Colin M Brand

Dec 23, 2023 | biorxiv.org | Erin N Gilbertson |Colin M Brand |Evonne McArthur |David C. Rinker

AbstractUnderstanding variation in chromatin contact patterns across human populations is critical for interpreting non-coding variants and their ultimate effects on gene expression and phenotypes. However, experimental determination of chromatin contacts at a population-scale is prohibitively expensive. To overcome this challenge, we develop and validate a machine learning method to quantify the diversity 3D chromatin contacts at 2 kilobase resolution from genome sequence alone.

Oct 26, 2023 | biorxiv.org | Colin M Brand |Shuzhen Kuang |Erin N Gilbertson |Evonne McArthur

AbstractPhenotypic divergence between closely related species, including bonobos and chimpanzees (genus Pan), is largely driven by variation in gene regulation. The 3D structure of the genome mediates gene expression; however, genome folding differences in Pan are not well understood. Here, we apply machine learning to predict genome-wide 3D genome contact maps from DNA sequence for 56 bonobos and chimpanzees, encompassing all five extant lineages.