Harvard Catalyst Profiles

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Peter Park, Ph.D.

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Overview

Research
research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
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  1. OT2OD032119 (PARK, PETER J) Sep 17, 2021 - Sep 16, 2023
    NIH
    Interoperability and Collaboration with the Common Fund Data Ecosystem to Improve Utility of 4DN Data
    Role: Principal Investigator
  2. R03CA249364 (PARK, PETER J) Jun 1, 2020 - May 31, 2022
    NIH
    Identification of Transposable Element Insertions in the Kids First Data
    Role: Principal Investigator
  3. U01CA200059 (PARK, PETER J) Sep 7, 2015 - Aug 31, 2025
    NIH
    4D Nucleome Network Data Coordination and Integration Center
    Role: Principal Investigator
  4. U01CA198935 (PARK, PETER J) Jun 1, 2015 - May 31, 2019
    NIH
    Visual Analysis of Genomic and Clinical Data from Large Patient Cohorts
    Role: Principal Investigator
  5. U01MH106883 (WALSH, CHRISTOPHER A.) May 1, 2015 - Jan 31, 2021
    NIH
    1/2-Somatic mosaicism and autism spectrum disorder
    Role: Principal Investigator

Bibliographic
selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Reiff SB, Schroeder AJ, Kirli K, Cosolo A, Bakker C, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, Öztürk SU, Çamoglu U, Mirny LA, Gehlenborg N, Alver BH, Park PJ. The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Nat Commun. 2022 May 02; 13(1):2365. PMID: 35501320.
    Citations:    Fields:    Translation:Cells
  2. Rajurkar M, Parikh AR, Solovyov A, You E, Kulkarni AS, Chu C, Xu KH, Jaicks C, Taylor MS, Wu C, Alexander KA, Good CR, Szabolcs A, Gerstberger S, Tran AV, Xu N, Ebright RY, Van Seventer EE, Vo KD, Tai EC, Lu C, Joseph-Chazan J, Raabe MJ, Nieman LT, Desai N, Arora KS, Ligorio M, Thapar V, Cohen L, Garden PM, Senussi Y, Zheng H, Allen JN, Blaszkowsky LS, Clark JW, Goyal L, Wo JY, Ryan DP, Corcoran RB, Deshpande V, Rivera MN, Aryee MJ, Hong TS, Berger SL, Walt DR, Burns KH, Park PJ, Greenbaum BD, Ting DT. Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer. Cancer Discov. 2022 Mar 23. PMID: 35320348.
    Citations:    Fields:    
  3. Jin Z, Huang W, Shen N, Li J, Wang X, Dong J, Park PJ, Xi R. Single-cell gene fusion detection by scFusion. Nat Commun. 2022 02 28; 13(1):1084. PMID: 35228538.
    Citations:    Fields:    
  4. Rigano A, Ehmsen S, Öztürk SU, Ryan J, Balashov A, Hammer M, Kirli K, Boehm U, Brown CM, Bellve K, Chambers JJ, Cosolo A, Coleman RA, Faklaris O, Fogarty KE, Guilbert T, Hamacher AB, Itano MS, Keeley DP, Kunis S, Lacoste J, Laude A, Ma WY, Marcello M, Montero-Llopis P, Nelson G, Nitschke R, Pimentel JA, Weidtkamp-Peters S, Park PJ, Alver BH, Grunwald D, Strambio-De-Castillia C. Author Correction: Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods. 2022 Feb; 19(2):256. PMID: 34952955.
    Citations:    Fields:    
  5. Lee S, Bakker C, Vitzthum C, Alver BH, Park PJ. Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs. Bioinformatics. 2022 Jan 03. PMID: 34978573.
    Citations: 1     Fields:    
  6. Cortés-Ciriano I, Gulhan DC, Lee JJ, Melloni GEM, Park PJ. Computational analysis of cancer genome sequencing data. Nat Rev Genet. 2022 May; 23(5):298-314. PMID: 34880424.
    Citations: 1     Fields:    Translation:Humans
  7. Rigano A, Ehmsen S, Öztürk SU, Ryan J, Balashov A, Hammer M, Kirli K, Boehm U, Brown CM, Bellve K, Chambers JJ, Cosolo A, Coleman RA, Faklaris O, Fogarty KE, Guilbert T, Hamacher AB, Itano MS, Keeley DP, Kunis S, Lacoste J, Laude A, Ma WY, Marcello M, Montero-Llopis P, Nelson G, Nitschke R, Pimentel JA, Weidtkamp-Peters S, Park PJ, Alver BH, Grunwald D, Strambio-De-Castillia C. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods. 2021 12; 18(12):1489-1495. PMID: 34862503.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  8. Borges-Monroy R, Chu C, Dias C, Choi J, Lee S, Gao Y, Shin T, Park PJ, Walsh CA, Lee EA. Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder. Mob DNA. 2021 Nov 27; 12(1):28. PMID: 34838103.
