Contact, publication, and social network information about Harvard faculty and fellows. Harvard Catalyst Profiles
Keywords
Last Name
Institution

Peter J. Park, PH.D.

TitleAssociate Professor of Pediatrics
InstitutionChildren's Hospital Boston
DepartmentPediatrics
AddressHMS Center for Biomedical Informatics
Countway Lib - Rm 318
10 Shattuck St
Boston MA 02115
Phone617/432-7373
Other Positions
TitleMember of the Affiliated Faculty of the Harvard-MIT Division of Health Sciences and Technology
InstitutionMassachusetts Institute of Technology
DepartmentHealth Sciences and Technology


 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.
List All   |   Timeline
  1. Li H, Park P, Liu W, Matney J, Liao Z, Balter P, Li Y, Zhang X, Li X, Zhu XR. Patient-specific quantification of respiratory motion-induced dose uncertainty for step-and-shoot IMRT of lung cancer. Med Phys. 2013 Dec; 40(12):121712.
    View in: PubMed
  2. Kim TM, Laird PW, Park PJ. The landscape of microsatellite instability in colorectal and endometrial cancer genomes. Cell. 2013 Nov 7; 155(4):858-68.
    View in: PubMed
  3. Ferrari F, Plachetka A, Alekseyenko AA, Jung YL, Ozsolak F, Kharchenko PV, Park PJ, Kuroda MI. "Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts. Cell Rep. 2013 Nov 14; 5(3):629-36.
    View in: PubMed
  4. Davoli T, Xu AW, Mengwasser KE, Sack LM, Yoon JC, Park PJ, Elledge SJ. Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell. 2013 Nov 7; 155(4):948-62.
    View in: PubMed
  5. Ajay AK, Kim TM, Ramirez-Gonzalez V, Park PJ, Frank DA, Vaidya VS. A bioinformatics approach identifies signal transducer and activator of transcription-3 and checkpoint kinase 1 as upstream regulators of kidney injury molecule-1 after kidney injury. J Am Soc Nephrol. 2014 Jan; 25(1):105-18.
    View in: PubMed
  6. Degennaro CM, Alver BH, Marguerat S, Stepanova E, Davis CP, Bähler J, Park PJ, Winston F. Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast. Mol Cell Biol. 2013 Dec; 33(24):4779-92.
    View in: PubMed
  7. Chang K, Creighton CJ, Davis C, Donehower L, Drummond J, Wheeler D, Ally A, Balasundaram M, Birol I, Butterfield YS, Chu A, Chuah E, Chun HJ, Dhalla N, Guin R, Hirst M, Hirst C, Holt RA, Jones SJ, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall AJ, Robertson AG, Schein JE, Sipahimalani P, Tam A, Thiessen N, Varhol RJ, Beroukhim R, Bhatt AS, Brooks AN, Cherniack AD, Freeman SS, Gabriel SB, Helman E, Jung J, Meyerson M, Ojesina AI, Pedamallu CS, Saksena G, Schumacher SE, Tabak B, Zack T, Lander ES, Bristow CA, Hadjipanayis A, Haseley P, Kucherlapati R, Lee S, Lee E, Luquette LJ, Mahadeshwar HS, Pantazi A, Parfenov M, Park PJ, Protopopov A, Ren X, Santoso N, Seidman J, Seth S, Song X, Tang J, Xi R, Xu AW, Yang L, Zeng D, Auman JT, Balu S, Buda E, Fan C, Hoadley KA, Jones CD, Meng S, Mieczkowski PA, Parker JS, Perou CM, Roach J, Shi Y, Silva GO, Tan D, Veluvolu U, Waring S, Wilkerson MD, Wu J, Zhao W, Bodenheimer T, Hayes DN, Hoyle AP, Jeffreys SR, Mose LE, Simons JV, Soloway MG, Baylin SB, Berman BP, Bootwalla MS, Danilova L, Herman JG, Hinoue T, Laird PW, Rhie SK, Shen H, Triche T, Weisenberger DJ, Carter SL, Cibulskis K, Chin L, Zhang J, Getz G, Sougnez C, Wang M, Saksena G, Carter SL, Cibulskis K, Chin L, Zhang J, Getz G, Dinh H, Doddapaneni HV, Gibbs R, Gunaratne P, Han Y, Kalra D, Kovar C, Lewis L, Morgan M, Morton D, Muzny D, Reid J, Xi L, Cho J, Dicara D, Frazer S, Gehlenborg N, Heiman DI, Kim J, Lawrence MS, Lin P, Liu Y, Noble MS, Stojanov P, Voet D, Zhang H, Zou L, Stewart C, Bernard B, Bressler R, Eakin A, Iype L, Knijnenburg T, Kramer R, Kreisberg R, Leinonen K, Lin J, Liu Y, Miller M, Reynolds SM, Rovira H, Shmulevich I, Thorsson V, Yang D, Zhang W, Amin S, Wu CJ, Wu CC, Akbani R, Aldape K, Baggerly KA, Broom B, Casasent TD, Cleland J, Creighton C, Dodda D, Edgerton M, Han L, Herbrich SM, Ju Z, Kim H, Lerner S, Li J, Liang H, Liu W, Lorenzi PL, Lu Y, Melott J, Mills GB, Nguyen L, Su X, Verhaak R, Wang W, Weinstein JN, Wong A, Yang Y, Yao J, Yao R, Yoshihara K, Yuan Y, Yung AK, Zhang N, Zheng S, Ryan M, Kane DW, Aksoy BA, Ciriello G, Dresdner G, Gao J, Gross B, Jacobsen A, Kahles A, Ladanyi M, Lee W, Lehmann KV, Miller ML, Ramirez R, Rätsch G, Reva B, Sander C, Schultz N, Senbabaoglu Y, Shen R, Sinha R, Sumer SO, Sun Y, Taylor BS, Weinhold N, Fei S, Spellman P, Benz C, Carlin D, Cline M, Craft B, Ellrott K, Goldman M, Haussler D, Ma S, Ng S, Paull E, Radenbaugh A, Salama S, Sokolov A, Stuart JM, Swatloski T, Uzunangelov V, Waltman P, Yau C, Zhu J, Hamilton SR, Getz G, Sougnez C, Abbott S, Abbott R, Dees ND, Delehaunty K, Ding L, Dooling DJ, Eldred JM, Fronick CC, Fulton R, Fulton LL, Kalicki-Veizer J, Kanchi KL, Kandoth C, Koboldt DC, Larson DE, Ley TJ, Lin L, Lu C, Magrini VJ, Mardis ER, McLellan MD, McMichael JF, Miller CA, O'Laughlin M, Pohl C, Schmidt H, Smith SM, Walker J, Wallis JW, Wendl MC, Wilson RK, Wylie T, Zhang Q, Burton R, Jensen MA, Kahn A, Pihl T, Pot D, Wan Y, Levine DA, Black AD, Bowen J, Frick J, Gastier-Foster JM, Harper HA, Helsel C, Leraas KM, Lichtenberg TM, McAllister C, Ramirez NC, Sharpe S, Wise L, Zmuda E, Chanock SJ, Davidsen T, Demchok JA, Eley G, Felau I, Ozenberger BA, Sheth M, Sofia H, Staudt L, Tarnuzzer R, Wang Z, Yang L, Zhang J, Omberg L, Margolin A, Raphael BJ, Vandin F, Wu HT, Leiserson MD, Benz SC, Vaske CJ, Noushmehr H, Knijnenburg T, Wolf D, Veer LV, Collisson EA, Anastassiou D, Ou Yang TH, Lopez-Bigas N, Gonzalez-Perez A, Tamborero D, Xia Z, Li W, Cho DY, Przytycka T, Hamilton M, McGuire S, Nelander S, Johansson P, Jörnsten R, Kling T, Sanchez J, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Sep 26; 45(10):1113-20.
