Li Lab

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==Recent News==
==Recent News==
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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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. 01/2013Zheng's 3'UTR paper was in revision in '''Nature'''. Fingers Crossed!
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. 02/2012Liguo Wang was offered a '''tenure-track Assistant Professor''' position at Mayo Clinic. Congratulations!
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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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. 11/2011Yuanxin's RRBSMAP paper was accepted to '''Bioinformatics'''.  
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. 12/2012Kaifu's variomics paper with Xuewen Pan lab was accepted to '''Cell Reports'''.
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. 09/2011Wei Li was promoted to tenured '''Associate Professor''' at BCM. Cheers!
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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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. 09/2011Deqiang's DNA methylation paper with Peggy Goodell lab was accepted to '''Nature Genetics'''.  
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. 11/2012Kaifu's nucleosome methodology paper DANPOS was 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'''.
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. 10/2012:  Kaifu's promoter nucleosome paper was accepted to '''Genome Research'''.
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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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. 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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. 07/2011: Liguo's FoxA1 cistrome paper was accepted to '''Cancer Research'''.
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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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. 07/2011: See our '''[http://www.genomeweb.com/node/973004 Genomic Regulation Technical Guide]''' on Genome Technology magazine
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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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. 07/2011: 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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. 08/2012: 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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. 05/2011: Dr.Bert O'Malley's coregulator network paper was published in '''Cell'''. Wei is a co-author on the paper.
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. 06/2012: Dr. Ira's Fun30 nucleosome remodeler paper was accepted to '''Nature'''. Kaifu is a co-author.
 +
 +
. 06/2012: Liguo's RNA-seq Quality Control paper was accepted to '''Bioinformatics'''.
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. 04/2011Yuanxin's epigenomic paper was invited for revision in '''Nature'''.
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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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. 04/2011Liguo's Prostate Cancer RNA-seq paper was officially accepted to  '''PNAS'''.
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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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. 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.  
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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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. 01/2011:  Yuanxin's fragile nucleosome paper was accepted to  '''Genome Research'''.
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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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+
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. 01/2011:  Yuanxin and Liguo's  Atoh1 targetome paper was accepted to  '''PNAS'''.
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. 12/2010:  Liguo's fly RNA-seq paper was published in  '''Genome Research'''.
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. 10/2010:  A Texas '''CPRIT grant''' was funded. We will work with Dr. Goodell at BCM to understand DNA Methylgransferase 3B in normal and malignant hematopoiesis.
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. 08/2010:  Our '''Pilot Project''' was funded by a NIH Stem Cell P01 Grant.
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. 07/2010:  The DNA methylation platform comparision paper was accepted to '''Nature Biotechnology'''.
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 +
. 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!
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[http://openwetware.org/wiki/Li_Lab:news News Archive]
[http://openwetware.org/wiki/Li_Lab:news News Archive]
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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 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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We have developed a number of widely used algorithms to detect and annotate genome-wide cis-regulatory regions, including a Hidden Markov Model ('''Bioinformatics''' 2005) and MAT ('''PNAS''' 2006) for analyzing ChIP-chip experiments on genome tiling arrays, CEAS ('''NAR''' 2006) for cis-regulatory element annotation, xMAN ('''BMC Genomics''' 2008) for microarray probe mapping, MACS ('''Genome Biology''' 2008) for model based analysis of ChIP-seq, BSMAP ('''BMC Bioinformatics''' 2009) for DNA methylation analysis using Bisulfite-seq, MMES ('''PLoS ONE''' 2010) for alternative splicing using RNA-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 > 30 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 remodeling (Mnase-seq); 4) Alternative splicing (RNA-seq).
+
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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We have extensive experience in collaborative research, such as Estrogen Receptor regulation in breast cancer ('''Cell''' 2005; '''Nature Genetics''' 2006), Androgen Receptor regulation in prostate cancer ('''Molecular Cell''' 2007; '''Cell''' 2009), chromatin factor FoxA1 in epigenetic regulation ('''Cell''' 2008), Atoh1 in neuron development ('''PNAS''' 2011), fly transcriptome using RNA-seq ('''Genome Res''' 2011), and chimerical RNA biomarkers in prostate cancer ('''PNAS''' 2011). My laboratory also plays an important role in the BCM Epigenomics Data Analysis and Coordination Center for a five-year NIH Roadmap Epigenomics Program.
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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).
   
   

Revision as of 15:24, 24 January 2013

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Recent News

. 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: Kaifu's variomics paper with Xuewen Pan lab was accepted to Cell Reports.

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

. 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!

. 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: Dr. Ira's Fun30 nucleosome remodeler paper was accepted to Nature. Kaifu is a co-author.

. 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.

. 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 was 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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