    Citations: 1     
  9. Luquette LJ, Park PJ. Somatic mutation accumulation seen through a single-molecule lens. Cell Res. 2021 09; 31(9):949-950. PMID: 34316001.
    Citations:    Fields:    
  10. Chu C, Borges-Monroy R, Viswanadham VV, Lee S, Li H, Lee EA, Park PJ. Comprehensive identification of transposable element insertions using multiple sequencing technologies. Nat Commun. 2021 06 22; 12(1):3836. PMID: 34158502.
    Citations: 6     Fields:    Translation:HumansCells
  11. Roberts Kingman GA, Vyas DN, Jones FC, Brady SD, Chen HI, Reid K, Milhaven M, Bertino TS, Aguirre WE, Heins DC, von Hippel FA, Park PJ, Kirch M, Absher DM, Myers RM, Di Palma F, Bell MA, Kingsley DM, Veeramah KR. Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. Sci Adv. 2021 Jun; 7(25). PMID: 34144992.
    Citations: 9     Fields:    
  12. Jain D, Chu C, Alver BH, Lee S, Lee EA, Park PJ. HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data. Bioinformatics. 2021 05 23; 37(8):1045-1051. PMID: 33136153.
    Citations: 1     Fields:    Translation:HumansCells
  13. Lonfat N, Wang S, Lee C, Garcia M, Choi J, Park PJ, Cepko C. Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors. Development. 2021 05 01; 148(9). PMID: 33929509.
    Citations:    Fields:    Translation:AnimalsCells
  14. Viktorovskaya O, Chuang J, Jain D, Reim NI, López-Rivera F, Murawska M, Spatt D, Churchman LS, Park PJ, Winston F. Essential histone chaperones collaborate to regulate transcription and chromatin integrity. Genes Dev. 2021 05 01; 35(9-10):698-712. PMID: 33888559.
    Citations: 4     Fields:    Translation:AnimalsCells
  15. Rodin RE, Dou Y, Kwon M, Sherman MA, D'Gama AM, Doan RN, Rento LM, Girskis KM, Bohrson CL, Kim SN, Nadig A, Luquette LJ, Gulhan DC, Park PJ, Walsh CA. Author Correction: The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing. Nat Neurosci. 2021 Apr; 24(4):611. PMID: 33753946.
    Citations: 2     Fields:    
  16. Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov A. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biol. 2021 03 29; 22(1):92. PMID: 33781308.
    Citations: 6     Fields:    Translation:HumansCells
  17. Bhasin A, Bregger M, Kluk M, Park P, Feinglass J, Barsuk J. Exertional hypoxia in patients without resting hypoxia is an early predictor of moderate to severe COVID-19. Intern Emerg Med. 2021 11; 16(8):2097-2103. PMID: 33770368.
    Citations: 1     Fields:    Translation:Humans
  18. Cook JH, Melloni GEM, Gulhan DC, Park PJ, Haigis KM. The origins and genetic interactions of KRAS mutations are allele- and tissue-specific. Nat Commun. 2021 03 22; 12(1):1808. PMID: 33753749.
    Citations: 16     Fields:    Translation:Humans
  19. Bizzotto S, Dou Y, Ganz J, Doan RN, Kwon M, Bohrson CL, Kim SN, Bae T, Abyzov A, Park PJ, Walsh CA. Landmarks of human embryonic development inscribed in somatic mutations. Science. 2021 03 19; 371(6535):1249-1253. PMID: 33737485.
    Citations: 9     Fields:    Translation:HumansCells
  20. Robinson DCL, Ritso M, Nelson GM, Mokhtari Z, Nakka K, Bandukwala H, Goldman SR, Park PJ, Mounier R, Chazaud B, Brand M, Rudnicki MA, Adelman K, Dilworth FJ. Negative elongation factor regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation. Dev Cell. 2021 04 05; 56(7):1014-1029.e7. PMID: 33735618.
