Li Lab
Computational Epigenomics and Transcriptomics Lab (PI: Wei Li)Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine |
Recent News. 12/2013: Kaifu's aging nucleosome accepted to Genes & Development . 12/2013: We received a 5-year NIH/NHGRI R01 grant to study DNA Methylation . 11/2013: Wei will serve on the Editorial Board of Molecular Endocrinology . 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. . 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 epigenetic mechanisms and transcription dynamics in normal development and diseases such as cancer. Since establishing the lab in early 2008, we have published more than 50 peer-reviewed papers with a Google Scholar H-index of 34. We developed a number of widely used algorithms to analyze next generation sequencing data from ChIP-seq (MACS, MACE, DyChIPS), DNA methylation Bisulfite-seq (BSMAP/RRBSMAP, BSeQC, MOABS), nucleosome positioning MNase-seq (DANPOS), and RNA-seq (CPAT, RSeQC, DaPars). These algorithms have been broadly adopted by thousands of academic users. For example, the MACS algorithm has gathered >1000 citations since 2008. In collaboration with experimental biologists, we used these algorithms to gain novel biological insights from various biological processes and disease models.
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