Publications


2008

Kharchenko PV, Tolstorukov M, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins, Nature Biotechnology, 6:1351-1359, 2008 [Pubmed]

Park PJ, Epiegenetics meets next-generation sequencing, Epigenetics, 3:318-321, 2008

Sural TH, Peng S, Li B, Workman JL, Park PJ, Kuroda MI. The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila X chromosome, Nature Structural and Molecular Biology, 15:1318-25, 2008 [Pubmed]

The Cancer Genome Atlas Research Network (including the Harvard Medical School/Dana-Farber Cancer Institute team: Chin L, Protopopov A, Zhang J, Perna I, Aronson S, Sathiamoorthy N, Ren G, Yao J, Wiedemeyer WR, Kim H, Won Kong S, Xiao Y, Kohane IS, Seidman J, Park PJ, Kucherlapati R), Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 255:1061-8, 2008 [Pubmed]

Dermody JL, Dreyfuss J, Villén J, Ogundipe B, Gygi SP, Park PJ, Ponticelli AS, Moore CL, Buratowski S, Bucheli ME. Unphosphorylated SR-like Protein Npl3 Stimulates RNA Polymerase II Elongation, PLoS ONE, 3:e3273, 2008 [Pubmed]

Kharchenko PV*, Woo CJ*, Tolstorukov MY, Kingston RE**, Park PJ**. Nucleosome positioning in human HOX gene clusters, Genome Research, 18:1554-61, 2008 (*equal contribution; **co-corresponding authors) [Pubmed]

Alekseyenko AA*, Peng S*, Larschan E, Gorchakov AA, Lee OK, Kharchenko PV, McGrath S, Wang CI, Mardis E, Park PJ**, Kuroda MI**. A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome, Cell, 134:599-609, 2008. (*equal contribution; **co-corresponding authors) [Pubmed] Highlighted in : Epigenetics: Sequence-guided entry for MSL, Nature Reviews Genetics, 9:732-733, 2008 [Journal]

Park PJ, Experimental Design and Data Analysis for Array Comparative Genomic Hybridization. Cancer Investigation, 26:923-928, 2008

Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ. nuScore: a web-interface for nucleosome positioning predictions, Bioinformatics, 24:1456-8, 2008 [Pubmed] [pdf from publisher]

Orford K*, Kharchenko PV*, Lai WR, Dao MC, Worhunsky D, Park PJ**, Scadden DT**. Differential H3K4 methylation identifies developmentally poised hematopoietic genes, Developmental Cell, 14:798-809, 2008 (*equal contribution; **co-corresponding authors) [Pubmed]

Mueller JL, Mahadevaiah SK, Park PJ, Warburton PE, Page DC, Turner JMA. The mouse X chromosome is enriched for multi-copy testis genes exhibiting post-meiotic expression, Nature Genetics, 40:794-9, 2008 [Pubmed]

Lai WR, Choudhary V, Park PJ. CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms. Bioinformatics 24:1014-1015, 2008 [Pubmed] [pdf from publisher]

Lee H, Kong SW, Park PJ. Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes, Bioinformatics 24:889-896, 2008 [Pubmed] [pdf from publisher]

Tun HW, Personett D, Baskerville KA, Menke DM, Jaeckle KA, Kreinest P, Edenfield B, Zubair AC, O'Neill BP, Lai WR, Park PJ, McKinney M. Pathway analysis of primary central nervous system lymphoma. Blood 111:3200-10, 2008 [Pubmed]

Claus EB, Park PJ, Carroll R, Chan J, Black PM. Specific genes expressed in association with progesterone receptors in meningioma. Cancer Research 68:314-22, 2008 [Pubmed]

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, 29:1874-93, 2008 (Epub Jun 11, 2007) [Pubmed]

2007

Larschan E, Alekseyenko AA, Gortchakov AA, Peng S, Li B, Yang P, Workman JL, Park PJ, Kuroda MI. MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism, Molecular Cell 28:121-33, 2007 [Pubmed]

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

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 [Pubmed]

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. [Pubmed]

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) [Pubmed]

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] Highlighted in: Gene regulation: Compensation culture, Nature Reviews Genetics, 7:335, 2006 (2006); Dosage compensation in high resolution: global up-regulation through local recruitment Genes & Development, 20:749-753, 2006

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]