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Structural and Computational Biology and Molecular Biophysics

Houston, Texas

A BCM research lab.
Structural and Computational Biology & Molecular Biophysics
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Wei Li, Ph.D.

Wei Li, Ph.D.Associate Professor, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology

Baylor College of Medicine

Education:

Ph.D., Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
Postdoctoral Training, Dana Farber Cancer Institute/Harvard School of Public Health, Boston

Research Interests:

Computational Epigenomics

Our lab is focused on the design and application of bioinformatics algorithms to elucidate global regulatory mechanism by integrating data from ChlP-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 ChlP-chip experiments on genome tiling arrays, MACS (Genome Biology 2008) for model based analysis of Chlp-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 (ChlP-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 esterogen receptors in prostate and breast cancers (Cell 2005; Nature Genetics 2006; Molecular Cell 2007; Cell2009), epigeneticr 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).

Selected Publications:

  • Yao J, Liu X, Sakuno T, Li W, Xi Y, Aravamudhan P, Joglekar A, Li W, Watanabe Y and He X. Plasticity and Epigenetic Inheritance of Centromere Specific Histone H3 (CENP-A) Containing Nucleosome Positioning in the Fission Yeast. J Biol Chem, [Epub ahead of print] (2013). PubMed
  • Hanley PJ, Mei Z, da Graca Cabreira-Hansen M, Klis M, Li W, Zhao Y, Durett AG, Zheng X, Wang Y, Gee AP and Horwitz EM. Manufacturing mesenchymal stromal cells for phase I clinical trials. Cytotherapy, 15(4):416-22 (2013). PubMed
  • Huang Z, Chen K, Zhang J, Li Y, Wang H, Cui D, Tang J, Liu Y, Shi X, Li W, Liu D, Chen R, Sucgang RS and Pan X. A functional variomics tool for discovering drug-resistance genes and drug targets. Cell Rep, 3(2):577-85 (2013). PubMed
  • Rijnkels M, Freeman-Zadrowski C, Hernandez J, Potluri V, Wang L, Li W and Lemay DG. Epigenetic modifications unlock the milk protein gene loci during mouse mammary gland development and differentiation. Cell Rep, 8(1):e53270 (2013). PubMed
  • Huang Z, Srinivasan S, Zhang J, Chen K, Li Y, Li W, Quiocho FA and Pan X. Discovering thiamine transporters as targets of chloroquine using a novel functional genomics strategy. PLoS Genet, 8(11):e1003083 (2012). PubMed
  • Chen K, Wilson MA, Hirsch C, Watson A, Liang S, Lu Y, Li W and Dent SYI. Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor. Genome Res, 23(2):312-22 (2013). PubMed
  • Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X and Li W. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res, 23(2): 341-51 (2013): PubMed

For more publications, see listing on PubMed.

Contact Information:

Department: Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology
Address: Baylor College of Medicine
One Baylor Plaza
Room 529DK
BCM305
Houston, TX 77030
Phone: 713-798-7854
E-mail: WL1@bcm.edu
Additional Links: http://lilab.openwetware.org/

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