Wei Li

Wei Li

Research Fellow
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Developing computational and statistical methods for the functional interpretation of coding and non-coding elements. I am interested in developing algorithms (1) to design and interpret genome-wide screening (especially CRISPR-Cas9 knockout screening) experiments targeting coding and non-coding elements in cancer; (2) to study the transcriptome dynamics (especially alternative splicing and isoform structure changes) from multiple high-throughput RNA sequencing data; and (3) to identify the functional roles of coding and non-coding elements by integrating large-scale genetic and epigenetic sequencing datasets.



Ph.D. in Computer Science and Engineering, University of California, Riverside, 2008-2012
Novartis Institutes for Biomedical Research, 2011
Master in Computer Science, Tsinghua University, Beijing China, 2006-2008
Bachelor in Computer Science, Tsinghua University, Beijing, China, 2002-2006

Select Publication

Wei Li, et al. SVM feature selection and sample regression for Chinese medicine research. 2008 International Conference on Information and Antomation (ICIA 2008), pp. 1773.
Wei Li, et al. COX-2 activity prediction in Chinese medicine using neural network based ensemble learning methods. International Joint Conference on Neural Networks (IJCNN 2008), pp. 1853.
Jianxing Feng, Wei Li, Tao Jiang. Inference of isoforms from short sequence reads. Research in Computational Molecular Biology (RECOMB 2010). Lecture Notes on Computer Science, 6044:138-157. Also appears in Journal of Computational Biology, 18(3):305-321, Mar. 2011
Wei Li, Paul Ruegger, James Borneman, Tao Jiang. Polony Identification Using the EM Algorithm Based on a Gaussian Mixture Model. IEEE International Conference on BioInformatics and BioEngineering (BIBE 2010), 220-225.
Wei Li, Jianxing Feng, Tao Jiang. IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly. Research in Computational Molecular Biology (RECOMB 2011). Lecture Notes in Computer Science, 6577:167-188. Also appears in Journal of Computational Biology, 18(11):1693-1707,Nov. 2011.
Wei Li, et al. Workshop: Transcriptome assembly from RNA-Seq data: Objectives, algorithms and challenges. IEEE 1st Computational Advances in Bio and Medical Sciences (ICCABS 2011), pp. 271
Wei Li, et al. Workshop: Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads. IEEE 2nd Computational Advances in Bio and Medical Sciences (ICCABS 2012), pp. 1
Wei Li and Tao Jiang. Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads. Bioinformatics (2012) 28(22):2914-2921.
Paul M. Ruegger, Elizabeth Bent, Wei Li, Daniel R. Jeske, Xinping Cui, Jonathan Braun, Tao Jiang, James Borneman. Improving Oligonucleotide Fingerprinting of rRNA Genes by Implementation of Polony Microarray Technology. Journal of Microbiological Methods (2012) 90(3):235-240.
Xiaoqi Zheng, Qian Zhao, Hua-Jun Wu, Wei Li, et al. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biology 2014, 15:419.
Masruba Tasnim, Shining Ma, Ei-Wen Yang, Tao Jiang* and Wei Li*. Accurate Inference of Isoforms from Multiple Sample RNA-Seq Data. To appear in 2015 Asian Pacific Bioinformatics Conference (APBC 2015).
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.


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CRISPR-Cas9 knockout screening, coding and non-coding elements in cancer, transcriptome dynamics, high-throughput RNA sequencing, epigenetic sequencing