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Publications

(*equal contribution; **co-corresponding authors)

2014

  • Comparative analysis of metazoan chromatin organization
    Ho JWK*, Jung YL*, Liu T*, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SCJ, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hofman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, LatorreI, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM**, Strome S**, Elgin SCR**, Liu XS**, Lieb JD**, Ahringer J**, Karpen GH**, Park PJ**
    Nature, in press.

  • Comparative analysis of the transcriptome across distant species
    Gerstein MB, Rozowsky J, Yan K, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach RK, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Green P, Guigo R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJP, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R.
    Nature, in press.

  • Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming
    West JA*, Cook A*, Alver BH, Stadtfeld M, Deaton A, Hochedlinger K, Park PJ**, Tolstorukov MY**, Kingston RE**
    Nature Communications, in press.

  • The somatic genomic landscape of chromophobe renal cell carcinoma
    Davis CF*, Ricketts C*, Wang M*, Yang L*, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA, The Cancer Genome Atlas Research Network, Chin L, Meyerson M, Kucherlapati R, Park W, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ.
    Cancer Cell, in press.

  • Comprehensivemolecular characterization of gastric adenocarcinoma
    The Cancer Genome Atlas Research Network
    Nature, in press.

  • Comprehensive molecular profiling of lung adenocarcinoma
    The Cancer Genome Atlas Research Network
    Nature, in press.

  • Impact of sequencing depth in ChIP-seq experiments
    Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen GH, Kuroda MI, Park PJ.
    Nucleic Acids Research, online Mar 5.

  • Comprehensive molecular characterization of urothelial bladder carcinoma
    The Cancer Genome Atlas Research Network
    Nature, 507:315-322, 2014.

  • Transcriptional control of a whole chromosome: emerging models for dosage compensation
    Ferrari F, Alekseyenko AA, Park PJ, Kuroda MI.
    Nat Struct Mol Biol., 21:118-25, 2014.

  • Large-scale quality analysis of published ChIP-seq data
    Marinov GK, Kundaje A, Park PJ, Wold BJ.
    G3, 4:209-23, 2014.

  • Rearranging the chromatin for pluripotency
    Apostolou E*, Ferrari, F*, Park PJ**, Hochedlinger K**.
    Cell Cycle, 13:167-8, 2014

  • 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
    Ajay AK, Kim TM, Ramirez-Gonzalez V, Park PJ, Frank DA, Vaidya VS
    J Am Soc Nephrology, 25:105-18, 2014.

2013

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

  • Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome
    Davoli T*, Xu AW*, Mengwasser KE, Sack LM, Yoon JC, Park PJ, Elledge SJ.
    Cell, 155:948-62, 2013.

  • "Jumpstart and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts
    Ferrari F*, Plachetka A*, Alekseyenko AA*, Jung YL, Ozsolak F, Kharchenko PV, Park PJ**, Kuroda MI**
    Cell Reports, 5:629-36, 2013.

  • Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast
    DeGennaro CM, Alver BH, Marguerat S, Stepanova E, Davis CP, Bahler J, Park PJ, Winston F.
    Molecular and Cellular Biology, 33:4779-92, 2013.

  • The somatic genomic landscape of glioblastoma
    Brennan CW et al. and TCGA Research Network
    Cell, 155:462-77, 2013.

  • The Cancer Genome Atlas Pan-Cancer analysis project
    Cancer Genome Atlas Research Network (including Park lab members Haseley P, Lee E, Lee S, Luquette LJ, Xi R, Xu AW, Yang L, Park PJ).
    Nature Genetics, 45:1113-20, 2013.

  • Primate genome architecture influences structural variation mechanisms and functional consequences
    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.
    Proc Natl Acad Sci USA, 110:15764-9, 2013.

  • Variable requirements for DNA-binding proteins at Polycomb-dependent repressive regions in the human HOX clusters
    Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE.
    Molecular and Cellular Biology, 33:3274-85, 2013.

  • The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation.
    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, and Larschan, E.
    Genes & Development, 27:1551-6, 2013.

  • Comprehensive molecular characterization of clear cell renal cell carcinoma
    Cancer Genome Atlas Research Network.
    Nature, 499:43-9, 2013.

  • Loss of Sh3gl2/endophilin A1 is a common event in urothelial carcinoma that promotes malignant behavior
    Majumdar S, Gong EM, Di Vizio D, Dreyfuss J, DeGraff DJ, Hager MH, Park PJ, Bellmunt J, Matusik RJ, Rosenberg JE, Adam RM.
    Neoplasia, 15:749-60.

