Li Lab: Difference between revisions

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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==
. 12/2012: Liguo and HJ's CPAT RNA coding potential prediction paper was in accepted to '''Nucleic Acids Research'''.
. 03/2021: Yipeng's single cell APA paper was accepted to '''Genome Research'''
 
. 11/2012:  Kaifu's nucleosome methodology paper DANPOS was accepted to '''Genome Research'''.
 
. 10/2012:  Kaifu's promoter nucleosome paper was accepted to '''Genome Research'''.
 
. 09/2012:  A '''NIH R01 grant''' was funded. We will work with Dr. Issa at Temple Univ. to understand DNA methylation in Cancer.


. 08/2012: A mouse ES nucleosome paper from Kaestner lab at Upenn was accepted to '''Cell'''. Kaifu and Wei used DANPOS to analyze the data and were listed as co-authors.
. 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'''


. 08/2011: Dr. Benjamin Rodriguez will join us as a '''Postdoc Associate'''. Ben has PhD in Integrated Biomedical Science from the Ohio State Univ. Eric B. Rutledge, a BCM MD/PhD student,  joined us for his term 2 '''rotation'''.  Welcome!
. 09/2020: Jie's DORGE cancer driver gene paper was accepted to '''Science Advances'''


. 08/2012:  A '''Mazzone Award ''' was funded. We will work with Dr. Balk at Harvard Medical School to understand the molecular features of aggressive prostate cancer.
. 08/2020: Jianfeng's CHALM methylation paper was accepted to '''Nature Communications'''


. 06/2012: Dr. Ira's Fun30 nucleosome remodeler paper was accepted to '''Nature'''. Kaifu is a co-author.
. 08/2020: Cui Ya's [https://wlcb.oit.uci.edu/NG-Circos NG-Circos] paper was accepted to '''NAR Genomics and Bioinformatics'''
. 06/2012: Liguo's RNA-seq Quality Control paper was accepted to '''Bioinformatics'''.


. 06/2012: A '''NIH R01 grant''' was funded. We will work with Dr. Goodell at BCM to understand DNA methylation in Hematopoietic Stem 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]


. 04/2012:  A '''NIH R01 grant''' was funded. We will work with Dr. Dent at MD Anderson to define USP22 functions during mammalian development.
. 01/2020: Lei's paper w/ Ryan Potts was accepted to '''Molecular Cell'''


. 04/2012: Dr.Dean Tang's prostate cancer stem cell paper was accepted in '''Cell Stem Cell'''. Wei is a co-author.
. 10/2019: Collaborative work with David Allis and Wen Hong was accepted to '''Nature''';


. 02/2012: Yuanxin's epigenetic paper with Katrin Chua lab at Stanford was accepted to '''Nature'''. Two years of hard work finally paid off!
. 10/2019: Collaborative work with Suming Huang was accepted to '''Cancer Cell''';


. 02/2012: Liguo Wang was offered a '''tenure-track Assistant Professor''' position at Mayo Clinic. Congratulations!
. 9/2019: Collaborative work with Costa-Mattioli's group was accepted to '''Science'''; 


. 02/2012: Justin Park will join us as a Postdoc Associate. Justin will graduate in May with a PhD in Computer Science from Rice University. Welcome!
. 05/2019: Collaborative work with Paolo Sassone-Corsi at UCI was published in '''Cell'''


. 11/2011: Yuanxin's RRBSMAP paper was accepted to '''Bioinformatics'''.  
. 02/2019: Our new 5-year '''NCI R01 grant''' regarding DNA methylation canyon was funded.


. 09/2011: Wei Li was promoted to tenured '''Associate Professor''' at BCM. Cheers!
. 07/2018: Jianzhong's DNA methylation canyon paper was accepted to '''Genome Biology'''.  


. 09/2011: Deqiang's DNA methylation paper with Peggy Goodell lab was accepted to '''Nature Genetics'''.  
. 06/2018: Jiejun’s paper was accepted to '''Nature Cell Biology'''.  


. 08/2011: Kaifu's NSD2 epigenetic paper with Or Gozani lab at Stanford was accepted to '''Molecular Cell'''.
. 06/2018: Xueqiu's DNMT3A binding paper was accepted to '''Genome Biology'''


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


. 07/2011: Liguo's FoxA1 cistrome paper was accepted to '''Cancer 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!


. 07/2011: See our '''[http://www.genomeweb.com/node/973004 Genomic Regulation Technical Guide]''' on Genome Technology magazine


. 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!


. 05/2011:  Dr.Bert O'Malley's coregulator network paper was published in '''Cell'''. Wei is a co-author on the paper.


. 04/2011:  Liguo's Prostate Cancer RNA-seq paper was officially accepted to  '''PNAS'''.


. 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.
. 01/2011:  Yuanxin's fragile nucleosome paper was accepted to  '''Genome Research'''.
. 01/2011:  Yuanxin and Liguo's  Atoh1 targetome paper was accepted to  '''PNAS'''.


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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 MAT ('''PNAS''' 2006) for analyzing ChIP-chip experiments on genome tiling arrays, MACS ('''Genome Biology''' 2008) for model based analysis of ChIP-seq, BSMAP/RRBSMAP ('''BMC Bioinformatics''' 2009; '''Bioinformatics''' 2012) for DNA methylation analysis using Bisulfite-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 > 50 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 dynamics (Mnase-seq); 4) Alternative splicing (RNA-seq).


We have extensive experience in collaborative research including androgen and estrogen receptors in prostate and breast cancers ('''Cell''' 2005; '''Nature Genetics''' 2006; '''Molecular Cell''' 2007; '''Cell''' 2009), epigenetic regulation by histone modifications ('''Cell''' 2008; '''PNAS''' 2011; '''Cancer Res.''' 2011; '''Molecular Cell''' 2011; '''Nature''' 2012), nucleosome positioning ('''Genome Res.''' 2011), DNA methylation ('''Nature Genetics''' 2012) and novel chimerical RNAs in prostate cancer ('''PNAS''' 2011).


   
   
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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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