Li Lab

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== '''Wei Li's Computational Epigenomics Lab''' ==  
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== '''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]
[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]
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==Recent News==
==Recent News==
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. 06/16: A new paper w/ MG Lee @ MD Anderson was accepted to '''Molecular Cell'''.
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. 06/2013: Our own DNA methylation bioinformatics '''R01 was scored at 6 percentile''' in its first submission.  
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. 05/16: Zheng Xia has been offered (in principle) a '''tenure-track faculty position'''. Congratulations!
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. 06/2013: Zheng's TCGA RNA-seq bioinformatics paper was under external review in '''Nature Biotechnology'''.
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. 04/16: Jianzhong's DNMT3A/TET2 paper (w/ Goodell lab) was accepted to '''Nature Genetics'''.  
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. 06/2013Deqiang's DNA methylation Canyon paper was in revision in '''Nature Genetics'''.
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. 04/16: Wei has been selected as a recipient of the 2016 [https://www.bcm.edu/news/awards-honors-faculty-staff/2016-debakey-research-award-science '''Michael E. DeBakey, M.D., Excellence in Research Award''']
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. 03/2013: Eric joined the lab for his PhD thesis study. Welcome back, Eric!
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. 04/16: Yuanxin has been offered a '''tenure-track faculty position''' at The University of Texas Health Science Center at Houston (UTHealth). Congratulations!
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. 01/2013Zheng's 3'UTR paper was in revision in '''Nature'''. Fingers Crossed!
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. 03/2016Ben's enhancer hypomethylation paper (w/ Goodell lab) was accepted to '''Cancer Cell'''.  
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. 01/2013[http://www.bcm.edu/news/item.cfm?newsID=6723 BCM News] and  [http://epigenie.com/danpos-reveals-dynamic-nucleosomes Epigenie Headline] about our recent work on nucleosome dynamics.
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. 02/2016Yuanxin's SIRT6 paper (w/ Chua lab at Stanford) was accepted to '''Nature Structural & Molecular Biology'''
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. 12/2012: Kaifu's variomics paper with Xuewen Pan lab was accepted to '''Cell Reports'''.
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. 01/2016: Welcome our new Postdoc Associate Dr. Jie Lyu.
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. 12/2012Liguo and HJ's CPAT RNA coding potential prediction paper was accepted to '''Nucleic Acids Research'''.
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. 12/2015Yuanxin's G9a paper (w/ Shi lab at MD Anderson) was accepted to '''Nature Communications. '''
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. 11/2012:  Kaifu's nucleosome methodology paper DANPOS was accepted to '''Genome Research'''.
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. 12/2015:  Kaifu's UTX paper (w/ Lee lab at MD Anderson) was accepted to '''Nucleic Acids Research '''.  
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. 10/2012: Kaifu's promoter nucleosome paper was accepted to '''Genome Research'''.
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. 11/2015: We received a new '''NIH/NCI R01''' grant (scored at 5%ile) to study 3`UTR alternations in human cancers.
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. 09/2012: A '''NIH R01 grant''' was funded. We will work with Dr. Issa at Temple Univ. to understand DNA methylation in Cancer.
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. 09/2015: Welcome our new Research Associate (and potential Graduate Student) YanBing Cheng.
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. 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.
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. 08/2015: Kaifu's Cancer Big-data analysis paper is published in '''Nature Genetics'''. This work links broad H3K4me3 to pan-cancer tumor suppressors. See reports in Nature Editor’s [http://blogs.nature.com/freeassociation/2015/08/methylation-marks-tumor-suppressors.html Blog], [http://cancerdiscovery.aacrjournals.org/content/early/2015/09/01/2159-8290.CD-RW2015-166.abstract Cancer Discovery], [http://www.ebiotrade.com/newsf/2015-8/2015825165005119.htm ebiotrade.com] (in Chinese), [http://fromthelabs.bcm.edu/2015/10/15/novel-epigenetic-signature-for-tumor-suppressors-in-normal-cells-found/ BCM news] and [http://cancer.osu.edu/news-and-media/news/studies-suggest-new-ways-to-inhibit-oncogenes-enhance-tumor-suppressor-activity OSU news]; and an error we found in a [http://www.cell.com/cell/fulltext/S0092-8674(15)01407-5 Cell paper].
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. 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!
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. 07/2015: Wei will become a regular member of the '''NIH GCAT''' (Genomics, Computational Biology and Technology) study section.
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. 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.
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. 06/2015: Kaifu will start his '''tenure-track faculty''' position at Cornell University & Methodist Hospital. Congratulations!
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. 06/2012: Dr. Ira's Fun30 nucleosome remodeler paper was accepted to '''Nature'''. Kaifu is a co-author.
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. 03/2015: Kaifu's MeCP2 mCH binding paper (w/ Zoghbi lab) is accepted to '''PNAS'''.
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+
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. 06/2012: Liguo's RNA-seq Quality Control paper was accepted to '''Bioinformatics'''.
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. 06/2012: A '''NIH R01 grant''' was funded. We will work with Dr. Goodell at BCM to understand DNA methylation in Hematopoietic Stem Cell.
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. 3/2015: We received a NEW '''CPRIT''' grant.
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. 04/2012A '''NIH R01 grant''' was funded. We will work with Dr. Dent at MD Anderson to define USP22 functions during mammalian development.
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. 01/2015Deqiang, HJ and Ben's HSC novel noncoding RNA paper is accepted to '''Cell Stem Cell''' -- the 100th paper we published.
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. 04/2012Dr.Dean Tang's prostate cancer stem cell paper was accepted in '''Cell Stem Cell'''. Wei is a co-author.
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. 12/2014Zheng Xia is awarded a '''Keck fellowship''' in Computational Cancer Biology.
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. 02/2012:  Yuanxin's epigenetic paper with Katrin Chua lab at Stanford was accepted to '''Nature'''. Two years of hard work finally paid off!
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. 11/2014:  Zheng's DaPars 3'UTR Pan Cancer analysis paper is published in '''Nature Communications'''.
 +
 
