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Sun, Shuying

Contact Information
Shuying Sun
Assistant Professor

Office: MCS 571
Phone: 512-245-3422
Research Interest
Statistical genetics and bioinformatics

Dr. Shuying Sun received her Ph.D. in statistics from the University of Toronto in Canada. Her research focuses on addressing challenging genetic and epigenetic questions using statistical and computational methods. In particular, Dr. Sun has been working on statistical genetics and bioinformatics with a focus on methylation microarray and sequencing data analysis, haplotype inference, mutation age estimation, and genetic variant identification. Dr. Sun has collaborated with biomedical researchers from different research groups in Canada and the United States on projects related to complex diseases (e.g., cancer and arthritis). She has also been developing statistical methodologies and software packages for genomic and epigenomic problems using Bayesian methods, hidden Markov models, Markov Chain Monte Carlo algorithms, and linear models. These methodologies and software packages have been published in more than 20 peer-reviewed research articles in high-impact journals. For these journals, the average impact factor is 4.3, and the average H index is 125.2.

Selected Publications:

  1. Sun S, Yu X: HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher's exact test. Stat Appl Genet Mol Biol 2016, 15(1):55-67.
  2. Yu X, Sun S: HMM-DM: identifying differentially methylated regions using a hidden Markov model. Stat Appl Genet Mol Biol 2016, 15(1):69-81.
  3. Yu X, Sun S: Comparing five statistical methods of differential methylation identification using bisulfite sequencing data. Stat Appl Genet Mol Biol 2016, 15(2):173-191.
  4. Tian S, Bertelsmann K, Yu L, Sun S: DNA Methylation Heterogeneity Patterns in Breast Cancer Cell Lines. Cancer Inform 2016, 15(Supple 4):1-9.
  5. Sun S, Li P: HMPL: A Pipeline for Identifying Hemimethylation Patterns by Comparing Two Samples. Cancer Inform 2015, 14(Suppl 2):235-245.
  6. Xu L, Mitra-Behura S, Alston B, Zong Z, Sun S: Identifying DNA Methylation Variation Patterns to Obtain Potential Breast Cancer Biomarker Genes. International Journal of Biomedical Data Mining 2015, 4(115).
  7. Sun S, Noviski A, Yu X: MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment. BMC Bioinformatics 2013, 14:259.
  8. Yu X, Sun S: Comparing a few SNP calling algorithms using low-coverage sequencing data. BMC Bioinformatics 2013, 14:274.
  9. Adams MD, Veigl ML, Wang Z, Molyneux N, Sun S, Guda K, Yu X, Markowitz SD, Willis J: Global mutational profiling of formalin-fixed human colon cancers from a pathology archive. Mod Pathol 2012, 25(12):1599-1608.
  10. Yu X, Guda K, Willis J, Veigl M, Wang Z, Markowitz S, Adams MD, Sun S: How do alignment programs perform on sequencing data with varying qualities and from repetitive regions? BioData Min 2012, 5(1):6.
  11. Sun S, Chen Z, Yan PS, Huang YW, Huang TH, Lin S: Identifying hypermethylated CpG islands using a quantile regression model. BMC Bioinformatics 2011, 12:54.
  12. Sun S, Huang YW, Yan PS, Huang TH, Lin S: Preprocessing differential methylation hybridization microarray data. BioData Min 2011, 4:13.
  13. Han L, Zheng S, Sun S, Huang T, Zhao Z: Genome-wide DNA methylation profiling in 40 breast cancer cell lines. Advanced Intelligent Computing Theories and Applications Lecture Notes in Computer Science 2010, 6215:277-284.
  14. Greenwood CM, Sun S, Veenstra J, Hamel N, Niell B, Gruber S, Foulkes WD: How old is this mutation? - a study of three Ashkenazi Jewish founder mutations. BMC genetics 2010, 11:39.
  15. Sun S, Yan PS, Huang TH, Lin S: Identifying differentially methylated genes using mixed effect and generalized least square models. BMC Bioinformatics 2009, 10:404.
  16. Clendenning M, Baze ME, Sun S, Walsh K, Liyanarachchi S, Fix D, Schunemann V, Comeras I, Deacon M, Lynch JF et al: Origins and prevalence of the American Founder Mutation of MSH2. Cancer Res 2008, 68(7):2145-2153.
  17. Clendenning M, Senter L, Hampel H, Robinson KL, Sun S, Buchanan D, Walsh MD, Nilbert M, Green J, Potter J et al: A frame-shift mutation of PMS2 is a widespread cause of Lynch syndrome. J Med Genet 2008, 45(6):340-345.
  18. Lin HJ, Zuo T, Lin CH, Kuo CT, Liyanarachchi S, Sun S, Shen R, Deatherage DE, Potter D, Asamoto L et al: Breast cancer-associated fibroblasts confer AKT1-mediated epigenetic silencing of Cystatin M in epithelial cells. Cancer Res 2008, 68(24):10257-10266.
  19. Sun S, Greenwood CM, Neal RM: Haplotype inference using a Bayesian Hidden Markov model. Genet Epidemiol 2007, 31(8):937-948.
  20. Rahman P, Sun S, Peddle L, Snelgrove T, Melay W, Greenwood C, Gladman D: Association between the interleukin-1 family gene cluster and psoriatic arthritis. Arthritis Rheum 2006, 54(7):2321-2325.
  21. Sun S, Greenwood CM, Thiffault I, Hamel N, Chong G, Foulkes WD: The HNPCC associated MSH2*1906G-->C founder mutation probably originated between 1440 CE and 1715 CE in the Ashkenazi Jewish population. J Med Genet 2005, 42(10):766-768.
  22. Butt C, Sun S, Greenwood C, Gladman D, Rahman P: Lack of association of SLC22A4, SLC22A5, SLC9A3R1 and RUNX1 variants in psoriatic arthritis. Rheumatology (Oxford) 2005, 44(6):820-821.
  23. Butt C, Sun S, Peddle L, Greenwood C, Hamilton S, Gladman D, Rahman P: Association of nuclear factor-kappaB in psoriatic arthritis. J Rheumatol 2005, 32(9):1742-1744.