PJP8PeterParkPeter Park, Ph.D.42.33837200000000-71.1032690000000062138Park, PeterJungsoo617/432-7373Professor of Biomedical Informaticscatalyst:eCommonsLogineCommons Loginprns:coAuthorOfcoauthor ofprns:endDateend dateFaculty Rankprns:fullNamefull nameprns:hasAuthorListauthor listprns:hasFacultyRankhas faculty rankprns:hasNetworkhas networkprns:hasPublicationVenuepublished inprns:informationResourceReferenceinformation resource referenceprns:isPrimaryPositionis primary positionprns:latitudelatitudeprns:longitudelongitudeprns:mainImagephotoprns:maxWeightmaximum weightprns:medlineTAjournal title abbreviationprns:meshDescriptorUIMeSH DescriptorUIprns:meshSemanticGroupNameMeSH semantic group nameprns:minWeightminimum weightprns:numberOfAuthorsnumber of authorsprns:numberOfConnectionsnumber of connectionsprns:numberOfPublicationsnumber of publicationsprns:personIdPerson IDprns:personInPrimaryPositionperson in primary positionprns:physicalNeighborOfphysical neighborprns:positionInDepartmentposition in departmentprns:positionInDivisionposition in divisionprns:predicateNodepredicate nodeprns:principalInvestigatorNameprincipal investigator nameprns:publicationDatepublication dateprns:similarTosimilar toprns:sortOrdersort orderprns:startDatestart dateprns:uniquenessWeightuniqueness weightprns:yearyearAcademic ArticleArticleDocumentbibo:pmidPubMed IdentifierAddressvivo:address1address line 1vivo:address2address line 2vivo:address3address line 3vivo:addressCitycityvivo:addressPostalCodepostal codevivo:addressStatestate or provincevivo:authorInAuthorshipselected publicationsvivo:authorRankauthor rank in publicationAuthorshipDepartmentDivisionGrantvivo:hasResearchArearesearch areasvivo:hasResearcherRoleresearch activitiesvivo:hrJobTitleHR job titleInformation Resourcevivo:linkAnchorTextlink anchor textvivo:linkedAuthorlinked authorvivo:linkedInformationResourcelinked information resourcevivo:mailingAddressmailing addressvivo:middleNamemiddle name or initialvivo:personInPositionpositionsvivo:phoneNumberphonePositionvivo:positionInOrganizationposition in organizationvivo:preferredTitlepreferred titleResearcher Rolevivo:researcherRoleOfresearcher role ofvivo:roleContributesTocontributes tovivo:sponsorAwardIdsponsor award idURLLinkvivo:webpagewebpagerdf:predicatepredicaterdf:typetyperdfs:labellabelConceptAgentfoaf:firstNamefirst namefoaf:lastNamelast nameOrganizationPerson15504239Hwang KB, Kong SW, Greenberg SA, Park PJBMC bioinformaticsCombining gene expression data from different generations of oligonucleotide arrays. BMC Bioinformatics. 2004 Oct 25; 5:159.BMC Bioinformatics2004-10-25T00:00:002004Combining gene expression data from different generations of oligonucleotide arrays.18477461Orford K, Kharchenko P, Lai W, Dao MC, Worhunsky DJ, Ferro A, Janzen V, Park PJ, Scadden DTDevelopmental cellDifferential H3K4 methylation identifies developmentally poised hematopoietic genes. Dev Cell. 2008 May; 14(5):798-809.Dev Cell2008-05-01T00:00:002008Differential H3K4 methylation identifies developmentally poised hematopoietic genes.19603527Hodge JC, Park PJ, Dreyfuss JM, Assil-Kishawi I, Somasundaram P, Semere LG, Quade BJ, Lynch AM, Stewart EA, Morton CCGenes, chromosomes & cancerIdentifying 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.Genes Chromosomes Cancer2009-10-01T00:00:002009Identifying the molecular signature of the interstitial deletion 7q subgroup of uterine leiomyomata using a paired analysis.19732454Dreyfuss JM, Johnson MD, Park PJMolecular cancerMeta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers. Mol Cancer. 2009 Sep 04; 8:71.Mol Cancer2009-09-04T00:00:002009Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers.Authorship 10571762Authorship 10574803221796861Gritt A, Park PLocal population studiesThe workhouse populations of Lancashire in 1881. Local Popul Stud. 2011; (86):37-65.Local Popul Stud2011-01-01T00:00:002011The workhouse populations of Lancashire in 1881.29625053Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding LCellComprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 04 05; 173(2):371-385.e18.Cell2018-04-05T00:00:002018Comprehensive Characterization of Cancer Driver Genes and Mutations.19797766Gorchakov AA, Alekseyenko AA, Kharchenko P, Park PJ, Kuroda MIGenes & developmentLong-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X. Genes Dev. 2009 Oct 01; 23(19):2266-71.Genes Dev2009-10-01T00:00:002009Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X.22844249Larschan E, Soruco MM, Lee OK, Peng S, Bishop E, Chery J, Goebel K, Feng J, Park PJ, Kuroda MIPLoS geneticsIdentification of chromatin-associated regulators of MSL complex targeting in Drosophila dosage compensation. PLoS Genet. 2012; 8(7):e1002830.PLoS Genet2012-07-26T00:00:002012Identification of chromatin-associated regulators of MSL complex targeting in Drosophila dosage compensation.23599463Ferrari F, Jung YL, Kharchenko PV, Plachetka A, Alekseyenko AA, Kuroda MI, Park PJScience (New York, N.Y.)Comment on "Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters". Science. 2013 Apr 19; 340(6130):273.Science2013-04-19T00:00:002013Comment on "Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters".Authorship 1065276429731376Dou Y, Gold HD, Luquette LJ, Park PJTrends in genetics : TIGDetecting Somatic Mutations in Normal Cells. Trends Genet. 2018 07; 34(7):545-557.Trends Genet2018-05-03T00:00:002018Detecting Somatic Mutations in Normal Cells.17592629Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJBMC bioinformaticsNormalization and experimental design for ChIP-chip data. BMC Bioinformatics. 2007 Jun 25; 8:219.BMC Bioinformatics2007-06-25T00:00:002007Normalization and experimental design for ChIP-chip data.18296463Lai W, Choudhary V, Park PJBioinformatics (Oxford, England)CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms. Bioinformatics. 2008 Apr 01; 24(7):1014-5.Bioinformatics2008-02-22T00:00:002008CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms.19549744Pihlajamäki J, Boes T, Kim EY, Dearie F, Kim BW, Schroeder J, Mun E, Nasser I, Park PJ, Bianco AC, Goldfine AB, Patti METhe Journal of clinical endocrinology and metabolismThyroid hormone-related regulation of gene expression in human fatty liver. J Clin Endocrinol Metab. 2009 Sep; 94(9):3521-9.J Clin Endocrinol Metab2009-06-23T00:00:002009Thyroid hormone-related regulation of gene expression in human fatty liver.20682713Goutagny S, Yang HW, Zucman-Rossi J, Chan J, Dreyfuss JM, Park PJ, Black PM, Giovannini M, Carroll RS, Kalamarides MClinical cancer research : an official journal of the American Association for Cancer ResearchGenomic 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.Clin Cancer Res2010-08-03T00:00:002010Genomic profiling reveals alternative genetic pathways of meningioma malignant progression dependent on the underlying NF2 status.20718989Kim TM, Luquette LJ, Xi R, Park PJBMC bioinformaticsrSW-seq: algorithm for detection of copy number alterations in deep sequencing data. BMC Bioinformatics. 2010 Aug 18; 11:432.BMC Bioinformatics2010-08-18T00:00:002010rSW-seq: algorithm for detection of copy number alterations in deep sequencing data.20932656Yoon 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 TFInternational journal of radiation oncology, biology, physicsPhase 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.Int J Radiat Oncol Biol Phys2010-10-06T00:00:002010Phase II study of neoadjuvant bevacizumab and radiotherapy for resectable soft tissue sarcomas.12490441Park PJ, Butte AJ, Kohane ISBioinformatics (Oxford, England)Comparing expression profiles of genes with similar promoter regions. Bioinformatics. 2002 Dec; 18(12):1576-84.Bioinformatics2002-12-01T00:00:002002Comparing expression profiles of genes with similar promoter regions.21885022Zacharek 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 CFCell stem cellLung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci. Cell Stem Cell. 2011 Sep 02; 9(3):272-81.Cell Stem Cell2011-09-02T00:00:002011Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci.22553175Jiang X, Xing H, Kim TM, Jung Y, Huang W, Yang HW, Song S, Park PJ, Carroll RS, Johnson MDStem cells (Dayton, Ohio)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.Stem Cells2012-07-01T00:00:002012Numb regulates glioma stem cell fate and growth by altering epidermal growth factor receptor and Skp1-Cullin-F-box ubiquitin ligase activity.23101622Evrony GD, Cai X, Lee E, Hills LB, Elhosary PC, Lehmann HS, Parker JJ, Atabay KD, Gilmore EC, Poduri A, Park PJ, Walsh CACellSingle-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell. 2012 Oct 26; 151(3):483-96.Cell2012-10-26T00:00:002012Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain.16877751Kong SW, Pu WT, Park PJBioinformatics (Oxford, England)A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics. 2006 Oct 01; 22(19):2373-80.Bioinformatics2006-07-28T00:00:002006A multivariate approach for integrating genome-wide expression data and biological knowledge.17571924Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif SPLoS geneticsNetwork-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet. 2007 Jun; 3(6):e96.PLoS Genet2007-06-01T00:00:002007Network-based analysis of affected biological processes in type 2 diabetes models.Authorship 10731011029898899Fan J, Lee HO, Lee S, Ryu DE, Lee S, Xue C, Kim SJ, Kim K, Barkas N, Park PJ, Park WY, Kharchenko PVGenome researchLinking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data. Genome Res. 2018 08; 28(8):1217-1227.Genome Res2018-06-13T00:00:002018Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data.Authorship 10767961029945864Zhang L, Ettou S, Khalid M, Taglienti M, Jain D, Jung YL, Seager C, Liu Y, Ng KH, Park PJ, Kreidberg JADevelopment (Cambridge, England)EED, a member of the polycomb group, is required for nephron differentiation and the maintenance of nephron progenitor cells. Development. 