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. 09/2014:  Liguo's ChIP-exo methodology paper (MACE) is accepted to '''Nucleic Acids Research'''.  MACE is recommended by Active Motif as the software solution for the company's new [https://www.activemotif.com/catalog/1050/chip-exo ChIP-exo kit and service].
 +
 
 +
. 09/2014: Deqiang will start his '''tenure-track assistant professor''' position. Job well done. 
 +
 
 +
. 09/2014:  Zheng's prostate cancer RNA-seq paper with Dr. Balk at Harvard is accepted to '''Molecular Cancer Research '''.
 +
 
 +
. 09/2014:  Yuanxin's work on H3K79 Methylation with Dr. Shi is accepted to '''Cell'''.
 +
 
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. 08/2014:  '''Three Collaborative CPRIT grants''' are funded: DNA methylation with Goodell lab, 3'UTR with Wagner lab and ZM11 with Shi lab.
 +
 
 +
. 06/2014:  Deqiang's Dnmt3a/3b double KO paper (w/ Goodell Lab) is accepted to '''Cell Stem Cell '''.
 +
 
 +
. 06/2014:  Zheng's alternative splicing paper (w/ Cooper Lab) is accepted to '''Molecular Cell '''.
 +
 
 +
. 02/2014:  Zheng's brain tumor 3'UTR regulator paper is accepted to '''Nature'''. This paper was initially rejected after review twice. We appealed twice with success and finally made it in the 3rd submission.
 +
 
 +
. 02/2014:  Welcome our new postdoc Jianzhong Su and graduate student Xueqiu Lin.
 +
 
 +
. 02/2014:  Deqiang's mouse HSC Aging Epigenomics paper is accepted in principle to '''Cell Stem Cell'''.
 +
 
 +
. 01/2014:  Deqiang's Methodology paper for the detection of differential DNA Methylation (MOABS) is accepted to '''Genome Biology'''.
 +
 
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. 01/2014:  Yuanxin and Zheng's ZM11 paper with Xiaobing Shi lab in MD Anderson is accepted to '''Nature'''. This work links transcription elongation to tumor suppression.
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. 02/2012:  Liguo Wang was offered a '''tenure-track Assistant Professor''' position at Mayo Clinic. Congratulations!
 
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. 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!
 
