BBS Faculty Member - Peter Park

Peter Park

HMS Department of 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: 12 postdoctoral fellows, 5 graduate students, 4 bioinformatics analysts, 6 software engineers
Visit my lab page here.



Mutational processes in cancer and normal cells; development of computational methods for genome and epigenome analysis.

We employ computational and statistical approaches to study various types of somatic mutations that arise in cancer cells and neurons. We are particularly interested in large-scale analysis of genome and epigenome sequencing data to investigate the role of non-coding mutations and mosaic mutations (present in a subpopulation of cells) as potential causes of cancer and neurodegenerative diseases, respectively.

To comprehensively identify somatic mutations, we have developed algorithms for various structural variations in whole-genome sequencing data, including copy number variation, complex structural variations, retrotransposition, and microsatellite instability. To study the role of non-coding mutations, we utilize histone modification and higher-order chromosomal interaction data. To detect extremely low-frequency mutations, we take advantage of single cell whole-genome DNA sequencing, which requires new computational approaches to account for amplification-associated artifacts.

We have played a major role in several large NIH consortia in the past, including The Cancer Genome Atlas (TCGA) and the model organism Encyclopedia of DNA Elements (ENCODE). We are part of the Harvard Ludwig Center, a group of investigators interested in developing strategies to overcome resistance to cancer therapies, and two NIH consortia—Brain Somatic Mosaicism Network for studying the genetic architecture of neuropsychiatric disorders and the 4D Nucleome Network for understanding the principles behind nuclear organization in space and time and its role in cellular function. These projects offer unprecedented opportunities for deriving biological insights from bioinformatic analysis of complex data sets.

We benefit from our interactions with a fabulous set of collaborators at HMS, including Mitzi Kuroda, Steve Elledge, Chris Walsh, Konrad Hochedlinger, George Daley, Fred Winston, and Bob Kingston. We welcome BBS rotation students with strong quantitative and programming skills. Joint thesis supervision with an experimentalist is a possibility.



Last Update: 1/4/2017



Publications

For a complete listing of publications click here.

 


 

Lodato MA*, Woodworth MB*, Lee S*, Evrony GD, Mehta BK, Karger A, Lee S, Chittenden TW, D'Gama AM, Cai X, Luquette LJ, Lee E, Park PJ**, Walsh CA**. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science, 350:94-8, 2015.

De Los Angeles A*, Ferrari F*, Fujiwara Y, Mathieu R, Lee S, Lee S, Tu H-C, Ross S, Chou S, Nguyen M, Wu Z, Theunissen TW, Powell BE, Imsoonthornruksa S, Chen J, Borkent M, Krupalnik V, Lujan E, Wernig M, Hanna JH, Hochedlinger K, Pei D, Jaenisch R, Deng H, Orkin SH, Park PJ**, Daley GQ**. Failure to replicate the STAP cell phenomenon. Nature, 525:E6-9, 2015

Ho JWK*, Jung YL*, Liu T*, Alver BH, Lee S, Ikegami K, Sohn K-A, Minoda A, Tolstorukov MY, Appert A, Parker SCJ, Gu T, Kundaje A, Riddle NC, Bishop EP, Egelhofer TA, Hu S'en S, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen BQ, Chen RA-J, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM**, Strome S**, Elgin SCR**, Liu XS**, Lieb JD**, Ahringer J**, Karpen GH**, Park PJ**. Comparative analysis of metazoan chromatin organization. Nature 512:449-52, 2014



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