2018 07 18; 145(14).Development2018-07-18T00:00:002018EED, a member of the polycomb group, is required for nephron differentiation and the maintenance of nephron progenitor cells.21399641Tolstorukov MY, Volfovsky N, Stephens RM, Park PJNature structural & molecular biologyImpact of chromatin structure on sequence variability in the human genome. Nat Struct Mol Biol. 2011 Apr; 18(4):510-5.Nat Struct Mol Biol2011-03-13T00:00:002011Impact of chromatin structure on sequence variability in the human genome.22684860Kim YJ, Lee HJ, Kim TM, Eisinger-Mathason TS, Zhang AY, Schmidt B, Karl DL, Nakazawa MS, Park PJ, Simon MC, Yoon SSInternational journal of cancerOvercoming 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 01; 132(1):29-41.Int J Cancer2012-06-26T00:00:002012Overcoming evasive resistance from vascular endothelial growth factor a inhibition in sarcomas by genetic or pharmacologic targeting of hypoxia-inducible factor 1a.22745252Lee 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 PJScience (New York, N.Y.)Landscape of somatic retrotransposition in human cancers. Science. 2012 Aug 24; 337(6097):967-71.Science2012-06-28T00:00:002012Landscape of somatic retrotransposition in human cancers.15313001Park PJ, Cao YA, Lee SY, Kim JW, Chang MS, Hart R, Choi SJournal of biotechnologyCurrent issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. J Biotechnol. 2004 Sep 09; 112(3):225-45.J Biotechnol2004-09-09T00:00:002004Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference.16174746Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJProceedings of the National Academy of Sciences of the United States of AmericaDiscovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A. 2005 Sep 20; 102(38):13544-9.Proc Natl Acad Sci U S A2005-09-08T00:00:002005Discovering statistically significant pathways in expression profiling studies.Authorship 1161051018263644Lee H, Kong SW, Park PJBioinformatics (Oxford, England)Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes. Bioinformatics. 2008 Apr 01; 24(7):889-96.Bioinformatics2008-02-08T00:00:002008Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes.19029915Kharchenko PV, Tolstorukov MY, Park PJNature biotechnologyDesign and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008 Dec; 26(12):1351-9.Nat Biotechnol2008-11-16T00:00:002008Design and analysis of ChIP-seq experiments for DNA-binding proteins.Authorship 10792662321156717Anchan 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 RLHuman molecular geneticsAmniocytes can serve a dual function as a source of iPS cells and feeder layers. Hum Mol Genet. 2011 Mar 01; 20(5):962-74.Hum Mol Genet2010-12-14T00:00:002010Amniocytes can serve a dual function as a source of iPS cells and feeder layers.Authorship 10825091329996110Zhang Y, Yang L, Kucherlapati M, Chen F, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Li W, Park PJ, Kucherlapati R, Creighton CJCell reportsA Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases. Cell Rep. 2018 07 10; 24(2):515-527.Cell Rep2018-07-10T00:00:002018A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases.29986673Holm IA, Agrawal PB, Ceyhan-Birsoy O, Christensen KD, Fayer S, Frankel LA, Genetti CA, Krier JB, LaMay RC, Levy HL, McGuire AL, Parad RB, Park PJ, Pereira S, Rehm HL, Schwartz TS, Waisbren SE, Yu TW, Green RC, Beggs AHBMC pediatricsThe BabySeq project: implementing genomic sequencing in newborns. BMC Pediatr. 2018 07 09; 18(1):225.BMC Pediatr2018-07-09T00:00:002018The BabySeq project: implementing genomic sequencing in newborns.18445607Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJBioinformatics (Oxford, England)nuScore: a web-interface for nucleosome positioning predictions. Bioinformatics. 2008 Jun 15; 24(12):1456-8.Bioinformatics2008-04-29T00:00:002008nuScore: a web-interface for nucleosome positioning predictions.18454149Mueller JL, Mahadevaiah SK, Park PJ, Warburton PE, Page DC, Turner JMNature geneticsThe mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression. Nat Genet. 2008 Jun; 40(6):794-9.Nat Genet2008-05-04T00:00:002008The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression.22506565Reis BY, Olson KL, Tian L, Bohn RL, Brownstein JS, Park PJ, Cziraky MJ, Wilson MD, Mandl KDDrug safetyA pharmacoepidemiological network model for drug safety surveillance: statins and rhabdomyolysis. Drug Saf. 2012 May 01; 35(5):395-406.Drug Saf2012-05-01T00:00:002012A pharmacoepidemiological network model for drug safety surveillance: statins and rhabdomyolysis.Authorship 1191885Authorship 10869183230096302Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding LCellComprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 08 09; 174(4):1034-1035.Cell2018-08-09T00:00:002018Comprehensive Characterization of Cancer Driver Genes and Mutations.18184868Tun HW, Personett D, Baskerville KA, Menke DM, Jaeckle KA, Kreinest P, Edenfield B, Zubair AC, O'Neill BP, Lai WR, Park PJ, McKinney MBloodPathway analysis of primary central nervous system lymphoma. Blood. 2008 Mar 15; 111(6):3200-10.Blood2008-01-09T00:00:002008Pathway analysis of primary central nervous system lymphoma.19429790Wang XP, O'Connell DJ, Lund JJ, Saadi I, Kuraguchi M, Turbe-Doan A, Cavallesco R, Kim H, Park PJ, Harada H, Kucherlapati R, Maas RLDevelopment (Cambridge, England)Apc inhibition of Wnt signaling regulates supernumerary tooth formation during embryogenesis and throughout adulthood. Development. 2009 Jun; 136(11):1939-49.Development2009-06-01T00:00:002009Apc inhibition of Wnt signaling regulates supernumerary tooth formation during embryogenesis and throughout adulthood.19648925Gelbart ME, Larschan E, Peng S, Park PJ, Kuroda MINature structural & molecular biologyDrosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation. Nat Struct Mol Biol. 2009 Aug; 16(8):825-32.Nat Struct Mol Biol2009-08-02T00:00:002009Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation.18723689Kharchenko PV, Woo CJ, Tolstorukov MY, Kingston RE, Park PJGenome researchNucleosome positioning in human HOX gene clusters. Genome Res. 2008 Oct; 18(10):1554-61.Genome Res2008-08-22T00:00:002008Nucleosome positioning in human HOX gene clusters.19029895Sural TH, Peng S, Li B, Workman JL, Park PJ, Kuroda MINature structural & molecular biologyThe 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.Nat Struct Mol Biol2008-11-23T00:00:002008The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster X chromosome.Authorship 10894081630143029Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, Hwang J, Lee S, Alver BH, Pfister H, Mirny LA, Park PJ, Gehlenborg NGenome biologyHiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018 08 24; 19(1):125.Genome Biol2018-08-24T00:00:002018HiGlass: web-based visual exploration and analysis of genome interaction maps.Authorship 11635222418008Balakrishnan A, Stearns AT, Park PJ, Dreyfuss JM, Ashley SW, Rhoads DB, Tavakkolizadeh AAnnals of surgeryUpregulation of proapoptotic microRNA mir-125a after massive small bowel resection in rats. Ann Surg. 2012 Apr; 255(4):747-53.Ann Surg2012-04-01T00:00:002012Upregulation of proapoptotic microRNA mir-125a after massive small bowel resection in rats.22955991Landt 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 MGenome researchChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31.Genome Res2012-09-01T00:00:002012ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.18818768Dermody JL, Dreyfuss JM, Villén J, Ogundipe B, Gygi SP, Park PJ, Ponticelli AS, Moore CL, Buratowski S, Bucheli MEPloS oneUnphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation. PLoS One. 2008 Sep 26; 3(9):e3273.PLoS One2008-09-26T00:00:002008Unphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation.19246569Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJGenome researchComparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Res. 2009 Jun; 19(6):967-77.Genome Res2009-02-26T00:00:002009Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes.Authorship 1063631722065754Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, Johnson MD, Muzny DM, Wheeler DA, Gibbs RA, Kucherlapati R, Park PJProceedings of the National Academy of Sciences of the United States of AmericaCopy 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.Proc Natl Acad Sci U S A2011-11-07T00:00:002011Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion.22120048Kharchenko PV, Xi R, Park PJNature geneticsEvidence for dosage compensation between the X chromosome and autosomes in mammals. Nat Genet. 2011 Nov 28; 43(12):1167-9; author reply 1171-2.Nat Genet2011-11-28T00:00:002011Evidence for dosage compensation between the X chromosome and autosomes in mammals.22323457Lachke SA, Ho JW, Kryukov GV, O'Connell DJ, Aboukhalil A, Bulyk ML, Park PJ, Maas RLInvestigative ophthalmology & visual scienceiSyTE: integrated Systems Tool for Eye gene discovery. Invest Ophthalmol Vis Sci. 2012 Mar; 53(3):1617-27.Invest Ophthalmol Vis Sci2012-03-21T00:00:002012iSyTE: integrated Systems Tool for Eye gene discovery.22570616Alekseyenko 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 PJPLoS geneticsSequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genet. 2012; 8(4):e1002646.PLoS Genet2012-04-26T00:00:002012Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context.Authorship 1110561229890820Jiang Y, Park P, Hong SM, Ban KMolecules and cellsMaturation of Cardiomyocytes Derived from Human Pluripotent Stem Cells: Current Strategies and Limitations. Mol Cells. 