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.


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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