    View in: PubMed
  8. Gokcumen O, Tischler V, Tica J, Zhu Q, Iskow RC, Lee E, Fritz MH, Langdon A, Stütz AM, Pavlidis P, Benes V, Mills RE, Park PJ, Lee C, Korbel JO. Primate genome architecture influences structural variation mechanisms and functional consequences. Proc Natl Acad Sci U S A. 2013 Sep 24; 110(39):15764-9.
    View in: PubMed
  9. Soruco MM, Chery J, Bishop EP, Siggers T, Tolstorukov MY, Leydon AR, Sugden AU, Goebel K, Feng J, Xia P, Vedenko A, Bulyk ML, Park PJ, Larschan E. The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation. Genes Dev. 2013 Jul 15; 27(14):1551-6.
    View in: PubMed
  10. Majumdar S, Gong EM, Di Vizio D, Dreyfuss J, Degraff DJ, Hager MH, Park PJ, Bellmunt J, Matusik RJ, Rosenberg JE, Adam RM. Loss of Sh3gl2/Endophilin A1 Is a Common Event in Urothelial Carcinoma that Promotes Malignant Behavior. Neoplasia. 2013 Jul; 15(7):749-60.
    View in: PubMed
  11. Creighton CJ, Morgan M, Gunaratne PH, Wheeler DA, Gibbs RA, Gordon Robertson A, Chu A, Beroukhim R, Cibulskis K, Signoretti S, Vandin Hsin-Ta Wu F, Raphael BJ, Verhaak RG, Tamboli P, Torres-Garcia W, Akbani R, Weinstein JN, Reuter V, Hsieh JJ, Rose Brannon A, Ari Hakimi A, Jacobsen A, Ciriello G, Reva B, Ricketts CJ, Marston Linehan W, Stuart JM, Rathmell WK, Shen H, Laird PW, Muzny D, Davis C, Morgan M, Xi L, Chang K, Kakkar N, Treviño LR, Benton S, Reid JG, Morton D, Doddapaneni H, Han Y, Lewis L, Dinh H, Kovar C, Zhu Y, Santibanez J, Wang M, Hale W, Kalra D, Creighton CJ, Wheeler DA, Gibbs RA, Getz G, Cibulskis K, Lawrence MS, Sougnez C, Carter SL, Sivachenko A, Lichtenstein L, Stewart C, Voet D, Fisher S, Gabriel SB, Lander E, Beroukhim R, Schumacher SE, Tabak B, Saksena G, Onofrio RC, Carter SL, Cherniack AD, Gentry J, Ardlie K, Sougnez C, Getz G, Gabriel SB, Meyerson M, Gordon Robertson A, Chu A, Chun HJ, Mungall AJ, Sipahimalani P, Stoll D, Ally A, Balasundaram M, Butterfield YS, Carlsen R, Carter C, Chuah E, Coope RJ, Dhalla N, Gorski S, Guin R, Hirst C, Hirst M, Holt RA, Lebovitz C, Lee D, Li HI, Mayo M, Moore RA, Pleasance E, Plettner P, Schein JE, Shafiei A, Slobodan JR, Tam A, Thiessen N, Varhol RJ, Wye N, Zhao Y, Birol I, Jones SJ, Marra MA, Auman JT, Tan D, Jones CD, Hoadley KA, Mieczkowski PA, Mose LE, Jefferys SR, Topal MD, Liquori C, Turman YJ, Shi Y, Waring S, Buda E, Walsh J, Wu J, Bodenheimer T, Hoyle AP, Simons JV, Soloway MG, Balu S, Parker JS, Neil Hayes D, Perou CM, Kucherlapati R, Park P, Shen H, Triche T, Weisenberger DJ, Lai PH, Bootwalla MS, Maglinte DT, Mahurkar S, Berman BP, Van Den Berg DJ, Cope L, Baylin SB, Laird PW, Creighton CJ, Wheeler DA, Getz G, Noble MS, Dicara D, Zhang H, Cho J, Heiman DI, Gehlenborg N, Voet D, Mallard W, Lin P, Frazer S, Stojanov P, Liu Y, Zhou L, Kim J, Lawrence MS, Chin L, Vandin F, Wu HT, Raphael BJ, Benz C, Yau C, Reynolds SM, Shmulevich I, Verhaak RG, Torres-Garcia W, Vegesna R, Kim H, Zhang W, Cogdell D, Jonasch E, Ding Z, Lu Y, Akbani R, Zhang N, Unruh AK, Casasent TD, Wakefield C, Tsavachidou D, Chin L, Mills GB, Weinstein JN, Jacobsen A, Rose Brannon A, Ciriello G, Schultz N, Ari Hakimi A, Reva B, Antipin Y, Gao J, Cerami E, Gross B, Arman Aksoy B, Sinha R, Weinhold N, Onur Sumer S, Taylor BS, Shen R, Ostrovnaya I, Hsieh JJ, Berger MF, Ladanyi M, Sander C, Fei SS, Stout A, Spellman PT, Rubin DL, Liu TT, Stuart JM, Ng S, Paull EO, Carlin D, Goldstein T, Waltman P, Ellrott K, Zhu J, Haussler D, Gunaratne PH, Xiao W, Shelton C, Gardner J, Penny R, Sherman M, Mallery D, Morris S, Paulauskis J, Burnett K, Shelton T, Signoretti S, Kaelin WG, Choueiri T, Atkins MB, Penny R, Burnett K, Mallery D, Curley E, Tickoo S, Reuter V, Rathmell WK, Thorne L, Boice L, Huang M, Fisher JC, Marston Linehan W, Vocke CD, Peterson J, Worrell R, Merino MJ, Schmidt LS, Tamboli P, Czerniak BA, Aldape KD, Wood CG, Boyd J, Weaver J, Iacocca MV, Petrelli N, Witkin G, Brown J, Czerwinski C, Huelsenbeck-Dill L, Rabeno B, Myers J, Morrison C, Bergsten J, Eckman J, Harr J, Smith C, Tucker K, Anne Zach L, Bshara W, Gaudioso C, Morrison C, Dhir R, Maranchie J, Nelson J, Parwani A, Potapova O, Fedosenko K, Cheville JC, Houston Thompson R, Signoretti S, Kaelin WG, Atkins MB, Tickoo S, Reuter V, Marston Linehan W, Vocke CD, Peterson J, Merino MJ, Schmidt LS, Tamboli P, Mosquera JM, Rubin MA, Blute ML, Rathmell WK, Pihl T, Jensen M, Sfeir R, Kahn A, Chu A, Kothiyal P, Snyder E, Pontius J, Ayala B, Backus M, Walton J, Baboud J, Berton D, Nicholls M, Srinivasan D, Raman R, Girshik S, Kigonya P, Alonso S, Sanbhadti R, Barletta S, Pot D, Sheth M, Demchok JA, Davidsen T, Wang Z, Yang L, Tarnuzzer RW, Zhang J, Eley G, Ferguson ML, Mills Shaw KR, Guyer MS, Ozenberger BA, Sofia HJ. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 Jul 4; 499(7456):43-9.
