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Chirag Nepal · SciRah

Researcher profile · Semantic Scholar

Chirag Nepal

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Chirag Nepal — researcher profile on SciRah

h-index: 17
Works: 38
Citations: 1,970

Most-cited papers

The genome sequence of Atlantic cod reveals a unique immune system
Bastiaan Star, A. Nederbragt, S. Jentoft, U. Grimholt +38 more
2011Nature777 citations Open access
Semantic Scholar
Two independent transcription initiation codes overlap on vertebrate core promoters
Vanja Haberle, Nan Li, Yavor Hadzhiev, C. Plessy +13 more
2014Nature179 citations Open access
Semantic Scholar
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
Chirag Nepal, Yavor Hadzhiev, C. Previti, Vanja Haberle +19 more
2013Genome Research128 citations Open access
Semantic Scholar
Genomic Perturbations Reveal Distinct Regulatory Networks in Intrahepatic Cholangiocarcinoma
Chirag Nepal, C. O'Rourke, D. V. Oliveira, Andrzej Taranta +10 more
2018Hepatology116 citations Open access
Semantic Scholar
MIR21 Drives Resistance to Heat Shock Protein 90 Inhibition in Cholangiocarcinoma
A. Lampis, P. Carotenuto, G. Vlachogiannis, L. Cascione +30 more
2017Gastroenterology110 citations Open access
Semantic Scholar
Association of Aflatoxin and Gallbladder Cancer'
J. Koshiol, Yu-Tang Gao, M. Dean, P. Egner +14 more
2017Gastroenterology84 citations Open access
Semantic Scholar
Neuropsychological Deficits in Mice Depleted of the Schizophrenia Susceptibility Gene CSMD1
V. Steen, Chirag Nepal, K. M. Ersland, Rita Holdhus +4 more
2013PLoS ONE83 citations Open access
Semantic Scholar
Neural stem cell quiescence and stemness are molecularly distinct outputs of the Notch3 signalling cascade in the vertebrate adult brain
Emmanuel Than-Trong, Sara Ortica-Gatti, S. Mella, Chirag Nepal +2 more
2018Development80 citations Open access
Semantic Scholar
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements
Damir Baranasic, Matthias Hörtenhuber, Piotr J. Balwierz, T. Zehnder +51 more
2022Nature Genetics79 citations Open access
Semantic Scholar
Integrative molecular characterization of gallbladder cancer reveals microenvironment-associated subtypes
Chirag Nepal, Bin Zhu, C. O'Rourke, D. Bhatt +23 more
2020Journal of Hepatology69 citations Open access
Semantic Scholar
Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing
Chirag Nepal, Yavor Hadzhiev, Piotr J. Balwierz, E. Tarifeño-Saldivia +8 more
2020Nature Communications49 citations Open access
Semantic Scholar
Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes
Chirag Nepal, J. Andersen
2023Nature Communications35 citations Open access
Semantic Scholar
IDENTIFICATION OF A PAN-GAMMA-SECRETASE INHIBITOR RESPONSE SIGNATURE FOR NOTCH-DRIVEN CHOLANGIOCARCINOMA
C. O'Rourke, M. Matter, Chirag Nepal, Rui Caetano-Oliveira +3 more
2019Hepatology34 citations Open access
Semantic Scholar
University of Birmingham Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.
Chirag Nepal, M. Coolen, Yavor Hadzhiev, Delphine Cussigh +8 more
201528 citations
Semantic Scholar
PRI‐Modeler: Extracting RNA structural elements from PDB files of protein–RNA complexes
Kyungsook Han, Chirag Nepal
2007FEBS Letters23 citations
Semantic Scholar
RevSex duplication-induced and sex-related differences in the SOX9 regulatory region chromatin landscape in human fibroblasts
Helle Lybæk, D. D. de Bruijn, Anke H. A. den Engelsman-van Dijk, Darya Vanichkina +3 more
2013Epigenetics21 citations Open access
Semantic Scholar
Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans
Chirag Nepal, Andrzej Taranta, Yavor Hadzhiev, S. Pundhir +4 more
2020iScience19 citations Open access
Semantic Scholar
The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome
S. Basu, Yavor Hadzhiev, Giuseppe Petrosino, Chirag Nepal +6 more
2016Scientific Reports16 citations Open access
Semantic Scholar
Spatial transcriptomics reveals distinct role of monocytes/macrophages with high FCGR3A expression in kidney transplant rejections
Yan Chen Wongworawat, Chirag Nepal, Mark Duhon, Wan-Qiu Chen +11 more