  • The Swi/Snf tumor suppressor complex establishes nucleosome occupancy at target promoters
    Tolstorukov MY*, Sansam CG*, Lu P, Koellhoffer EC, Helming KC, Alvera BH, Tillman EJ, Evans JA, Wilson BG, Park PJ**, Roberts CWM**.
    Proc Natl Acad Sci USA, 110:10165-70, 2013.

  • Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation and reprogramming
    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**.
    Cell Stem Cell, 12:699-712.

  • A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity.
    Zhang B, Day DS, Ho JW, Song L, Cao J, Christodoulou D, Seidman JG, Crawford GE, Park PJ, Pu WT.
    Genome Research, 23:917-27.
  • Diverse mechanisms of somatic structural variations in human cancer genomes
    Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh C, Zhang C, Ren X, Protopopov A, Chin L, Kucherlapati R, Lee C, Park PJ.
    Cell, 153:919-29, 2013.

  • Integrated genomic characterization of endometrial carcinoma
    Cancer Genome Atlas Network
    Nature, 497:67-73, 2013.

  • Comment on "Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters"
    Ferrari F*, Jung YL*, Kharchenko PV, Plachetka A, Alekseyenko AA, Kuroda M**, Park PJ**
    Science, 340:273, 2013.

  • Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila
    Alekseyenko AA, Ellison CE, Gorchakov AA, Zhou Q, Kaiser VB, Toda N, Walton Z, Peng S, Park PJ, Bachtrog D, Kuroda MI.
    Genes & Development, 27:853-8, 2013.

  • Nozzle: a report generation toolkit for data analysis pipelines.
    Gehlenborg N, Noble MS, Getz G, Chin L, Park PJ.
    Bioinformatics, 29:1089-91, 2013.
  • KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs.
    Tzatsos A, Paskaleva P, Ferrari F, Deshpande V, Stoykova S, Contino G, Wong KK, Lan F, Trojer P, Park PJ, Bardeesy N.
    J Clin Invest, 123:727-39, 2013.

  • Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes
    Kim TM, Xi R, Luquette LJ, Park RW, Johnson MD, Park PJ.
    Genome Research, 23:217-27, 2013.

  • Overcoming evasive resistance from vascular endothelial growth factor A inhibition in sarcomas by genetic or pharmacologic targeting of hypoxia inducible factor 1alpha
    Kim YJ, Lee HJ, Kim TM, Eisinger-Mathason TSK, Zhang AY, Schmidt B, Karl DL, Lee YJ, Nakazawa MS, Park PJ, Kirsch DG, Simon MC, Yoon SS.
    International Journal of Cancer, 132:29-41, 2013.

2012

  • Single neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain (cover)
    Evrony GD*, Cai X*, Lee E, Hills LB, Elhosary PC, Parker JJ, Atabay KD, Lehmann HS, Gilmore EC, Poduri A, Park PJ, Walsh CA.
    Cell, 151:483-96, 2012.

  • Systematic identification of synergistic drug pairs targeting HIV
    Tan X, Hu L*, Luquette LJ III*, Gao G, Liu Y, Qu H, Xi R, Lu ZJ, Park PJ, Elledge SJ.
    Nature Biotechnology, 30:1125-30, 2012.

  • Comprehensive molecular portraits of human breast tumours [open access]
    Cancer Genome Atlas Network.
    Nature, 490:61-70, 2012.
    Media coverage: NY Times / NPR / ABC News

  • Comprehensive genomic characterization of squamous cell lung cancers [open access]
    Cancer Genome Atlas Network
    Nature, 489:519-25, 2012.
    Media coverage: NY Times

  • Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain
    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 SCR**.
    PLoS Genetics, 8:e1002954, 2012.

  • Landscape of somatic retrotransposition in human cancers
    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**, and The Cancer Genome Atlas Research Network
    Science, 337:967-71, 2012 (online 6/28/2012).
    Full text is available from this website only, courtesy of Science author reprint service: PDF
    Software: Transposable element analyzer (Tea)
    Media coverage: The Scientist / GenomeWeb / Cancer Discovery (requires subscription) / TCGA Research Brief

  • Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells (cover)
    Tolstorukov MY*, Goldman JA*, Gilbert C, Ogryzko V, Kingston RE**, Park PJ**
    Molecular Cell, 47:596-607, 2012 (online 7/12/2012).

