Li Lab

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Recent News

. 08/2011: Kaifu's NSD2 epigenetic paper with Or Gozani lab at Stanford has been accepted to Molecular Cell.

. 08/2011: Deqiang's DNA methylation paper with Peggy Goodell lab has been invited for revision in Nature Genetics. Fingers crossed!

. 08/2011: A NIH R01 grant has been funded. We will work with Dr. Wang at the Ohio State University to understand the role of histone methylations in prostate cancer.

. 07/2011: Liguo's FoxA1 cistrome paper has been accepted to Cancer Research.

. 07/2011: See our Genomic Regulation Technical Guide on Genome Technology magazine

. 07/2011: Dr. Zheng Xia will join us as a postdoc fellow. Zheng has PhD in Control Theory and Engineering Computer Science from Zhejiang University in China. Welcome!

. 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 invited for revision 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.


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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 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.


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