Publications


2007

Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ. Normalization and Experimental Design for ChIP-chip Data, BMC Bioinformatics 8:219, 2007

Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S. Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models. PLoS Genetics 3:e96, 2007

Baskerville KA, Kent C, Personett D, Lai WR, Park PJ, Coleman P, McKinney M. Aging elevates metabolic gene expression in brain cholinergic neurons. Neurobiology of Aging, 2007

2006

Larschan E, Alekseyenko AA, Lai WR, Park PJ, Kuroda MI. MSL complex associates with clusters of actively transcribed genes along the Drosophila male X chromosome. Cold Spring Harb Symp Quant Biol. 2006;71:385-94.

Liu F*, Park PJ*, Lai WR, Maher E, Chakravarti A, Durso L, Jiang X, yu Y, Brosius A, Thomas M, Chin L, Brennan C, DePinho RA, Kohane IS, Carroll RS, Black PM Johnson MD*. A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma, Cancer Research 66: 10815-10823, 2006 (*equal contribution)

Kong SW, Pu WT, Park PJ. A multivariate approach for integrating genome-wide expression data and biological knowledge, Bioinformatics 22:2373-80, 2006 [Pubmed]

Yoon SS, Segal NH, Park PJ, Detwiller KY, Fernando NT, Ryeom SW, Brennan MF, Singer S. Angiogenic profile of soft tissue sarcomas based on analysis of circulating factors and microarray gene expression, Journal of Surgical Research 135(2):282-90, 2006 [Pubmed]

Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TA. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies, Nature Biotechnology 24(7):832-40, 2006 [Pubmed]

Namekawa SH, Park PJ, Zhang LF, Shima JE, McCarrey JR, Griswold MD, Lee JT. Post-meiotic sex chromatin in the male germline of mice, Currrent Biology 16:660-7, 2006 [Pubmed]

Alekseyenko AA, Larschan E, Lai WR, Park PJ*, Kuroda MI*. High resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome, Genes and Development 20:848-57, 2006 (*co-corresponding authors) [Pubmed] [Supplementary Website]

Hamada FN*, Park PJ*, Gordadze PR, Kuroda MI. Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster, Genes and Development 19:2289-94, 2005 (*co-first authors) [Pubmed] [Supplementary Website]

Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profling studies, Proc Natl Acad Sci USA 102:13544-9, 2005 [Pubmed] [PDF] [Journal Website] [Supplementary Website]

Lai W, Johnson MJ, Kucherlapati R, Park PJ. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data, Bioinformatics 21:3763-4770, 2005 [Pubmed] [Journal Website] [Supplementary Website]

Greenberg SA, Pinkus JL, Pinkus GS, Burleson T, Sanoudou D, Tawil R, Barohn RJ, Saperstein DS, Briemberg HR, Ericsson M, Park P, Amato AA. Interferon-alpha/beta-mediated innate immune mechanisms in dermatomyositis, Annals of Neurology 57:664-678, 2005 [Pubmed]

Kong SW, Hwang KB, Kim RD, Zhang BT, Greenberg SA, Kohane IS, Park PJ. CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays, Bioinformatics 21:2116-7, 2005 [Pubmed]

Park PJ, Gene Expression Data and Survival Analysis, in Shoemaker, JS and Lin, SM, Editors, Methods of Microarray Data Analysis IV, Springer, New York, 2005

2004

Hwang KB, Kong SW, Greenberg SA, Park PJ. Combining Gene Expression Data from Different Generations of Oligonucleotide Arrays, BMC Bioinformatics 5:159, 2004 [Pubmed] [PDF] [Journal Website][Linke to Data in GEO]

Kim R, Park PJ. Improving identification of Differentially Expressed Genes Using Public Databases, Genome Biology 5:R70, 2004 [Pubmed] [PDF] [Journal Website]

Park PJ, Cao YA, Lee SY, Kim JW, Chang MS, Hart R, Choi S. Current issues of DNA microarrays: platform comparison, double amplification, and universal standard, Journal of Biotechnology 112:225-45, 2004 [Pubmed]

Park PJ, Hou TY. Multiscale Numerical Methods for Singularly Perturbed Convection-Diffusion Equations. International Journal of Computational Methods 1:17-65, 2004

Park PJ, Kohane IS, Kim JH. Rank-Based Nonlinear Normalization of Oligonucleotide Arrays, Genomics & Informatics 1:94-100,

2003

Koopman LA, Kopcow HD, Rybalov B, Boyson JE, Orange JS, Schatz F, Masch R, Lockwood CJ, Schachter AD, Park PJ, Strominger JL. Human decidual natural killer cells are a unique NK cell subset with immunomodulatory potential, J Exp Med 198:1201-12, 2003 [Pubmed]

Kulldorff M, Tango M, Park PJ. Power Comparisons for Disease Clustering Tests, Computational Statistics and Data Analysis 42:665-684, 2003

Blackshaw S, Kuo WP, Park PJ, Tsujikawa M, Gunnersen JM, Scott HS, Boon W, Tan S, Cepko CL. MicroSage is highly reproducible, but reveals major difference in gene expression among samples obtained from identical tissues, Genome Biology 4(3):R17, 2003 [Pubmed] [PDF] [Journal Website]

Kuo WP, Whipple ME, Jenssen TK, Todd R, Epstein JB, Ohno-Machado L, Sonis ST, Park PJ. Microarrays and clinical dentistry, J Am Dent Assoc 134:456-62, 2003 [Pubmed]

Kuo WP, Mendez E, Chen C, Whipple M, Farell G, Agoff N, Park PJ. Functional Relationships Between Gene Pairs in Oral Squamous Cell Carcinoma, Proceedings American Medical Informatics Association Symposium 371-5, 2003 [Pubmed]

2002

Kuo WP, Jenssen TK, Park PJ, Lingen MW, Hasina R, Ohno-Machado L. Gene Expression Levels In Different Stages of Progression in Oral Squamous Cell Carcinoma, Proceedings American Medical Informatics Association Symposium 2002:415-9, 2002 [Pubmed]

Park PJ, Butte A, Kohane IS. Comparing Expression Profiles of Genes with Similar Promoter Regions, Bioinformatics 18(12):1576-84, 2002 [Pubmed]

Park PJ, Tian L, Kohane IS. Linking Expression Data with Patient Survival Times Using Partial Least Squares, Bioinformatics 18:S120-7, 2002 (Presented at ISMB 2002) [Pubmed]

Kuruvilla F, Park PJ, Schreiber SL. Vector Algebra in the Analysis of Genome-wide Expression Data, Genome Biology 3(3): research0011.1-0011.11, 2002 [Pubmed] [PDF] [Journal Website]

2001

Park PJ, Pagano M, Bonetti M. A Nonparametric Scoring Algorithm for Identifying Informative Genes from Microarray Data, Pacific Symposium on Biocomputing 6:52-63, 2001 [Pubmed]