    Citations: 5     Fields:    Translation:AnimalsCells
  21. Färkkilä A, Rodríguez A, Oikkonen J, Gulhan DC, Nguyen H, Domínguez J, Ramos S, Mills CE, Pérez-Villatoro F, Lazaro JB, Zhou J, Clairmont CS, Moreau LA, Park PJ, Sorger PK, Hautaniemi S, Frias S, D'Andrea AD. Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells. Cancer Res. 2021 05 15; 81(10):2774-2787. PMID: 33514515.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  22. Yang HW, Lee S, Yang D, Dai H, Zhang Y, Han L, Zhao S, Zhang S, Ma Y, Johnson MF, Rattray AK, Johnson TA, Wang G, Zheng S, Carroll RS, Park PJ, Johnson MD. Deletions in CWH43 cause idiopathic normal pressure hydrocephalus. EMBO Mol Med. 2021 03 05; 13(3):e13249. PMID: 33459505.
    Citations: 9     Fields:    Translation:HumansAnimals
  23. Jung YL, Kirli K, Alver BH, Park PJ. Resources and challenges for integrative analysis of nuclear architecture data. Curr Opin Genet Dev. 2021 04; 67:103-110. PMID: 33450522.
    Citations: 1     Fields:    Translation:HumansCells
  24. Rodin RE, Dou Y, Kwon M, Sherman MA, D'Gama AM, Doan RN, Rento LM, Girskis KM, Bohrson CL, Kim SN, Nadig A, Luquette LJ, Gulhan DC, Park PJ, Walsh CA. The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing. Nat Neurosci. 2021 02; 24(2):176-185. PMID: 33432195.
    Citations: 18     Fields:    Translation:HumansCells
  25. Sherman MA, Rodin RE, Genovese G, Dias C, Barton AR, Mukamel RE, Berger B, Park PJ, Walsh CA, Loh PR. Large mosaic copy number variations confer autism risk. Nat Neurosci. 2021 02; 24(2):197-203. PMID: 33432194.
    Citations: 8     Fields:    Translation:Humans
  26. Kwon M, Lee S, Berselli M, Chu C, Park PJ. BamSnap: a lightweight viewer for sequencing reads in BAM files. Bioinformatics. 2021 Jan 08. PMID: 33416869.
    Citations:    Fields:    
  27. Reim NI, Chuang J, Jain D, Alver BH, Park PJ, Winston F. The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae. Nucleic Acids Res. 2020 10 09; 48(18):10241-10258. PMID: 32941642.
    Citations: 3     Fields:    Translation:AnimalsCells
  28. Haider S, Tyekucheva S, Prandi D, Fox NS, Ahn J, Xu AW, Pantazi A, Park PJ, Laird PW, Sander C, Wang W, Demichelis F, Loda M, Boutros PC. Systematic Assessment of Tumor Purity and Its Clinical Implications. JCO Precis Oncol. 2020; 4. PMID: 33015524.
    Citations: 4     Fields:    
  29. Chu C, Zhao B, Park PJ, Lee EA. Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data. Curr Protoc Hum Genet. 2020 09; 107(1):e102. PMID: 32662945.
    Citations: 4     Fields:    Translation:HumansCells
  30. Ettou S, Jung YL, Miyoshi T, Jain D, Hiratsuka K, Schumacher V, Taglienti ME, Morizane R, Park PJ, Kreidberg JA. Epigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury. Sci Adv. 2020 07; 6(30):eabb5460. PMID: 32754639.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  31. Goldman MJ, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O'Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein JN, Huber W, Valencia A, Park PJ, Papatheodorou I, Zhu J, Ferretti V, Vazquez M. A user guide for the online exploration and visualization of PCAWG data. Nat Commun. 2020 07 07; 11(1):3400. PMID: 32636365.
    Citations: 7     Fields:    Translation:Humans
  32. Yun JW, Yang L, Park HY, Lee CW, Cha H, Shin HT, Noh KW, Choi YL, Park WY, Park PJ. Dysregulation of cancer genes by recurrent intergenic fusions. Genome Biol. 2020 07 06; 21(1):166. PMID: 32631391.
    Citations: 6     Fields:    Translation:Humans
  33. Huang AY, Li P, Rodin RE, Kim SN, Dou Y, Kenny CJ, Akula SK, Hodge RD, Bakken TE, Miller JA, Lein ES, Park PJ, Lee EA, Walsh CA. Parallel RNA and DNA analysis after deep sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain. Proc Natl Acad Sci U S A. 2020 06 23; 117(25):13886-13895. PMID: 32522880.