2025Frontiers in Immunology11 citations Open access
Semantic Scholar
Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs
Chirag Nepal, M. Coolen, Yavor Hadzhiev, Delphine Cussigh +7 more
2015Nucleic Acids Research10 citations Open access
Semantic Scholar
Maternal e-cigarette exposure alters DNA methylome, site-specific CpG and CH methylation, and transcriptomic signatures in the neonatal brain
Andrew Walayat, M. Hosseini, Chirag Nepal, Yong Li +7 more
2024Scientific Reports7 citations Open access
Semantic Scholar
Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish
Damir Baranasic, Matthias Hörtenhuber, Piotr J. Balwierz, T. Zehnder +48 more
20216 citations Open access
Semantic Scholar
Spatial Transcriptomics Using Archived Formalin-Fixed Paraffin-Embedded Core Needle Biopsy Tissues Revealed Unique Transcriptomic Signatures in Kidney Transplant Rejections
Y. C. Wongworawat, Chirag Nepal, Mark Duhon, Wan-Qiu Chen +10 more
2025bioRxiv3 citations
Semantic Scholar
Epigenomic, transcriptomic, and proteomic characterization of breast cancer cell line reference samples
Chirag Nepal, Wan-Qiu Chen, Zhong Chen, J. Wrobel +8 more
2026Cell Reports Methods2 citations Open access
Semantic Scholar
HOTAIR ancient sequence suggests regulatory roles both in cis and trans
Chirag Nepal, Yavor Hadzheiv, S. Pundhir, P. Mydel +3 more
2018bioRxiv1 citations Open access
Semantic Scholar
Predicting Binding Sites of Hepatitis C Virus Complexes Using Residue Binding Propensity and Sequence Entropy
Guang-Zheng Zhang, Chirag Nepal, Kyungsook Han
2007International Conference on Conceptual Structures1 citations Open access
Semantic Scholar
Prenatal e-cigarette exposure induces region- and cell type-specific metabolic and developmental reprogramming
Wan-Qiu Chen, Zhong Chen, Chirag Nepal, Xue Pan +7 more
2026bioRxiv0 citations
Semantic Scholar
A Comprehensive DNA Methylome BodyMap across 12 Organs/Tissues from Spaceflight Mice
Zhong Chen, Chirag Nepal, Xiao W. Mao, Feng Zeng +3 more
2026bioRxiv0 citations Open access
Semantic Scholar
Epigenomic, transcriptomic and proteomic characterizations of reference samples
Chirag Nepal, Wan-Qiu Chen, Zhong Chen, J. Wrobel +8 more
2024bioRxiv0 citations Open access
Semantic Scholar
Alternative promoters in CpG depleted regions pervasively account for epigenetic misregulation of cancer transcriptomes
Chirag Nepal, J. Andersen
2022bioRxiv0 citations Open access
Semantic Scholar
PS-044-Identification of a pan-gamma-secretase inhibitor response signature for notch-driven cholangiocarcinoma
Colm O. Rourke, M. Matter, Chirag Nepal, P. Ton +2 more
2019Journal of Hepatology0 citations
Semantic Scholar
Intertwined canonical and non-canonical initiation in dual promoters are pervasive and differentially regulate Polymerase II transcription
Chirag Nepal, Yavor Hadzhiev, E. Tarifeño-Saldivia, Ryan Cardenas +6 more
20180 citations Open access
Semantic Scholar
Abstract LB-157: Association of aflatoxin and gallbladder cancer in Shanghai
J. Koshiol, Yu-Tang Gao, M. Dean, P. Egner +14 more
20170 citations
Semantic Scholar
single nucleotide resolution during vertebrate embryogenesis Dynamic regulation of the transcription initiation landscape at Material Supplemental
Chirag Nepal, Yavor Hadzhiev, C. Previti, Vanja Haberle +19 more
20130 citations
Semantic Scholar
Regulatory mechanisms of non-coding RNAs during zebrafish embryogenesis
Chirag Nepal
20130 citations
Semantic Scholar
Analysis of HCV Envelope Proteins Interacting with Human Proteins
Chirag Nepal, Kyungsook Han
2007Frontiers in the Convergence of Bioscience and Information Technologies0 citations
Semantic Scholar
Mining Molecular Structure Data for the Patterns of Interactions Between Protein and RNA
Kyungsook Han, Chirag Nepal
2007International Conference on Conceptual Structures0 citations Open access
Semantic Scholar
Spatial Reasoning for Collision Detection and Hardware Implementation
Chirag Nepal, S. Nam, Dohyung Kim, Kyungsook Han
20060 citations
Semantic Scholar

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