2018 Jul 31; 41(7):613-621.Mol Cells2018-06-12T00:00:002018Maturation of Cardiomyocytes Derived from Human Pluripotent Stem Cells: Current Strategies and Limitations.21076395Jagani 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 MNature medicineLoss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway. Nat Med. 2010 Dec; 16(12):1429-33.Nat Med2010-11-14T00:00:002010Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway.21356108Ho JW, Bishop E, Karchenko PV, Nègre N, White KP, Park PJBMC genomicsChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics. 2011 Feb 28; 12:134.BMC Genomics2011-02-28T00:00:002011ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.Authorship 1125421128983899Park PJ, Cole SS, Bercu ZL, Martin J, Newsome JThe journal of vascular accessUnderstanding patient preferences for femoral central venous catheterization among patients with sickle cell disease. J Vasc Access. 2018 03; 19(2):199-200.J Vasc Access2018-02-19T00:00:002018Understanding patient preferences for femoral central venous catheterization among patients with sickle cell disease.19098449Park PJEpigeneticsEpigenetics meets next-generation sequencing. Epigenetics. 2008 Nov; 3(6):318-21.Epigenetics2008-11-22T00:00:002008Epigenetics meets next-generation sequencing.20085705Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RECellA region of the human HOXD cluster that confers polycomb-group responsiveness. Cell. 2010 Jan 08; 140(1):99-110.Cell2010-01-08T00:00:002010A region of the human HOXD cluster that confers polycomb-group responsiveness.Authorship 112725117Authorship 1128258930683134Zhao Y, Huang W, Kim TM, Jung Y, Menon LG, Xing H, Li H, Carroll RS, Park PJ, Yang HW, Johnson MDJournal of experimental & clinical cancer research : CRMicroRNA-29a activates a multi-component growth and invasion program in glioblastoma. J Exp Clin Cancer Res. 2019 Jan 25; 38(1):36.J Exp Clin Cancer Res2019-01-25T00:00:002019MicroRNA-29a activates a multi-component growth and invasion program in glioblastoma.30670628Wang S, Chen J, Garcia SP, Liang X, Zhang F, Yan P, Yu H, Wei W, Li Z, Wang J, Le H, Han Z, Luo X, Day DS, Stevens SM, Zhang Y, Park PJ, Liu ZJ, Sun K, Yuan GC, Pu WT, Zhang BGenome researchA dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA. Genome Res. 2019 02; 29(2):193-207.Genome Res2019-01-22T00:00:002019A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA.http://compbio.med.harvard.eduPark LabAuthorship 11323932430755442Howard TP, Arnoff TE, Song MR, Giacomelli AO, Wang X, Hong AL, Dharia NV, Wang S, Vazquez F, Pham MT, Morgan AM, Wachter F, Bird GH, Kugener G, Oberlick EM, Rees MG, Tiv HL, Hwang JH, Walsh KH, Cook A, Krill-Burger JM, Tsherniak A, Gokhale PC, Park PJ, Stegmaier K, Walensky LD, Hahn WC, Roberts CWMCancer researchMDM2 and MDM4 Are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors. Cancer Res. 2019 05 01; 79(9):2404-2414.Cancer Res2019-02-12T00:00:002019MDM2 and MDM4 Are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors.D020411DevicesProcedures143939220.515471Oligonucleotide Array Sequence AnalysisD015894Genes & Molecular Sequences120744190.377767Genome, Human30988514Gulhan DC, Lee JJ, Melloni GEM, Cortés-Ciriano I, Park PJNature geneticsDetecting the mutational signature of homologous recombination deficiency in clinical samples. Nat Genet. 2019 05; 51(5):912-919.Nat Genet2019-04-15T00:00:002019Detecting the mutational signature of homologous recombination deficiency in clinical samples.D056915Physiology80219360.52468DNA Copy Number VariationsD047369Procedures4648880.775384Chromatin ImmunoprecipitationAuthorship 11410105D017422Procedures167747910.431712Sequence Analysis, DNAAuthorship 11434901430886424Bohrson CL, Barton AR, Lodato MA, Rodin RE, Luquette LJ, Viswanadham VV, Gulhan DC, Cortés-Ciriano I, Sherman MA, Kwon M, Coulter ME, Galor A, Walsh CA, Park PJNature geneticsLinked-read analysis identifies mutations in single-cell DNA-sequencing data. Nat Genet. 2019 04; 51(4):749-754.Nat Genet2019-03-18T00:00:002019Linked-read analysis identifies mutations in single-cell DNA-sequencing data.Authorship 11489672Authorship 11495421431015438Wang X, Wang S, Troisi EC, Howard TP, Haswell JR, Wolf BK, Hawk WH, Ramos P, Oberlick EM, Tzvetkov EP, Ross A, Vazquez F, Hahn WC, Park PJ, Roberts CWMNature communicationsBRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors. Nat Commun. 2019 04 23; 10(1):1881.Nat Commun2019-04-23T00:00:002019BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors.30154013Ambur V, Park P, Gaughan JP, Golarz S, Schmieder F, Van Bemmelen P, Choi E, Dhanisetty RJournal of vascular surgeryThe impact of chronic kidney disease on lower extremity bypass outcomes in patients with critical limb ischemia. J Vasc Surg. 2019 02; 69(2):491-496.J Vasc Surg2018-08-25T00:00:002018The impact of chronic kidney disease on lower extremity bypass outcomes in patients with critical limb ischemia.Authorship 1222057Authorship 1151805631077294Lee S, Johnson J, Vitzthum C, Kirli K, Alver BH, Park PJBioinformatics (Oxford, England)Tibanna: software for scalable execution of portable pipelines on the cloud. Bioinformatics. 2019 11 01; 35(21):4424-4426.Bioinformatics2019-11-01T00:00:002019Tibanna: software for scalable execution of portable pipelines on the cloud.GeneticsMedicinePediatricsGeneticsImmunologyBrigham and Women's HospitalBoston Children's HospitalHarvard Medical SchoolMassachusetts General HospitalYJ12YoungsookJungYoungsook Lucy Jung, Ph.D.36044Jung, YoungsookInstructor in PediatricsAuthorship 1320223GEM4GustavoMartinez-NoelGustavo E.C. Martinez-Noel, Ph.D.42.33837200000000-71.1032690000000010687Martinez-Noel, GustavoResearch Associate in ImmunologyMEG15MarnieGelbartMarnie Gelbart, Ph.D.42.33837200000000-71.1032690000000074104Gelbart, MarnieResearch Associate in GeneticsREK1RobertKingstonRobert Edward Kingston, Ph.D.42.36241700000000-71.0689370000000073338Kingston, RobertProfessor of GeneticsCW11ChristopherWalshChristopher A. Walsh, M.D., Ph.D.42.33849900000000-71.104460000000009592Walsh, ChristopherBullard Professor of Pediatrics and Neurology31155235Lee JJ, Park S, Park H, Kim S, Lee J, Lee J, Youk J, Yi K, An Y, Park IK, Kang CH, Chung DH, Kim TM, Jeon YK, Hong D, Park PJ, Ju YS, Kim YTCellTracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma. Cell. 2019 06 13; 177(7):1842-1857.e21.Cell2019-05-30T00:00:002019Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma.CJT1CliffordTabinClifford J. Tabin, Ph.D.42.33837200000000-71.1032690000000073820Tabin, CliffordGeorge Jacob and Jacqueline Hazel Leder Professor of GeneticsIAA3IvanAdzhubeyIvan A. Adzhubey, Ph.D.42.33837200000000-71.1032690000000013588Adzhubey, IvanResearch Associate in Biomedical InformaticsAuthorship 115860516SRS14ShamilSunyaevShamil R. Sunyaev, Ph.D.42.33837200000000-71.1032690000000065871Sunyaev, ShamilProfessor of Biomedical InformaticsFSA2FowzanAlkurayaFowzan Sami Alkuraya, M.B.,B.S.42.33837200000000-71.1032690000000041121Alkuraya, FowzanInstructor in PediatricsMIK1MitziKurodaMitzi Kuroda, Ph.D.42.33837200000000-71.1032690000000065836Kuroda, MitziProfessor of GeneticsJTL3JeannieLeeJeannie T. Lee, M.D.,Ph.D.42.36125700000000-71.0655270000000032135Lee, JeannieProfessor of GeneticsNP7NorbertPerrimonNorbert Perrimon, Ph.D.42.33837200000000-71.103269000000006247Perrimon, NorbertJames Stillman Professor of Developmental Biology11297selected publications3.11890.00461147879research areas3.58640.0168605269coauthor of151.63434.105360similar to23665121Apostolou 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 KCell stem cellGenome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell. 2013 Jun 06; 12(6):699-712.Cell Stem Cell2013-05-09T00:00:002013Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming.Authorship 1342536Authorship 144359631416464Yang L, Wang S, Lee JJ, Lee S, Lee E, Shinbrot E, Wheeler DA, Kucherlapati R, Park PJGenome biologyAn enhanced genetic model of colorectal cancer progression history. Genome Biol. 2019 08 15; 20(1):168.Genome Biol2019-08-15T00:00:002019An enhanced genetic model of colorectal cancer progression history.Authorship 11845139Authorship 11852964Authorship 11846632131461650Oberlick EM, Rees MG, Seashore-Ludlow B, Vazquez F, Nelson GM, Dharia NV, Weir BA, Tsherniak A, Ghandi M, Krill-Burger JM, Meyers RM, Wang X, Montgomery P, Root DE, Bieber JM, Radko S, Cheah JH, Hon CS, Shamji AF, Clemons PA, Park PJ, Dyer MA, Golub TR, Stegmaier K, Hahn WC, Stewart EA, Schreiber SL, Roberts CWMCell reportsSmall-Molecule and CRISPR Screening Converge to Reveal Receptor Tyrosine Kinase Dependencies in Pediatric Rhabdoid Tumors. Cell Rep. 2019 08 27; 28(9):2331-2344.e8.Cell Rep2019-08-27T00:00:002019Small-Molecule and CRISPR Screening Converge to Reveal Receptor Tyrosine Kinase Dependencies in Pediatric Rhabdoid Tumors.31467286Luquette LJ, Bohrson CL, Sherman MA, Park PJNature communicationsIdentification of somatic mutations in single cell DNA-seq using a spatial model of allelic imbalance. Nat Commun. 2019 08 29; 10(1):3908.Nat Commun2019-08-29T00:00:002019Identification of somatic mutations in single cell DNA-seq using a spatial model of allelic imbalance.Authorship 145913Authorship 11934421431558726Wang X, Wang S, Troisi EC, Howard TP, Haswell JR, Wolf BK, Hawk WH, Ramos P, Oberlick EM, Tzvetkov EP, Ross A, Vazquez F, Hahn WC, Park PJ, Roberts CWMNature communicationsAuthor Correction: BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors. Nat Commun. 