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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


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
Houston, TX 77030
Phone: 713-798-7854
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