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== '''Please visit our new lab website [https://sites.uci.edu/weililab https://sites.uci.edu/weililab] ''' ==


== '''Wei Li's Computational Epigenomics Lab''' ==  
== '''Computational Cancer Epigenomics and Transcriptomics (PI: Wei Li)''' ==  
 
[http://www.bcm.edu/cancercenter/ Dan L. Duncan Cancer Center], [http://www.bcm.edu/mcb/index.html Department of Molecular and Cellular Biology], [http://www.bcm.edu/ Baylor College of Medicine]


Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine
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==Recent News==
==Recent News==
. 02/2012: Yuanxin's epigenetic paper w/ Katrin Chua lab at Stanford was accepted to '''Nature'''. Two years of hard work finally paid off!
. 03/2021: Yipeng's single cell APA paper was accepted to '''Genome Research'''


. 02/2012: Liguo Wang was offered a '''tenure-track Assistant Professor''' position at Mayo Clinic. Congratulations!
. 02/2021: Lei's 3'aQTL paper entitled "An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability" was accepted to '''Nature Genetics'''


. 11/2011: Yuanxin's RRBSMAP paper was accepted to '''Bioinformatics'''.
. 09/2020: Jie's DORGE cancer driver gene paper was accepted to '''Science Advances'''


. 09/2011: Wei Li was promoted to tenured '''Associate Professor''' at BCM. Cheers!
. 08/2020: Jianfeng's CHALM methylation paper was accepted to '''Nature Communications'''


. 09/2011: Deqiang's DNA methylation paper with Peggy Goodell lab was accepted to '''Nature Genetics'''.
. 08/2020: Cui Ya's [https://wlcb.oit.uci.edu/NG-Circos NG-Circos] paper was accepted to '''NAR Genomics and Bioinformatics'''


. 08/2011: Kaifu's NSD2 epigenetic paper with Or Gozani lab at Stanford was accepted to '''Molecular Cell'''.
. 01/2020: Our lab has moved to [https://start.emailopen.com/public1/BrView.aspx?idc=197231&cc1=j7WFn6r3B8J&s5=47494aca951f49d1b1531a572c5754f8WVUa880hkbx84Pd.343068638%40emailopen.com University of California Irvine]


. 08/2011:  A '''NIH R01 grant''' was funded. We will work with Dr. Wang at the Ohio State University to understand the role of histone methylations in prostate cancer.
. 01/2020: Lei's paper w/ Ryan Potts was accepted to '''Molecular Cell'''


. 07/2011: Liguo's FoxA1 cistrome paper was accepted to '''Cancer Research'''.
. 10/2019: Collaborative work with David Allis and Wen Hong was accepted to '''Nature''';


. 07/2011: See our '''[http://www.genomeweb.com/node/973004 Genomic Regulation Technical Guide]''' on Genome Technology magazine
. 10/2019: Collaborative work with Suming Huang was accepted to '''Cancer Cell''';


. 07/2011: Dr. Zheng Xia will join us as a postdoc fellow. Zheng has PhD in Control Theory and Engineering Computer Science from Zhejiang University in China. Welcome!
. 9/2019: Collaborative work with Costa-Mattioli's group was accepted to '''Science'''; 


. 05/2011: Dr.Bert O'Malley's coregulator network paper was published in '''Cell'''. Wei is a co-author on the paper.
. 05/2019: Collaborative work with Paolo Sassone-Corsi at UCI was published in '''Cell'''


. 04/2011: Yuanxin's epigenomic paper was invited for revision in '''Nature'''.
. 02/2019: Our new 5-year '''NCI R01 grant''' regarding DNA methylation canyon was funded.


. 04/2011: Liguo's Prostate Cancer RNA-seq paper was officially accepted to '''PNAS'''.
. 07/2018: Jianzhong's DNA methylation canyon paper was accepted to '''Genome Biology'''.  


