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Peter J. Park, PhD

Publications

  • Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen GH, Kuroda MI, Park PJ.Impact of sequencing depth in ChIP-seq experiments.Nucleic Acids Res. 2014 Mar 5.
    24598259
  • Marinov GK, Kundaje A, Park PJ, Wold BJ.Large-scale quality analysis of published ChIP-seq data.G3 (Bethesda, Md.). 2014 Feb;4(2):209-23.
    24347632
  • Ferrari F, Alekseyenko AA, Park PJ, Kuroda MI.Transcriptional control of a whole chromosome: emerging models for dosage compensation.Nat Struct Mol Biol. 2014 Feb;21(2):118-25. Review.
    24500429
  • Ferrari F, Apostolou E, Park PJ, Hochedlinger K.Rearranging the chromatin for pluripotency.Cell Cycle. 2014 Jan 15;13(2):167-8.
    24241209
  • 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.
    24158981
  • 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.
    24100010
  • 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.
    24183666
  • 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.
    24209623
  • 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.
    24183448
  • 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.
    24014587
  • 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.
    23775117
  • 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.
    23873939
  • 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.
    23814487
  • 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.
    23723349
  • 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.
    23665121
  • 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.
    23663786
  • 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.
    23419376
  • 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 Apr 1.
    23547170
  • 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 Jan 16.
    23321669
  • 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. 2012 Nov 6.
    23132910
  • 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.
    22767387
  • 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 1α.Int J Cancer. 2013 Jan 1;132(1):29-41.
    22684860
  • 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.
    23074071
  • 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.
    23028361
  • , 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, Zhengdong Z, Brent M, Haussler D, Kellis M, Valencia A, Gerstein M, Raymond A, Guigó R, Harrow J, Hubbard TJ, Landt SG, Frietze S, Abyzov A, Addleman N, Alexander RP, Auerbach RK, Balasubramanian S, Bettinger K, Bhardwaj N, Boyle AP, Cao AR, Cayting P, Charos A, Cheng Y, Cheng C, Eastman C, Euskirchen G, Fleming JD, Grubert F, Habegger L, Hariharan M, Harmanci A, Iyenger S, Jin VX, Karczewski KJ, Kasowski M, Lacroute P, Lam H, Larnarre-Vincent N, Leng J, Lian J, Lindahl-Allen M, Min R, Miotto B, Monahan H, Moqtaderi Z, Mu XJ, O'Geen H, Ouyang Z, Patacsil D, Pei B, Raha D, Ramirez L, Reed B, Rozowsky J, Sboner A, Shi M, Sisu C, Slifer T, Witt H, Wu L, Xu X, Yan KK, Yang X, Yip KY, Zhang Z, Struhl K, Weissman SM, Gerstein M, Farnham PJ, Snyder M, Tenebaum SA, Penalva LO, Doyle F, Karmakar S, Landt SG, Bhanvadia RR, Choudhury A, Domanus M, Ma L, Moran J, Patacsil D, Slifer T, Victorsen A, Yang X, Snyder M, White KP, Auer T, Centarin L, Eichenlaub M, Gruhl F, Heerman S, Hoeckendorf B, Inoue D, Kellner T, Kirchmaier S, Mueller C, Reinhardt R, Schertel L, Schneider S, Sinn R, Wittbrodt B, Wittbrodt J, Weng Z, Whitfield TW, Wang J, Collins PJ, Aldred SF, Trinklein ND, Partridge EC, Myers RM, Dekker J, Jain G, Lajoie BR, Sanyal A, Balasundaram G, Bates DL, Byron R, Canfield TK, Diegel MJ, Dunn D, Ebersol AK, Ebersol AK, Frum T, Garg K, Gist E, Hansen RS, Boatman L, Haugen E, Humbert R, Jain G, Johnson AK, Johnson EM, Kutyavin TM, Lajoie BR, Lee K, Lotakis D, Maurano MT, Neph SJ, Neri FV, Nguyen ED, Qu H, Reynolds AP, Roach V, Rynes E, Sabo P, Sanchez ME, Sandstrom RS, Sanyal A, Shafer AO, Stergachis AB, Thomas S, Thurman RE, Vernot B, Vierstra J, Vong S, Wang H, Weaver MA, Yan Y, Zhang M, Akey JA, Bender M, Dorschner MO, Groudine M, MacCoss MJ, Navas P, Stamatoyannopoulos G, Kaul R, Dekker J, Stamatoyannopoulos JA, Dunham I, Beal K, Brazma A, Flicek P, Herrero J, Johnson N, Keefe D, Lukk M, Luscombe NM, Sobral D, Vaquerizas JM, Wilder SP, Batzoglou S, Sidow A, Hussami N, Kyriazopoulou-Panagiotopoulou S, Libbrecht MW, Schaub MA, Kundaje A, Hardison RC, Miller W, Giardine B, Harris RS, Wu W, Bickel PJ, Banfai B, Boley NP, Brown JB, Huang H, Li Q, Li JJ, Noble WS, Bilmes JA, Buske OJ, Hoffman MM, Sahu AO, Kharchenko PV, Park PJ, Baker D, Taylor J, Weng Z, Iyer S, Dong X, Greven M, Lin X, Wang J, Xi HS, Zhuang J, Gerstein M, Alexander RP, Balasubramanian S, Cheng C, Harmanci A, Lochovsky L, Min R, Mu XJ, Rozowsky J, Yan KK, Yip KY, Birney E.An integrated encyclopedia of DNA elements in the human genome.Nature. 2012 Sep 6;489(7414):57-74.