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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.  
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Our lab is focused on the design and application of bioinformatics algorithms to elucidate global epigenetic mechanisms and transcription dynamics in normal development and diseases such as cancer. Since establishing the lab in early 2008, we have
 +
* '''Published''' >86 peer-reviewed papers through solid methodology development and extensive collaboration research, including >34 in '''Nature, Science and Cell''' series.
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 +
* '''Been well-funded''' by NIH and Texas CPRIT with total external funding >$1.3 million per year. Dr Li is the PI on the following 4 major grants: NIH R01HG007538 (2013-2018) and R01CA193466 (2015-2020); CPRIT RP110471-C3 (2011-2016) and RP150292 (2015-2018).
 +
 +
* '''Mentored''' the first 3 postdoc trainees to start their tenure track faculty positions in prestigious research institutions in the US.
 +
 
 +
We have developed a number of widely used algorithms to analyze next generation sequencing data from ChIP-seq (MACS, MACE), DNA methylation Bisulfite-seq (BSMAP/RRBSMAP, BSeQC, MOABS), nucleosome positioning MNase-seq (DANPOS), and RNA-seq (CPAT, RSeQC, DaPars). These algorithms have been broadly adopted by thousands of academic users. For example, the MACS algorithm has gathered >1900 citations since 2008.
 +
 
 +
In collaboration with experimental biologists, we used these algorithms to gain novel biological insights from various biological processes and disease models.
 +
 
 +
* '''Chromatin Factors''': ER in breast cancer, AR in prostate cancer, FoxA1 pioneer factor, Atoh1 in neuron development, NSD2 in oncogenic programming, SIRT7 in cancer transformation, ZM11 in transcription elongation, and p53 in ES differentiation..
 +
 
 +
* '''DNA Methylation''': DNA methylation Canyon, Epigenetic changes in HSC aging, Dnmt3a in HSC differentiation and cancer transformation.  
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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).
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* '''Nucleosome Organization''': Fragile nucleosome in stress-response, Promoter nucleosome with Tup1, Nucleosome dynamics in ES differentiation, and Global nucleosome loss in yeast aging.
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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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* '''Transcriptome''': chimeric RNA in prostate cancer, Long non-coding RNA in HSC, 3’UTR deletion in cancer and its master regulator CFIm25. .
   
   

Current revision

Home        People        Publications        Collaborations        Software        Positions        Contact       


Recent News

. 06/16: A new paper w/ MG Lee @ MD Anderson was accepted to Molecular Cell.

. 05/16: Zheng Xia has been offered (in principle) a tenure-track faculty position. Congratulations!

. 04/16: Jianzhong's DNMT3A/TET2 paper (w/ Goodell lab) was accepted to Nature Genetics.

. 04/16: Wei has been selected as a recipient of the 2016 Michael E. DeBakey, M.D., Excellence in Research Award

. 04/16: Yuanxin has been offered a tenure-track faculty position at The University of Texas Health Science Center at Houston (UTHealth). Congratulations!

. 03/2016: Ben's enhancer hypomethylation paper (w/ Goodell lab) was accepted to Cancer Cell.

. 02/2016: Yuanxin's SIRT6 paper (w/ Chua lab at Stanford) was accepted to Nature Structural & Molecular Biology

. 01/2016: Welcome our new Postdoc Associate Dr. Jie Lyu.

. 12/2015: Yuanxin's G9a paper (w/ Shi lab at MD Anderson) was accepted to Nature Communications.

. 12/2015: Kaifu's UTX paper (w/ Lee lab at MD Anderson) was accepted to Nucleic Acids Research .

. 11/2015: We received a new NIH/NCI R01 grant (scored at 5%ile) to study 3`UTR alternations in human cancers.

. 09/2015: Welcome our new Research Associate (and potential Graduate Student) YanBing Cheng.

. 08/2015: Kaifu's Cancer Big-data analysis paper is published in Nature Genetics. This work links broad H3K4me3 to pan-cancer tumor suppressors. See reports in Nature Editor’s Blog, Cancer Discovery, ebiotrade.com (in Chinese), BCM news and OSU news; and an error we found in a Cell paper.

. 07/2015: Wei will become a regular member of the NIH GCAT (Genomics, Computational Biology and Technology) study section.

. 06/2015: Kaifu will start his tenure-track faculty position at Cornell University & Methodist Hospital. Congratulations!

. 03/2015: Kaifu's MeCP2 mCH binding paper (w/ Zoghbi lab) is accepted to PNAS.

