TDP-43 pathology activates immune cells in ALS, linking it to immune dysfunction and suggesting immune monitoring as a diagnostic tool.

The paper uses MPRA to identify functional regulatory variants associated with schizophrenia and shows they differ from eQTLs in genomic location and regulatory impact.

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.

The paper assesses the transcriptional response of in vitro innate immune cell models to synthetic amyloid beta and finds no robust response, but identifies LPS and INFγ as better activators of microglia-like cells.

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

This study examines the transcriptional response of human chondrocytes to fibronectin fragments, finding similarities to osteoarthritis gene expression patterns.

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

The paper identifies off-target effects in CRISPR-Cas9 screens for non-coding elements and shows that strict filtering with specificity scores improves the identification of essential regulatory regions.

Coral provides an interactive web tool for visualizing human kinome data with customizable features and high-resolution outputs.

The paper identifies multi-loop activation hubs during macrophage development using Hi-C data, showing they are enriched for AP-1 binding and driven by cell-type specific transcription factors.