Li Lab: Difference between revisions
Wei Li Bcm (talk | contribs) |
Wei Li Bcm (talk | contribs) |
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==Recent News== | ==Recent News== | ||
. | . 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: [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: 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]] | [[Image:Banner.jpg]] | ||
[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. | ||
We have developed a number of widely used algorithms to detect and annotate genome-wide cis-regulatory regions, including | 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). | ||
We have extensive experience in collaborative research | 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 19:36, 12 March 2013
Wei Li's Computational Epigenomics LabDan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine |
Recent News. 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: 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!
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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. 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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