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The Sun group is interested in developing statistical methods for analyzing systems-biology data, including genome-wide DNA polymorphism information (e.g., SNP genotypes, DNA copy number variations), epigenetic information (e.g., nucleosome occupancy, histone modifications), genome-wide gene expression, protein interaction data, as well as phenotype data. More specific areas of interest include:
(1) eQTL studies: eQTL (gene expression quantitative trait loci) studies aim to identify the genetic determinants of gene-expression levels. One direction the Sun group is working on in this area is to analyze transcription-regulation data to determine how specific genetic variants affect gene-expression levels. Another research direction is to identify dynamic linkages among gene-expression traits, which can be extended to other phenotypes such as physiology, disease states, etc.
(2) Tiling microarray data analysis: Tiling microarray data provide unprecedented resolution for genomic studies, but also present significant challenges for data analysis. The Sun group has developed statistical methods for such data including nucleosome occupancy (ChIP-chip) and SNP array data.
(3) Cancer classification and survival-time prediction: In their analysis of gene-expression data, the Sun group uses a combination of prior feature selection and dimension reduction to select for a small subgroup of genes whose expression can predict specific cancer subtypes or patients' survival time.
(4) Large-scale association studies: In analyzing the genotypes of millions of SNPs in thousands of patients a major challenge is the multiple-testing problem posed by the large number of SNPs. The Sun group has been working on incorporating haplotype blocks in large-scale association studies and developing new statistical methods to address the multiple-testing problem.
Selected Publications
Sun W, Yu T, Li KC. (2007) Detection of eQTL modules mediated by activity levels of transcription factors. Bioinformatics. Jun 28; [Epub ahead of print]
Yu T, Ye H, Sun W, Li KC, Chen Z, Jacobs S, Bailey DK, Wong DT, Zhou X. (2007) A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array. BMC Bioinformatics. 8:145.
Yu T, Sun W, Yuan S, Li KC. (2005) Study of coordinative gene expression at the biological process level. Bioinformatics. 21(18):3651-7.
Li KC, Liu CT, Sun W, Yuan S, Yu T. (2004) A system for enhancing genome-wide coexpression dynamics study. Proc Natl Acad Sci U S A. 101(44):15561-6.
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