Li Lab: Difference between revisions
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== '''Wei Li | == '''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== | ||
. | . 09/2013: Deqiang's DNA methylation Canyon paper accepted to '''Nature Genetics'''. | ||
. 08/ | . 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/ | . 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: [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 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/ | . 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/ | . 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]] | [[Image:Banner.jpg]] |
Revision as of 12:44, 9 October 2013
Wei Li Computational Epigenomics and Transcriptomics LabDan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine |
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!
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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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