Li Lab

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== '''Wei Li's Computational Epigenomics Lab''' ==  
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== '''Computational Epigenomics and Transcriptomics Lab (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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. 12/2012Liguo and HJ's CPAT RNA coding potential prediction paper was in accepted to '''Nucleic Acids Research'''.
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. 09/2013Zheng's prostate cancer RNA-seq paper with Dr. Balk at Harvard is accepted in '''Molecular Cancer Research '''.
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. 11/2012Kaifu's nucleosome methodology paper DANPOS was accepted to '''Genome Research'''.
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. 08/2013Zheng's DaPars 3'UTR Pan Cancer analysis paper is accepted in principle in '''Nature Communications'''.
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. 10/2012Kaifu's promoter nucleosome paper was accepted to '''Genome Research'''.
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. 08/2014Liguo's RSeQC paper is ranked No. 15 in the [http://bioinformatics.oxfordjournals.org/reports/most-cited Most-Cited Articles] in Bioinformatics as of August 1, 2014.
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. 09/2012A '''NIH R01 grant''' was funded. We will work with Dr. Issa at Temple Univ. to understand DNA methylation in Cancer.
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. 08/2014:  '''Three Collaboration CPRIT grants''' are funded: DNA methylation with Goodell lab, 3'UTR with Wagner lab and ZM11 with Shi lab.
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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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. 08/2014: Kaifu's "super promoter" paper is under review in '''Nature Genetics'''.  
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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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. 06/2014: Deqiang's Dnmt3a/3b double KO paper (with the Goodell Lab) is accepted to '''Cell Stem Cell '''.  
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. 08/2012A '''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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. 06/2014Zheng's alternative splicing paper (with the Cooper Lab) is accepted to '''Molecular Cell '''.  
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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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. 04/2014:  Liguo's ChIP-exo methodology paper (MACE) is accepted in principle in '''Nucleic Acids Research'''.  
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. 06/2012: Liguo's RNA-seq Quality Control paper was accepted to '''Bioinformatics'''.
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. 06/2012A '''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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. 02/2014DQ and HJ's HSC LncRNA paper (with the Goodell Lab) is in revision in '''Cell Stem Cell'''.  
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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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. 02/2014Zheng's collaborative work on alternative splicing in heart development is accepted to '''Nature Communications'''.  
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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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. 02/2014Zheng'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.
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. 02/2012Yuanxin'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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. 02/2014Welcome our new postdoc Jianzhong Su and graduate student Xueqiu Lin.
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. 02/2012Liguo Wang was offered a '''tenure-track Assistant Professor''' position at Mayo Clinic. Congratulations!
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. 02/2014Deqiang's mouse HSC Aging Epigenomics paper is accepted in principle to '''Cell Stem Cell'''.
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. 02/2012Justin 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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. 01/2014Deqiang's Methodology paper for the detection of differential DNA Methylation (MOABS) is accepted to '''Genome Biology'''.
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. 11/2011Yuanxin's RRBSMAP paper was accepted to '''Bioinformatics'''.  
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. 01/2014Our collaborative work on Breast Cancer Epigenetics is accepted to '''Science Translational Medicine'''.
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. 09/2011Wei Li was promoted to tenured '''Associate Professor''' at BCM. Cheers!
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. 01/2014Yuanxin 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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. 09/2011: Deqiang's DNA methylation paper with Peggy Goodell lab was accepted to '''Nature Genetics'''.
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. 12/2013: Kaifu's aging nucleosome paper is accepted to ''' Genes & Development'''  
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. 08/2011: Kaifu's NSD2 epigenetic paper with Or Gozani lab at Stanford was accepted to '''Molecular Cell'''.
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. 12/2013: We received a 5-year NIH/NHGRI '''R01''' grant (scored at 6 percentile in its first submission) to study DNA Methylation
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. 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.
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. 11/2013: Wei will serve on the Editorial Board of '''Molecular Endocrinology'''
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. 07/2011Liguo's FoxA1 cistrome paper was accepted to '''Cancer Research'''.
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. 09/2013Deqiang's DNA methylation Canyon paper is accepted to '''Nature Genetics'''.
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. 07/2011: See our '''[http://www.genomeweb.com/node/973004 Genomic Regulation Technical Guide]''' on Genome Technology magazine
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. 09/2013: Xueqiu's bisulfite sequencing quality control paper (BSeQC) is accepted to '''Bioinformatics'''.
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. 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!
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. 08/2013: Kadir's p53 paper is accepted to '''Nucleic Acids Research'''
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. 05/2011Dr.Bert O'Malley's coregulator network paper was published in '''Cell'''. Wei is a co-author on the paper.
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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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. 04/2011:  Liguo's Prostate Cancer RNA-seq paper was officially accepted to  '''PNAS'''.
 
