Yue Xue

This study maps how 269 human transcription factors recognize DNA sequences on nucleosomes, revealing a second regulatory code in chromatin that influences gene regulation.

The paper introduces INF, an algorithm that integrates protein and gene level information to analyze regulatory circuits and their role in cellular responses and identity.

HiCGen predicts and perturbs chromatin organization, revealing loop domains' role in higher-order structures like TADs and compartments.

The paper analyzes Hi-C data to show that chromatin contact networks in cancer and leukemia have reduced information transmission efficiency and shallower hierarchy compared to normal tissues.

The paper develops CTG, a diffusion-based method to improve Hi-C data reliability and reveal structural genomic regulation.

This study examines how CpG density distribution around transcription start sites influences gene transcription and regulation patterns in human genes.

The paper examines chromatin structural changes and epigenetic reprogramming during mouse and human embryonic development, showing domain segregation correlates with genetic and epigenetic changes.