    Citations: 10     Fields:    Translation:HumansCells
  34. Färkkilä A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C, Chen YA, Schapiro D, Zhou Y, Graham JR, Dezube BJ, Munster P, Santagata S, Garcia E, Rodig S, Lako A, Chowdhury D, Shapiro GI, Matulonis UA, Park PJ, Hautaniemi S, Sorger PK, Swisher EM, D'Andrea AD, Konstantinopoulos PA. Author Correction: Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Nat Commun. 2020 05 18; 11(1):2543. PMID: 32424117.
    Citations: 2     Fields:    
  35. Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, Park PJ. Publisher Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet. 2020 May 13. PMID: 32404988.
    Citations: 3     Fields:    
  36. Gulhan DC, Garcia E, Lee EK, Lindemann NI, Liu JF, Matulonis UA, Park PJ, Konstantinopoulos PA. Genomic Determinants of De Novo Resistance to Immune Checkpoint Blockade in Mismatch Repair-Deficient Endometrial Cancer. JCO Precis Oncol. 2020; 4:492-497. PMID: 32494760.
    Citations: 2     Fields:    
  37. Horton CA, Alver BH, Park PJ. GiniQC: a measure for quantifying noise in single-cell Hi-C data. Bioinformatics. 2020 05 01; 36(9):2902-2904. PMID: 32003786.
    Citations: 2     Fields:    Translation:Cells
  38. Touat M, Li YY, Boynton AN, Spurr LF, Iorgulescu JB, Bohrson CL, Cortes-Ciriano I, Birzu C, Geduldig JE, Pelton K, Lim-Fat MJ, Pal S, Ferrer-Luna R, Ramkissoon SH, Dubois F, Bellamy C, Currimjee N, Bonardi J, Qian K, Ho P, Malinowski S, Taquet L, Jones RE, Shetty A, Chow KH, Sharaf R, Pavlick D, Albacker LA, Younan N, Baldini C, Verreault M, Giry M, Guillerm E, Ammari S, Beuvon F, Mokhtari K, Alentorn A, Dehais C, Houillier C, Laigle-Donadey F, Psimaras D, Lee EQ, Nayak L, McFaline-Figueroa JR, Carpentier A, Cornu P, Capelle L, Mathon B, Barnholtz-Sloan JS, Chakravarti A, Bi WL, Chiocca EA, Fehnel KP, Alexandrescu S, Chi SN, Haas-Kogan D, Batchelor TT, Frampton GM, Alexander BM, Huang RY, Ligon AH, Coulet F, Delattre JY, Hoang-Xuan K, Meredith DM, Santagata S, Duval A, Sanson M, Cherniack AD, Wen PY, Reardon DA, Marabelle A, Park PJ, Idbaih A, Beroukhim R, Bandopadhayay P, Bielle F, Ligon KL. Mechanisms and therapeutic implications of hypermutation in gliomas. Nature. 2020 04; 580(7804):517-523. PMID: 32322066.
    Citations: 112     Fields:    Translation:HumansAnimalsCells
  39. Miller DT, Cortés-Ciriano I, Pillay N, Hirbe AC, Snuderl M, Bui MM, Piculell K, Al-Ibraheemi A, Dickson BC, Hart J, Jones K, Jordan JT, Kim RH, Lindsay D, Nishida Y, Ullrich NJ, Wang X, Park PJ, Flanagan AM. Genomics of MPNST (GeM) Consortium: Rationale and Study Design for Multi-Omic Characterization of NF1-Associated and Sporadic MPNSTs. Genes (Basel). 2020 04 02; 11(4). PMID: 32252413.
    Citations: 3     Fields:    Translation:HumansCells
  40. Wang S, Lee S, Chu C, Jain D, Kerpedjiev P, Nelson GM, Walsh JM, Alver BH, Park PJ. HiNT: a computational method for detecting copy number variations and translocations from Hi-C data. Genome Biol. 2020 03 23; 21(1):73. PMID: 32293513.
    Citations: 17     Fields:    Translation:Cells
  41. Färkkilä A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C, Chen YA, Schapiro D, Zhou Y, Graham JR, Dezube BJ, Munster P, Santagata S, Garcia E, Rodig S, Lako A, Chowdhury D, Shapiro GI, Matulonis UA, Park PJ, Hautaniemi S, Sorger PK, Swisher EM, D'Andrea AD, Konstantinopoulos PA. Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Nat Commun. 2020 03 19; 11(1):1459. PMID: 32193378.
    Citations: 59     Fields:    Translation:HumansCellsCTClinical Trials
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