  • Nature and function of insulator protein binding sites in the Drosophila genome.
    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.
    Genome Research, published online 7/5/2012.

  • Expression, circulation and excretion profile of microRNA-21, -155, and -18a following acute kidney injury
    Saikumar J, Hoffmann D, Kim T, Gonzalez VR, Zhang Q, Goering PL, Brown RP, Bijol V, Park P, Waiker S, Vaidya VS.
    Toxicological Sciences, 129:256-67, 2012.

  • An integrated encyclopedia of DNA elements in the human genome [open access]
    ENCODE consortium
    Nature, 489:57-74, 2012.
    Media coverage: NY Times / Wall Street Journal / The Economist / Discover / ScienceDaily / Nature site

  • Comprehensive molecular characterization of human colon and rectal tumors [open access]
    The Cancer Genome Atlas Research Network
    Nature, 487:330-337, 2012.
    Media coverage: NY Times / Business Week and many others

  • ChIP-seq guidelines and practices used by the ENCODE and modENCODE consortia
    Landt S, Marinov GK, Kheradpour P, Kundaje A, Pauli F, Batzoglou S, Bernstein B, Bickel P, Brown B, Cayting P, Chen Y, Epstein C, Euskirchen G, Fisher-Aylor K, Gerstein M, Gertz J, Guigo R, Hartemink AJ, Hoffman MM, Iyer V, Jung YL, Karmakar S, Kellis M, Kharchenko P, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Pery MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stammatoyonnopoulous J, Tolstorukov M, White K, Xi S, Farnham PJ, Lieb J, Wold B, Snyder M
    Genome Research, 22:1813-31, 2012.

  • A survey of copy number variation detection tools based on high-throughput sequencing data
    Xi R, Lee S, Park PJ.
    Current Protocols in Human Genetics, Chapter 7:Unit7.19, 2012.

  • Identification of chromatin-associated regulators of MSL complex targeting in Drosophila dosage compensation
    Larschan E, Soruco MML, Lee O-K, Peng S, Bishop E, Chery J, Goebel K, Feng J, Park PJ, Kuroda MI.
    PLoS Genetics, 8:e1002830, 2012 (online 7/26/2012).

  • Numb Regulates Glioma Stem Cell Fate and Growth by Altering EGFR and SCF Ubiquitin Ligase Activity
    Jiang X, Xing H, Kim TM, Jung Y, Huang W, Yang HW, Song S, Park PJ, Carroll RS, Johnson MD.
    Stem Cells, 30:1313-26, 2012.

  • StratomeX: Visual analysis of large-scale heterogeneous genomics data for cancer subtype characterization
    Lex A, Streit M., Schulz H.-J., Partl C, Schmalstieg D, Park PJ, Gehlenborg N
    Computer Graphics Forum (EuroVis '12), 31:1175-84, 2012.

  • Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context
    Alekseyenko AA*, Ho JWK*, Peng S*, Gelbart M, Tolstorukov M, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E, Gu T, Minoda A, Riddle NC, Schwartz YB, Elgin SCR, Karpen GH, Pirrotta V, Kuroda MI**, Park PJ**.
    PLoS Genetics8:e1002646, 2012.

  • Expression profiling of uterine leiomyomata cytogenetic subgroups reveals distinct signatures in matched myometrium: transcriptional profiling of the t(12;14) and evidence in support of predisposing genetic heterogeneity
    Hodge JC, Kim TM, Dreyfuss JM, Somasundaram P, Christacos NC, Rousselle M, Quade BJ, Park PJ, Stewart EA, Morton CC.
    Human Molecular Genetics 21:2312-29, 2012.

  • Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all–iPS cell mice from terminally differentiated B cells
    Stadtfeld M, Apostolou E, Ferrari F, Choi J, Walsh RM, Chen T, Oi S, Kim SY, Bestor T, Shioda T, Park PJ, Hochedlinger K.
    Nature Genetics, 44:398-405, 2012.

  • A pharmacoepidemiological network model for drug safety surveillance: Statins and rhabdomyolysis
    Reis BY, Olson KL, Tian L, Bohn RL, Brownstein JS, Park PJ, Cziraky MJ, Wilson MD, Mandl KD.
    Drug Safety, 35:395-406, 2012.