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. 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.
 
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. 01/2011:  Yuanxin's fragile nucleosome paper was accepted to  '''Genome Research'''.
 
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. 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.  
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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 more than 50 peer-reviewed papers in high profile journals, such as Nature, Cell, Nature Genetics, Molecular Cell, Genome Research, Genome Biology, Genes and Development, Nucleic Acids Research, Cancer Research, PNAS and Bioinformatics.
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We developed a number of widely used algorithms to analyze next generation sequencing data from Chromatin Factor ChIP-seq (MACS, MACE, DyChIPS), 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 >1000 citations since 2008.
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In collaboration with experimental biologists, we used these algorithms to gain novel biological insights from various biological processes and disease models.
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* 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.
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* DNA Methylation: Dnmt3a in HSC differentiation, DNA methylation Canyon, HSC aging.  
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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 gene poising, promoter nucleosome with Tup1, nucleosome dynamics in ES differentiation, global nucleosome loss in 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 their master regulators.
   
   

Current revision

Home        People        Publications        Collaborations        Software        Positions        Contact       


Recent News

. 09/2013: Zheng's prostate cancer RNA-seq paper with Dr. Balk at Harvard is accepted in Molecular Cancer Research .

. 08/2013: Zheng's DaPars 3'UTR Pan Cancer analysis paper is accepted in principle in Nature Communications.

. 08/2014: Liguo's RSeQC paper is ranked No. 15 in the Most-Cited Articles in Bioinformatics as of August 1, 2014.

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

. 08/2014: Kaifu's "super promoter" paper is under review in Nature Genetics.

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

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

. 04/2014: Liguo's ChIP-exo methodology paper (MACE) is accepted in principle in Nucleic Acids Research.

. 02/2014: DQ and HJ's HSC LncRNA paper (with the Goodell Lab) is in revision in Cell Stem Cell.

. 02/2014: Zheng's collaborative work on alternative splicing in heart development is accepted to Nature Communications.

. 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: Our collaborative work on Breast Cancer Epigenetics is accepted to Science Translational Medicine.

. 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.

. 12/2013: Kaifu's aging nucleosome paper is accepted to Genes & Development

. 12/2013: We received a 5-year NIH/NHGRI R01 grant (scored at 6 percentile in its first submission) to study DNA Methylation

. 11/2013: Wei will serve on the Editorial Board of Molecular Endocrinology

. 09/2013: Deqiang's DNA methylation Canyon paper is accepted to Nature Genetics.

. 09/2013: Xueqiu's bisulfite sequencing quality control paper (BSeQC) is accepted to Bioinformatics.

. 08/2013: Kadir's p53 paper is accepted to Nucleic Acids Research

. 01/2013: BCM News and Epigenie Headline about our recent work on nucleosome dynamics.


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 more than 50 peer-reviewed papers in high profile journals, such as Nature, Cell, Nature Genetics, Molecular Cell, Genome Research, Genome Biology, Genes and Development, Nucleic Acids Research, Cancer Research, PNAS and Bioinformatics.

We developed a number of widely used algorithms to analyze next generation sequencing data from Chromatin Factor ChIP-seq (MACS, MACE, DyChIPS), 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 >1000 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: Dnmt3a in HSC differentiation, DNA methylation Canyon, HSC aging.
  • Nucleosome Organization: fragile nucleosome in gene poising, promoter nucleosome with Tup1, nucleosome dynamics in ES differentiation, global nucleosome loss in aging.
  • Transcriptome: chimeric RNA in prostate cancer, Long non-coding RNA in HSC, 3’UTR deletion in cancer and their master regulators.


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