    View in: PubMed
  12. Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE. Variable Requirements for DNA-Binding Proteins at Polycomb-Dependent Repressive Regions in Human HOX Clusters. Mol Cell Biol. 2013 Aug; 33(16):3274-85.
    View in: PubMed
  13. Tolstorukov MY, Sansam CG, Lu P, Koellhoffer EC, Helming KC, Alver BH, Tillman EJ, Evans JA, Wilson BG, Park PJ, Roberts CW. Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters. Proc Natl Acad Sci U S A. 2013 Jun 18; 110(25):10165-70.
    View in: PubMed
  14. Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, Kharchenko PV, Park PJ, Hochedlinger K. Genome-wide Chromatin Interactions of the Nanog Locus in Pluripotency, Differentiation, and Reprogramming. Cell Stem Cell. 2013 Jun 6; 12(6):699-712.
    View in: PubMed
  15. Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh CH, 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. 2013 May 9; 153(4):919-29.
    View in: PubMed
  16. Getz G, Gabriel SB, Cibulskis K, Lander E, Sivachenko A, Sougnez C, Lawrence M, Kandoth C, Dooling D, Fulton R, Fulton L, Kalicki-Veizer J, McLellan MD, O'Laughlin M, Schmidt H, Wilson RK, Ye K, Ding L, Mardis ER, Ally A, Balasundaram M, Birol I, Butterfield YS, Carlsen R, Carter C, Chu A, Chuah E, Chun HJ, Dhalla N, Guin R, Hirst C, Holt RA, Jones SJ, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall AJ, Plettner P, Schein JE, Sipahimalani P, Tam A, Varhol RJ, Gordon Robertson A, Cherniack AD, Pashtan I, Saksena G, Onofrio RC, Schumacher SE, Tabak B, Carter SL, Hernandez B, Gentry J, Salvesen HB, Ardlie K, Getz G, Winckler W, Beroukhim R, Gabriel SB, Meyerson M, Hadjipanayis A, Lee S, Mahadeshwar HS, Park P, Protopopov A, Ren X, Seth S, Song X, Tang J, Xi R, Yang L, Zeng D, Kucherlapati R, Chin L, Zhang J, Todd Auman J, Balu S, Bodenheimer T, Buda E, Neil Hayes D, Hoyle AP, Jefferys SR, Jones CD, Meng S, Mieczkowski PA, Mose LE, Parker JS, Perou CM, Roach J, Shi Y, Simons JV, Soloway MG, Tan D, Topal MD, Waring S, Wu J, Hoadley KA, Baylin SB, Bootwalla MS, Lai PH, Triche TJ, Van Den Berg DJ, Weisenberger DJ, Laird PW, Shen H, Chin L, Zhang J, Getz G, Cho J, Dicara D, Frazer S, Heiman D, Jing R, Lin P, Mallard W, Stojanov P, Voet D, Zhang H, Zou L, Noble M, Lawrence M, Reynolds SM, Shmulevich I, Arman Aksoy B, Antipin Y, Ciriello G, Dresdner G, Gao J, Gross B, Jacobsen A, Ladanyi M, Reva B, Sander C, Sinha R, Onur Sumer S, Taylor BS, Cerami E, Weinhold N, Schultz N, Shen R, Benz S, Goldstein T, Haussler D, Ng S, Szeto C, Stuart J, Benz CC, Yau C, Zhang W, Annala M, Broom BM, Casasent TD, Ju Z, Liang H, Liu G, Lu Y, Unruh AK, Wakefield C, Weinstein JN, Zhang N, Liu Y, Broaddus R, Akbani R, Mills GB, Adams C, Barr T, Black AD, Bowen J, Deardurff J, Frick J, Gastier-Foster JM, Grossman T, Harper HA, Hart-Kothari M, Helsel C, Hobensack A, Kuck H, Kneile K, Leraas KM, Lichtenberg TM, McAllister C, Pyatt RE, Ramirez NC, Tabler TR, Vanhoose N, White P, Wise L, Zmuda E, Barnabas N, Berry-Green C, Blanc V, Boice L, Button M, Farkas A, Green A, Mackenzie J, Nicholson D, Kalloger SE, Blake Gilks C, Karlan BY, Lester J, Orsulic S, Borowsky M, Cadungog M, Czerwinski C, Huelsenbeck-Dill L, Iacocca M, Petrelli N, Rabeno B, Witkin G, Nemirovich-Danchenko E, Potapova O, Rotin D, Berchuck A, Birrer M, Disaia P, Monovich L, Curley E, Gardner J, Mallery D, Penny R, Dowdy SC, Winterhoff B, Dao L, Gostout B, Meuter A, Teoman A, Dao F, Olvera N, Bogomolniy F, Garg K, Soslow RA, Levine DA, Abramov M, Bartlett JM, Kodeeswaran S, Parfitt J, Moiseenko F, Clarke BA, Goodman MT, Carney ME, Matsuno RK, Fisher J, Huang M, Rathmell WK, Thorne L, Van Le L, Dhir R, Edwards R, Elishaev E, Zorn K, Broaddus R, Goodfellow PJ, Mutch D, Schultz N, Liu Y, Akbani R, Cherniack AD, Cerami E, Weinhold N, Shen H, Hoadley KA, Kahn AB, Bell DW, Pollock PM, Wang C, A Wheeler D, Shinbrot E, Karlan BY, Berchuck A, Dowdy SC, Winterhoff B, Goodman MT, Gordon Robertson A, Beroukhim R, Pashtan I, Salvesen HB, Laird PW, Noble M, Stuart J, Ding L, Kandoth C, Blake Gilks C, Soslow RA, Goodfellow PJ, Mutch D, Broaddus R, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA, Ayala B, Chu AL, Jensen MA, Kothiyal P, Pihl TD, Pontius J, Pot DA, Snyder EE, Srinivasan D, Kahn AB, Mills Shaw KR, Sheth M, Davidsen T, Eley Martin L Ferguson G, Demchok JA, Yang L, Guyer MS, Ozenberger BA, Sofia HJ, Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Gordon Robertson A, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA. Integrated genomic characterization of endometrial carcinoma. Nature. 2013 May 2; 497(7447):67-73.
