Wei Li, Ph.D.
Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology
Ph.D.: Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
Postdoctoral training: Dana Farber Cancer Institute/Harvard School of Public Health, Boston
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 including androgen and estrogen receptors in prostate and breast cancers (Cell 2005; Nature Genetics 2006; Molecular Cell 2007; Cell 2009), epigenetic 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).
- Wang L, Wang S, Li W*. (2012). RseQC: Quality Control of RNA-seq experiments. Bioinformatics. Accepted
- Barber MF^, Michishita E^, Xi Y^, Tasselli L, Kioi M, Moqtaderi Z, Tennen RI, Paredes S, Young NL, Chen K, Struhl K, Garcia BA, Gozani O, Li W*(joint corresponding author), Chua KF*. (2012). SIRT7 is a histone H3 lysine 18 deacetylase that stabilizes the transformed state of cancer cells. Nature Accepted.
- Xi Y, Bock C, Muller F, Sun D, Meissner A, Li W. (2012). RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing. Bioinformatics 28 430-432. PMCID: PMC3268241.
- Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, Xi Y, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JJ, Godley LA, Li W*(joint corresponding author), Goodell MA*. (2012). Dnmt3a is Essential for Hematopoietic Stem Cell Differentiation. Nature Genetics 44. 23-31.
- Kuo AJ^, Cheung P^, Chen K^, Zee BM, Lauring J, Xi Y, Park BH, Shi X, Kioi M, Garcia BA, Li W* (joint corresponding author), Gozani O*. (2011) NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. Molecular Cell 44. 609-620.
- Zhang C^, Wang L^, Wu D, Chen H, Chen Z, Thomas-Ahner JM, Zynger DL, Eeckhoute J, Yu J, Luo J, Brown M, Clinton SK, Nephew KP, Huang TH, Li W* (joint corresponding author), Wang Q*. (2011) Definition of a FoxA1 cistrome that is crucial for G1-S phase cell cycle transit in castration resistant prostate cancer. Cancer Res 71. 6738-6748.
- Kannan K, Wang L, Wang J, Ittmann M, Li W* (joint corresponding author), Yen L*. (2011). Recurrent chimeric RNAs enriched in human prostate cancer identified by deep-sequencing. PNAS 108. 9172-9177. PMCID: PMC3107329.
- Xi Y, Yao J, Chen R*, Li W* (joint corresponding author), He X*. (2011). Nucleosome fragility marks novel functional states of nucleosomes throughout the yeast genome. Genome Res 21 718-724. PMCID: PMC3083088.
- Klisch T, Xi Y, Flora A, Wang L, Li W* (joint corresponding author), Zoghbi H*. (2011). In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development. PNAS 108. 3288-3293. PMCID: PMC3044384.
- Wang Q^, Li W^ (joint first author), Zhang Y, Yuan X, ..., Kantoff PW, Liu XS, Brown M. (2009). Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer. Cell 138. 245-256 (Featured Article). PMCID: PMC2726827