Publications by authors named "Chirag Nepal"

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Spatial transcriptomics reveals distinct role of monocytes/macrophages with high expression in kidney transplant rejections.
Yan Chen Wongworawat, Chirag Nepal, Mark Duhon, Wanqiu Chen, Minh-Tri Nguyen

Front Immunol· October 2025

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Maternal e-cigarette exposure alters DNA methylome, site-specific CpG and CH methylation, and transcriptomic signatures in the neonatal brain.
Andrew Walayat, Maryam Hosseini, Chirag Nepal, Yong Li, Wanqiu Chen

Sci Rep· October 2024

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Epigenomic, transcriptomic and proteomic characterizations of reference samples.
Chirag Nepal, Wanqiu Chen, Zhong Chen, John A Wrobel, Ling Xie

bioRxiv· September 2024

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Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes.
Chirag Nepal, Jesper B Andersen

Nat Commun· May 2023

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Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Damir Baranasic, Matthias Hörtenhuber, Piotr J Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal

Nat Genet· July 2022

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Integrative molecular characterisation of gallbladder cancer reveals micro-environment-associated subtypes.
Chirag Nepal, Bin Zhu, Colm J O'Rourke, Deepak Kumar Bhatt, Donghyuk Lee

J Hepatol· May 2021

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Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans.
Chirag Nepal, Andrzej Taranta, Yavor Hadzhiev, Sachin Pundhir, Piotr Mydel

iScience· April 2020

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Identification of a Pan-Gamma-Secretase Inhibitor Response Signature for Notch-Driven Cholangiocarcinoma.
Colm J O'Rourke, Matthias S Matter, Chirag Nepal, Rui Caetano-Oliveira, Phuongnga T Ton

Hepatology· January 2020

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Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing.
Chirag Nepal, Yavor Hadzhiev, Piotr Balwierz, Estefanía Tarifeño-Saldivia, Ryan Cardenas

Nat Commun· January 2020

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Genomic perturbations reveal distinct regulatory networks in intrahepatic cholangiocarcinoma.
Chirag Nepal, Colm J O'Rourke, Douglas V N P Oliveira, Andrzej Taranta, Steven Shema

Hepatology· September 2018

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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, Sébastien Mella, Chirag Nepal, Alessandro Alunni

Development· May 2018

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MIR21 Drives Resistance to Heat Shock Protein 90 Inhibition in Cholangiocarcinoma.
Andrea Lampis, Pietro Carotenuto, Georgios Vlachogiannis, Luciano Cascione, Somaieh Hedayat, Chirag Nepal

Gastroenterology· March 2018

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Association of Aflatoxin and Gallbladder Cancer.
Jill Koshiol, Yu-Tang Gao, Michael Dean, Patricia Egner, Chirag Nepal

Gastroenterology· August 2017

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The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome.
Swaraj Basu, Yavor Hadzhiev, Giuseppe Petrosino, Chirag Nepal, Jochen Gehrig

Sci Rep· September 2016

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Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.
Chirag Nepal, Marion Coolen, Yavor Hadzhiev, Delphine Cussigh, Piotr Mydel

Nucleic Acids Res· April 2016

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Neuropsychological deficits in mice depleted of the schizophrenia susceptibility gene CSMD1.
Vidar M Steen, Chirag Nepal, Kari M Ersland, Rita Holdhus, Marianne Nævdal

PLoS One· November 2014

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RevSex duplication-induced and sex-related differences in the SOX9 regulatory region chromatin landscape in human fibroblasts.
Helle Lybæk, Diederik de Bruijn, Anke H A den Engelsman-van Dijk, Darya Vanichkina, Chirag Nepal

Epigenetics· March 2014

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Two independent transcription initiation codes overlap on vertebrate core promoters.
Vanja Haberle, Nan Li, Yavor Hadzhiev, Charles Plessy, Christopher Previti, Chirag Nepal

Nature· March 2014

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Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis.
Chirag Nepal, Yavor Hadzhiev, Christopher Previti, Vanja Haberle, Nan Li

Genome Res· November 2013

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The genome sequence of Atlantic cod reveals a unique immune system.
Bastiaan Star, Alexander J Nederbragt, Sissel Jentoft, Unni Grimholt, Martin Malmstrøm, Chirag Nepal

Nature· August 2011

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PRI-Modeler: extracting RNA structural elements from PDB files of protein-RNA complexes.
Kyungsook Han, Chirag Nepal

FEBS Lett· May 2007

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