Li Lab

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== '''Wei Li's Computational Epigenomics Lab''' ==  
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== '''Wei Li Computational Epigenomics and Transcriptomics Lab''' ==  
[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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. 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.
+
. 09/2013: Deqiang's DNA methylation Canyon paper 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!
+
. 09/2013: Xueqiu's bisulfite sequencing quality control paper (BSeQC) accepted to '''Bioinformatics'''.
-
. 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.
+
. 08/2013Yuanxin's transcription elongation paper in revision in '''Nature'''.
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. 06/2012: Dr. Ira's Fun30 nucleosome remodeler paper was accepted to '''Nature'''. Kaifu is a co-author.
+
. 08/2013Kadir's p53 paper accepted to '''Nucleic Acids Research'''
-
   
+
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. 06/2012: Liguo's RNA-seq Quality Control paper was accepted to '''Bioinformatics'''.
+
-
. 06/2012A '''NIH R01 grant''' was funded. We will work with Dr. Goodell at BCM to understand DNA methylation in Hematopoietic Stem Cell.
+
. 07/2013Deqiang's aging epigenomics paper was under external review in '''Cell'''.
-
. 04/2012A '''NIH R01 grant''' was funded. We will work with Dr. Dent at MD Anderson to define USP22 functions during mammalian development.
+
. 06/2013Our own DNA methylation bioinformatics '''R01 was scored at 6 percentile''' in its first submission.  
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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.
+
. 06/2013Zheng's TCGA RNA-seq bioinformatics paper was under review in '''Nature Biotechnology'''.
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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!
+
. 05/2013Kaifu's nucleosome aging paper was under review in '''Nature'''.
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. 02/2012Liguo Wang was offered a '''tenure-track Assistant Professor''' position at Mayo Clinic. Congratulations!
+
. 03/2013Eric joined the lab for his PhD thesis study. Welcome back, Eric!
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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!
+
. 01/2013Zheng's 3'UTR paper was in revision in '''Nature'''. Fingers Crossed!
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. 11/2011Yuanxin's RRBSMAP paper was accepted to '''Bioinformatics'''.  
+
. 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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. 09/2011Wei Li was promoted to tenured '''Associate Professor''' at BCM. Cheers!
+
. 12/2012Liguo and HJ's CPAT RNA coding potential prediction paper accepted to '''Nucleic Acids Research'''.
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. 09/2011Deqiang's DNA methylation paper with Peggy Goodell lab was accepted to '''Nature Genetics'''.  
+
. 11/2012Kaifu's nucleosome methodology paper DANPOS accepted to '''Genome Research'''.
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. 08/2011:  Kaifu's NSD2 epigenetic paper with Or Gozani lab at Stanford was accepted to '''Molecular Cell'''.
+
. 10/2012:  Kaifu's promoter nucleosome paper accepted to '''Genome Research'''.
-
. 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.
+
. 09/2012:  A '''NIH R01 grant''' was funded. We will work with Dr. Issa at Temple Univ. to understand DNA methylation in Cancer.
-
. 07/2011: Liguo's FoxA1 cistrome paper was accepted to '''Cancer Research'''.
+
. 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.
-
. 07/2011: See our '''[http://www.genomeweb.com/node/973004 Genomic Regulation Technical Guide]''' on Genome Technology magazine
+
. 08/2011: Dr. Benjamin Rodriguez will join us as a '''Postdoc Associate'''. Ben has PhD in Integrated Biomedical Science from the Ohio State Univ. Welcome!
-
. 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!
+
. 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.
 +
 +
. 06/2012: Liguo's RNA-seq Quality Control paper accepted to '''Bioinformatics'''.
-
. 05/2011Dr.Bert O'Malley's coregulator network paper was published in '''Cell'''. Wei is a co-author on the paper.
+
. 06/2012A '''NIH R01 grant''' was funded. We will work with Dr. Goodell at BCM to understand DNA methylation in Hematopoietic Stem Cell.
-
. 04/2011Liguo's Prostate Cancer RNA-seq paper was officially accepted to  '''PNAS'''.
+
. 04/2012A '''NIH R01 grant''' was funded. We will work with Dr. Dent at MD Anderson to define USP22 functions during mammalian development.
-
. 03/2011Our 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.  
+
. 04/2012Dr.Dean Tang's prostate cancer stem cell paper was accepted in '''Cell Stem Cell'''. Wei is a co-author.
-
. 01/2011:  Yuanxin's fragile nucleosome paper was accepted to '''Genome Research'''.
+
. 02/2012:  Yuanxin's epigenetic paper with Katrin Chua lab at Stanford accepted to '''Nature'''. Two years of hard work finally paid off!
-
. 01/2011Yuanxin and Liguo's  Atoh1 targetome paper was accepted to  '''PNAS'''.
+
. 02/2012:  Liguo Wang was 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]]
[[Image:Banner.jpg‎‎]]

Revision as of 15:44, 9 October 2013

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Recent News

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

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

. 08/2013: Yuanxin's transcription elongation paper in revision in Nature.

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

. 07/2013: Deqiang's aging epigenomics paper was under external review in Cell.

. 06/2013: Our own DNA methylation bioinformatics R01 was scored at 6 percentile in its first submission.

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

. 05/2013: Kaifu's nucleosome aging paper was under review in Nature.

. 03/2013: Eric joined the lab for his PhD thesis study. Welcome back, Eric!

. 01/2013: Zheng's 3'UTR paper was in revision in Nature. Fingers Crossed!

. 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 accepted to Nucleic Acids Research.

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

. 10/2012: Kaifu's promoter nucleosome paper 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.

. 08/2011: 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 was 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 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.

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

. 02/2012: Yuanxin's epigenetic paper with Katrin Chua lab at Stanford 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!

. 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 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.

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 Res 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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Image:WeiLi.jpg‎


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