Publications

Yu Zhao
Equal contribution
, Ran Zhou
Equal contribution
, Zepeng Mu, Peter Carbonetto, Xiaoyuan Zhong, Bingqing Xie, Kaixuan Luo, Candace M Cham, Jason Koval, Xin He, Andrew W Dahl, Xuanyao Liu, Eugene B Chang, Anindita Basu
Corresponding
, Sebastian Pott
Corresponding
(2026). Single-Cell Analysis of Chromatin Accessibility in the Human Intestine Identifies Regulatory Programs and Clarifies Genetic Associations in Crohn’s Disease. Nature Genetics.
DOI DOI
Yoshihiko Tomofuji
First
, Zepeng Mu, Hafsa Mire, Yu Zhao, Cassidy Liu, Vidya Jayanthi, Nicholas Sugiarto, Accelerating Medicines Partnership RA/SLE Network, Jeffrey A. Sparks, Soumya Raychaudhuri
Corresponding
(2026). Identifying the causal allele in the CD40 autoimmune locus enables discovery of context-specific trans-effects in B cells. bioRxiv.
URL DOI
Haley E Randolph
First
, Raul Aguirre-Gamboa, Elsa Brunet-Ratnasingham, Takahiro Nakanishi, Zepeng Mu, Vitor Locher, Emma Ketter, Caitlin Brandolino, Catherine Larochelle, Alexandre Prat, Nathalie Arbour, Anne Dumaine, Andres Finzi, Madeleine Durand, J. Brent Richards, Daniel E Kaufmann, Luis B Barreiro
Corresponding
(2026). Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients. Nature Communications.
URL DOI
Zepeng Mu
First
, Haley E Randolph, Raúl Aguirre-Gamboa, Ellen Ketter, Anne Dumaine, Veronica Locher, Cary Brandolino, Xuanyao Liu, Daniel E Kaufmann, Luis B Barreiro
Corresponding
, Yang I Li
Corresponding
(2025). Impact of disease-associated chromatin accessibility QTLs across immune cell types and contexts. Cell Genomics.
Zenodo SRA DOI
Yuriy Baglaenko
Corresponding, equal contribution
, Zepeng Mu
Equal contribution
, Michelle Curtis, Hafsa M Mire, Vidyashree Jayanthi, Majd Al Suqri, Cassidy Liu, Ryan Agnew, Aparna Nathan, Annelise Yoo Mah-Som, David R Liu, Gregory a Newby, Soumya Raychaudhuri
Corresponding
(2025). Precisely defining disease variant effects in CRISPR-edited single cells. Nature.
DOI
Guimin Gao
Equal contribution
, Julian McClellan
Equal contribution
, Alvaro N Barbeira
Equal contribution
, Peter N Fiorica, James L Li, Zepeng Mu, Olufunmilayo I Olopade, Dezheng Huo
Corresponding
, Hae Kyung Im
Corresponding
(2024). A multi-tissue, splicing-based joint transcriptome-wide association study identifies susceptibility genes for breast cancer. The American Journal of Human Genetics.
Haley E Randolph
First
, Katherine a Aracena, Yen-Lung Lin, Zepeng Mu, Luis B Barreiro
Corresponding
(2024). Shaping immunity: The influence of natural selection on population immune diversity. Immunological Reviews.
URL DOI
Katherine a Aracena
First
, Yen-Lung Lin, Kaixuan Luo, Alain Pacis, Saideep Gona, Zepeng Mu, Vania Yotova, Renata Sindeaux, Albena Pramatarova, Marie-Michelle Simon, Xun Chen, Cristian Groza, David Lougheed, Romain Gregoire, David Brownlee, Carly Boye, Roger Pique-Regi, Yang Li, Xin He, David Bujold, Tomi Pastinen, Guillaume Bourque
Corresponding
, Luis B Barreiro
Corresponding
(2024). Epigenetic variation impacts individual differences in the transcriptional response to influenza infection. Nature Genetics.
DOI
Zepeng Mu
Equal contribution
, Wei Wei
Equal contribution
, Benjamin Jung Fair, Jinlin Miao, Ping Zhu
Corresponding
, Yang I Li
Corresponding
(2021). The impact of cell-type and context-dependent regulatory variants on human immune traits. Genome Biology.
EGA Archive Full Summ Stats PDF Zenodo DOI
Mengjie Chen
Corresponding, First
, Qi Zhan, Zepeng Mu, Lili Wang, Zhaohui Zheng, Jinlin Miao, Ping Zhu
Corresponding
, Yang I Li
Corresponding
(2021). Alignment of single-cell RNA-seq samples without over-correction using kernel density matching. Genome Research.
DOI