The paper uses population-based modeling of Hi-C data to analyze the nuclear microenvironment's role in gene function, revealing structural variability and functional heterogeneity.

bioRxiv · Jul 11, 2021 · PreprintGenomics

Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis

Shuo Li, Zorawar Singh Noor, Weihua Zeng, Mary L. Stackpole, Xiaohui Ni, Yonggang Zhou, Zuyang Yuan, Wing Hung Wong, Vatche Garen Agopian, Steven M. Dubinett, Frank Alber, Wenyuan Li, Edward B. Garon, Xianghong Jasmine Zhou

This paper introduces cfSNV, a somatic SNV caller for cfDNA that outperforms existing tools in detecting low-frequency mutations and applies it to immunotherapy prognosis in non-small-cell lung cancer.

Nature Communications · Jul 7, 2021Peer-reviewedGenetic & Genomic Medicine

PGS: a dynamic and automated population-based genome structure software

Nan Hua, Harianto Tjong, Hanjun Shin, Ke Qin Gong, Xianghong Jasmine Zhou, Frank Alber

PGS generates a population of 3D genome structures from Hi-C data to better understand genome organization and provides analysis tools.

Nature Protocols · Apr 5, 2018Peer-reviewedBioinformatics

The 3D genome organization of Drosophila melanogaster through data integration

Qingjiao Li, Harianto Tjong, Xiao Li, Ke Qin Gong, Xianghong Jasmine Zhou, Irene Chiolo, Frank Alber

This paper integrates Hi-C and lamina-DamID data to compute 3D genome structures for Drosophila melanogaster, revealing structural features and functional insights.

Genome biology · Jul 31, 2017Peer-reviewedBioinformatics