    View in: PubMed
  17. Ferrari F, Jung YL, Kharchenko PV, Plachetka A, Alekseyenko AA, Kuroda MI, Park PJ. Comment on "Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters". Science. 2013 Apr 19; 340(6130):273; discussion 273.
    View in: PubMed
  18. Alekseyenko AA, Ellison CE, Gorchakov AA, Zhou Q, Kaiser VB, Toda N, Walton Z, Peng S, Park PJ, Bachtrog D, Kuroda MI. Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila. Genes Dev. 2013 Apr 15; 27(8):853-8.
    View in: PubMed
  19. Zhang B, Day DS, Ho JW, Song L, Cao J, Christodoulou D, Seidman JG, Crawford GE, Park PJ, Pu WT. A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. Genome Res. 2013 Jun; 23(6):917-27.
    View in: PubMed
  20. Sui SH, Merrill E, Gehlenborg N, Haseley P, Sytchev I, Park R, Rocca-Serra P, Corlosquet S, Gonzalez-Beltran A, Maguire E, Hofmann O, Park P, Das S, Sansone SA, Hide W. The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework. AMIA Summits Transl Sci Proc. 2013; 2013:70.
    View in: PubMed
  21. Gehlenborg N, Noble MS, Getz G, Chin L, Park PJ. Nozzle: a report generation toolkit for data analysis pipelines. Bioinformatics. 2013 Apr 15; 29(8):1089-91.
    View in: PubMed
  22. Tzatsos A, Paskaleva P, Ferrari F, Deshpande V, Stoykova S, Contino G, Wong KK, Lan F, Trojer P, Park PJ, Bardeesy N. KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs. J Clin Invest. 2013 Feb 1; 123(2):727-39.
    View in: PubMed
  23. Kim TM, Xi R, Luquette LJ, Park RW, Johnson MD, Park PJ. Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Res. 2013 Feb; 23(2):217-27.
    View in: PubMed
  24. Evrony GD, Cai X, Lee E, Hills LB, Elhosary PC, Lehmann HS, Parker JJ, Atabay KD, Gilmore EC, Poduri A, Park PJ, Walsh CA. Single-neuron sequencing analysis of l1 retrotransposition and somatic mutation in the human brain. Cell. 2012 Oct 26; 151(3):483-96.
    View in: PubMed
  25. Tan X, Hu L, Luquette LJ, Gao G, Liu Y, Qu H, Xi R, Lu ZJ, Park PJ, Elledge SJ. Systematic identification of synergistic drug pairs targeting HIV. Nat Biotechnol. 2012 Nov; 30(11):1125-30.
    View in: PubMed
  26. Xi R, Lee S, Park PJ. A survey of copy-number variation detection tools based on high-throughput sequencing data. Curr Protoc Hum Genet. 2012 Oct; Chapter 7:Unit7.19.
    View in: PubMed
  27. Riddle NC, Jung YL, Gu T, Alekseyenko AA, Asker D, Gui H, Kharchenko PV, Minoda A, Plachetka A, Schwartz YB, Tolstorukov MY, Kuroda MI, Pirrotta V, Karpen GH, Park PJ, Elgin SC. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genet. 2012 Sep; 8(9):e1002954.
    View in: PubMed
  28. Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee BK, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey TS, Gerstein M, Giardine B, Greven M, Hardison RC, Harris RS, Herrero J, Hoffman MM, Iyer S, Kelllis M, Khatun J, Kheradpour P, Kundaje A, Lassman T, Li Q, Lin X, Marinov GK, Merkel A, Mortazavi A, Parker SC, Reddy TE, Rozowsky J, Schlesinger F, Thurman RE, Wang J, Ward LD, Whitfield TW, Wilder SP, Wu W, Xi HS, Yip KY, Zhuang J, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Pazin MJ, Lowdon RF, Dillon LA, Adams LB, Kelly CJ, Zhang J, Wexler JR, Green ED, Good PJ, Feingold EA, Bernstein BE, Birney E, Crawford GE, Dekker J, Elinitski L, Farnham PJ, Gerstein M, Giddings MC, Gingeras TR, Green ED, Guigó R, Hardison RC, Hubbard TJ, Kellis M, Kent WJ, Lieb JD, Margulies EH, Myers RM, Snyder M, Starnatoyannopoulos JA, Tennebaum SA, Weng Z, White KP, Wold B, Khatun J, Yu Y, Wrobel J, Risk BA, Gunawardena HP, Kuiper HC, Maier CW, Xie L, Chen X, Giddings MC, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Kheradpour P, Mikkelsen TS, Gillespie S, Goren A, Ram O, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Eaton ML, Kellis M, Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Batut P, Bell I, Bell K, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena HP, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Li G, Luo OJ, Park E, Preall JB, Presaud K, Ribeca P, Risk BA, Robyr D, Ruan X, Sammeth M, Sandu KS, Schaeffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Hayashizaki Y, Harrow J, Gerstein M, Hubbard TJ, Reymond A, Antonarakis SE, Hannon GJ, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR, Rosenbloom KR, Sloan CA, Learned K, Malladi VS, Wong MC, Barber GP, Cline MS, Dreszer TR, Heitner SG, Karolchik D, Kent WJ, Kirkup VM, Meyer LR, Long JC, Maddren M, Raney BJ, Furey TS, Song L, Grasfeder LL, Giresi PG, Lee BK, Battenhouse A, Sheffield NC, Simon JM, Showers KA, Safi A, London D, Bhinge AA, Shestak C, Schaner MR, Kim SK, Zhang ZZ, Mieczkowski PA, Mieczkowska JO, Liu Z, McDaniell RM, Ni Y, Rashid NU, Kim MJ, Adar S, Zhang Z, Wang T, Winter D, Keefe D, Birney E, Iyer VR, Lieb JD, Crawford GE, Li G, Sandhu KS, Zheng M, Wang P, Luo OJ, Shahab A, Fullwood MJ, Ruan X, Ruan Y, Myers RM, Pauli F, Williams BA, Gertz J, Marinov GK, Reddy TE, Vielmetter J, Partridge EC, Trout D, Varley KE, Gasper C, Bansal A, Pepke S, Jain P, Amrhein H, Bowling KM, Anaya M, Cross MK, King B, Muratet MA, Antoshechkin I, Newberry KM, McCue K, Nesmith AS, Fisher-Aylor KI, Pusey B, DeSalvo G, Parker SL, Balasubramanian S, Davis NS, Meadows SK, Eggleston T, Gunter C, Newberry JS, Levy SE, Absher DM, Mortazavi A, Wong WH, Wold B, Blow MJ, Visel A, Pennachio LA, Elnitski L, Margulies EH, Parker SC, Petrykowska HM, Abyzov A, Aken B, Barrell D, Barson G, Berry A, Bignell A, Boychenko V, Bussotti G, Chrast J, Davidson C, Derrien T, Despacio-Reyes G, Diekhans M, Ezkurdia I, Frankish A, Gilbert J, Gonzalez JM, Griffiths E, Harte R, Hendrix DA, Howald C, Hunt T, Jungreis I, Kay M, Khurana E, Kokocinski F, Leng J, Lin MF, Loveland J, Lu Z, Manthravadi D, Mariotti M, Mudge J, Mukherjee G, Notredame C, Pei B, Rodriguez JM, Saunders G, Sboner A, Searle S, Sisu C, Snow C, Steward C, Tanzer A, Tapanan E, Tress ML, van Baren MJ, Walters N, Washieti S, Wilming L, Zadissa A, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6; 489(7414):57-74.