    22955616
  • 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.
    22955991
  • 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.
    22795134
  • 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.
    22745252
  • 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.
    22844249
  • 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.
    22553175
  • 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.
    22065754
  • 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.
    21399641
  • 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.
    21179089
  • 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.
    21356108
  • Kim TM, Huang W, Park R, Park PJ, Johnson MD.A developmental taxonomy of glioblastoma defined and maintained by microRNAs.Cancer Res. 2011 Mar 8.
    21385897
  • 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.
    21368835
  • 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.
    21177972
  • 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.
    21156717
  • 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.
    21216738
  • 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.
    21131980
  • , 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.
    21177974
  • Kim TM, Park PJ.Advances in analysis of transcriptional regulatory networks.Wiley Interdisciplinary Reviews. Systems Biology And Medicine.;3(1):21-35. Review.
    21069662
  • 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.
    21076395
  • 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.
    21124451
  • 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. 2010 Oct 5.
    20932656
  • 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.
    20718989
  • 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.
    20682713
  • Peng S, Kuroda MI, Park PJ.Quantized correlation coefficient for measuring reproducibility of ChIP-chip data.BMC Bioinformatics. 2010;11:399.
    20663215
  • Day DS, Luquette LJ, Park PJ, Kharchenko PV.Estimating enrichment of repetitive elements from high-throughput sequence data.Genome Biol. 2010;11(6):R69.
    20584328
  • 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.
    20417597
  • 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.
    20080666
  • 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.
    20085705
  • 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.
    19797766
  • Park PJ.ChIP-seq: advantages and challenges of a maturing technology.Nat Rev Genet. 2009 Oct;10(10):669-80. Review.
    19736561
  • Dreyfuss JM, Johnson MD, Park PJ.Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers.Mol Cancer. 2009;8:71.
    19732454
  • 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.
    19603527
  • 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.
    19648925
  • 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.
    19420357
  • 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.
    19545786
  • 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.
    19429790
  • 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.
    19246569
  • Park PJ.Epigenetics meets next-generation sequencing.Epigenetics. 2008 Nov;3(6):318-21.
    19098449
  • Park PJ.Experimental design and data analysis for array comparative genomic hybridization.Cancer Invest. 2008 Nov;26(9):923-8. Review.
    19034774
  • 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.
    19029915
  • 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.
    19029895
  • Dermody JL,Dreyfuss JM,Villen 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.
    18818768
  • 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.
    18724933
  • 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.
    18723689
  • The Cancer Genome Atlas Research Network.Comprehensive genomic characterization defines human glioblastoma genes and core pathways.Nature.;455(7216):1061-8.
  • 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.
    18445607
  • 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.
    18454149
  • 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.
    18477461
  • Park PJ, Ahn CB, Jeon YJ, Je JY.Renin inhibition activity by chitooligosaccharides.Bioorg Med Chem Lett. 2008 Apr 1;18(7):2471-4.
    18313296
  • 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.
    18296463
  • 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.
    18263644
  • 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.
    18184868
  • Lee HM, Kim HJ, Won KJ, Choi WS, Park SH, Song H, Park PJ, Park TK, Lee CK, Kim B.Soluble form of vascular cell adhesion molecule 1 induces migration and proliferation of vascular smooth muscle cells.J Vasc Res. 2008;45(3):259-68.
    18182825
  • 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.
    18172325
  • 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.
    17936709
  • Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ.Normalization and experimental design for ChIP-chip data.BMC Bioinformatics. 2007;8:219.
    17592629
  • 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.
    17571924
  • 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.
    17560690
  • 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.
    17381321
  • 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.
    17090523
  • 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.
    16877751
  • 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.
    16603191
  • 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.
    16581510
  • 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.
    16547173
  • 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.
    16204180
  • 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.
    16174746
  • 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.
    16081473
  • 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.
    15684227
  • 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.
    15504239
  • Kim RD, Park PJ.Improving identification of differentially expressed genes in microarray studies using information from public databases.Genome Biol. 2004;5(9):R70.
    15345054
  • 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.
    15313001
  • 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.
    14728197
  • 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.
    14568979
  • 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.
    12620102
  • Park PJ, Butte AJ, Kohane IS.Comparing expression profiles of genes with similar promoter regions.Bioinformatics. 2002 Dec;18(12):1576-84.
    12490441
  • 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.
    12474876
  • 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.
    12169539
  • Kuruvilla FG, Park PJ, Schreiber SL.Vector algebra in the analysis of genome-wide expression data.Genome Biol. 2002;3(3):RESEARCH0011.
    11897023
  • Park PJ, Pagano M, Bonetti M.A nonparametric scoring algorithm for identifying informative genes from microarray data.Proc AMIA Symp. 2001:52-63.
    11262969