2019 Sep 26; 10(1):4445.Nat Commun2019-09-26T00:00:002019Author Correction: BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors.31597037Kim J, Hu C, Moufawad El Achkar C, Black LE, Douville J, Larson A, Pendergast MK, Goldkind SF, Lee EA, Kuniholm A, Soucy A, Vaze J, Belur NR, Fredriksen K, Stojkovska I, Tsytsykova A, Armant M, DiDonato RL, Choi J, Cornelissen L, Pereira LM, Augustine EF, Genetti CA, Dies K, Barton B, Williams L, Goodlett BD, Riley BL, Pasternak A, Berry ER, Pflock KA, Chu S, Reed C, Tyndall K, Agrawal PB, Beggs AH, Grant PE, Urion DK, Snyder RO, Waisbren SE, Poduri A, Park PJ, Patterson A, Biffi A, Mazzulli JR, Bodamer O, Berde CB, Yu TWThe New England journal of medicinePatient-Customized Oligonucleotide Therapy for a Rare Genetic Disease. N Engl J Med. 2019 10 24; 381(17):1644-1652.N Engl J Med2019-10-09T00:00:002019Patient-Customized Oligonucleotide Therapy for a Rare Genetic Disease.Authorship 15169211Authorship 119643042Authorship 11973732131610796Zhang Y, Yang L, Kucherlapati M, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Park PJ, Kucherlapati R, Creighton CJGenome biologyGlobal impact of somatic structural variation on the DNA methylome of human cancers. Genome Biol. 2019 10 15; 20(1):209.Genome Biol2019-10-15T00:00:002019Global impact of somatic structural variation on the DNA methylome of human cancers.true1Research Associate in ImmunologyResearch Associate in Immunologytrue1Professor of GeneticsProfessor of Geneticstrue1James Stillman Professor of Developmental BiologyJames Stillman Professor of Developmental BiologyAuthorship 12169121031907404Dou Y, Kwon M, Rodin RE, Cortés-Ciriano I, Doan R, Luquette LJ, Galor A, Bohrson C, Walsh CA, Park PJNature biotechnologyAccurate detection of mosaic variants in sequencing data without matched controls. Nat Biotechnol. 2020 03; 38(3):314-319.Nat Biotechnol2020-01-06T00:00:002020Accurate detection of mosaic variants in sequencing data without matched controls.Authorship 11632512Authorship 1222392332003786Horton CA, Alver BH, Park PJBioinformatics (Oxford, England)GiniQC: a measure for quantifying noise in single-cell Hi-C data. Bioinformatics. 2020 05 01; 36(9):2902-2904.Bioinformatics2020-05-01T00:00:002020GiniQC: a measure for quantifying noise in single-cell Hi-C data.Authorship 122384712Authorship 122386740Authorship 12230351132024998Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PA, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine KM, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, Campbell PJ, Tubio JMCNature geneticsPan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020 03; 52(3):306-319.Nat Genet2020-02-05T00:00:002020Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.32025003Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, Park PJNature geneticsComprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet. 2020 03; 52(3):331-341.Nat Genet2020-02-05T00:00:002020Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.32024817Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, Brors B, Rippe K, Jones DTW, Feuerbach LNature communicationsGenomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun. 2020 02 05; 11(1):733.Nat Commun2020-02-05T00:00:002020Genomic footprints of activated telomere maintenance mechanisms in cancer.Authorship 12311401Authorship 12319642232193378Färkkilä A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C, Chen YA, Schapiro D, Zhou Y, Graham JR, Dezube BJ, Munster P, Santagata S, Garcia E, Rodig S, Lako A, Chowdhury D, Shapiro GI, Matulonis UA, Park PJ, Hautaniemi S, Sorger PK, Swisher EM, D'Andrea AD, Konstantinopoulos PANature communicationsImmunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Nat Commun. 2020 03 19; 11(1):1459.Nat Commun2020-03-19T00:00:002020Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer.32062997Park PJ, Kokabi N, Nadendla P, Lindsey T, Dariushnia SRCanadian Association of Radiologists journal = Journal l'Association canadienne des radiologistesEfficacy of Intraprocedural Superior Hypogastric Nerve Block in Reduction of Postuterine Artery Embolization Narcotic Analgesia Use. Can Assoc Radiol J. 2020 Feb; 71(1):75-80.Can Assoc Radiol J2020-01-27T00:00:002020Efficacy of Intraprocedural Superior Hypogastric Nerve Block in Reduction of Postuterine Artery Embolization Narcotic Analgesia Use.Authorship 12394371832252413Miller DT, Cortés-Ciriano I, Pillay N, Hirbe AC, Snuderl M, Bui MM, Piculell K, Al-Ibraheemi A, Dickson BC, Hart J, Jones K, Jordan JT, Kim RH, Lindsay D, Nishida Y, Ullrich NJ, Wang X, Park PJ, Flanagan AMGenesGenomics of MPNST (GeM) Consortium: Rationale and Study Design for Multi-Omic Characterization of NF1-Associated and Sporadic MPNSTs. Genes (Basel). 2020 04 02; 11(4).Genes (Basel)2020-04-02T00:00:002020Genomics of MPNST (GeM) Consortium: Rationale and Study Design for Multi-Omic Characterization of NF1-Associated and Sporadic MPNSTs.32322066Touat M, Li YY, Boynton AN, Spurr LF, Iorgulescu JB, Bohrson CL, Cortes-Ciriano I, Birzu C, Geduldig JE, Pelton K, Lim-Fat MJ, Pal S, Ferrer-Luna R, Ramkissoon SH, Dubois F, Bellamy C, Currimjee N, Bonardi J, Qian K, Ho P, Malinowski S, Taquet L, Jones RE, Shetty A, Chow KH, Sharaf R, Pavlick D, Albacker LA, Younan N, Baldini C, Verreault M, Giry M, Guillerm E, Ammari S, Beuvon F, Mokhtari K, Alentorn A, Dehais C, Houillier C, Laigle-Donadey F, Psimaras D, Lee EQ, Nayak L, McFaline-Figueroa JR, Carpentier A, Cornu P, Capelle L, Mathon B, Barnholtz-Sloan JS, Chakravarti A, Bi WL, Chiocca EA, Fehnel KP, Alexandrescu S, Chi SN, Haas-Kogan D, Batchelor TT, Frampton GM, Alexander BM, Huang RY, Ligon AH, Coulet F, Delattre JY, Hoang-Xuan K, Meredith DM, Santagata S, Duval A, Sanson M, Cherniack AD, Wen PY, Reardon DA, Marabelle A, Park PJ, Idbaih A, Beroukhim R, Bandopadhayay P, Bielle F, Ligon KLNatureMechanisms and therapeutic implications of hypermutation in gliomas. Nature. 2020 04; 580(7804):517-523.Nature2020-04-15T00:00:002020Mechanisms and therapeutic implications of hypermutation in gliomas.32293513Wang S, Lee S, Chu C, Jain D, Kerpedjiev P, Nelson GM, Walsh JM, Alver BH, Park PJGenome biologyHiNT: a computational method for detecting copy number variations and translocations from Hi-C data. Genome Biol. 2020 03 23; 21(1):73.Genome Biol2020-03-23T00:00:002020HiNT: a computational method for detecting copy number variations and translocations from Hi-C data.Authorship 12407859Authorship 124181973Authorship 124940512Authorship 12467222232424117Färkkilä A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C, Chen YA, Schapiro D, Zhou Y, Graham JR, Dezube BJ, Munster P, Santagata S, Garcia E, Rodig S, Lako A, Chowdhury D, Shapiro GI, Matulonis UA, Park PJ, Hautaniemi S, Sorger PK, Swisher EM, D'Andrea AD, Konstantinopoulos PANature communicationsAuthor Correction: Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Nat Commun. 2020 05 18; 11(1):2543.Nat Commun2020-05-18T00:00:002020Author Correction: Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer.32404988Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, Park PJNature geneticsPublisher Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet. 2023 May; 55(5):893.Nat Genet2023-05-01T00:00:002023Publisher Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.Authorship 1252910732494760Gulhan DC, Garcia E, Lee EK, Lindemann NI, Liu JF, Matulonis UA, Park PJ, Konstantinopoulos PAJCO precision oncologyGenomic Determinants of De Novo Resistance to Immune Checkpoint Blockade in Mismatch Repair-Deficient Endometrial Cancer. JCO Precis Oncol. 2020; 4:492-497.JCO Precis Oncol2020-05-08T00:00:002020Genomic Determinants of De Novo Resistance to Immune Checkpoint Blockade in Mismatch Repair-Deficient Endometrial Cancer.2022-05-31PARK, PETER J2020-06-01Identification of Transposable Element Insertions in the Kids First DataR03CA249364Principal InvestigatorAuthorship 12558951232522880Huang AY, Li P, Rodin RE, Kim SN, Dou Y, Kenny CJ, Akula SK, Hodge RD, Bakken TE, Miller JA, Lein ES, Park PJ, Lee EA, Walsh CAProceedings of the National Academy of Sciences of the United States of AmericaParallel RNA and DNA analysis after deep sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain. Proc Natl Acad Sci U S A. 2020 06 23; 117(25):13886-13895.Proc Natl Acad Sci U S A2020-06-10T00:00:002020Parallel RNA and DNA analysis after deep sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain.Authorship 126564810Authorship 12653632032631391Yun JW, Yang L, Park HY, Lee CW, Cha H, Shin HT, Noh KW, Choi YL, Park WY, Park PJGenome biologyDysregulation of cancer genes by recurrent intergenic fusions. Genome Biol. 2020 07 06; 21(1):166.Genome Biol2020-07-06T00:00:002020Dysregulation of cancer genes by recurrent intergenic fusions.32636365Goldman MJ, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O'Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein JN, Huber W, Valencia A, Park PJ, Papatheodorou I, Zhu J, Ferretti V, Vazquez MNature communicationsA user guide for the online exploration and visualization of PCAWG data. Nat Commun. 2020 07 07; 11(1):3400.Nat Commun2020-07-07T00:00:002020A user guide for the online exploration and visualization of PCAWG data.Authorship 1545821Authorship 1566543Authorship 1268290332662945Chu C, Zhao B, Park PJ, Lee EACurrent protocols in human geneticsIdentification and Genotyping of Transposable Element Insertions From Genome Sequencing Data. Curr Protoc Hum Genet. 2020 09; 107(1):e102.Curr Protoc Hum Genet2020-09-01T00:00:002020Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data.Authorship 17084Authorship 1274862932754639Ettou S, Jung YL, Miyoshi T, Jain D, Hiratsuka K, Schumacher V, Taglienti ME, Morizane R, Park PJ, Kreidberg JAScience advancesEpigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury. Sci Adv. 2020 07; 6(30):eabb5460.Sci Adv2020-07-24T00:00:002020Epigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury.Authorship 1395324Authorship 1288525532941642Reim NI, Chuang J, Jain D, Alver BH, Park PJ, Winston FNucleic acids researchThe conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae. Nucleic Acids Res. 2020 10 09; 48(18):10241-10258.Nucleic Acids Res2020-10-09T00:00:002020The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae.Authorship 1293192833015524Haider S, Tyekucheva S, Prandi D, Fox NS, Ahn J, Xu AW, Pantazi A, Park PJ, Laird PW, Sander C, Wang W, Demichelis F, Loda M, Boutros PCJCO precision oncologySystematic Assessment of Tumor Purity and Its Clinical Implications. JCO Precis Oncol. 