Li Lab

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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.  
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.  
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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 Re'''s 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).
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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 Re'''s 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, 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.
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.

Revision as of 00:09, 21 April 2012

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Recent News

. 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!

. 11/2011: Yuanxin's RRBSMAP paper was accepted to Bioinformatics.

. 09/2011: Wei Li was promoted to tenured Associate Professor at BCM. Cheers!

. 09/2011: Deqiang's DNA methylation paper with Peggy Goodell lab was accepted to Nature Genetics.

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

. 08/2011: A NIH R01 grant was 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 was 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 was published in Cell. Wei is a co-author on the paper.

. 04/2011: Liguo's Prostate Cancer RNA-seq paper was officially accepted to PNAS.

. 03/2011: Our Texas CPRIT Multi-Investigator grant was 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 was accepted to Genome Research.

. 01/2011: Yuanxin and Liguo's Atoh1 targetome paper was accepted to PNAS.

. 12/2010: Liguo's fly RNA-seq paper was published in Genome Research.

. 10/2010: A Texas CPRIT grant was funded. We will work with Dr. Goodell at BCM to understand DNA Methylgransferase 3B in normal and malignant hematopoiesis.

. 08/2010: Our Pilot Project was funded by a NIH Stem Cell P01 Grant.

. 07/2010: The DNA methylation platform comparision paper was 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 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, 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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