Li Lab

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Welcome to Wei Li's Computational Genomics Lab Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine

Recent News . 06/2011: Kaifu's epigenetic paper has been invited for revision in Molecular Cell. . 05/2011: Dr.Bert O'Malley's coregulator network paper has been published in Cell. Wei is a co-author on the paper. . 04/2011: Yuanxin's epigenomic paper has been considered for publication in Nature. . 04/2011: Liguo's Prostate Cancer RNA-seq paper has been officially accepted to PNAS. . 03/2011: Our Texas CPRIT Multi-Investigator grant has been 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. . 01/2011: Yuanxin's fragile nucleosome paper has been accepted to Genome Research. . 01/2011: Yuanxin and Liguo's Atoh1 targetome paper has been accepted to PNAS. . 12/2010: Liguo's fly RNA-seq paper has been published in Genome Research. . 10/2010: A Texas CPRIT grant has been funded. We will work with Dr. Goodell at BCM to understand DNA Methylgransferase 3B in normal and malignant hematopoiesis. . 08/2010: Our Pilot Project has been funded by a NIH Stem Cell P01 Grant. . 07/2010: The DNA methylation platform comparision paper has been accepted to Nature Biotechnology. . 06/2010: Hao Zhao will join us as a postdoc fellow. Hao has a PhD in Computer Science from City University of Hong Kong. Welcome! . 05/2010: Our paper titled "Histone modifications and chromatin organization in prostate cancer" has been accepted by Epigenomics. . 01/2010: A Texas CPRIT grant has been funded. We will use ChIP-seq and RNA-seq to analyze Androgen Receptor (AR) function in Prostate Cancer with Dr. Weigel at BCM. . 01/2010: Wei Li is an invited speaker in the American Association for Cancer Research (AACR) Special Conference on Cancer Epigenetics at Puerto Rico. News Archive

A Genomic View of Epigenetic and Transcriptional Regulation 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 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 Res 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 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. Lab Intranet openwetware

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