2020; 4.JCO Precis Oncol2020-09-04T00:00:002020Systematic Assessment of Tumor Purity and Its Clinical Implications.Authorship 19571933136153Jain D, Chu C, Alver BH, Lee S, Lee EA, Park PJBioinformatics (Oxford, England)HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data. Bioinformatics. 2021 05 23; 37(8):1045-1051.Bioinformatics2021-05-23T00:00:002021HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data.Authorship 13042046Authorship 2165054Authorship 1316832533416869Kwon M, Lee S, Berselli M, Chu C, Park PJBioinformatics (Oxford, England)BamSnap: a lightweight viewer for sequencing reads in BAM files. Bioinformatics. 2021 Apr 19; 37(2):263-264.Bioinformatics2021-04-19T00:00:002021BamSnap: a lightweight viewer for sequencing reads in BAM files.Authorship 1476765Authorship 132064915Authorship 13218458Authorship 132212716Authorship 1321086433432195Rodin RE, Dou Y, Kwon M, Sherman MA, D'Gama AM, Doan RN, Rento LM, Girskis KM, Bohrson CL, Kim SN, Nadig A, Luquette LJ, Gulhan DC, Park PJ, Walsh CANature neuroscienceThe landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing. Nat Neurosci. 2021 02; 24(2):176-185.Nat Neurosci2021-01-11T00:00:002021The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing.33432194Sherman MA, Rodin RE, Genovese G, Dias C, Barton AR, Mukamel RE, Berger B, Park PJ, Walsh CA, Loh PRNature neuroscienceLarge mosaic copy number variations confer autism risk. Nat Neurosci. 2021 02; 24(2):197-203.Nat Neurosci2021-01-11T00:00:002021Large mosaic copy number variations confer autism risk.33459505Yang HW, Lee S, Yang D, Dai H, Zhang Y, Han L, Zhao S, Zhang S, Ma Y, Johnson MF, Rattray AK, Johnson TA, Wang G, Zheng S, Carroll RS, Park PJ, Johnson MDEMBO molecular medicineDeletions in CWH43 cause idiopathic normal pressure hydrocephalus. EMBO Mol Med. 2021 03 05; 13(3):e13249.EMBO Mol Med2021-01-18T00:00:002021Deletions in CWH43 cause idiopathic normal pressure hydrocephalus.33450522Jung YL, Kirli K, Alver BH, Park PJCurrent opinion in genetics & developmentResources and challenges for integrative analysis of nuclear architecture data. Curr Opin Genet Dev. 2021 04; 67:103-110.Curr Opin Genet Dev2021-01-12T00:00:002021Resources and challenges for integrative analysis of nuclear architecture data.Authorship 13237181433514515Färkkilä A, Rodríguez A, Oikkonen J, Gulhan DC, Nguyen H, Domínguez J, Ramos S, Mills CE, Pérez-Villatoro F, Lazaro JB, Zhou J, Clairmont CS, Moreau LA, Park PJ, Sorger PK, Hautaniemi S, Frias S, D'Andrea ADCancer researchHeterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells. Cancer Res. 2021 05 15; 81(10):2774-2787.Cancer Res2021-01-29T00:00:002021Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells.Authorship 13391108Authorship 13396221133735618Robinson DCL, Ritso M, Nelson GM, Mokhtari Z, Nakka K, Bandukwala H, Goldman SR, Park PJ, Mounier R, Chazaud B, Brand M, Rudnicki MA, Adelman K, Dilworth FJDevelopmental cellNegative elongation factor regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation. Dev Cell. 2021 04 05; 56(7):1014-1029.e7.Dev Cell2021-03-17T00:00:002021Negative elongation factor regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation.33737485Bizzotto S, Dou Y, Ganz J, Doan RN, Kwon M, Bohrson CL, Kim SN, Bae T, Abyzov A, Park PJ, Walsh CAScience (New York, N.Y.)Landmarks of human embryonic development inscribed in somatic mutations. Science. 2021 03 19; 371(6535):1249-1253.Science2021-03-19T00:00:002021Landmarks of human embryonic development inscribed in somatic mutations.Authorship 13412044Authorship 134129915Authorship 1342061433753946Rodin RE, Dou Y, Kwon M, Sherman MA, D'Gama AM, Doan RN, Rento LM, Girskis KM, Bohrson CL, Kim SN, Nadig A, Luquette LJ, Gulhan DC, Park PJ, Walsh CANature neuroscienceAuthor Correction: The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing. Nat Neurosci. 2021 Apr; 24(4):611.Nat Neurosci2021-04-01T00:00:002021Author Correction: The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing.33770368Bhasin A, Bregger M, Kluk M, Park P, Feinglass J, Barsuk JInternal and emergency medicineExertional hypoxia in patients without resting hypoxia is an early predictor of moderate to severe COVID-19. Intern Emerg Med. 2021 11; 16(8):2097-2103.Intern Emerg Med2021-03-26T00:00:002021Exertional hypoxia in patients without resting hypoxia is an early predictor of moderate to severe COVID-19.33753749Cook JH, Melloni GEM, Gulhan DC, Park PJ, Haigis KMNature communicationsThe origins and genetic interactions of KRAS mutations are allele- and tissue-specific. Nat Commun. 2021 03 22; 12(1):1808.Nat Commun2021-03-22T00:00:002021The origins and genetic interactions of KRAS mutations are allele- and tissue-specific.Authorship 13453424033781308Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov AGenome biologyComprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biol. 2021 03 29; 22(1):92.Genome Biol2021-03-29T00:00:002021Comprehensive identification of somatic nucleotide variants in human brain tissue.true1Professor of Biomedical InformaticsProfessor of Biomedical InformaticsAuthorship 13471806Authorship 1350144933929509Lonfat N, Wang S, Lee C, Garcia M, Choi J, Park PJ, Cepko CDevelopment (Cambridge, England)Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors. Development. 2021 05 01; 148(9).Development2021-04-30T00:00:002021Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors.33888559Viktorovskaya O, Chuang J, Jain D, Reim NI, López-Rivera F, Murawska M, Spatt D, Churchman LS, Park PJ, Winston FGenes & developmentEssential histone chaperones collaborate to regulate transcription and chromatin integrity. Genes Dev. 2021 05 01; 35(9-10):698-712.Genes Dev2021-04-22T00:00:002021Essential histone chaperones collaborate to regulate transcription and chromatin integrity.Authorship 13645201234144992Roberts Kingman GA, Vyas DN, Jones FC, Brady SD, Chen HI, Reid K, Milhaven M, Bertino TS, Aguirre WE, Heins DC, von Hippel FA, Park PJ, Kirch M, Absher DM, Myers RM, Di Palma F, Bell MA, Kingsley DM, Veeramah KRScience advancesPredicting future from past: The genomic basis of recurrent and rapid stickleback evolution. Sci Adv. 2021 Jun; 7(25).Sci Adv2021-06-18T00:00:002021Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution.Authorship 13700637Authorship 1373587334158502Chu C, Borges-Monroy R, Viswanadham VV, Lee S, Li H, Lee EA, Park PJNature communicationsComprehensive identification of transposable element insertions using multiple sequencing technologies. Nat Commun. 2021 06 22; 12(1):3836.Nat Commun2021-06-22T00:00:002021Comprehensive identification of transposable element insertions using multiple sequencing technologies.25407859Liu W, Mohan R, Park P, Liu Z, Li H, Li X, Li Y, Wu R, Sahoo N, Dong L, Zhu XR, Grosshans DRPractical radiation oncologyDosimetric benefits of robust treatment planning for intensity modulated proton therapy for base-of-skull cancers. Pract Radiat Oncol. 2014 Nov-Dec; 4(6):384-91.Pract Radiat Oncol2014-01-14T00:00:002014Dosimetric benefits of robust treatment planning for intensity modulated proton therapy for base-of-skull cancers.Authorship 1380325234316001Luquette LJ, Park PJCell researchSomatic mutation accumulation seen through a single-molecule lens. Cell Res. 2021 09; 31(9):949-950.Cell Res2021-09-01T00:00:002021Somatic mutation accumulation seen through a single-molecule lens.2023-09-16PARK, PETER J2021-09-17Interoperability and Collaboration with the Common Fund Data Ecosystem to Improve Utility of 4DN DataOT2OD032119Principal InvestigatorAuthorship 14146818Authorship 14103133034838103Borges-Monroy R, Chu C, Dias C, Choi J, Lee S, Gao Y, Shin T, Park PJ, Walsh CA, Lee EAMobile DNAWhole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder. Mob DNA. 2021 Nov 27; 12(1):28.Mob DNA2021-11-27T00:00:002021Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder.34862503Rigano A, Ehmsen S, Öztürk SU, Ryan J, Balashov A, Hammer M, Kirli K, Boehm U, Brown CM, Bellve K, Chambers JJ, Cosolo A, Coleman RA, Faklaris O, Fogarty KE, Guilbert T, Hamacher AB, Itano MS, Keeley DP, Kunis S, Lacoste J, Laude A, Ma WY, Marcello M, Montero-Llopis P, Nelson G, Nitschke R, Pimentel JA, Weidtkamp-Peters S, Park PJ, Alver BH, Grunwald D, Strambio-De-Castillia CNature methodsMicro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods. 2021 12; 18(12):1489-1495.Nat Methods2021-12-03T00:00:002021Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications.34880424Cortés-Ciriano I, Gulhan DC, Lee JJ, Melloni GEM, Park PJNature reviews. GeneticsComputational analysis of cancer genome sequencing data. Nat Rev Genet. 2022 05; 23(5):298-314.Nat Rev Genet2021-12-08T00:00:002021Computational analysis of cancer genome sequencing data.Authorship 14184605Authorship 1624613Authorship 14198453034952955Rigano A, Ehmsen S, Öztürk SU, Ryan J, Balashov A, Hammer M, Kirli K, Boehm U, Brown CM, Bellve K, Chambers JJ, Cosolo A, Coleman RA, Faklaris O, Fogarty KE, Guilbert T, Hamacher AB, Itano MS, Keeley DP, Kunis S, Lacoste J, Laude A, Ma WY, Marcello M, Montero-Llopis P, Nelson G, Nitschke R, Pimentel JA, Weidtkamp-Peters S, Park PJ, Alver BH, Grunwald D, Strambio-De-Castillia CNature methodsAuthor Correction: Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods. 2022 Feb; 19(2):256.Nat Methods2022-02-01T00:00:002022Author Correction: Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications.Authorship 1422465534978573Lee S, Bakker CR, Vitzthum C, Alver BH, Park PJBioinformatics (Oxford, England)Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs. Bioinformatics. 