  • iSyTE: integrated Systems Tool for Eye gene discovery
    Lachke SA, Ho JW, Kryukov GV, O'Connell DJ, Aboukhalil A, Bulyk ML, Park PJ, Maas RL.
    Invest Ophthalmol Vis Sci, 53:1617-27, 2012.
  • Alternative splicing of CHEK2 and co-deletion with NF2 promote chromosomal instability in meningioma
    Yang HW, Kim TM, Song SS, Shrinath N, Park R, Kalamarides M, Park PJ, Black PM, Carroll RS, Johnson MD.
    Neoplasia, 14:20-8, 2012.

  • Upregulation of pro-apoptotic microRNA mir-125a following massive small bowel resection in rats
    Balakrishnan A, Stearns AT, Park PJ, Dreyfuss JM, Ashley SW, Rhoads DB, Tavakkolizadeh A.
    Annals of Surgery, 255:747-53, 2012.

  • Wnt/Bmp feedback circuit controls inter-tissue signaling dynamics in tooth organogenesis
    O'Connell DJ*, Ho JWK*, Mammoto T, Turbe-Doan A, O'Connell JT, Haseley PS, Koo S, Kamiya N, Ingber DE, Park PJ, Maas RL.
    Science Signalling, 5:ra4, 2012 (cover).

  • Genome-wide mapping of protein-DNA interactions by ChIP-seq
    Ho JWK, Alekseyenko AA, Kuroda MI, Park PJ.
    Tag-based Approaches for Next Generation Sequencing (Eds, Kahl, Harbers), Weinheim, Germany: Wiley, 139-152, 2012.

2011

  • Evidence for dosage compensation between the X and autosomes in mammals
    Kharchenko PV, Xi R, Park PJ.
    Nature Genetics, 43:1167-9,2011.

  • Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion
    Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, Johnson MD, Muzny DM, Wheeler DA, Gibbs RA, Kucherlapati R, Park PJ.
    Proc Natl Acad Sci USA, 108:E1128-36, 2011.

  • Gene expression analysis reveals the cell cycle and kinetochore genes participating in ischemia reperfusion injury and early development in kidney
    Kim T-M, Ramírez V, Barrera-Chimal J, Bobadilla NA, Park PJ, Vaidya VS.
    PLoS ONE, 6(9): e25679, 2011.

  • Lung stem cell self-renewal relies on Bmi1-dependent control of expression at imprinted loci
    Zacharek SJ, Fillmore CM, Lau AN, Gludish DW, Chou A, Ho JWK, 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.
    Cell Stem Cell, 9:272-81, 2011.

  • Expression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis
    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**.
    Cell Metabolism, 14:208-18, 2011.

  • Integrated genomic analyses of ovarian carcinoma
    Cancer Genome Atlas Research Network (including Park lab members: Kim TM, Park RW, Lee E, Park PJ as part of Harvard/Broad Genomic Data Analysis Center and Harvard Genome Characterization Center).
    Nature, 474:609-15, 2011.

  • Amniocytes can serve a dual function as a source of iPS cells and feeder layers
    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.
    Human Molecular Genetics 20:962-74, 2011.

  • A developmental taxonomy of glioblastoma defined and maintained by microRNAs
    Kim TM, Huang W, Park R, Park PJ**, Johnson MD**.
    Cancer Research, 71:3387-99, 2011.

  • Impact of chromatin structure on sequence variability in the human genome
    Tolstorukov MY, Volfovsky N, Stephens RM, Park PJ.
    Nature Structural & Molecular Biology, 8:510-5, 2011.

  • ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis
    Ho JWK, Bishop E, Kharchenko PV, Negre N, White K, Park PJ.
    BMC Genomics, 12:134, 2011.

  • X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila
    Larschan E*, Bishop EP*, Kharchenko PV, Core L, Lis JT, Park PJ**, Kuroda MI**.
    Nature, 472:115-8, 2011.

  • Advances in analysis of transcriptional regulatory networks
    Kim TM, Park PJ.
    Wiley Interdisciplinary Reviews Systems Biology and Medicine, 3:21-35, 2011.

  • Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
    Riddle NC*, Minoda A*, Kharchenko PV*, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy A, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SCR**, Karpen GH**.
    Genome Research, 21:147-63, 2011 (Epub 2010 Dec 22).

  • Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
    Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TP, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SCR, Kuroda MI, Pirrotta V, Karpen GH**, Park PJ**.
    Nature, 471:480-5, 2011 (online Dec 22, 2010).

