Outer membrane protein G (OmpG) from Escherichia coli has exhibited pH-dependent
gating that can be employed by bacteria to alter the permeability of their outer membranes in …

Chromatin interactions are important for gene regulation and cellular specialization. Emerging
evidence suggests many-body spatial interactions play important roles in condensing …

Single-cell chromatin studies provide insights into how chromatin structure relates to
functions of individual cells. However, balancing high-resolution and genome wide-coverage …

We report the structure-based pathogenicity relationship identifier (SPRI), a novel computational
tool for accurate evaluation of pathological effects of missense single mutations and …

Computational three-dimensional chromatin modeling has helped uncover principles of
genome organization. Here, we discuss methods for modeling three-dimensional chromatin …

Genome resequencing with short reads generated from pyrosequencing generally relies on
mapping the short reads against a single reference genome. However, mapping of reads …

Despite thousands of reported studies unveiling gene-level signatures for complex diseases,
few of these techniques work at the single-sample level with explicit underpinning of …

Missense mutations are among the most frequently occurring variants in exon regions and
may lead to pathogenic phenotypes. Computational methods predicting effects of missense …

Motivation: 3D structures of proteins provide rich information for understanding their biochemical
roles. Identifying the representative protein structures for protein sequences is essential …

In this study, we focus on the following question: do genomic regions enriched in cancer
variant mutations have significantly different chromatin folding patterns? We utilize publicly …