2022 03 04; 38(6):1729-1731.Bioinformatics2022-03-04T00:00:002022Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs.Authorship 14413537Authorship 14382304735320348Rajurkar M, Parikh AR, Solovyov A, You E, Kulkarni AS, Chu C, Xu KH, Jaicks C, Taylor MS, Wu C, Alexander KA, Good CR, Szabolcs A, Gerstberger S, Tran AV, Xu N, Ebright RY, Van Seventer EE, Vo KD, Tai EC, Lu C, Joseph-Chazan J, Raabe MJ, Nieman LT, Desai N, Arora KS, Ligorio M, Thapar V, Cohen L, Garden PM, Senussi Y, Zheng H, Allen JN, Blaszkowsky LS, Clark JW, Goyal L, Wo JY, Ryan DP, Corcoran RB, Deshpande V, Rivera MN, Aryee MJ, Hong TS, Berger SL, Walt DR, Burns KH, Park PJ, Greenbaum BD, Ting DTCancer discoveryReverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer. Cancer Discov. 2022 06 02; 12(6):1462-1481.Cancer Discov2022-06-02T00:00:002022Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer.35228538Jin Z, Huang W, Shen N, Li J, Wang X, Dong J, Park PJ, Xi RNature communicationsSingle-cell gene fusion detection by scFusion. Nat Commun. 2022 02 28; 13(1):1084.Nat Commun2022-02-28T00:00:002022Single-cell gene fusion detection by scFusion.Authorship 2904975Authorship 14446182335501320Reiff SB, Schroeder AJ, Kirli K, Cosolo A, Bakker C, Mercado L, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, Öztürk SU, Çamoglu U, Mirny LA, Gehlenborg N, Alver BH, Park PJNature communicationsThe 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Nat Commun. 2022 05 02; 13(1):2365.Nat Commun2022-05-02T00:00:002022The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data.true1Research Associate in Biomedical InformaticsResearch Associate in Biomedical Informatics36163278Luquette LJ, Miller MB, Zhou Z, Bohrson CL, Zhao Y, Jin H, Gulhan D, Ganz J, Bizzotto S, Kirkham S, Hochepied T, Libert C, Galor A, Kim J, Lodato MA, Garaycoechea JI, Gawad C, West J, Walsh CA, Park PJNature geneticsSingle-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements. Nat Genet. 2022 10; 54(10):1564-1571.Nat Genet2022-09-26T00:00:002022Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements.Authorship 150263623Authorship 148501120Authorship 14802661836048535Batalini F, Gulhan DC, Mao V, Tran A, Polak M, Xiong N, Tayob N, Tung NM, Winer EP, Mayer EL, Knappskog S, Lønning PE, Matulonis UA, Konstantinopoulos PA, Solit DB, Won H, Eikesdal HP, Park PJ, Wulf GMClinical cancer research : an official journal of the American Association for Cancer ResearchMutational Signature 3 Detected from Clinical Panel Sequencing is Associated with Responses to Olaparib in Breast and Ovarian Cancers. Clin Cancer Res. 2022 11 01; 28(21):4714-4723.Clin Cancer Res2022-11-01T00:00:002022Mutational Signature 3 Detected from Clinical Panel Sequencing is Associated with Responses to Olaparib in Breast and Ovarian Cancers.36323678Reiff SB, Schroeder AJ, Kirli K, Cosolo A, Bakker C, Mercado L, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, Öztürk SU, Çamoglu U, Mirny LA, Gehlenborg N, Alver BH, Park PJNature communicationsAuthor Correction: The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Nat Commun. 2022 Nov 02; 13(1):6561.Nat Commun2022-11-02T00:00:002022Author Correction: The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data.Authorship 15097141136481818Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, Brors B, Rippe K, Jones DTW, Feuerbach LNature communicationsAuthor Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun. 2022 Dec 08; 13(1):7574.Nat Commun2022-12-08T00:00:002022Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer.36598417Cortes-Ciriano I, Steele CD, Piculell K, Al-Ibraheemi A, Eulo V, Bui MM, Chatzipli A, Dickson BC, Borcherding DC, Feber A, Galor A, Hart J, Jones KB, Jordan JT, Kim RH, Lindsay D, Miller C, Nishida Y, Proszek PZ, Serrano J, Sundby RT, Szymanski JJ, Ullrich NJ, Viskochil D, Wang X, Snuderl M, Park PJ, Flanagan AM, Hirbe AC, Pillay N, Miller DTCancer discoveryGenomic Patterns of Malignant Peripheral Nerve Sheath Tumor (MPNST) Evolution Correlate with Clinical Outcome and Are Detectable in Cell-Free DNA. Cancer Discov. 2023 03 01; 13(3):654-671.Cancer Discov2023-03-01T00:00:002023Genomic Patterns of Malignant Peripheral Nerve Sheath Tumor (MPNST) Evolution Correlate with Clinical Outcome and Are Detectable in Cell-Free DNA.Authorship 1521280936711756Ganz J, Luquette LJ, Bizzotto S, Bohrson CL, Jin H, Miller MB, Zhou Z, Galor A, Park PJ, Walsh CAbioRxiv : the preprint server for biologyContrasting patterns of somatic mutations in neurons and glia reveal differential predisposition to disease in the aging human brain. bioRxiv. 2023 Jan 14.bioRxiv2023-01-14T00:00:002023Contrasting patterns of somatic mutations in neurons and glia reveal differential predisposition to disease in the aging human brain.Authorship 15341471236944733Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, Park PJNature geneticsAuthor Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet. 2023 Jun; 55(6):1076.Nat Genet2023-06-01T00:00:002023Author Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.36944736Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PA, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine KM, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, Campbell PJ, Tubio JMCNature geneticsAuthor Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2023 Jun; 55(6):1080.Nat Genet2023-06-01T00:00:002023Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.Authorship 19563111Authorship 19561Authorship 15504815Authorship 155391940Authorship 155265222Authorship 155583823Authorship 156426115Authorship 15533412737198482Lee JJ, Jung YL, Cheong TC, Espejo Valle-Inclan J, Chu C, Gulhan DC, Ljungström V, Jin H, Viswanadham VV, Watson EV, Cortés-Ciriano I, Elledge SJ, Chiarle R, Pellman D, Park PJNatureERa-associated translocations underlie oncogene amplifications in breast cancer. Nature. 2023 Jun; 618(7967):1024-1032.Nature2023-05-17T00:00:002023ERa-associated translocations underlie oncogene amplifications in breast cancer.37419111Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong SMolecular cellSpatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Mol Cell. 2023 08 03; 83(15):2624-2640.Mol Cell2023-07-06T00:00:002023Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.36698984Cheng AL, Downs DL, Brady BK, Hong BA, Park P, Prather H, Hunt DMJB & JS open accessInterpretation of PROMIS Depression and Anxiety Measures Compared with DSM-5 Diagnostic Criteria in Musculoskeletal Patients. JB JS Open Access. 2023 Jan-Mar; 8(1).JB JS Open Access2023-01-24T00:00:002023Interpretation of PROMIS Depression and Anxiety Measures Compared with DSM-5 Diagnostic Criteria in Musculoskeletal Patients.37438524Kim J, Woo S, de Gusmao CM, Zhao B, Chin DH, DiDonato RL, Nguyen MA, Nakayama T, Hu CA, Soucy A, Kuniholm A, Thornton JK, Riccardi O, Friedman DA, El Achkar CM, Dash Z, Cornelissen L, Donado C, Faour KNW, Bush LW, Suslovitch V, Lentucci C, Park PJ, Lee EA, Patterson A, Philippakis AA, Margus B, Berde CB, Yu TWNatureA framework for individualized splice-switching oligonucleotide therapy. Nature. 2023 Jul; 619(7971):828-836.Nature2023-07-12T00:00:002023A framework for individualized splice-switching oligonucleotide therapy.Authorship 22996511Authorship 35692111Authorship 159037215Authorship 15846613Authorship 15862772037576891Chen CC, Liu J, Park P, Shim A, Huang S, Wong S, Tsai P, Lin H, Choi JIFrontiers in oncologyCase Report: Cumulative proton dose reconstruction using CBCT-based synthetic CT for interfraction metallic port variability in breast tissue expanders. Front Oncol. 2023; 13:1132178.Front Oncol2023-07-27T00:00:002023Case Report: Cumulative proton dose reconstruction using CBCT-based synthetic CT for interfraction metallic port variability in breast tissue expanders.37644260Rodin RE, Dou Y, Kwon M, Sherman MA, D'Gama AM, Doan RN, Rento LM, Girskis KM, Bohrson CL, Kim SN, Nadig A, Luquette LJ, Gulhan DC, Park PJ, Walsh CANature neuroscienceAuthor Correction: The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing. Nat Neurosci. 2023 Oct; 26(10):1833.Nat Neurosci2023-10-01T00:00:002023Author Correction: The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing.37773632Marino-Enriquez A, Novotny JP, Gulhan DC, Klooster I, Tran AV, Kasbo M, Lundberg MZ, Ou WB, Tao DL, Pilco-Janeta DF, Mao VY, Zenke FT, Leeper BA, Gokhale PC, Cowley GS, Baker LH, Ballman KV, Root DE, Albers J, Park PJ, George S, Fletcher JAClinical cancer research : an official journal of the American Association for Cancer ResearchHyper-Dependence on NHEJ Enables Synergy between DNA-PK Inhibitors and Low-Dose Doxorubicin in Leiomyosarcoma. Clin Cancer Res. 2023 Dec 15; 29(24):5128-5139.Clin Cancer Res2023-12-15T00:00:002023Hyper-Dependence on NHEJ Enables Synergy between DNA-PK Inhibitors and Low-Dose Doxorubicin in Leiomyosarcoma.true1Member of the Faculty of MedicineMember of the Faculty of MedicineAuthorship 15972181037823611Chu C, Lin EW, Tran A, Jin H, Ho NI, Veit A, Cortes-Ciriano I, Burns KH, Ting DT, Park PJNucleic acids researchThe landscape of human SVA retrotransposons. Nucleic Acids Res. 2023 Nov 27; 51(21):11453-11465.Nucleic Acids Res2023-11-27T00:00:002023The landscape of human SVA retrotransposons.true1George Jacob and Jacqueline Hazel Leder Professor of GeneticsGeorge Jacob and Jacqueline Hazel Leder Professor of Geneticstrue1Research Fellow in Biomedical InformaticsResearch Fellow in Biomedical Informaticstrue1Professor of Biomedical InformaticsProfessor of Biomedical Informaticstrue1Professor of GeneticsProfessor of Geneticstrue1Professor of GeneticsProfessor of Geneticstrue1Research Associate in GeneticsResearch Associate in GeneticsAuthorship 15987949Authorship 1599211737914857L'Yi S, Maziec D, Stevens V, Manz T, Veit A, Berselli M, Park PJ, Glodzik D, Gehlenborg NNature methodsChromoscope: interactive multiscale visualization for structural variation in human genomes. Nat Methods. 