Publications

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

Selected publications

*first/co-first author; #corresponding/co-corresponding author

  • 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, in press.

  • 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 ChuHe HuangJin 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.
  • Chen-Hao Chen*, Tengfei Xiao*, Han Xu, Peng Jiang, Cliff Meyer, Wei Li#, Myles Brown#, X. Shirley Liu#. Integrative design and analysis of CRISPR Knockout Screens. Bioinformatics 2018, 34 (23) 4095–4101. [Link]
  • Qingyi Cao, Jian Ma, Chen-Hao Chen, Han Xu, Zhi Chen#, Wei Li#, X. Shirley Liu#. CRISPR-FOCUS: a web server for designing focused CRISPR screening experiments. PLoS ONE 2017; 12(9): e0184281.
  • 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: >300; >50k 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

  • Xiaolong Cheng*, Zexu Li*, Ruocheng Shan, Zihan Li, Lumen Chao, Jian Peng, Teng Fei#, Wei Li#. Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches. bioRxiv 2021. [Link]
  • Zexu Li*, Zihan Li*, Xiaolong Cheng*, Xiaofeng Wang, Shixin Ma, Shengnan Wang, Zhiyan Lu, Han Zhang, Wenchang Zhao, Zhisong Chen, Yingjia Yao, Lumen ChaoWei Li#, Teng Fei#. Intrinsic RNA targeting constrains the utility of CRISPR-Cas13 systems. bioRxiv 2022. [Link]