Li Lab

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Recent News

. 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 external review in Nature Biotechnology.

. 06/2013: Deqiang's DNA methylation Canyon was in revision in Nature Genetics.

. 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: Kaifu's variomics paper with Xuewen Pan lab was accepted to Cell Reports.

. 12/2012: Liguo and HJ's CPAT RNA coding potential prediction paper was accepted to Nucleic Acids Research.

. 11/2012: Kaifu's nucleosome methodology paper DANPOS was accepted to Genome Research.

. 10/2012: Kaifu's promoter nucleosome paper was 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. Eric B. Rutledge, a BCM MD/PhD student, joined us for his term 2 rotation. 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: Dr. Ira's Fun30 nucleosome remodeler paper was accepted to Nature. Kaifu is a co-author.

. 06/2012: Liguo's RNA-seq Quality Control paper was 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 was 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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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).


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