2023 Dec; 20(12):1834-1835.Nat Methods2023-12-01T00:00:002023Chromoscope: interactive multiscale visualization for structural variation in human genomes.37904053Gao T, Kastriti ME, Ljungström V, Heinzel A, Tischler AS, Oberbauer R, Loh PR, Adameyko I, Park PJ, Kharchenko PVNature geneticsA pan-tissue survey of mosaic chromosomal alterations in 948 individuals. Nat Genet. 2023 Nov; 55(11):1901-1911.Nat Genet2023-10-30T00:00:002023A pan-tissue survey of mosaic chromosomal alterations in 948 individuals.Authorship 160805022Authorship 16079782337985666Garrison MA, Jang Y, Bae T, Cherskov A, Emery SB, Fasching L, Jones A, Moldovan JB, Molitor C, Pochareddy S, Peters MA, Shin JH, Wang Y, Yang X, Akbarian S, Chess A, Gage FH, Gleeson JG, Kidd JM, McConnell M, Mills RE, Moran JV, Park PJ, Sestan N, Urban AE, Vaccarino FM, Walsh CA, Weinberger DR, Wheelan SJ, Abyzov AScientific dataGenomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases. Sci Data. 2023 11 20; 10(1):813.Sci Data2023-11-20T00:00:002023Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases.37986891Kim SN, Viswanadham VV, Doan RN, Dou Y, Bizzotto S, Khoshkhoo S, Huang AY, Yeh R, Chhouk B, Truong A, Chappell KM, Beaudin M, Barton A, Akula SK, Rento L, Lodato M, Ganz J, Szeto RA, Li P, Tsai JW, Hill RS, Park PJ, Walsh CAbioRxiv : the preprint server for biologyCell lineage analysis with somatic mutations reveals late divergence of neuronal cell types and cortical areas in human cerebral cortex. bioRxiv. 2023 Nov 06.bioRxiv2023-11-06T00:00:002023Cell lineage analysis with somatic mutations reveals late divergence of neuronal cell types and cortical areas in human cerebral cortex.Authorship 1615873738100419Yang HW, Lee S, Berry BC, Yang D, Zheng S, Carroll RS, Park PJ, Johnson MDProceedings of the National Academy of Sciences of the United States of AmericaA role for mutations in AK9 and other genes affecting ependymal cells in idiopathic normal pressure hydrocephalus. Proc Natl Acad Sci U S A. 2023 Dec 19; 120(51):e2300681120.Proc Natl Acad Sci U S A2023-12-15T00:00:002023A role for mutations in AK9 and other genes affecting ependymal cells in idiopathic normal pressure hydrocephalus.Authorship 5160288Authorship 5492693Authorship 5718906Authorship 16261941638293061Gulhan DC, Viswanadham V, Muyas F, Jin H, Foote MB, Lee JJ, Barras D, Jung YL, Ljungstrom V, Rousseau B, Galor A, Diplas BH, Maron SB, Cleary JM, Cortés-Ciriano I, Park PJmedRxiv : the preprint server for health sciencesPredicting response to immune checkpoint blockade therapy among mismatch repair-deficient patients using mutational signatures. medRxiv. 2024 Jan 21.medRxiv2024-01-21T00:00:002024Predicting response to immune checkpoint blockade therapy among mismatch repair-deficient patients using mutational signatures.38342659Boiarsky D, Gulhan DC, Savignano H, Lakshminarayanan G, McClure HM, Silver R, Hirsch MS, Sholl LM, Choudhury AD, Ananda G, Park PJ, Tewari AK, Berchuck JEClinical genitourinary cancerA Panel-Based Mutational Signature of Mismatch Repair Deficiency is Associated With Durable Response to Pembrolizumab in Metastatic Castration-Resistant Prostate Cancer. Clin Genitourin Cancer. 2024 Apr; 22(2):558-568.e3.Clin Genitourin Cancer2024-01-20T00:00:002024A Panel-Based Mutational Signature of Mismatch Repair Deficiency is Associated With Durable Response to Pembrolizumab in Metastatic Castration-Resistant Prostate Cancer.38388848Watson EV, Lee JJ, Gulhan DC, Melloni GEM, Venev SV, Magesh RY, Frederick A, Chiba K, Wooten EC, Naxerova K, Dekker J, Park PJ, Elledge SJNature geneticsChromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns. Nat Genet. 2024 Feb 22.Nat Genet2024-02-22T00:00:002024Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns.Authorship 163077311Authorship 16316107Authorship 163317412Authorship 1629401338361034Jin H, Gulhan DC, Geiger B, Ben-Isvy D, Geng D, Ljungström V, Park PJNature geneticsAccurate and sensitive mutational signature analysis with MuSiCal. Nat Genet. 2024 Feb 15.Nat Genet2024-02-15T00:00:002024Accurate and sensitive mutational signature analysis with MuSiCal.38405315Choi JI, McCormick B, Park P, Millar M, Walker K, Tung CC, Huang S, Florio P, Chen CC, Lozano A, Hanlon AL, Fox J, Xu AJ, Zinovoy M, Mueller B, Bakst R, LaPlant Q, Braunstein LZ, Khan AJ, Powell SN, Cahlon OAdvances in radiation oncologyComparative Evaluation of Proton Therapy and Volumetric Modulated Arc Therapy for Brachial Plexus Sparing in the Comprehensive Reirradiation of High-Risk Recurrent Breast Cancer. Adv Radiat Oncol. 2024 Feb; 9(2):101355.Adv Radiat Oncol2023-08-18T00:00:002023Comparative Evaluation of Proton Therapy and Volumetric Modulated Arc Therapy for Brachial Plexus Sparing in the Comprehensive Reirradiation of High-Risk Recurrent Breast Cancer.Authorship 2242437Authorship 16349341138453887Jung YL, Zhao W, Li I, Jain D, Epstein CB, Bernstein BE, Parangi S, Sherwood R, Robinson-Cohen C, Hsu YH, Park PJ, Mannstadt MNature communicationsEpigenetic profiling reveals key genes and cis-regulatory networks specific to human parathyroids. Nat Commun. 2024 Mar 07; 15(1):2106.Nat Commun2024-03-07T00:00:002024Epigenetic profiling reveals key genes and cis-regulatory networks specific to human parathyroids.true1Instructor in PediatricsInstructor in Pediatricstrue1Instructor in PediatricsInstructor in Pediatricstrue1Bullard Professor of Pediatrics and NeurologyBullard Professor of Pediatrics and NeurologyAuthorship 29268631Authorship 3182843Authorship 2375531Authorship 64641613Authorship 6498949Authorship 66250417Authorship 6594117Authorship 6472475Authorship 65023615Authorship 6433993Authorship 64978113Authorship 6661611Authorship 6549641Authorship 6677047Authorship 6462014Authorship 64937410Authorship 65601212Authorship 6636199Authorship 65935810Authorship 667330923419376Gehlenborg N, Noble MS, Getz G, Chin L, Park PJBioinformatics (Oxford, England)Nozzle: a report generation toolkit for data analysis pipelines. Bioinformatics. 2013 Apr 15; 29(8):1089-91.Bioinformatics2013-02-17T00:00:002013Nozzle: a report generation toolkit for data analysis pipelines.20406344Park PJ, Bell MAJournal of evolutionary biologyVariation of telencephalon morphology of the threespine stickleback (Gasterosteus aculeatus) in relation to inferred ecology. J Evol Biol. 2010 Jun 01; 23(6):1261-77.J Evol Biol2010-04-08T00:00:002010Variation of telencephalon morphology of the threespine stickleback (Gasterosteus aculeatus) in relation to inferred ecology.23547170Zhang B, Day DS, Ho JW, Song L, Cao J, Christodoulou D, Seidman JG, Crawford GE, Park PJ, Pu WTGenome researchA dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. Genome Res. 2013 Jun; 23(6):917-27.Genome Res2013-04-01T00:00:002013A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity.23873939Soruco 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 EGenes & developmentThe CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation. Genes Dev. 2013 Jul 15; 27(14):1551-6.Genes Dev2013-07-15T00:00:002013The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation.23723349Tolstorukov MY, Sansam CG, Lu P, Koellhoffer EC, Helming KC, Alver BH, Tillman EJ, Evans JA, Wilson BG, Park PJ, Roberts CWProceedings of the National Academy of Sciences of the United States of AmericaSwi/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.Proc Natl Acad Sci U S A2013-05-30T00:00:002013Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters.23663786Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh CH, Zhang C, Ren X, Protopopov A, Chin L, Kucherlapati R, Lee C, Park PJCellDiverse mechanisms of somatic structural variations in human cancer genomes. Cell. 2013 May 09; 153(4):919-29.Cell2013-05-09T00:00:002013Diverse mechanisms of somatic structural variations in human cancer genomes.23792563NatureComprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 Jul 04; 499(7456):43-9.Nature2013-06-23T00:00:002013Comprehensive molecular characterization of clear cell renal cell carcinoma.23636398Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DANatureIntegrated genomic characterization of endometrial carcinoma. Nature. 2013 May 02; 497(7447):67-73.Nature2013-05-02T00:00:002013Integrated genomic characterization of endometrial carcinoma.23814487Majumdar S, Gong EM, Di Vizio D, Dreyfuss J, Degraff DJ, Hager MH, Park PJ, Bellmunt J, Matusik RJ, Rosenberg JE, Adam RMNeoplasia (New York, N.Y.)Loss of Sh3gl2/endophilin A1 is a common event in urothelial carcinoma that promotes malignant behavior. Neoplasia. 