. 03/2011: Our Texas '''CPRIT Multi-Investigator grant''' was funded with a total direct cost of  ~$10M for 5 years. This project will bring together a "dream team" in cancer epigenetic research.  We will direct the bioinformatics component for LONESTAR.  
. 06/2018: Jiejun’s paper was accepted to '''Nature Cell Biology'''.  


. 01/2011: Yuanxin's fragile nucleosome paper was accepted to '''Genome Research'''.
. 06/2018: Xueqiu's DNMT3A binding paper was accepted to '''Genome Biology'''


. 01/2011: Yuanxin and Liguo's Atoh1 targetome paper was accepted to '''PNAS'''.
. 03/2018: HJ Park's papers were accepted to '''PLOS Computational Biology''' and '''Cell Reports''', respectively.  


. 12/2010: Liguo's fly RNA-seq paper was published in  '''Genome Research'''.
. 01/2018: HJ Park's 3'UTR vs ceRNA paper was finally accepted to '''Nature Genetics''' after 1.5 years and 3 rounds of revisions/appeals. A good start to the new year!


. 10/2010:  A Texas '''CPRIT grant''' was funded. We will work with Dr. Goodell at BCM to understand DNA Methylgransferase 3B in normal and malignant hematopoiesis.


. 08/2010:  Our '''Pilot Project''' was funded by a NIH Stem Cell P01 Grant.


. 07/2010:  The DNA methylation platform comparision paper was accepted to '''Nature Biotechnology'''.






[[Image:Banner.jpg‎‎]]
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[http://openwetware.org/wiki/Li_Lab:news News Archive]
[http://openwetware.org/wiki/Li_Lab:news News Archive]
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Our lab is focused on the design and application of bioinformatics algorithms to elucidate global regulatory mechanism by integrating data from ChIP-seq, DNA methylation, Nucleosome positioning, and RNA-seq.  We are also working with bench and clinical collaborators to understand epigenetic gene regulation and transcription dynamics in various biological processes and disease models.  
Our lab 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 in developing widely used open-source bioinformatics software, such as MACS (>7,000 citations) for ChIP-seq and RSeqQC (>800 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 areas of expertise include 1) DNA methylation using Bisulfite-seq; 2) Epigenetic regulation using ChIP-seq; 3) Alternative Polyadenylation (APA); 4) Non-coding RNA; 5) Nucleosome organization using MNase-seq. Since establishing our own bioinformatics lab in early 2008, we have (as of Febuary 2020)
* '''Published''' 143 peer-reviewed papers through solid methodology development and extensive collaboration research, including 20 senior-author papers in '''Nature''' and '''Cell''' series.
 
* '''Been well-funded''' with total external funding >$1.0 million per year, including 4 PI grants from NIH: NIH R01HG007538 (2013-2020), R01CA193466 (2015-2020), R01CA228140 (2019-2024) and U54CA217297 (2017-2022).
* '''Mentored''' the first 7 postdoc trainees to start their tenure track faculty positions in prestigious research institutions in the US (6) and China (1).


We have developed a number of widely used algorithms to detect and annotate genome-wide cis-regulatory regions, including a Hidden Markov Model ('''Bioinformatics''' 2005) and MAT ('''PNAS''' 2006) for analyzing ChIP-chip experiments on genome tiling arrays, CEAS ('''NAR''' 2006) for cis-regulatory element annotation, xMAN ('''BMC Genomics''' 2008) for microarray probe mapping, MACS ('''Genome Biology''' 2008) for model based analysis of ChIP-seq, BSMAP ('''BMC Bioinformatics''' 2009) for DNA methylation analysis using Bisulfite-seq, MMES ('''PLoS ONE''' 2010) for alternative splicing using RNA-seq, and fragile nucleosomes ('''Genome Re'''s 2011) using MNase-seq. These algorithms have gathered thousands of academic users worldwide and hundreds of citations, including > 30 papers in Cell and Nature series. We are currently working on bioinformatics development for 1) Transcription factor binding and histone modifications (ChIP-seq); 2) DNA methylation at single nucleotide resolution (Bisulfite-seq); 3) Nucleosome remodeling (Mnase-seq); 4) Alternative splicing (RNA-seq).


