@article{Wang01022023,
author = {Wang, Jingyao and Xue, Yue and He, Yueying and Quan, Hui and Zhang, Jun and Gao, Yi Qin}, 
title = {Characterization of network hierarchy reflects cell state specificity in genome organization},
volume = {33}, 
number = {2}, 
pages = {247-260}, 
year = {2023}, 
doi = {10.1101/gr.277206.122}, 
abstract ={Dynamic chromatin structure acts as the regulator of transcription program in crucial processes including cancer and cell development, but a unified framework for characterizing chromatin structural evolution remains to be established. Here, we performed graph inferences on Hi-C data sets and derived the chromatin contact networks. We discovered significant decreases in information transmission efficiencies in chromatin of colorectal cancer (CRC) and T-cell acute lymphoblastic leukemia (T-ALL) compared to corresponding normal controls through graph statistics. Using network embedding in the Poincaré disk, the hierarchy depths of chromatin from CRC and T-ALL patients were found to be significantly shallower compared to their normal controls. A reverse trend of change in chromatin structure was observed during early embryo development. We found tissue-specific conservation of hierarchy order in chromatin contact networks. Our findings reveal the top-down hierarchy of chromatin organization, which is significantly attenuated in cancer.}, 
URL = {http://genome.cshlp.org/content/33/2/247.abstract}, 
eprint = {http://genome.cshlp.org/content/33/2/247.full.pdf+html}, 
journal = {Genome Research} 
}