Research & Publications

With the advance of array/sequencing techniques and the accumulation of different types of genomic data, the study of a living organism in system level has become feasible and necessary. Such genomic data may include genome-wide DNA polymorphism (e.g., genotypes of thousands to millions of SNPs, DNA copy number variations), epigenetic information (e.g., nucleosome occupancy, histone modification), mRNA/miRNA expression, protein abundance/phosphorylation, and protein-protein interaction, as well as phenotype data. My research focus is on analyzing such comprehensive genomic data, and their associations or casual relations with complex traits, such as human cancer.


QTL/eQTL (Expression Quantitative Trait Loci)

Yijuan Hu, Jung-Ying Tzeng, Charles M. Perou, and Wei Sun (2015), Proper Use of Allele-Specific Expression Improves Statistical Power for cis-eQTL Mapping with RNA-Seq DataJ Am Stat Assoc 110(511): 962-74. A list of 2,509 eQTLs

Wei Sun and Yijuan Hu (2013), eQTL mapping using RNA-seq dataStatistics in Biosciences, 2013 May;5(1):198-219.

Wei Sun (2012), A Statistical Framework for eQTL Mapping Using RNA-seq DataBiometrics, 2012 Mar;68(1):1-11.     Download data and results        Slides

Fred Wright, Patrick Sullivan, Andrew Brooks, Fei Zou, Wei Sun et al. (2014) Heritability and genomics of gene expression in peripheral bloodNature Genetics, 46(5), 430-437.

Wei Sun and Lexin Li, (2012), Model-free Variable Selection for Small-n-Large-p Regressions, with Application to Genome-wide Multiple Loci Mapping, Biometrics, 2012 Mar;68(1):12-22 Epub 2011 Aug 12.

Wei Sun and Fred A. Wright, (2010), A geometric interpretation of the permutation p-value and its application in eQTL studiesAnnals of Applied Statistics, 4(2), 1014-1033.

Wei Sun, Joseph G. Ibrahim, and Fei Zou (2010), Genome-wide Multiple Loci Mapping in Experimental Crosses by the Iterative Adaptive Penalized Regression, Genetics, Vol. 185, 349-359.

Wei Sun*, Shinsheng Yuan*, and Ker-Chau Li (2008), Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation studyBMC Genomics 2008, 9:242. (*Authors contributed equally)

Wei Sun, Tianwei Yu, and Ker-Chau Li (2007), Detection of eQTL modules mediated by activity levels of transcription factorsBioinformatics, 23(17), 2290-2297.


RNA-seq

James J Crowley*, Vasyl Zhabotynsky*, Wei Sun*, ..., Fernando Pardo-Manuel de Villena (2015) Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalanceNature Genetics 47(4):353-60. 

Calabrese JM, Sun W, Song L, Mugford J, Williams L, Yee D, Starmer J, Mieczkowski P, Crawford G, Magnuson T (2012) Site-specific silencing of regulatory elements as a mechanism of X-inactivationCell,  Nov 21;151(5):951-63.


Epigenetic Studies

Wei Sun, Michael J Buck, Mukund Patel, and Ian J Davis (2009), Improved ChIP-chip analysis by mixture model approachBMC Bioinformatics, 10:173. 

Wei Sun*, Wei Xie*, Feng Xu, Michael Grunstein, Ker-Chau Li (2009), Dissecting Nucleosome Free Regions by a Segmental Semi-Markov ModelPLoS One, 4(3):e4721, (*Authors contribute equally) 

Naim Rashid, Paul Giresi, Joe Ibrahim, Wei Sun*, Jason Lieb* (2011) ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regionsGenome Biology, 12(7):R67, 

Naim Rashid, Wei Sun, Joe Ibrahim (2014), Some Statistical Strategies for DAE-seq Data Analysis: Variable Selection and Modeling Dependencies among ObservationsJournal of the American Statistical Association, 109(505):78-94 


Copy Number Studies

Szatkiewicz JP, Wang W, Sullivan PF, Wang W, Sun W (2013), Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentationNucleic Acids Research, 1;41(3):1519-32

Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, Perou CM, Børresen-Dale AL, and Kristensen VN. (2010), Allele-specific copy number analysis of tumorsPNAS, 107(39):16910-5 

Wei Sun, Fred Wright, Zhengzheng Tang, Silje H. Nordgard, Peter Van Loo, Tianwei Yu, Vessela Kristensen, and Charles Perou (2009), Integrated study of copy number states and genotype calls using high density SNP arraysNucleic Acid Research, 37(16):5365-77  Supplemenatry Materials 

Tianwei Yu, Hui Ye, Wei Sun, Ker-Chau Li, Zugen Chen, Sharoni Jacobs, Dione K Bailey, David T Wong and Xiaofeng Zhou, (2007), A forward-backward fragment assembling algorithm for the identification of amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) arrayBMC bioinformatics, 8:145 


Review Papers

Richardson S, Tseng GC, Sun W (2016), Statistical Methods in Integrative GenomicsAnnual Review of Statistics and Its Application 3(1):181-209.