Li Lab

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Wei Li Computational Epigenomics and Transcriptomics Lab Dan 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! 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). Lab Intranet openwetware

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