Li, Wei - University of California, Irvine

个人简介

Endowed Chair & Professor of Bioinformatics: 2019 – present Division of Computational Biomedicine Department of Biological Chemistry School of Medicine University of California, Irvine Dan L Duncan Chair Professor: 07/2018 – 2019 Professor (tenured): 08/2016 – present Associate Professor (tenured): 10/2011 – 07/2016 Assistant Professor (tenure track): 11/2007 – 09/2011 Division of Biostatistics, Dan L. Duncan Cancer Center Department of Molecular and Cellular Biology Baylor College of Medicine. Postdoctoral Fellow: 06/2004 – 10/2007 Department of Biostatistics & Computational Biology Dana Farber Cancer Institute Harvard School of Public Health, Boston Advisor: Prof. Xiaole Shirley Liu Bioinformatics Group Leader: 01/2000 – 05/2004 Beijing Genomics Institute (BGI) Chinese Academy of Sciences, Beijing, China Ph.D. in Bioinformatics: 09/1998 – 09/2003 Institute of Biophysics Chinese Academy of Sciences, Beijing, China Advisor: Prof. Runsheng Chen Awards: * Michael E. DeBakey Excellence in Research Award (2016): the most prestigious honor given annually to 5 out of ~3,500 Baylor faculty who have made the most significant published scientific contribution to clinical or basic biomedical research in the past three years.

研究领域

Our research is focused on the design and application of bioinformatics algorithms to elucidate global regulatory mechanisms in normal development and diseases such as cancer. We have a solid track record in large-scale genomics data analysis and the development of widely used open-source bioinformatics software, such as MACS (>9,000 citations) for ChIP-seq and RSeqQC (>1,200 citations) for RNA-seq. In collaboration with experimental biologists, we have used bioinformatics to gain novel biological insights into development, aging, stem cell, neurologic disorders, and various cancers. Our major contributions to science include the following: (1) We uncovered several novel links between chromatin modifications and cancer driver gene regulation; (2) Our work on alternative polyadenylation (APA) is the first of its kind to connect APA regulation to many human complex traits and diseases. (3) Our work regarding cell heterogeneity in DNA methylation has now been quickly adopted in clinical trials for early cancer detection by liquid biopsy.

近期论文

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Gao Y, Li L, Amos CI, Li W: Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression Genome Research 6 (2021), 31 Highlighted in GenomeWeb.com Li L, Huang KL, Gao Y, Cui Y, Wang G, Elrod ND , Li Y, Chen YE, Ji P, Peng F, Russell WK, Wagner EJ, Li W: An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability. Nature Genetics 53 (2021), 1-12 UCI-led study sheds light on mysterious genotype-phenotype associations; Highlighted in BioArt and Highlighted in ebiotrade Xu J, Shi J, Cui X, Cui Y, Li JJ, Goel A, Chen X, Issa JP, Su J, Li W: Heterogeneity–Adjusted cLonal Methylation (CHALM) improves prediction of gene expression. Nature Communications 12 (2021), 1-9 New study points to better diagnostics for cancer Cui Y, Cui Z, Xu J, Hao D, Shi J, Wang D, Xiao H, Duan X, Chen R, Li W: NG-Circos: next-generation Circos for data visualization and interpretation. NAR Genomics and Bioinformatics 2 (2020) Lyu J, Li JJ, Su J, Peng F, Chen YE, Ge X, Li W: DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features. Science Advances 6 (2020), eaba6784 New prediction algorithm identifies previously undetected cancer driver genes Park HJ, Ji P, Kim S, Xia Z, Rodriguez B, Li L, Su J, Chen K, Masamha CP, Baillat D, Fontes-Garfias CR, Shyu AB, Neilson JR, Wagner EJ, Li W: 3′ UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk. Nature Genetics 50 (2018) 783-789. PMCID Gu T^, Lin X^, Cullen SM^, Luo M, Jeong M, Estecio M, Shen J, Hardikar S, Sun D, Su J, Rux D, Guzman A, Lee M, Qi LS, Chen JJ, Kyba M, Huang Y, Chen T, Li W*, Goodell MA*: DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells. Genome Biol 19 (2018) 88. PMCID. Su J^, Huang YH^, Cui X, Wang X, Zhang X, Lei Y, Xu J, Lin X, Chen K, Lv J, Goodell MA*, Li W*: Homeobox oncogene activation by pan-cancer DNA hypermethylation. Genome Biol 19 (2018) 108. PMCID Lin X, Su J, Chen K, Rodrigues B, Li W*: Sparse conserved under-methylated CpGs are associated with high-order chromatin structure. Genome Biology 18 (2017) 163 Zhang X^, Su J^, Jeong M, Ko M, Huang Y, Park HJ, Guzman A, Lei Y, Huang YH, Rao A, Li W*, Goodell MA*: DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells. Nature Genetics 48 (2016) 1014-1023. PMCID: PMC4957136 Luo M^, Jeong M^, Sun D^, Park HJ^, Rodrigues B^, Xia Z, Yang L, Zhang X, Darlington GJ, Li W*!, Goodell MA*: Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function. Cell Stem Cell 16 (2015) 426–438 Chen K^, Chen Z^, Wu D, Zhang L, Lin X, Su J, Rodriguez B, Xi Y, Xia Z, Chen X, Shi X, Wang Q, Li W*: Broad H3K4me3 is Asscoated with Increased Transcription Elongation and Enhancer Activity at Tumor Suppressor Genes. Nature Genetics 47 (2015) 1149-1157 Chen L^, Chen K^, Lavery LA, Baker SA, Shaw C, Li W*, Zoghbi HY*: MeCP2 binds to mCH as neurons mature, influencing transcription and onset of Rett syndrome. PNAS 112 (2015) 5509-5514 Sun D, Xi Y, Rodriguez B, Park HJ, Pan T, Meong M, Goodell MA, Li W: MOABS: Model based Analysis of Bisulfite Sequencing data. Genome Biol 15 (2014) R38. PMCID Wang L*, Chen J, Wang C, Uuskula-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP*, Li W*: MACE: Model based Analysis of ChIP-exo.Nucleic Acids Res. 42 (2014) e156. Sun D^, Luo M^, Jeong M^, Rodriguez B, Xia Z, Hannah R, Wang H, Le T, Faull KF, Chen R, Gu H, Bock C, Meissner A, Gottgens B, Darlington GJ*, Li W*, Goodell MA*: Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal.Cell Stem Cell 14 (2014) 673-688 Xia Z, Donehower L, Cooper TA, Neilson JR, Wheeler DA, Wagner EJ, Li W*: Dynamic Analyses of Alternative Polyadenylation from RNA-Seq Reveal 3′-UTR Landscape Across 7 Tumor Types. Nature Communications 5 (2014) 5274 Masamha CP^, Xia Z^, Yang J, Albrecht TR, Li M, Shyu A, Li W, Wagner EJ*: CFIm25 links Alternative Polyadenylation to Glioblastoma Tumor Suppression. Nature 510 (2014) 412-416 Jeong M^, Sun D^, Luo M^, Huang Y, Challen GA, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim S, Yang L, Ko M, Chen R, Gottgens B, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, Li W*!, Goodell MA*: Large conserved domains of low DNA methylation maintained by Dnmt3a. Nature Genetics 46 (2014) 17-23. Wen H^, Li Y^, Xi Y^, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, Xia Z, Wu J, Li B, Barton MC, Li W*!, Li H*, Shi X*: ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature 508 (2014) 263-268