  • An assessment of histone-modification antibody quality
    Egelhofer TA*, Minoda A*, Klugman S*, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung M, 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 SCR, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ**, Karpen GH**, Hawkins RD**, Lieb JD**.
    Nature Structural & Molecular Biolology, 18:91-3, 2011 (online Dec 5, 2010).

2010

  • Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
    modENCODE consortium (includes Kharchenko PV*, Tolstorukov MY, Bishop EP, Jung YL, Park PJ).
    Science, 330:1787-97, 2010.

  • Dosage compensation in Drosophila: sequence-specific initiation and sequence-independent spreading of MSL complex to the active genes on the male X chromosome
    Gorchakov AA, Alekseenko AA, Kharchenko PV, Park P, Kuroda M.
    Genetika, 46:1430-4, 2011 (Russian).

  • Detecting structural variations in the human genome using next-generation sequencing
    Xi R, Kim TM, Park PJ.
    Briefings in Functional Genomics, 9:405-15, 2010.

  • Loss of the Tumor Suppressor Snf5 Leads to Aberrant Activation of the Hedgehog-Gli Pathway
    Jagani Z, Mora-Blanco L, Sansam CG, Wilson B, Chen D, Klekota J, Tamayo P, McKenna E, Nguyen PTL, Tolstorukov M, Park PJ, Cho Y, Hsiao K, Pomeroy SL, Mesirov JP, Ruffner H, Bouwmeester T, Luchansky S, Murtie J, Kelleher J, Warmuth M, Sellers WR, Roberts CWM, Dorsch M.
    Nature Medicine, 16:1429-1433, 2010.

  • Lkb1 regulates stem cell quiescence, energy metabolism, and cell survival in the hematopoietic system
    Gurumurthy S, Xie SZ, Alagesan B, Kim J, Yusuf RZ, Saez B, Tzatsos A, Oszolak F, Milos P, Ferrari F, Park PJ, Shirihai O, Scadden DT, Bardeesy N.
    Nature, 468:659-63, 2010.

  • rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data
    Kim TM, Luquette LJ, Xi R, Park PJ.
    BMC Bioinformatics, 11:432, 2010.

  • Quantized correlation coefficient for measuring reproducibility of ChIP-chip data
    Peng S, Kuroda MI, Park PJ.
    BMC Bioinformatics, 11:339, 2010.

  • MicroRNA mir-16 is anti-proliferative in enterocytes and exhibits diurnal rhythmicity in intestinal crypts
    Balakrishnan A, Stearns AT, Park PJ, Dreyfuss JM, Ashley SW, Rhoads DB, Tavakkolizadeh A.
    Experimental Cell Research, 316:3512-21, 2010.

  • Estimating enrichment of repetitive elements from high-throughput sequence data
    Day DS, Luquette LJ, Park PJ, Kharchenko PV.
    Genome Biology, 11:R69, 2010.

  • Phase II Study of Neoadjuvant Bevacizumab and Radiation Therapy for Resectable Soft Tissue Sarcomas
    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.
    Int J Radiat Oncol Biol Phys, online Oct 5, 2010.

  • Genomic profiling reveals alternative genetic pathways of meningioma malignant progression dependent upon the underlying NF2 status
    Goutagn S, Yan HW, Zucman-Rossi J, Chan J, Dreyfuss JM, Park PJ, Black PM, Giovannini M, Carroll RS, Kalamarides M.
    Clinical Cancer Research, 16:4155-64, 2010.

  • CpG islands recruit a histone H3 lysine 36 demethylase
    Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJ.
    Molecular Cell, 38:179-90, 2010.

  • Integrative Genome Analysis Reveals an Oncomir/Oncogene Cluster Regulating Glioblastoma Survivorship
    Kim H*, Huang W*, Jiang X, Pennicooke B, Park PJ**, Johnson MD**.
    Proc Natl Acad Sci USA, 107:2183-8, 2010.

  • Analysis of primary chromatin structure from next-generation sequencing
    Tolstorukov MY, Kharchenko PV, Park PJ.
    Epigenomics, 2:187-197, 2010.

  • A Region of Human HOXD that Confers Polycomb-Group Responsiveness
    Woo C, Kharchenko PV, Daheron L, Park PJ, Kingston RE.
    Cell, 140:99-110, 2010.

2009

  • ChIP-seq: advantages and challenges of a maturing technology
    Park PJ.
    Nature Reviews Genetics, 10:669-80, 2009.

  • Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance
    Park PJ, Kong SW, Tebaldi T, Lai WR, Kasif S, Kohane IS.
    Bioinformatics, 25:3121-3127, 2009.

  • Meta-analysis of Glioblastoma multiforme versus Anaplastic astrocytoma identifies robust gene markers
    Dreyfuss JD, Johnson MD, Park PJ.
    Molecular Cancer, 8:71, 2009.

  • Long range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X
    Gorchakov AA, Alekseyenko AA, Kharchenko PV, Park PJ, Kuroda MI.
    Genes and Development, 23:2266-71, 2009.

  • MSL complex globally acetylates H4 K16 on the male X chromosome for dosage compensation in Drosophila
    Gelbart M, Larschan E, Peng S, Park PJ, Kuroda MI.
    Nature Structural and Molecular Biology, 16:825-32, 2009.

  • Thyroid Hormone-Related Regulation of Gene Expression in Human Fatty Liver
    Pihlajamäki J, Boes T, Kim EY, Dearie F, Kim BW, Schroeder J, Mun E, Nasser I, Park PJ, Bianco AC, Goldfine AB, Patti ME.
    J Clin Endocrinol Metab, 94:3521-9, 2009.

  • Surface antigen phenotypes of hematopoietic stem cells from embryos and murine embryonic stem cells
    McKinney-Freeman SL, Naveiras O, Yates F, Loewer S, Philitas M, Curran M, Park PJ, Daley GQ.
    Blood, 114:268-78, 2009.

  • A Permutation Test for determining significance of clusters with applications to spatial and gene expression data
    Park PJ, Manjourides J, Bonetti M, Pagano M.
    Computational Statistics and Data Analysis, 53:4290-4300, 2009.

  • Identifying the Molecular Signature of the Interstitial Deletion 7q Subgroup of Uterine Leiomyomata Using a Paired Analysis
    Hodge JC, Park PJ, Dreyfuss JM, Assil-Kishawi I, Somasundaram P, Semere LG, Quade B, Lynch AM, Stewart EA, Morton CC.
    Genes, Chromosomes, & Cancer, 48:865-85.

  • Efficacy of sunitinib and radiotherapy in genetically engineered mouse model of soft-tissue sarcoma
    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.
    Int J Radiat Oncol Biol Phys, 74:1207-16, 2009.

  • Apc inhibition of Wnt signaling regulates supernumerary tooth formation during embryogenesis and throughout adulthood
    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.
    Development, 136:1939-49, 2009.

  • Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes
    Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ.
    Genome Res, 19:967-77, 2009.

2008

  • Design and analysis of ChIP-seq experiments for DNA-binding proteins
    Kharchenko PV, Tolstorukov M, Park PJ.
    Nature Biotechnology, 6:1351-1359, 2008.

  • Epiegenetics meets next-generation sequencing
    Park PJ.
    Epigenetics, 3:318-321, 2008.

  • The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila X chromosome
    Sural TH, Peng S, Li B, Workman JL, Park PJ, Kuroda MI.
    Nature Structural and Molecular Biology, 15:1318-25, 2008.

  • Comprehensive genomic characterization defines human glioblastoma genes and core pathways
    The Cancer Genome Atlas Research Network (including the Harvard Medical School/Dana-Farber Cancer Institute team: Chin L, Protopopov A, Zhang J, Perna I, Aronson S, Sathiamoorthy N, Ren G, Yao J, Wiedemeyer WR, Kim H, Won Kong S, Xiao Y, Kohane IS, Seidman J, Park PJ, Kucherlapati R).
    Nature, 255:1061-8, 2008.

  • Unphosphorylated SR-like Protein Npl3 Stimulates RNA Polymerase II Elongation
    Dermody JL, Dreyfuss J, Villén J, Ogundipe B, Gygi SP, Park PJ, Ponticelli AS, Moore CL, Buratowski S, Bucheli ME.
    PLoS ONE, 3:e3273, 2008.

  • Nucleosome positioning in human HOX gene clusters
    Kharchenko PV*, Woo CJ*, Tolstorukov MY, Kingston RE**, Park PJ**.
    Genome Research, 18:1554-61, 2008.

