Wei Li Lab publications
Selected papers and preprints from the lab and our collaborators.
Our work spans AI-guided genome engineering, CRISPR screening, single-cell functional genomics, and computational methods for transcriptome analysis.
Selected publications
* first or co-first author; # corresponding or co-corresponding author. Bold names identify Li Lab members at the time of the work.
Genome Biology · 2026
An integrated multi-omics and network analysis of neutrophil differentiation from initial- to late-stage
Qing Chen*#, Tianchang Yang*, Yingping Hou*, Kai Wang, Tingting Li, Longteng Wang, Cuiyun Dou, Panpan Cheng, Minglei Shi#, and Wei Li#.
Nature Cell Biology · 2025
Decoding heterogeneous single-cell perturbation responses
Bicna Song, Dingyu Liu, Weiwei Dai, Natalie McMyn, Qingyang Wang, Dapeng Yang, Adam Krejci, Anatoly Vasilyev, Nicole Untermoser, Anke Loregger, Dongyuan Song, Breanna Williams, Bess Rosen, Xiaolong Cheng, Lumen Chao, Hanuman T. Kale, Hao Zhang, Yarui Diao, Tilmann Burckstummer, Jenet M. Siliciano, Jingyi Jessica Li, Robert Siliciano, Danwei Huangfu, and Wei Li.
Nature Biomedical Engineering · 2023
Intrinsic RNA targeting constrains the utility of CRISPR-Cas13 systems
Zexu Li*, Zihan Li*, Xiaolong Cheng*, Shengnan Wang, Xiaofeng Wang, Shixin Ma, Zhiyan Lu, Han Zhang, Wenchang Zhao, Zhisong Chen, Yingjia Yao, Cheng Zhang, Lumen Chao, Wei Li#, and Teng Fei#.
Nature Communications · 2023
Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches
Xiaolong Cheng*, Zexu Li*, Ruocheng Shan, Zihan Li, Shengnan Wang, Wenchang Zhou, Han Zhang, Lumen Chao, Jian Peng, Teng Fei#, and Wei Li#.
Science Translational Medicine · 2022
Genome-wide CRISPR screens identify combinations of candidate latency reversal agents for targeting the latent HIV-1 reservoir
Weiwei Dai, Fengting Wu, Natalie McMyn, Bicna Song, Victoria E. Walker-Sperling, Joseph Varriale, Hao Zhang, Dan H. Barouch, Janet D. Siliciano, Wei Li#, and Robert F. Siliciano#.
Nature Reviews Methods Primers · 2022
High-content CRISPR screening
Christoph Bock, Paul Datlinger, Florence Chardon, Matthew A. Coelho, Matthew B. Dong, Keith A. Lawson, Tian Lu, Laetitia Maroc, Thomas M. Norman, Bicna Song, Geoff Stanley, Sidi Chen, Mathew Garnett, Wei Li, Jason Moffat, Lei S. Qi, Rebecca S. Shapiro, Jay Shendure, Jonathan S. Weissman, and Xiaowei Zhuang.
Nucleic Acids Research · 2021
CRISP-view: a database of functional genetic screens spanning multiple phenotypes
Yingbo Cui*, Xiaolong Cheng*, Qing Chen, Bicna Song, Anthony Chiu, Yuan Gao, Tyson Dawson, Lumen Chao, Wubing Zhang, Dian Li, Zexiang Zeng, Jijun Yu, Zexu Li, Teng Fei, Shaoliang Peng, and Wei Li#.
Genome Biology · 2020
Linking genotypes with multiple phenotypes in single-cell CRISPR screens
Lin Yang*, Yuqing Zhu*, Hua Yu*, Xiaolong Cheng, Sitong Chen, Yulan Chu, He Huang, Jin Zhang#, and Wei Li#.
