Hank W. Bass

The paper uses MOA-seq to map transcription factor occupancy in hypoxia-treated human endothelial cells, identifying thousands of hypoxia-responsive sites and clustering them into HIF1A-associated and independent TF groups.

The paper analyzes chromatin accessibility of maize knobs using DNS-seq data across four tissues, revealing tissue-specific dynamics in K180 knobs compared to TR-1 and centromeres.

The paper uses Hi-C and 3D FISH to show maize euchromatin has two distinct interphase subcompartments, early-S and middle-S, defined by replication timing and chromatin organization.

The paper identifies thousands of alternative splicing events in human vascular endothelial cells under hypoxia, revealing a more complex and dynamic transcriptional response than conventional RNA-seq suggests.

The paper examines nucleosome dynamics during monocyte to macrophage differentiation, finding that nucleosome sensitivity changes dynamically while distribution remains largely static.

The paper shows that LPS stimulation causes transient nucleosome redistribution and increased MNase sensitivity in a subset of promoters, while most promoters show sensitivity changes uncoupled from gene expression.

The paper identifies genetic variants at transcription factor binding sites that explain a large portion of phenotypic heritability in maize under different water conditions.

SCsnvcna places SNVs on a CNA tree using independent cell sets, improving accuracy in predicting SNV placement and losses due to copy number changes.

iSeg is an efficient algorithm for genomic and epigenomic segmentation that uses dynamic programming and a novel data structure to identify and refine segments with statistical significance.