  • A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome
    Alekseyenko AA*, Peng S*, Larschan E, Gorchakov AA, Lee OK, Kharchenko PV, McGrath S, Wang CI, Mardis E, Park PJ**, Kuroda MI**.
    Cell, 134:599-609, 2008.
    Highlighted in : Epigenetics: Sequence-guided entry for MSL, Nature Reviews Genetics, 9:732-733, 2008

  • Experimental Design and Data Analysis for Array Comparative Genomic Hybridization
    Park PJ.
    Cancer Investigation, 26:923-928, 2008.

  • nuScore: a web-interface for nucleosome positioning predictions
    Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ.
    Bioinformatics, 24:1456-8, 2008.

  • Differential H3K4 methylation identifies developmentally poised hematopoietic genes
    Orford K*, Kharchenko PV*, Lai WR, Dao MC, Worhunsky D, Park PJ**, Scadden DT**.
    Developmental Cell, 14:798-809, 2008.

  • The mouse X chromosome is enriched for multi-copy testis genes exhibiting post-meiotic expression
    Mueller JL, Mahadevaiah SK, Park PJ, Warburton PE, Page DC, Turner JMA.
    Nature Genetics, 40:794-9, 2008.

  • CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms
    Lai WR, Choudhary V, Park PJ.
    Bioinformatics, 24:1014-1015, 2008.

  • Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes
    Lee H, Kong SW, Park PJ.
    Bioinformatics, 24:889-896, 2008.

  • Pathway analysis of primary central nervous system lymphoma
    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.
    Blood, 111:3200-10, 2008.

  • Specific genes expressed in association with progesterone receptors in meningioma
    Claus EB, Park PJ, Carroll R, Chan J, Black PM.
    Cancer Research, 68:314-22, 2008.

  • Aging elevates metabolic gene expression in brain cholinergic neuron
    Baskerville KA, Kent C, Personett D, Lai WR, Park PJ, Coleman P, McKinney M.
    Neurobiology of Aging, 29:1874-93, 2008 (Epub Jun 11, 2007).

2007

  • MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism
    Larschan E, Alekseyenko AA, Gortchakov AA, Peng S, Li B, Yang P, Workman JL, Park PJ, Kuroda MI.
    Molecular Cell, 28:121-33, 2007.

  • Normalization and Experimental Design for ChIP-chip Data
    Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ.
    BMC Bioinformatics, 8:219, 2007.

  • Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models
    Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S.
    PLoS Genetics, 3:e96, 2007.

2006

  • MSL complex associates with clusters of actively transcribed genes along the Drosophila male X chromosome
    Larschan E, Alekseyenko AA, Lai WR, Park PJ, Kuroda MI.
    Cold Spring Harb Symp Quant Biol, 71:385-94, 2006.

  • A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma
    Liu F*, Park PJ*, Lai WR, Maher E, Chakravarti A, Durso L, Jiang X, yu Y, Brosius A, Thomas M, Chin L, Brennan C, DePinho RA, Kohane IS, Carroll RS, Black PM Johnson MD* (*equal contribution).
    Cancer Research, 66: 10815-10823, 2006.

  • A multivariate approach for integrating genome-wide expression data and biological knowledge
    Kong SW, Pu WT, Park PJ.
    Bioinformatics, 22:2373-80, 2006.

  • Angiogenic profile of soft tissue sarcomas based on analysis of circulating factors and microarray gene expression
    Yoon SS, Segal NH, Park PJ, Detwiller KY, Fernando NT, Ryeom SW, Brennan MF, Singer S.
    Journal of Surgical Research, 135(2):282-90, 2006.

  • A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
    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 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TA.
    Nature Biotechnology, 24(7):832-40, 2006.

  • Post-meiotic sex chromatin in the male germline of mice
    Namekawa SH, Park PJ, Zhang LF, Shima JE, McCarrey JR, Griswold MD, Lee JT.
    Currrent Biology, 16:660-7, 2006.

  • High resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome
    Alekseyenko AA, Larschan E, Lai WR, Park PJ**, Kuroda MI**.
    Genes and Development, 20:848-57, 2006.
    Highlighted in: Gene regulation: Compensation culture, Nature Reviews Genetics, 7:335, 2006 (2006); Dosage compensation in high resolution: global up-regulation through local recruitment Genes & Development, 20:749-753, 2006

2005
  • Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster
    Hamada FN*, Park PJ*, Gordadze PR, Kuroda MI (*co-first authors).
    Genes and Development, 19:2289-94, 2005.

  • Discovering statistically significant pathways in expression profling studies
    Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ.
    Proc Natl Acad Sci USA, 102:13544-9, 2005.

  • Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data
    Lai W, Johnson MJ, Kucherlapati R, Park PJ.
    Bioinformatics, 21:3763-4770, 2005.

  • Interferon-alpha/beta-mediated innate immune mechanisms in dermatomyositis
    Greenberg SA, Pinkus JL, Pinkus GS, Burleson T, Sanoudou D, Tawil R, Barohn RJ, Saperstein DS, Briemberg HR, Ericsson M, Park P, Amato AA.
    Annals of Neurology, 57:664-678, 2005.

  • CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays
    Kong SW, Hwang KB, Kim RD, Zhang BT, Greenberg SA, Kohane IS, Park PJ.
    Bioinformatics, 21:2116-7, 2005.

  • Gene Expression Data and Survival Analysis
    Park PJ.
    Methods of Microarray Data Analysis IV, Shoemaker, JS and Lin, SM, Editors; Springer, New York, 2005.

2004

  • Combining Gene Expression Data from Different Generations of Oligonucleotide Arrays
    Hwang KB, Kong SW, Greenberg SA, Park PJ.
    BMC Bioinformatics, 5:159, 2004.

  • Improving identification of Differentially Expressed Genes Using Public Databases
    Kim R, Park PJ.
    Genome Biology, 5:R70, 2004.

  • Current issues of DNA microarrays: platform comparison, double amplification, and universal standard
    Park PJ, Cao YA, Lee SY, Kim JW, Chang MS, Hart R, Choi S.
    Journal of Biotechnology, 112:225-45, 2004.

  • Multiscale Numerical Methods for Singularly Perturbed Convection-Diffusion Equations
    Park PJ, Hou TY.
    International Journal of Computational Methods, 1:17-65, 2004.

  • Rank-Based Nonlinear Normalization of Oligonucleotide Arrays
    Park PJ, Kohane IS, Kim JH.
    Genomics & Informatics, 1:94-100, 2004.

2003

  • Human decidual natural killer cells are a unique NK cell subset with immunomodulatory potential
    Koopman LA, Kopcow HD, Rybalov B, Boyson JE, Orange JS, Schatz F, Masch R, Lockwood CJ, Schachter AD, Park PJ, Strominger JL.
    J Exp Med, 198:1201-12, 2003.

  • Power Comparisons for Disease Clustering Tests
    Kulldorff M, Tango M, Park PJ.
    Computational Statistics and Data Analysis, 42:665-684, 2003.

  • MicroSage is highly reproducible, but reveals major difference in gene expression among samples obtained from identical tissues
    Blackshaw S, Kuo WP, Park PJ, Tsujikawa M, Gunnersen JM, Scott HS, Boon W, Tan S, Cepko CL.
    Genome Biology, 4(3):R17, 2003.

  • Microarrays and clinical dentistry
    Kuo WP, Whipple ME, Jenssen TK, Todd R, Epstein JB, Ohno-Machado L, Sonis ST, Park PJ.
    J Am Dent Assoc, 134:456-62, 2003.

  • Functional Relationships Between Gene Pairs in Oral Squamous Cell Carcinoma
    Kuo WP, Mendez E, Chen C, Whipple M, Farell G, Agoff N, Park PJ.
    Proceedings American Medical Informatics Association Symposium, 371-5, 2003.

2002

  • Gene Expression Levels In Different Stages of Progression in Oral Squamous Cell Carcinoma
    Kuo WP, Jenssen TK, Park PJ, Lingen MW, Hasina R, Ohno-Machado L.
    Proceedings American Medical Informatics Association Symposium, 2002:415-9, 2002.

  • Comparing Expression Profiles of Genes with Similar Promoter Regions
    Park PJ, Butte A, Kohane IS.
    Bioinformatics, 18(12):1576-84, 2002.

  • Linking Expression Data with Patient Survival Times Using Partial Least Squares
    Park PJ, Tian L, Kohane IS.
    Bioinformatics, 18:S120-7, 2002 (Presented at ISMB 2002).

  • Vector Algebra in the Analysis of Genome-wide Expression Data
    Kuruvilla F, Park PJ, Schreiber SL.
    Genome Biology, 3(3): research0011.1-0011.11, 2002.

2001

  • A Nonparametric Scoring Algorithm for Identifying Informative Genes from Microarray Data
    Park PJ, Pagano M, Bonetti M.
    Pacific Symposium on Biocomputing 6:52-63, 2001