Jonathan H. Dennis

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 examines nucleosome positioning and sensitivity in the purple sea urchin genome, revealing unique patterns distinct from other eukaryotes.

This study shows that SARS-CoV-2 nucleocapsid protein alters chromatin structure at gene promoters linked to immune and metabolic pathways in severe COVID-19.

The paper identifies genomic locations with altered nucleosome sensitivity that distinguish cancer-free from cancer-associated colon polyps and suggests their potential as biomarkers for early cancer detection.

The paper maps nucleosome position and sensitivity in GM12878 cells stimulated with Salmonella typhimurium, showing dynamic changes in promoter chromatin structure linked to transcription factor binding and gene expression.

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.

The paper maps nucleosome distributions in lung and colon adenocarcinoma using mTSS-seq, showing early, widespread nucleosome redistribution driven by DNA sequence and transcription factor binding.