BBS Faculty Member - Peter Park

Peter Park

HMS Center for Biomedical Informatics
Informatics Program, Children's Hospital Boston
Division of Genetics, Brigham and Women's Hospital


Harvard Medical School
Countway Library Room 318
10 Shattuck St.
Boston, MA 02115
Tel: 617-432-7373
Fax: 617-432-0693
Email: peter_park@harvard.edu
Lab Members: 10 postdoctoral fellows, 2 graduate students, 2 bioinformatics analysts
Visit my lab page here.



Computational Analysis of Genomic Data

With the advances in high-throughput DNA sequencing technology, the size and complexity of genomic data sets are increasing rapidly. We specialize in development and application of rigorous and comprehensive computational methods to gain new insights in two areas.

In epigenomics, we have developed tools for analysis of ChIP-seq datasets for profiling DNA-protein interactions and histone modifications to study chromatin structure and its relationship to gene regulation. In collaboration with experimental laboratories, we have examined mechanisms of epigenetic regulation in several model systems, especially in human and
Drosophila. We have also played a major role in the model organism Encyclopedia of DNA Elements (ENCODE) project to map more than a hundred chromatin-associated proteins and histone modifications in multiple tissues and developmental stages, and to analyze their combinatorial patterns.

In cancer genomics, we have developed novel algorithms for characterizing various structural variations in whole-genome sequencing data. We have carried out comprehensive analysis of copy number variation, somatic retrotransposition, complex structural variations, microsatellite instability, and clonal heterogeneity of tumor genomes. Our integrative analysis has revealed a detailed view of these genomic alterations with single-nucleotide resolution and described their impact in tumorigenesis. We have also played active roles in several large-scale projects including The Cancer Genome Atlas (TCGA).

We welcome BBS rotation students with strong quantitative and programming skills. Joint supervision with an experimentalist is a possibility.



Last Update: 6/24/2014



Publications

For a complete listing of publications click here.

 


 

Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh C, Zhang C, Ren X, Protopopov A, Chin L, Kucherlapati R, Lee C, Park PJ. Diverse mechanisms of somatic structural variations in human cancer genomes, Cell, 153:919-29, 2013.

Kim TM, Laird PW, Park PJ. The landscape of microsatellite instability in colorectal and endometrial cancer genomes, Cell, 155:858-68, 2013.

Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ 3rd, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C,Kharchenko PV*, Park PJ*, The Cancer Genome Atlas Research Network (2012), Landscape of Somatic Retrotransposition in Human Cancers, Science, 337:967-71, 2012.

Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TP, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SCR, Kuroda MI, Pirrotta V, Karpen GH*, Park PJ* (2011). Comprehensive analysis of the chromatin landscape in Drosophila melanogaster, Nature, 471:480-5, 2011.



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