Publications

2026

Jul 16

Cross-platform Hi-C meta-analysis identifies functional insulators that actively block enhancer-promoter interactions

Jian Cui, Wanying Xu, Xiuyuan Lang, Shanshan Zhang, Leina Lu, Xiaoxiao Liu, Yan Li, Fulai Jin

Nature Communications · DOI: 10.1038/s41467-026-75801-3 · PMID: 42463675

Apr 13

Proinsulin regulators identified with CRISPR screen and in vivo mouse QTL mapping

Sisi Lai, Mark P. Keller, Jinglin Zhang, Zhou Fang, Ying Xie, Chen Weng, Saixian Zhang, Shanshan Zhang, Peidong Gao, Luxin Ke, Yuntong Wang, ..., Fulai Jin, Alan D. Attie, Yan Li

Nature Communications · DOI: 10.1038/s41467-026-71726-z · PMID: 41974708

2025

Oct 14

A comprehensive benchmark of single-cell Hi-C embedding tools

Dylan Plummer, Xiuyuan Lang, Shanshan Zhang, Yan Li, Jing Li, Fulai Jin

Nature Communications · DOI: 10.1038/s41467-025-64186-4 · PMID: 41087414

Jul 2

The Somatic Mosaicism across Human Tissues Network

Tim H. H. Coorens, Ji Won Oh, Yujin Angelina Choi, Nam Seop Lim, Boxun Zhao, ..., Fulai Jin, ..., Yan Li, ..., Eunjung Alice Lee, Flora M. Vaccarino, The Somatic Mosaicism across Human Tissues Network

Nature · DOI: 10.1038/s41586-025-09096-7 · PMID: 40604182

2024

Oct 30

Heterogeneous enhancer states orchestrate β cell responses to metabolic stress

Liu Wang, Jie Wu, Madeline Sramek, S. M. Bukola Obayomi, Peidong Gao, Yan Li, Aleksey V. Matveyenko, Zong Wei

Nature Communications · DOI: 10.1038/s41467-024-53717-0 · PMID: 39472434

2023

Sep 5

Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A

Chen Weng, Anniya Gu, Shanshan Zhang, Leina Lu, Luxin Ke, Peidong Gao, Xiaoxiao Liu, Yuntong Wang, Peinan Hu, Dylan Plummer, Elise MacDonald, Saixian Zhang, Jiajia Xi, Sisi Lai, Konstantin Leskov, Kyle Yuan, Fulai Jin, Yan Li

Nature Communications · DOI: 10.1038/s41467-023-41228-3 · PMID: 37669939

2022

Jul 11

DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution

Shanshan Zhang, Dylan Plummer, Leina Lu, Jian Cui, Wanying Xu, Miao Wang, Xiaoxiao Liu, ..., Yan Li, Jing Li, Fulai Jin

Nature Genetics · DOI: 10.1038/s41588-022-01116-w · PMID: 35817982

2021

Aug 23

INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants

Chenyang Dong, Shane P Simonett, Sunyoung Shin, Donnie S Stapleton, Kathryn L Schueler, Gary A Churchill, Leina Lu, Xiaoxiao Liu, Fulai Jin, Yan Li, Alan D Attie, Mark P Keller, Sündüz Keleş

Genome Biology · DOI: 10.1186/s13059-021-02450-8 · PMID: 34425882

2020

Nov 30

Single-cell lineage analysis reveals extensive multimodal transcriptional control during directed beta-cell differentiation

Chen Weng, Jiajia Xi, Haiyan Li, Jian Cui, Anniya Gu, Sisi Lai, Konstantin Leskov, Luxin Ke, Fulai Jin, Yan Li

Nature Metabolism · DOI: 10.1038/s42255-020-00314-2 · PMID: 33257854

Oct 15

Aberrant methylation underlies insulin gene expression in human insulinoma

Esra Karakose, Huan Wang, William Inabnet, Rajesh V Thakker, Steven Libutti, ..., Yan Li, Xiaoxiao Liu, Fulai Jin, ..., Andrew F Stewart, Donald K Scott, Luca Lambertini

Nature Communications · DOI: 10.1038/s41467-020-18839-1 · PMID: 33060578

Sep 29

TWO‐SIGMA: A novel two‐component single cell model‐based association method for single‐cell RNA‐seq data

Eric Van Buren, Ming Hu, Chen Weng, Fulai Jin, Yan Li, Di Wu, Yun Li

Genetic Epidemiology · DOI: 10.1002/gepi.22361 · PMID: 32989764

Jun 26

Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases

Leina Lu, Xiaoxiao Liu, Wei-Kai Huang, Paola Giusti-Rodríguez, Jian Cui, Shanshan Zhang, Wanying Xu, ..., Guo-Li Ming, Yan Li, Fulai Jin

Molecular Cell · DOI: 10.1016/j.molcel.2020.06.007 · PMID: 32592681

Apr 30

Myt Transcription Factors Prevent Stress-Response Gene Overactivation to Enable Postnatal Pancreatic β Cell Proliferation, Function, and Survival

Ruiying Hu, Emily Walker, Chen Huang, Yanwen Xu, Chen Weng, ..., Yan Li, Roland Stein, Guoqiang Gu

Developmental Cell · DOI: 10.1016/j.devcel.2020.04.003 · PMID: 32359405

2019

Oct 17

Exploring the Trans‐Cleavage Activity of CRISPR‐Cas12a (cpf1) for the Development of a Universal Electrochemical Biosensor

Yifan Dai, Rodrigo A Somoza, Liu Wang, Jean F Welter, Yan Li, Arnold I Caplan, Chung Chiun Liu

Angewandte Chemie · DOI: 10.1002/anie.201910772 · PMID: 31568601

Mar 12

Single-Cell Heterogeneity Analysis and CRISPR Screen Identify Key β-Cell-Specific Disease Genes

Zhou Fang, Chen Weng, Haiyan Li, Ran Tao, Weihua Mai, Xiaoxiao Liu, Leina Lu, Sisi Lai, ..., Yanxin Pei, Fulai Jin, Yan Li

Cell Reports · DOI: 10.1016/j.celrep.2019.02.043 · PMID: 30865899

2018

Aug 23

Chemical Screening Identifies Enhancers of Mutant Oligodendrocyte Survival and Unmasks a Distinct Pathological Phase in Pelizaeus-Merzbacher Disease

Matthew S Elitt, H Elizabeth Shick, Mayur Madhavan, Kevin C Allan, Benjamin L L Clayton, Chen Weng, ..., Yan Li, Fulai Jin, Drew J Adams, Paul J Tesar

Stem Cell Reports · DOI: 10.1016/j.stemcr.2018.07.015 · PMID: 30146490