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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. 01/2013: [http://www.bcm.edu/news/item.cfm?newsID=6723 BCM News] and [http://epigenie.com/danpos-reveals-dynamic-nucleosomes headline at Epigenie] about our recent work on nucleosome dynamics
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. 06/2014Deqiang's Dnmt3a/3b double KO paper (with the Goodell Lab) is accepted to '''Cell Stem Cell '''.  
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. 12/2012Kaifu's variomics paper with Xuewen Pan lab was accepted to '''Cell Reports'''.
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. 06/2014Zheng's alternative splicing paper (with the Cooper Lab) is accepted to '''Molecular Cell '''.  
-
. 12/2012:  Liguo and HJ's CPAT RNA coding potential prediction paper was accepted to '''Nucleic Acids Research'''.
+
. 04/2014:  Liguo's ChIP-exo methodology paper (MACE) is accepted in principle in '''Nucleic Acids Research'''.  
-
. 11/2012Kaifu's nucleosome methodology paper DANPOS was accepted to '''Genome Research'''.
+
. 02/2014DQ and HJ's HSC LncRNA paper (with the Goodell Lab) is in revision in '''Cell Stem Cell'''.  
-
. 10/2012Kaifu's promoter nucleosome paper was accepted to '''Genome Research'''.
+
. 02/2014Zheng's collaborative work on alternative splicing in heart development is accepted to '''Nature Communications'''.  
-
. 09/2012A '''NIH R01 grant''' was funded. We will work with Dr. Issa at Temple Univ. to understand DNA methylation in Cancer.
+
. 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.
-
. 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.
+
. 02/2014: Welcome our new postdoc Jianzhong Su and graduate student Xueqiu Lin.
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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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. 02/2014: Deqiang's mouse HSC Aging Epigenomics paper is accepted in principle 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.
+
. 01/2014Deqiang's Methodology paper for the detection of differential DNA Methylation (MOABS) is accepted to '''Genome Biology'''.
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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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. 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'''
 +
 
 +
. 06/2013:  Zheng's TCGA RNA-seq bioinformatics paper is under review in '''Nature Biotechnology'''.
 +
 
 +
. 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.
 +
 
 +
. 12/2012: Liguo and HJ's CPAT RNA coding potential prediction paper is accepted to '''Nucleic Acids Research'''.
 +
 
 +
. 11/2012:  Kaifu's nucleosome methodology paper DANPOS is accepted to '''Genome Research'''.
 +
 
 +
. 10/2012:  Kaifu's promoter nucleosome paper is 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 is accepted to '''Cell'''. Kaifu and Wei used DANPOS to analyze the data and were listed as co-authors.
 +
 
 +
. 08/2012: Dr. Benjamin Rodriguez will join us as a '''Postdoc Associate'''. Ben has PhD in Integrated Biomedical Science from the Ohio State Univ. Welcome!
 +
 
 +
. 08/2012:  A '''Mazzone Award ''' is funded. We will work with Dr. Balk at Harvard Medical School to understand the molecular features of aggressive prostate cancer.
   
   
-
. 06/2012: Liguo's RNA-seq Quality Control paper was accepted to '''Bioinformatics'''.
+
. 06/2012: Liguo's RNA-seq Quality Control paper is 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.
+
. 06/2012:  A '''NIH R01 grant''' is funded. We will work with Dr. Goodell at BCM to understand DNA methylation in Hematopoietic Stem Cell.
-
. 04/2012:  A '''NIH R01 grant''' was funded. We will work with Dr. Dent at MD Anderson to define USP22 functions during mammalian development.
+
. 04/2012:  A '''NIH R01 grant''' is funded. We will work with Dr. Dent at MD Anderson to define USP22 functions during mammalian development.
-
. 04/2012:  Dr.Dean Tang's prostate cancer stem cell paper was accepted in '''Cell Stem Cell'''. Wei is a co-author.
+
. 04/2012:  Dr.Dean Tang's prostate cancer stem cell paper is accepted in '''Cell Stem Cell'''. Wei is a co-author.
-
. 02/2012:  Yuanxin's epigenetic paper with Katrin Chua lab at Stanford was accepted to '''Nature'''. Two years of hard work finally paid off!
+
. 02/2012:  Yuanxin's epigenetic paper with Katrin Chua lab at Stanford is accepted to '''Nature'''. Two years of hard work finally paid off!
-
. 02/2012:  Liguo Wang was offered a '''tenure-track Assistant Professor''' position at Mayo Clinic. Congratulations!
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. 02/2012:  Liguo Wang is offered a '''tenure-track Assistant Professor''' position at Mayo Clinic. Congratulations!
. 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!
. 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.  
+
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.  
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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).
+
* 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

. 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

. 06/2013: Zheng's TCGA RNA-seq bioinformatics paper is under review in Nature Biotechnology.

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

. 12/2012: Liguo and HJ's CPAT RNA coding potential prediction paper is accepted to Nucleic Acids Research.

. 11/2012: Kaifu's nucleosome methodology paper DANPOS is accepted to Genome Research.

. 10/2012: Kaifu's promoter nucleosome paper is 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 is accepted to Cell. Kaifu and Wei used DANPOS to analyze the data and were listed as co-authors.

. 08/2012: Dr. Benjamin Rodriguez will join us as a Postdoc Associate. Ben has PhD in Integrated Biomedical Science from the Ohio State Univ. Welcome!

. 08/2012: A Mazzone Award is funded. We will work with Dr. Balk at Harvard Medical School to understand the molecular features of aggressive prostate cancer.

. 06/2012: Liguo's RNA-seq Quality Control paper is accepted to Bioinformatics.

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

. 04/2012: A NIH R01 grant is funded. We will work with Dr. Dent at MD Anderson to define USP22 functions during mammalian development.

. 04/2012: Dr.Dean Tang's prostate cancer stem cell paper is accepted in Cell Stem Cell. Wei is a co-author.

. 02/2012: Yuanxin's epigenetic paper with Katrin Chua lab at Stanford is accepted to Nature. Two years of hard work finally paid off!

. 02/2012: Liguo Wang is offered a tenure-track Assistant Professor position at Mayo Clinic. Congratulations!

. 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!

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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Image:WeiLi.jpg‎


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