. 3/2015: We received a NEW CPRIT grant.

. 01/2015: Deqiang, HJ and Ben's HSC novel noncoding RNA paper is accepted to Cell Stem Cell -- the 100th paper we published.

. 12/2014: Zheng Xia is awarded a Keck fellowship in Computational Cancer Biology.

. 11/2014: Zheng's DaPars 3'UTR Pan Cancer analysis paper is published in Nature Communications.

. 09/2014: Liguo's ChIP-exo methodology paper (MACE) is accepted to Nucleic Acids Research. MACE is recommended by Active Motif as the software solution for the company's new ChIP-exo kit and service.

. 09/2014: Deqiang will start his tenure-track assistant professor position. Job well done.

. 09/2014: Zheng's prostate cancer RNA-seq paper with Dr. Balk at Harvard is accepted to Molecular Cancer Research .

. 09/2014: Yuanxin's work on H3K79 Methylation with Dr. Shi is accepted to Cell.

. 08/2014: Three Collaborative CPRIT grants are funded: DNA methylation with Goodell lab, 3'UTR with Wagner lab and ZM11 with Shi lab.

. 06/2014: Deqiang's Dnmt3a/3b double KO paper (w/ Goodell Lab) is accepted to Cell Stem Cell .

. 06/2014: Zheng's alternative splicing paper (w/ Cooper Lab) is accepted to Molecular Cell .

. 02/2014: Zheng's brain tumor 3'UTR regulator paper is accepted to Nature. This paper was initially rejected after review twice. We appealed twice with success and finally made it in the 3rd submission.

. 02/2014: Welcome our new postdoc Jianzhong Su and graduate student Xueqiu Lin.

. 02/2014: Deqiang's mouse HSC Aging Epigenomics paper is accepted in principle to Cell Stem Cell.

. 01/2014: Deqiang's Methodology paper for the detection of differential DNA Methylation (MOABS) is accepted to Genome Biology.

. 01/2014: Yuanxin and Zheng's ZM11 paper with Xiaobing Shi lab in MD Anderson is accepted to Nature. This work links transcription elongation to tumor suppression.


Image:Banner.jpg‎‎

News Archive




Our lab is focused on the design and application of bioinformatics algorithms to elucidate global epigenetic mechanisms and transcription dynamics in normal development and diseases such as cancer. Since establishing the lab in early 2008, we have

  • Published >86 peer-reviewed papers through solid methodology development and extensive collaboration research, including >34 in Nature, Science and Cell series.
  • Been well-funded by NIH and Texas CPRIT with total external funding >$1.3 million per year. Dr Li is the PI on the following 4 major grants: NIH R01HG007538 (2013-2018) and R01CA193466 (2015-2020); CPRIT RP110471-C3 (2011-2016) and RP150292 (2015-2018).
  • Mentored the first 3 postdoc trainees to start their tenure track faculty positions in prestigious research institutions in the US.

We have developed a number of widely used algorithms to analyze next generation sequencing data from ChIP-seq (MACS, MACE), DNA methylation Bisulfite-seq (BSMAP/RRBSMAP, BSeQC, MOABS), nucleosome positioning MNase-seq (DANPOS), and RNA-seq (CPAT, RSeQC, DaPars). These algorithms have been broadly adopted by thousands of academic users. For example, the MACS algorithm has gathered >1900 citations since 2008.

In collaboration with experimental biologists, we used these algorithms to gain novel biological insights from various biological processes and disease models.

  • Chromatin Factors: ER in breast cancer, AR in prostate cancer, FoxA1 pioneer factor, Atoh1 in neuron development, NSD2 in oncogenic programming, SIRT7 in cancer transformation, ZM11 in transcription elongation, and p53 in ES differentiation..
  • DNA Methylation: DNA methylation Canyon, Epigenetic changes in HSC aging, Dnmt3a in HSC differentiation and cancer transformation.
  • Nucleosome Organization: Fragile nucleosome in stress-response, Promoter nucleosome with Tup1, Nucleosome dynamics in ES differentiation, and Global nucleosome loss in yeast aging.
  • Transcriptome: chimeric RNA in prostate cancer, Long non-coding RNA in HSC, 3’UTR deletion in cancer and its master regulator CFIm25. .


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Image:WeiLi.jpg‎


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