PNAS · 2019
Deciphering essential cistromes using genome-wide CRISPR screens
Teng Fei*, Wei Li*, Jingyu Peng, Tengfei Xiao, Chen-Hao Chen, Alexander Wu, Jialiang Huang, Chongzhi Zang, X. Shirley Liu#, and Myles Brown#.
Nature Protocols · 2019
Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute
Binbin Wang*, Mei Wang*, Wubing Zhang*, Tengfei Xiao, Chen-Hao Chen, Alexander Wu, Feizhen Wu, Nicole Traugh, Xiaoqing Wang, Ziyi Li, Shenglin Mei, Yingbo Cui, Sailing Shi, Jesse Jonathan Lipp, Matthias Hinterndorfer, Johannes Zuber, Myles Brown, Wei Li#, and X. Shirley Liu#.
PNAS · 2018
Estrogen-regulated feedback loop limits the efficacy of estrogen receptor-targeted breast cancer therapy
Tengfei Xiao*, Wei Li*, Xiaoqing Wang, Han Xu, Qiu Wu, Peng Jiang, Jixin Yang, Teng Fei, Chongzhi Zang, Qi Liao, Jonathan Rennhack, Eran Andrechek, Rinath M. Jeselsohn, X. Shirley Liu#, and Myles Brown#.
Nature Biotechnology · 2016
CRISPR/Cas9-mediated genomic deletion screening for long non-coding RNAs using paired-gRNAs
Shiyou Zhu*, Wei Li*, Jingze Liu, Chen-Hao Chen, Qi Liao, Han Xu, Tengfei Xiao, Zhongzheng Cao, Jingyu Peng, Pengfei Yuan, Myles Brown, Xiaole Shirley Liu, and Wensheng Wei.
Genome Biology · 2015
Quality control, modeling and visualization of genome-wide CRISPR screens using MAGeCK-VISPR
Wei Li*, Johannes Koster*, Tengfei Xiao, Han Xu, Chen-Hao Chen, Jun S. Liu, Myles Brown, and Xiaole S. Liu.
BMC Genomics · 2015
Accurate inference of isoforms from multiple-sample RNA-seq data
Masruba Tasnim, Shining Ma, Ei-Wen Yang, Tao Jiang#, and Wei Li. Also presented at APBC 2015, where it received the Best Paper Award.
Preprints
Preprints are listed separately from peer-reviewed publications.
pertTF: context-aware AI modeling for genome-scale and cross-system perturbation prediction
Yangqi Su, Dingyu Liu, Vipin Menon, Bicna Song, Samuel Boccara, Nan Zhang, Huan Zhao, Jiahui Hazel Zhao, Lei Wang, Nan Hu, Mpathi Nzima, Alon Katz, Bharath Kumar Swargam, Seth A. Ament, Yarui Diao, Hanrui Zhang, Lumen Chao, Gary Hon, Danwei Huangfu, and Wei Li. bioRxiv, 2026.
A stem cell knockout village reveals lineage rewiring and a non-canonical islet cell fate in monogenic diabetes
Dingyu Liu, Bicna Song, Zhaoheng Li, Stephen Zhang, Tabassum Fabiha, Jiahui Zhao, Ayaka Inoki, Julie Piccand, ChewLi Soh, Gary Dixon, Aaron Zhong, Nan Hu, Renhe Luo, Batu Ozlusen, Vipin Menon, Ting Zhou, Xiaojie Qiu, Gerard Gradwohl, Dapeng Yang, Kushal Dey, Wei Sun, Wei Li, and Danwei Huangfu. bioRxiv, 2025.
Perturb-seq reveals distinct responses to pluripotency regulator dosages underlying the control of self-renewal and differentiation
Jielin Yan, Hyein S. Cho, Renhe Luo, Michael A. Beer, Wei Li, and Danwei Huangfu. bioRxiv, 2025.
Reducing false positives in CRISPR/Cas9 screens from copy-number variations
Alexander Wu, Tengfei Xiao, Teng Fei, X. Shirley Liu, and Wei Li. bioRxiv, 2018.