Li Lab

Home        People        Publications        Collaborations        Software        Positions        Contact       

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

Recent News . 01/23/2010, Conference on Cancer Epigenetics Wei Li is an invited speaker in the American Association for Cancer Research (AACR) Special Conference on Cancer Epigenetics at Puerto Rico. . 12/24/2009, New Paper Dr.Bert O'Malley's paper, Global Characterization of Transcriptional Impact of the SRC-3 Coregulator, has been accepted by Molecular Endocrinology. Liguo and Wei are co-authors on the paper. . 12/08/2009, New Paper Liguo's paper titled 'A Statistical Method for the Detection of Alternative Splicing Using RNA-seq' has been accepted by PLoS ONE. Congratulations Liguo! . 11/13/2009, New Grant Wei Li received a New Investigator Award from the Department of Defense (DOD) Prostate Cancer Research Program (PCRP). Cheers! . 11/07/2009, Keynote Presentation Wei Li gave a Keynote Presentation at the Symposium on Advances in Cell Signaling, Cancer Prevention and Therapy at South Padre Island, Texas. . 09/29/2009, New Grant A prestigious NIH Challenge grant was funded. We will use ChIP-seq to analyze RXRa binding in mouse liver with Dr. Karpen at Texas Children's Hospital. . 09/17/2009, New Grant A two-year $2.5 million NIH Grand Opportunity (GO) grant was funded. We will study aging epigenomics with Drs. Darlington and Goodell at BCM. . 09/15/2009, New Grant A prestigious NIH Challenge grant was funded. We will use RNA-seq to characterize patient cardiac progenitors with Dr. Pu at Harvard Medical School. . 06/05/2009, New BMC Bioinformatics Paper Yuanxin's paper titled 'BSMAP: whole genome Bisulfite Sequence MAPping program' has been accepted by BMC Bioinformatics. Congratulations Yuanxin! . 06/04/2009, New Postdoc (joint with Prof. Xuewen Pan) Kaifu Chen has accepted our postdoc offer. Kaifu has a PhD in Genomics and Bioinformatics from Beijing Institute of Genomics, Chinese Academy of Sciences. Welcome Kaifu! . 03/26/2009, New Cell Paper A paper titled 'Reprogrammed Androgen Receptor Function in Androgen-Independent Prostate Cancer' has finally been accepted by Cell. . 03/20/2009, Cancer Epigenomics Workshop Please join us on May 2nd (Saturday) 2009 at MD Anderson Cancer Center. This meeting is organized by Steffi Oesterreich, Wei Li and Jean-Pierre Issa. News Archive

A Genomic View of Epigenetic and Transcriptional Regulation Our lab is focused on the design and application of statistical and computational algorithms to elucidate global epigenetic and transcriptional regulatory mechanism, by interpreting and integrating data from ChIP-chip/seq, DNA methylation, Nucleosome positioning, Alternative splicing and Motif finding. An elaborate system of epigenetic and transcription regulation is responsible for the morphological and behavioral complexity in higher eukaryotes. This regulatory system consists of diverse trans-acting protein factors, cis-acting regulatory DNA sequences and the underlying epigenomic background, such as histone modifications, DNA methylation and Nucleosome localizations. Recently, Chromatin ImmunoPrecipitation coupled with whole genome tiled microarray (ChIP-chip) and/or next-generation sequencing (Solexa, SOLiD and 454) has evolved as a powerful and unbiased technique to study this genome-wide regulatory system. The application of this technology to multiple factors and/or in multiple conditions allows biologists to study how transcription is differentially regulated in a combinatorial manner. However, it also poses great challenges for the development of effective algorithms, the key link between massive raw data and biological hypotheses. We developed a series of algorithms to reliably detect and annotate ChIP-enriched regions using Next-generation sequencing (MACS; Genome Biology 2008) and Affymetrix whole-genome tiling arrays, including 1) Model-based Analysis of Tiling-arrays (MAT; PNAS 2006) and a hidden Markov model (Bioinformatics 2005) for ChIP-region detection, 2) extreme MApping of OligoNucleotide (xMAN; BMC Genomics 2008) for microarray probe mapping, 3) Cis-regulatory Element Annotation System (CEAS; NAR 2006) for ChIP-region annotation. Since the inception in early 2006, they have been adopted by hundreds of academic users and are now considered as the ChIP-chip data analysis standard in many labs. We worked with ENCODE consortium to systematically analyze the performance variability introduced in ChIP-chip protocols, array platforms, and analysis methods (Genome Res. 2008). Furthermore, we are also in close collaboration with several labs on identifying global regulation targets of several key transcription factors, including Estrogen Receptor (Cell 2005; Nature Genetics 2006); Androgen Receptor (Molecular Cell 2007; Cell 2009) and FoxA1 (Cell 2008). We are currently collaborating with many BCM laboratories to use the Next generation sequencing to study 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). 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