#2 · Structural bio & protein design

Chromatin structure and nucleosome states inferred from sequencing and contact maps

The dominant thread is computational inference of regulatory state from indirect genomic readouts. CRUSH refines A/B compartments to 1 kb from low-depth data across cell types, single cells, and an ancient mammoth sample. A polymer-physics ensemble and an Activity-by-Multiway-Contact model, built from Hi-C and Micro-C maps, link multiway enhancer-promoter interactions to expression changes in cancer. IDLI classifies long-read single-molecule footprints to detect pervasive nucleosome distortion and TF-linked regulation, while YeIP predicts expression hotspots at yeast integration sites from genomic context. The items do not bridge modalities in the same way; the shared element is mapping one layer of chromatin or sequence information onto another. What is new here is resolution: kilobase-scale compartments from low-depth data and nucleosome-level distortion read from individual chromatin fibres.