About Chirag Nepal, PhD

My research interest is focused in understanding how coordinated changes at transcription, translation and epigenetic levels alter gene regulation in normal cells that favor initiation of tumor. We do integrative analyses on various kinds (RNA-seq, ChIP-seq, CAGE-seq, small RNAs, RRBS, single cell RNA) of large-scale genomics data on cancer patients’, human cell lines and mouse models. We analyze publicly available sequencing data and generate new data through collaboration. I am currently focused in understanding:

Transcription start sites selection in translation regulation in cancer

Understanding the mechanism of CpG islands hypermethylation in cancer

The roles of onco-histones in shaping SNV and CNV landscapes.


Key Publications

Alternative promoters in CpG depleted regions pervasively account for epigenetic misregulation of cancer transcriptomes. Nepal. C. et al, BioRxiv




Integrative molecular characterization of gallbladder cancer presents microenvironment-associated subtypes related to survival. Nepal. C. et al, Journal of Hepatology, 2020 Dec 1


Editorial: https://www.journal-of-hepatology.eu/article/S0168-8278(21)00007-6/fulltext


Genomic Perturbations Reveal Distinct Regulatory Networks in Intrahepatic Cholangiocarcinoma. Nepal. C. et al, Hepatology, 2018 Sep


Editorial: https://aasldpubs.onlinelibrary.wiley.com/doi/10.1002/hep.29830

Cover article: https://aasldpubs.onlinelibrary.wiley.com/toc/15273350/2018/68/3


Ancestrally duplicated conserved noncoding element suggests dual regulatory roles of HOTAIR in cis and trans. Nepal. C. et al, iScience, Volume 23, 2020



Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing. Nepal. C. et al, Nature Communications, 2020



Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Baranasic D et al, Nature Genetics. 2022