    View in: PubMed
  29. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31.
    View in: PubMed
  30. Larschan E, Soruco MM, Lee OK, Peng S, Bishop E, Chery J, Goebel K, Feng J, Park PJ, Kuroda MI. Identification of chromatin-associated regulators of MSL complex targeting in Drosophila dosage compensation. PLoS Genet. 2012; 8(7):e1002830.
    View in: PubMed
  31. Tolstorukov MY, Goldman JA, Gilbert C, Ogryzko V, Kingston RE, Park PJ. Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. Mol Cell. 2012 Aug 24; 47(4):596-607.
    View in: PubMed
  32. Schwartz YB, Linder-Basso D, Kharchenko PV, Tolstorukov MY, Kim M, Li HB, Gorchakov AA, Minoda A, Shanower G, Alekseyenko AA, Riddle NC, Jung YL, Gu T, Plachetka A, Elgin SC, Kuroda MI, Park PJ, Savitsky M, Karpen GH, Pirrotta V. Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res. 2012 Nov; 22(11):2188-98.
    View in: PubMed
  33. Jiang X, Xing H, Kim TM, Jung Y, Huang W, Yang HW, Song S, Park PJ, Carroll RS, Johnson MD. Numb regulates glioma stem cell fate and growth by altering epidermal growth factor receptor and Skp1-Cullin-F-box ubiquitin ligase activity. Stem Cells. 2012 Jul; 30(7):1313-26.
    View in: PubMed
  34. Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ. Landscape of somatic retrotransposition in human cancers. Science. 2012 Aug 24; 337(6097):967-71.
    View in: PubMed
  35. Kim YJ, Lee HJ, Kim TM, Eisinger-Mathason TS, Zhang AY, Schmidt B, Karl DL, Nakazawa MS, Park PJ, Simon MC, Yoon SS. Overcoming evasive resistance from vascular endothelial growth factor a inhibition in sarcomas by genetic or pharmacologic targeting of hypoxia-inducible factor 1a. Int J Cancer. 2013 Jan 1; 132(1):29-41.
    View in: PubMed
  36. Saikumar J, Hoffmann D, Kim TM, Gonzalez VR, Zhang Q, Goering PL, Brown RP, Bijol V, Park PJ, Waikar SS, Vaidya VS. Expression, circulation, and excretion profile of microRNA-21, -155, and -18a following acute kidney injury. Toxicol Sci. 2012 Oct; 129(2):256-67.
    View in: PubMed
  37. Reis BY, Olson KL, Tian L, Bohn RL, Brownstein JS, Park PJ, Cziraky MJ, Wilson MD, Mandl KD. A pharmacoepidemiological network model for drug safety surveillance: statins and rhabdomyolysis. Drug Saf. 2012 May 1; 35(5):395-406.
    View in: PubMed
  38. Alekseyenko AA, Ho JW, Peng S, Gelbart M, Tolstorukov MY, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E, Gu T, Minoda A, Riddle NC, Schwartz YB, Elgin SC, Karpen GH, Pirrotta V, Kuroda MI, Park PJ. Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genet. 2012; 8(4):e1002646.
    View in: PubMed
  39. Balakrishnan A, Stearns AT, Park PJ, Dreyfuss JM, Ashley SW, Rhoads DB, Tavakkolizadeh A. Upregulation of proapoptotic microRNA mir-125a after massive small bowel resection in rats. Ann Surg. 2012 Apr; 255(4):747-53.
    View in: PubMed
  40. Lachke SA, Ho JW, Kryukov GV, O'Connell DJ, Aboukhalil A, Bulyk ML, Park PJ, Maas RL. iSyTE: integrated Systems Tool for Eye gene discovery. Invest Ophthalmol Vis Sci. 2012 Mar; 53(3):1617-27.
    View in: PubMed
  41. Stadtfeld M, Apostolou E, Ferrari F, Choi J, Walsh RM, Chen T, Ooi SS, Kim SY, Bestor TH, Shioda T, Park PJ, Hochedlinger K. Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nat Genet. 2012 Apr; 44(4):398-405, S1-2.
    View in: PubMed
  42. Hodge JC, Kim TM, Dreyfuss JM, Somasundaram P, Christacos NC, Rousselle M, Quade BJ, Park PJ, Stewart EA, Morton CC. Expression profiling of uterine leiomyomata cytogenetic subgroups reveals distinct signatures in matched myometrium: transcriptional profilingof the t(12;14) and evidence in support of predisposing genetic heterogeneity. Hum Mol Genet. 2012 May 15; 21(10):2312-29.
    View in: PubMed
  43. Ahn HS, Shin YS, Park PJ, Kang KN, Kim Y, Lee HJ, Yang HK, Kim CW. Serum biomarker panels for the diagnosis of gastric adenocarcinoma. Br J Cancer. 2012 Feb 14; 106(4):733-9.
    View in: PubMed
  44. O'Connell DJ, Ho JW, Mammoto T, Turbe-Doan A, O'Connell JT, Haseley PS, Koo S, Kamiya N, Ingber DE, Park PJ, Maas RL. A Wnt-bmp feedback circuit controls intertissue signaling dynamics in tooth organogenesis. Sci Signal. 2012 Jan 10; 5(206):ra4.
    View in: PubMed
  45. Yang HW, Kim TM, Song SS, Shrinath N, Park R, Kalamarides M, Park PJ, Black PM, Carroll RS, Johnson MD. Alternative splicing of CHEK2 and codeletion with NF2 promote chromosomal instability in meningioma. Neoplasia. 2012 Jan; 14(1):20-8.
    View in: PubMed
  46. Kharchenko PV, Xi R, Park PJ. Evidence for dosage compensation between the X chromosome and autosomes in mammals. Nat Genet. 2011 Dec; 43(12):1167-9; author reply 1171-2.
