Yang Yang

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

MCIBox is a toolkit for analyzing single-molecule chromatin interactions and identifying micro-domains through visualization and clustering algorithms.

The paper introduces a machine learning method to predict DNA replication timing from sequence features and identifies genome-wide sequence elements that modulate replication timing.

This paper introduces Phylo-HMRF, a probabilistic model to analyze 3D genome organization across species using Hi-C data, revealing evolutionary patterns in chromatin structure.

This paper introduces SPEID, a deep learning model that predicts enhancer-promoter interactions using sequence features, showing effectiveness across six cell types and application to melanoma mutations.

This paper introduces a probabilistic model to compare multi-species functional genomic data, showing it can identify genomic regions with distinct evolutionary patterns of DNA replication timing across primates.

This study examines how two tartary buckwheat varieties respond to low nitrogen stress by secreting organic acids, showing differences in soil pH, nutrient content, and organic acid levels.

This study identifies sequence-based features that predict CTCF-mediated chromatin loops using a machine learning model called CTCF-MP.