We have extensive experience in collaborative research, such as Estrogen Receptor regulation in breast cancer ('''Cell''' 2005; '''Nature Genetics''' 2006), Androgen Receptor regulation in prostate cancer ('''Molecular Cell''' 2007; '''Cell''' 2009), chromatin factor FoxA1 in epigenetic regulation ('''Cell''' 2008), Atoh1 in neuron development ('''PNAS''' 2011), fly transcriptome using RNA-seq ('''Genome Res''' 2011), and chimerical RNA biomarkers in prostate cancer ('''PNAS''' 2011). My laboratory also plays an important role in the BCM Epigenomics Data Analysis and Coordination Center for a five-year NIH Roadmap Epigenomics Program.


   
   
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Latest revision as of 22:26, 7 May 2021

Home        People        Publications        Collaborations        Software        Positions        Contact       


Please visit our new lab website https://sites.uci.edu/weililab

Computational Cancer Epigenomics and Transcriptomics (PI: Wei Li)

Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine

Recent News

. 03/2021: Yipeng's single cell APA paper was accepted to Genome Research

. 02/2021: Lei's 3'aQTL paper entitled "An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability" was accepted to Nature Genetics

. 09/2020: Jie's DORGE cancer driver gene paper was accepted to Science Advances

. 08/2020: Jianfeng's CHALM methylation paper was accepted to Nature Communications

. 08/2020: Cui Ya's NG-Circos paper was accepted to NAR Genomics and Bioinformatics

. 01/2020: Our lab has moved to University of California Irvine

. 01/2020: Lei's paper w/ Ryan Potts was accepted to Molecular Cell

. 10/2019: Collaborative work with David Allis and Wen Hong was accepted to Nature;

. 10/2019: Collaborative work with Suming Huang was accepted to Cancer Cell;

. 9/2019: Collaborative work with Costa-Mattioli's group was accepted to Science;

. 05/2019: Collaborative work with Paolo Sassone-Corsi at UCI was published in Cell

. 02/2019: Our new 5-year NCI R01 grant regarding DNA methylation canyon was funded.

. 07/2018: Jianzhong's DNA methylation canyon paper was accepted to Genome Biology.

. 06/2018: Jiejun’s paper was accepted to Nature Cell Biology.

. 06/2018: Xueqiu's DNMT3A binding paper was accepted to Genome Biology

. 03/2018: HJ Park's papers were accepted to PLOS Computational Biology and Cell Reports, respectively.

. 01/2018: HJ Park's 3'UTR vs ceRNA paper was finally accepted to Nature Genetics after 1.5 years and 3 rounds of revisions/appeals. A good start to the new year!




News Archive




Our lab 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 in developing widely used open-source bioinformatics software, such as MACS (>7,000 citations) for ChIP-seq and RSeqQC (>800 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 areas of expertise include 1) DNA methylation using Bisulfite-seq; 2) Epigenetic regulation using ChIP-seq; 3) Alternative Polyadenylation (APA); 4) Non-coding RNA; 5) Nucleosome organization using MNase-seq. Since establishing our own bioinformatics lab in early 2008, we have (as of Febuary 2020)

  • Published 143 peer-reviewed papers through solid methodology development and extensive collaboration research, including 20 senior-author papers in Nature and Cell series.
  • Been well-funded with total external funding >$1.0 million per year, including 4 PI grants from NIH: NIH R01HG007538 (2013-2020), R01CA193466 (2015-2020), R01CA228140 (2019-2024) and U54CA217297 (2017-2022).
  • Mentored the first 7 postdoc trainees to start their tenure track faculty positions in prestigious research institutions in the US (6) and China (1).



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