Welcome to Wei Li lab

Publications

For a full list of published papers, see the google scholar page.

Selected publications

*first/co-first author; #corresponding/co-corresponding author; Li lab members.

  • 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, Wei Li. Decoding Heterogeneous Single-cell Perturbation Responses. Nature Cell Biology 2025. [Link] Also in bioRxiv 2023. [Link]
  • Bicna Song, Wei Li. Factoring Single-cell Perturbations. Nature Methods 2023. [Link]
  • 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#, Teng Fei#. Intrinsic RNA targeting constrains the utility of CRISPR-Cas13 systems. Nature Biomedical Engineering 2023.  [Link]. 
  • Xiaolong Cheng*, Zexu Li*, Ruocheng Shan, Zihan Li, Shengnan Wang, Wenchang Zhou, Han Zhang, Lumen Chao, Jian Peng, Teng Fei#, Wei Li#. Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches. Nature Communications 2023, 14 (752). Also on bioRxiv 2021. [Link][website]
  • Weiwei Dai, Fengting Wu, Natalie McMyn, Bicna Song, Victoria E. Walker-Sperling, Joseph Varriale, Hao Zhang, Dan H. Barouch, Janet D. Siliciano, Wei Li#, Robert F. Siliciano# . Genome-wide CRISPR screens identify combinations of candidate latency reversal agents for targeting the latent HIV-1 reservoir. Science Translational Medicine 2022, 14 (667) abh3351. [Link]
  • 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 & Xiaowei Zhuang. High-content CRISPR screening. Nature Reviews Methods Primers, 2, Article number: 8 (2022). [Link]
  • 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, Wei Li#. CRISP-view: a database of functional genetic screens spanning multiple phenotypes. Nucleic Acids Research 2021, 49 (D1) D848-854. [Link][Website]
  • Lin Yang*, Yuqing Zhu*, Hua Yu*, Xiaolong Cheng, Sitong Chen, Yulan Chu, He Huang, Jin Zhang#, Wei Li#. Linking genotypes with multiple phenotypes in single-cell CRISPR screens. Genome Biology 2020, 21, 19. [Link][Software].
  • Teng Fei*, Wei Li*, Jingyu Peng, Tengfei Xiao, Chen-Hao Chen, Alexander Wu, Jialiang Huang, Chongzhi Zang, X. Shirley Liu#, and Myles Brown#. Deciphering essential cistromes using genome-wide CRISPR screens. PNAS 2019. [Link]
  • 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#, Myles Brown#. Estrogen-regulated Feedback Loop Limits the Efficacy of Estrogen Receptor-targeted Breast Cancer Therapy. PNAS 2018, 115 (31), 7869-7878. [Link]
  • 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#, X. Shirley Liu#. Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute. Nature Protocols 2019, (14) 756-780.
  • 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 & Wensheng Wei. CRISPR/Cas9-mediated genomic deletion screening for long non-coding RNAs using paired-gRNAs. Nature Biotechnology 2016, 34:1279-1286. [Link]
  • Wei Li*, Han Xu*, Tengfei Xiao, Le Cong, Feng Zhang, Jun S. Liu, Myles Brown, X. Shirley Liu. MAGeCK enables robust identification of essential genes from genome-scale CRISPR-Cas9 knockout screens. Genome Biology 2014, 15:554. Citation: >2000; >150k software downloads. [Link][Software]
  • Wei Li*, Johannes Koster*, Tengfei Xiao, Han Xu, Chen-Hao Chen, Jun S. Liu, Myles Brown, Xiaole S. Liu. Quality control, modeling and visualization of genome-wide CRISPR screens using MAGeCK-VISPR. Genome Biology 2015, 16:281. [Link]
  • Masruba Tasnim, Shining Ma, Ei-Wen Yang, Tao Jiang# and Wei Li. Accurate Inference of Isoforms from Multiple Sample RNA-Seq Data. BMC Genomics 2015, 16 (S2):S15. Also appear in 2015 Asian Pacific Bioinformatics Conference (APBC 2015). APBC 2015 Best Paper Award. [Link]

Preprints

  • Alexander Wu, Tengfei Xiao, Teng Fei, X. Shirley Liu, Wei Li. Reducing false positives in CRISPR/Cas9 screens from copy number variations. bioRxiv 2018. [Link]