    View in: PubMed
  47. Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, Johnson MD, Muzny DM, Wheeler DA, Gibbs RA, Kucherlapati R, Park PJ. Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Natl Acad Sci U S A. 2011 Nov 15; 108(46):E1128-36.
    View in: PubMed
  48. Kim TM, Ramírez V, Barrera-Chimal J, Bobadilla NA, Park PJ, Vaidya VS. Gene expression analysis reveals the cell cycle and kinetochore genes participating in ischemia reperfusion injury and early development in kidney. PLoS One. 2011; 6(9):e25679.
    View in: PubMed
  49. Zacharek SJ, Fillmore CM, Lau AN, Gludish DW, Chou A, Ho JW, Zamponi R, Gazit R, Bock C, Jäger N, Smith ZD, Kim TM, Saunders AH, Wong J, Lee JH, Roach RR, Rossi DJ, Meissner A, Gimelbrant AA, Park PJ, Kim CF. Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci. Cell Stem Cell. 2011 Sep 2; 9(3):272-81.
    View in: PubMed
  50. Pihlajamäki J, Lerin C, Itkonen P, Boes T, Floss T, Schroeder J, Dearie F, Crunkhorn S, Burak F, Jimenez-Chillaron JC, Kuulasmaa T, Miettinen P, Park PJ, Nasser I, Zhao Z, Zhang Z, Xu Y, Wurst W, Ren H, Morris AJ, Stamm S, Goldfine AB, Laakso M, Patti ME. Expression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis. Cell Metab. 2011 Aug 3; 14(2):208-18.
    View in: PubMed
  51. Hwang S, Yu YD, Park GC, Choi YI, Park PJ, Jung SW, Namgoong JM, Yoon SY, Ha HS, Hong JJ, Kim IO, Jeon MK, Ma JE, Choi SY, Yun JS, Jung DH, Song GW, Ha TY, Moon DB, Kimy KH, Ahn CS, Lee SG. Safety of ultra-rapid intravenous infusion of hepatitis B immunoglobulin in liver transplant recipients. Transplant Proc. 2011 Jun; 43(5):1780-2.
    View in: PubMed
  52. Tolstorukov MY, Volfovsky N, Stephens RM, Park PJ. Impact of chromatin structure on sequence variability in the human genome. Nat Struct Mol Biol. 2011 Apr; 18(4):510-5.
    View in: PubMed
  53. Kim TM, Huang W, Park R, Park PJ, Johnson MD. A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs. Cancer Res. 2011 May 1; 71(9):3387-99.
    View in: PubMed
  54. Larschan E, Bishop EP, Kharchenko PV, Core LJ, Lis JT, Park PJ, Kuroda MI. X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature. 2011 Mar 3; 471(7336):115-8.
    View in: PubMed
  55. Ho JW, Bishop E, Karchenko PV, Nègre N, White KP, Park PJ. ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics. 2011; 12:134.
    View in: PubMed
  56. Xi R, Kim TM, Park PJ. Detecting structural variations in the human genome using next generation sequencing. Brief Funct Genomics. 2010 Dec; 9(5-6):405-15.
    View in: PubMed
  57. Kim TM, Park PJ. Advances in analysis of transcriptional regulatory networks. Wiley Interdiscip Rev Syst Biol Med. 2011 Jan-Feb; 3(1):21-35.
    View in: PubMed
  58. 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 TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011 Mar 24; 471(7339):480-5.
    View in: PubMed
  59. Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SC, Karpen GH. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res. 2011 Feb; 21(2):147-63.
    View in: PubMed
  60. Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97.
    View in: PubMed
  61. Anchan RM, Quaas P, Gerami-Naini B, Bartake H, Griffin A, Zhou Y, Day D, Eaton JL, George LL, Naber C, Turbe-Doan A, Park PJ, Hornstein MD, Maas RL. Amniocytes can serve a dual function as a source of iPS cells and feeder layers. Hum Mol Genet. 2011 Mar 1; 20(5):962-74.
    View in: PubMed
  62. Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SC, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD. An assessment of histone-modification antibody quality. Nat Struct Mol Biol. 2011 Jan; 18(1):91-3.
    View in: PubMed
  63. Gurumurthy S, Xie SZ, Alagesan B, Kim J, Yusuf RZ, Saez B, Tzatsos A, Ozsolak F, Milos P, Ferrari F, Park PJ, Shirihai OS, Scadden DT, Bardeesy N. The Lkb1 metabolic sensor maintains haematopoietic stem cell survival. Nature. 2010 Dec 2; 468(7324):659-63.
    View in: PubMed
  64. Park GC, Hwang S, Yu YD, Park PJ, Choi YI, Song GW, Jung DH, Ahn CS, Kim KH, Moon DB, Ha TY, Lee SG. Intractable recurrent hepatitis A virus infection requiring repeated liver transplantation: a case report. Transplant Proc. 2010 Dec; 42(10):4658-60.
    View in: PubMed
  65. Jagani Z, Mora-Blanco EL, Sansam CG, McKenna ES, Wilson B, Chen D, Klekota J, Tamayo P, Nguyen PT, Tolstorukov M, Park PJ, Cho YJ, Hsiao K, Buonamici S, Pomeroy SL, Mesirov JP, Ruffner H, Bouwmeester T, Luchansky SJ, Murtie J, Kelleher JF, Warmuth M, Sellers WR, Roberts CW, Dorsch M. Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway. Nat Med. 2010 Dec; 16(12):1429-33.
    View in: PubMed
  66. Yoon SS, Duda DG, Karl DL, Kim TM, Kambadakone AR, Chen YL, Rothrock C, Rosenberg AE, Nielsen GP, Kirsch DG, Choy E, Harmon DC, Hornicek FJ, Dreyfuss J, Ancukiewicz M, Sahani DV, Park PJ, Jain RK, Delaney TF. Phase II study of neoadjuvant bevacizumab and radiotherapy for resectable soft tissue sarcomas. Int J Radiat Oncol Biol Phys. 2011 Nov 15; 81(4):1081-90.
    View in: PubMed
  67. Gorchakov AA, Alekseenko AA, Kharchenko PV, Park P, Kuroda M. [Dosage compensation in drosophila: sequence-specific initiation and sequence-independent spreading of MSL complex to the active genes on the male X chromosome]. Genetika. 2010 Oct; 46(10):1430-4.
    View in: PubMed
  68. Hwang S, Kim KH, Song GW, Yu YD, Park GC, Kim KW, Choi NK, Park PJ, Choi YI, Jung DH, Ahn CS, Moon DB, Ha TY, Lee SG. Peritransplant monitoring of immune cell function in adult living donor liver transplantation. Transplant Proc. 2010 Sep; 42(7):2567-71.
    View in: PubMed
  69. Kim TM, Luquette LJ, Xi R, Park PJ. rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. BMC Bioinformatics. 2010; 11:432.
