Publications

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

Selected publications

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

  • 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. In press, PNAS.
  • 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. In press, Nature Protocol.
  • 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. In press, Bioinformatics.
  • 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: 115; >27k 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]
  • Wei Li, Jianxing Feng, Tao Jiang. IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly. Journal of Computational Biology 2011, 18(11):1693-1707. Also appear in the Research in Computational Molecular Biology (RECOMB 2011). Citation: 149. [Link][Software]
  • Wei Li*# and Tao Jiang. Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads. Bioinformatics 2012, 28(22):2914-2921. Citation: 63. [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]