    View in: PubMed
  70. Goutagny S, Yang HW, Zucman-Rossi J, Chan J, Dreyfuss JM, Park PJ, Black PM, Giovannini M, Carroll RS, Kalamarides M. Genomic profiling reveals alternative genetic pathways of meningioma malignant progression dependent on the underlying NF2 status. Clin Cancer Res. 2010 Aug 15; 16(16):4155-64.
    View in: PubMed
  71. Peng S, Kuroda MI, Park PJ. Quantized correlation coefficient for measuring reproducibility of ChIP-chip data. BMC Bioinformatics. 2010; 11:399.
    View in: PubMed
  72. Balakrishnan A, Stearns AT, Park PJ, Dreyfuss JM, Ashley SW, Rhoads DB, Tavakkolizadeh A. MicroRNA mir-16 is anti-proliferative in enterocytes and exhibits diurnal rhythmicity in intestinal crypts. Exp Cell Res. 2010 Dec 10; 316(20):3512-21.
    View in: PubMed
  73. Day DS, Luquette LJ, Park PJ, Kharchenko PV. Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol. 2010; 11(6):R69.
    View in: PubMed
  74. Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJ. CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell. 2010 Apr 23; 38(2):179-90.
    View in: PubMed
  75. Park PJ, Bell MA. Variation of telencephalon morphology of the threespine stickleback (Gasterosteus aculeatus) in relation to inferred ecology. J Evol Biol. 2010 Jun 1; 23(6):1261-77.
    View in: PubMed
  76. Kim H, Huang W, Jiang X, Pennicooke B, Park PJ, Johnson MD. Integrative genome analysis reveals an oncomir/oncogene cluster regulating glioblastoma survivorship. Proc Natl Acad Sci U S A. 2010 Feb 2; 107(5):2183-8.
    View in: PubMed
  77. Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE. A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell. 2010 Jan 8; 140(1):99-110.
    View in: PubMed
  78. Hodge JC, Park PJ, Dreyfuss JM, Assil-Kishawi I, Somasundaram P, Semere LG, Quade BJ, Lynch AM, Stewart EA, Morton CC. Identifying the molecular signature of the interstitial deletion 7q subgroup of uterine leiomyomata using a paired analysis. Genes Chromosomes Cancer. 2009 Oct; 48(10):865-85.
    View in: PubMed
  79. Gorchakov AA, Alekseyenko AA, Kharchenko P, Park PJ, Kuroda MI. Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X. Genes Dev. 2009 Oct 1; 23(19):2266-71.
    View in: PubMed
  80. Park PJ, Kong SW, Tebaldi T, Lai WR, Kasif S, Kohane IS. Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Bioinformatics. 2009 Dec 1; 25(23):3121-7.
    View in: PubMed
  81. Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009 Oct; 10(10):669-80.
    View in: PubMed
  82. Dreyfuss JM, Johnson MD, Park PJ. Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers. Mol Cancer. 2009; 8:71.
    View in: PubMed
  83. Gelbart ME, Larschan E, Peng S, Park PJ, Kuroda MI. Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation. Nat Struct Mol Biol. 2009 Aug; 16(8):825-32.
    View in: PubMed
  84. Yoon SS, Stangenberg L, Lee YJ, Rothrock C, Dreyfuss JM, Baek KH, Waterman PR, Nielsen GP, Weissleder R, Mahmood U, Park PJ, Jacks T, Dodd RD, Fisher CJ, Ryeom S, Kirsch DG. Efficacy of sunitinib and radiotherapy in genetically engineered mouse model of soft-tissue sarcoma. Int J Radiat Oncol Biol Phys. 2009 Jul 15; 74(4):1207-16.
    View in: PubMed
  85. Pihlajamäki J, Boes T, Kim EY, Dearie F, Kim BW, Schroeder J, Mun E, Nasser I, Park PJ, Bianco AC, Goldfine AB, Patti ME. Thyroid hormone-related regulation of gene expression in human fatty liver. J Clin Endocrinol Metab. 2009 Sep; 94(9):3521-9.
    View in: PubMed
  86. Wang XP, O'Connell DJ, Lund JJ, Saadi I, Kuraguchi M, Turbe-Doan A, Cavallesco R, Kim H, Park PJ, Harada H, Kucherlapati R, Maas RL. Apc inhibition of Wnt signaling regulates supernumerary tooth formation during embryogenesis and throughout adulthood. Development. 2009 Jun; 136(11):1939-49.
    View in: PubMed
  87. McKinney-Freeman SL, Naveiras O, Yates F, Loewer S, Philitas M, Curran M, Park PJ, Daley GQ. Surface antigen phenotypes of hematopoietic stem cells from embryos and murine embryonic stem cells. Blood. 2009 Jul 9; 114(2):268-78.
    View in: PubMed
  88. Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ. Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Res. 2009 Jun; 19(6):967-77.
    View in: PubMed
  89. 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 melanogaster X chromosome. Nat Struct Mol Biol. 2008 Dec; 15(12):1318-25.
    View in: PubMed
  90. Park PJ. Epigenetics meets next-generation sequencing. Epigenetics. 2008 Nov; 3(6):318-21.
    View in: PubMed
  91. Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008 Dec; 26(12):1351-9.
    View in: PubMed
  92. Park PJ. Experimental design and data analysis for array comparative genomic hybridization. Cancer Invest. 2008 Nov; 26(9):923-8.
    View in: PubMed
  93. Dermody JL, Dreyfuss JM, 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. 2008; 3(9):e3273.
    View in: PubMed
  94. Kharchenko PV, Woo CJ, Tolstorukov MY, Kingston RE, Park PJ. Nucleosome positioning in human HOX gene clusters. Genome Res. 2008 Oct; 18(10):1554-61.
    View in: PubMed
  95. Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee OK, Kharchenko P, McGrath SD, Wang CI, Mardis ER, Park PJ, Kuroda MI. A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell. 2008 Aug 22; 134(4):599-609.
    View in: PubMed
  96. Mueller JL, Mahadevaiah SK, Park PJ, Warburton PE, Page DC, Turner JM. The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression. Nat Genet. 2008 Jun; 40(6):794-9.
    View in: PubMed
  97. Orford K, Kharchenko P, Lai W, Dao MC, Worhunsky DJ, Ferro A, Janzen V, Park PJ, Scadden DT. Differential H3K4 methylation identifies developmentally poised hematopoietic genes. Dev Cell. 2008 May; 14(5):798-809.
    View in: PubMed
  98. Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ. nuScore: a web-interface for nucleosome positioning predictions. Bioinformatics. 2008 Jun 15; 24(12):1456-8.
    View in: PubMed
  99. Lai W, Choudhary V, Park PJ. CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms. Bioinformatics. 2008 Apr 1; 24(7):1014-5.
    View in: PubMed
  100. Lee H, Kong SW, Park PJ. Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes. Bioinformatics. 2008 Apr 1; 24(7):889-96.
    View in: PubMed
  101. 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. 2008 Mar 15; 111(6):3200-10.
    View in: PubMed
  102. Claus EB, Park PJ, Carroll R, Chan J, Black PM. Specific genes expressed in association with progesterone receptors in meningioma. Cancer Res. 2008 Jan 1; 68(1):314-22.
    View in: PubMed
  103. 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. Mol Cell. 2007 Oct 12; 28(1):121-33.
    View in: PubMed
  104. Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ. Normalization and experimental design for ChIP-chip data. BMC Bioinformatics. 2007; 8:219.
    View in: PubMed
  105. Baskerville KA, Kent C, Personett D, Lai WR, Park PJ, Coleman P, McKinney M. Aging elevates metabolic gene expression in brain cholinergic neurons. Neurobiol Aging. 2008 Dec; 29(12):1874-93.
    View in: PubMed
  106. 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 Genet. 2007 Jun; 3(6):e96.
    View in: PubMed
  107. Vukovic B, Beheshti B, Park P, Lim G, Bayani J, Zielenska M, Squire JA. Correlating breakage-fusion-bridge events with the overall chromosomal instability and in vitro karyotype evolution in prostate cancer. Cytogenet Genome Res. 2007; 116(1-2):1-11.
    View in: PubMed
  108. Liu F, Park PJ, Lai W, Maher E, Chakravarti A, Durso L, Jiang X, Yu Y, Brosius A, Thomas M, Chin L, Brennan C, DePinho RA, Kohane I, 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 Res. 2006 Nov 15; 66(22):10815-23.
    View in: PubMed
  109. 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. J Surg Res. 2006 Oct; 135(2):282-90.
    View in: PubMed
  110. Kong SW, Pu WT, Park PJ. A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics. 2006 Oct 1; 22(19):2373-80.
    View in: PubMed
  111. 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, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol. 2006 Jul; 24(7):832-40.
    View in: PubMed
  112. Namekawa SH, Park PJ, Zhang LF, Shima JE, McCarrey JR, Griswold MD, Lee JT. Postmeiotic sex chromatin in the male germline of mice. Curr Biol. 2006 Apr 4; 16(7):660-7.
    View in: PubMed
  113. 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 Dev. 2006 Apr 1; 20(7):848-57.
    View in: PubMed
  114. 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.
    View in: PubMed
  115. Hamada FN, Park PJ, Gordadze PR, Kuroda MI. Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster. Genes Dev. 2005 Oct 1; 19(19):2289-94.
    View in: PubMed
  116. Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A. 2005 Sep 20; 102(38):13544-9.
    View in: PubMed
  117. Lai WR, Johnson MD, Kucherlapati R, Park PJ. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics. 2005 Oct 1; 21(19):3763-70.
    View in: PubMed
  118. 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. Ann Neurol. 2005 May; 57(5):664-78.
    View in: PubMed
  119. 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. 2005 May 1; 21(9):2116-7.
    View in: PubMed
  120. Hwang KB, Kong SW, Greenberg SA, Park PJ. Combining gene expression data from different generations of oligonucleotide arrays. BMC Bioinformatics. 2004 Oct 25; 5:159.
    View in: PubMed
  121. Park PJ, Cao YA, Lee SY, Kim JW, Chang MS, Hart R, Choi S. Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. J Biotechnol. 2004 Sep 9; 112(3):225-45.
    View in: PubMed
  122. Kim RD, Park PJ. Improving identification of differentially expressed genes in microarray studies using information from public databases. Genome Biol. 2004; 5(9):R70.
    View in: PubMed
  123. 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. 2003 Oct 20; 198(8):1201-12.
    View in: PubMed
  124. 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. 2003 Apr; 134(4):456-62.
    View in: PubMed
  125. Blackshaw S, Kuo WP, Park PJ, Tsujikawa M, Gunnersen JM, Scott HS, Boon WM, Tan SS, Cepko CL. MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues. Genome Biol. 2003; 4(3):R17.
    View in: PubMed
  126. Kuo WP, Mendez E, Chen C, Whipple ME, Farell G, Agoff N, Park PJ. Functional relationships between gene pairs in oral squamous cell carcinoma. AMIA Annu Symp Proc. 2003; 371-5.
    View in: PubMed
  127. Park PJ, Butte AJ, Kohane IS. Comparing expression profiles of genes with similar promoter regions. Bioinformatics. 2002 Dec; 18(12):1576-84.
    View in: PubMed
  128. Kuruvilla FG, Park PJ, Schreiber SL. Vector algebra in the analysis of genome-wide expression data. Genome Biol. 2002; 3(3):RESEARCH0011.
    View in: PubMed
  129. Park PJ, Tian L, Kohane IS. Linking gene expression data with patient survival times using partial least squares. Bioinformatics. 2002; 18 Suppl 1:S120-7.
    View in: PubMed
  130. 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. Proc AMIA Symp. 2002; 415-9.
    View in: PubMed
  131. Lee KM, Park P. Application of life-cycle assessment to type III environmental declarations. Environ Manage. 2001 Oct; 28(4):533-46.
    View in: PubMed
  132. Kim SK, Park PJ, Yang HP, Han SS. Subacute toxicity of chitosan oligosaccharide in Sprague-Dawley rats. Arzneimittelforschung. 2001 Sep; 51(9):769-74.
    View in: PubMed
  133. Park P, Haas M, Cunningham PN, Alexander JJ, Bao L, Guthridge JM, Kraus DM, Holers VM, Quigg RJ. Inhibiting the complement system does not reduce injury in renal ischemia reperfusion. J Am Soc Nephrol. 2001 Jul; 12(7):1383-90.
    View in: PubMed
  134. Kim SK, Byun HG, Park PJ, Shahidi F. Angiotensin I converting enzyme inhibitory peptides purified from bovine skin gelatin hydrolysate. J Agric Food Chem. 2001 Jun; 49(6):2992-7.
    View in: PubMed
  135. Park PJ, Pagano M, Bonetti M. A nonparametric scoring algorithm for identifying informative genes from microarray data. Pac Symp Biocomput. 2001; 52-63.
    View in: PubMed
  136. Park P, Copeland W, Yang L, Wang T, Botchan MR, Mohr IJ. The cellular DNA polymerase alpha-primase is required for papillomavirus DNA replication and associates with the viral E1 helicase. Proc Natl Acad Sci U S A. 1994 Aug 30; 91(18):8700-4.
    View in: PubMed
Local representatives can answer questions about the Profiles website or help with editing a profile or issues with profile data. For assistance with this profile: HMS/HSDM faculty should contact Human Resources at faculty_serviceshms.harvard.edu.
Park's Networks
Click the "See All" links for more information and interactive visualizations!
Concepts
_
Co-Authors
_
Similar People
_
Same Department
Physical Neighbors
_