2013 Jul; 15(7):749-60.Neoplasia2013-07-01T00:00:002013Loss of Sh3gl2/endophilin A1 is a common event in urothelial carcinoma that promotes malignant behavior.17268171Vukovic B, Beheshti B, Park P, Lim G, Bayani J, Zielenska M, Squire JACytogenetic and genome researchCorrelating 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.Cytogenet Genome Res2007-01-01T00:00:002007Correlating breakage-fusion-bridge events with the overall chromosomal instability and in vitro karyotype evolution in prostate cancer.23630075Alekseyenko AA, Ellison CE, Gorchakov AA, Zhou Q, Kaiser VB, Toda N, Walton Z, Peng S, Park PJ, Bachtrog D, Kuroda MIGenes & developmentConservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila. Genes Dev. 2013 Apr 15; 27(8):853-8.Genes Dev2013-04-15T00:00:002013Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila.23775117Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston REMolecular and cellular biologyVariable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters. Mol Cell Biol. 2013 Aug; 33(16):3274-85.Mol Cell Biol2013-06-17T00:00:002013Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters.Authorship 1835449ImmunologyAuthorship 5076555Authorship 2283996Authorship 67668213Authorship 67802524071849Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JMNature geneticsThe Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct; 45(10):1113-20.Nat Genet2013-10-01T00:00:002013The Cancer Genome Atlas Pan-Cancer analysis project.24014587Gokcumen 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 JOProceedings of the National Academy of Sciences of the United States of AmericaPrimate genome architecture influences structural variation mechanisms and functional consequences. Proc Natl Acad Sci U S A. 2013 Sep 24; 110(39):15764-9.Proc Natl Acad Sci U S A2013-09-06T00:00:002013Primate genome architecture influences structural variation mechanisms and functional consequences.Authorship 254530324183666Ferrari F, Plachetka A, Alekseyenko AA, Jung YL, Ozsolak F, Kharchenko PV, Park PJ, Kuroda MICell reports"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.Cell Rep2013-10-31T00:00:002013"Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts.24241209Ferrari F, Apostolou E, Park PJ, Hochedlinger KCell cycle (Georgetown, Tex.)Rearranging the chromatin for pluripotency. Cell Cycle. 2014; 13(2):167-8.Cell Cycle2013-11-15T00:00:002013Rearranging the chromatin for pluripotency.Authorship 6921896Authorship 692702324209623Kim TM, Laird PW, Park PJCellThe landscape of microsatellite instability in colorectal and endometrial cancer genomes. Cell. 2013 Nov 07; 155(4):858-68.Cell2013-11-07T00:00:002013The landscape of microsatellite instability in colorectal and endometrial cancer genomes.24183448Davoli T, Xu AW, Mengwasser KE, Sack LM, Yoon JC, Park PJ, Elledge SJCellCumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell. 2013 Nov 07; 155(4):948-62.Cell2013-10-31T00:00:002013Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome.Authorship 6934877Authorship 694352724100010DeGennaro CM, Alver BH, Marguerat S, Stepanova E, Davis CP, Bähler J, Park PJ, Winston FMolecular and cellular biologySpt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast. Mol Cell Biol. 2013 Dec; 33(24):4779-92.Mol Cell Biol2013-10-07T00:00:002013Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast.Authorship 6988181224303302Ho Sui S, 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 WAMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational ScienceThe Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework. AMIA Jt Summits Transl Sci Proc. 2013; 2013:70.AMIA Jt Summits Transl Sci Proc2013-03-18T00:00:002013The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework.Authorship 700177424158981Ajay AK, Kim TM, Ramirez-Gonzalez V, Park PJ, Frank DA, Vaidya VSJournal of the American Society of Nephrology : JASNA 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.J Am Soc Nephrol2013-10-24T00:00:002013A 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.Authorship 246852424500429Ferrari F, Alekseyenko AA, Park PJ, Kuroda MINature structural & molecular biologyTranscriptional control of a whole chromosome: emerging models for dosage compensation. Nat Struct Mol Biol. 2014 Feb; 21(2):118-25.Nat Struct Mol Biol2014-02-05T00:00:002014Transcriptional control of a whole chromosome: emerging models for dosage compensation.24598259Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen GH, Kuroda MI, Park PJNucleic acids researchImpact of sequencing depth in ChIP-seq experiments. Nucleic Acids Res. 2014 May; 42(9):e74.Nucleic Acids Res2014-03-05T00:00:002014Impact of sequencing depth in ChIP-seq experiments.Authorship 2721241Authorship 3189136Authorship 31586816Authorship 2008549Authorship 7236443Authorship 7197823Authorship 711493324347632Marinov GK, Kundaje A, Park PJ, Wold BJG3 (Bethesda, Md.)Large-scale quality analysis of published ChIP-seq data. G3 (Bethesda). 2014 Feb 19; 4(2):209-23.G3 (Bethesda)2014-02-19T00:00:002014Large-scale quality analysis of published ChIP-seq data.Authorship 73111511Authorship 40534319Authorship 33510410Authorship 3934553Authorship 396697525158628West JA, Cook A, Alver BH, Stadtfeld M, Deaton AM, Hochedlinger K, Park PJ, Tolstorukov MY, Kingston RENature communicationsNucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming. Nat Commun. 2014 Aug 27; 5:4719.Nat Commun2014-08-27T00:00:002014Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming.Authorship 74644978Authorship 74653663Authorship 7456717Authorship 747975725164756Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, 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, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJNatureComparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52.Nature2014-08-28T00:00:002014Comparative analysis of metazoan chromatin organization.25164755Gerstein MB, Rozowsky J, Yan KK, 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 R, 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, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, 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 RNatureComparative analysis of the transcriptome across distant species. Nature. 2014 Aug 28; 512(7515):445-8.Nature2014-08-28T00:00:002014Comparative analysis of the transcriptome across distant species.25166867Streit M, Lex A, Gratzl S, Partl C, Schmalstieg D, Pfister H, Park PJ, Gehlenborg NNature methodsGuided visual exploration of genomic stratifications in cancer. Nat Methods. 2014 Sep; 11(9):884-885.Nat Methods2014-09-01T00:00:002014Guided visual exploration of genomic stratifications in cancer.Authorship 5031974Authorship 5181801Authorship 5303564Authorship 7564223925155756Davis CF, Ricketts CJ, 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, Chin L, Meyerson M, Kucherlapati R, Park WY, 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 CJCancer cellThe somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 2014 Sep 08; 26(3):319-330.Cancer Cell2014-08-21T00:00:002014The somatic genomic landscape of chromophobe renal cell carcinoma.Authorship 3542438Authorship 7655663225313082Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati RProceedings of the National Academy of Sciences of the United States of AmericaCharacterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):15544-9.Proc Natl Acad Sci U S A2014-10-13T00:00:002014Characterization of HPV and host genome interactions in primary head and neck cancers.Authorship 885819Authorship 976264Authorship 3666293Authorship 4789356Authorship 4805482Authorship 776296525453105Merlo P, Frost B, Peng S, Yang YJ, Park PJ, Feany MProceedings of the National Academy of Sciences of the United States of Americap53 prevents neurodegeneration by regulating synaptic genes. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):18055-60.Proc Natl Acad Sci U S A2014-12-01T00:00:002014p53 prevents neurodegeneration by regulating synaptic genes.Authorship 4883963Authorship 77790310Authorship 777156225371413Kim TM, Park PJCancer researchA genome-wide view of microsatellite instability: old stories of cancer mutations revisited with new sequencing technologies. Cancer Res. 2014 Nov 15; 74(22):6377-82.Cancer Res2014-11-04T00:00:002014A genome-wide view of microsatellite instability: old stories of cancer mutations revisited with new sequencing technologies.25569347Evrony GD, Lee E, Mehta BK, Benjamini Y, Johnson RM, Cai X, Yang L, Haseley P, Lehmann HS, Park PJ, Walsh CANeuronCell lineage analysis in human brain using endogenous retroelements. Neuron. 2015 Jan 07; 85(1):49-59.Neuron2015-01-07T00:00:002015Cell lineage analysis in human brain using endogenous retroelements.Authorship 51031Authorship 5226689Authorship 44802589Authorship 46207312Authorship 5315341Authorship 5583142Authorship 55374816Authorship 804002Authorship 24339510Authorship 3082693Authorship 3531204Authorship 4405257Authorship 4607131Authorship 4856044Authorship 501525Authorship 2767874Authorship 23010230Authorship 2363201Authorship 2455613Authorship 3839205Authorship 5217648Authorship 3321985Authorship 4105593Authorship 4161379Authorship 5188062Authorship 7889556Authorship 8036362Authorship 8047134Authorship 8042941625644941Park RW, Kim TM, Kasif S, Park PJMolecular cancerIdentification of rare germline copy number variations over-represented in five human cancer types. Mol Cancer. 2015 Feb 03; 14:25.Mol Cancer2015-02-03T00:00:002015Identification of rare germline copy number variations over-represented in five human cancer types.23920954McClay J, Park P, Marr SD, Langford LHStudies in health technology and informaticsThe HL7 standards-based model of emergency care information. Stud Health Technol Inform. 2013; 192:1180.Stud Health Technol Inform2013-01-01T00:00:002013The HL7 standards-based model of emergency care information.25574027Biagioli M, Ferrari F, Mendenhall EM, Zhang Y, Erdin S, Vijayvargia R, Vallabh SM, Solomos N, Manavalan P, Ragavendran A, Ozsolak F, Lee JM, Talkowski ME, Gusella JF, Macdonald ME, Park PJ, Seong ISHuman molecular geneticsHtt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation. Hum Mol Genet. 2015 May 01; 24(9):2442-57.Hum Mol Genet2015-01-08T00:00:002015Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation.26063573Kang H, McElroy KA, Jung YL, Alekseyenko AA, Zee BM, Park PJ, Kuroda MIGenes & developmentSex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila. Genes Dev. 2015 Jun 01; 29(11):1136-50.Genes Dev2015-06-01T00:00:002015Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila.Authorship 69223Authorship 3276876Authorship 33700811Authorship 3430695Authorship 41763213Authorship 4100492Biomedical InformaticsAuthorship 809598140Authorship 808939525725496Sohn KA, Ho JW, Djordjevic D, Jeong HH, Park PJ, Kim JHBioinformatics (Oxford, England)hiHMM: Bayesian non-parametric joint inference of chromatin state maps. Bioinformatics. 2015 Jul 01; 31(13):2066-74.Bioinformatics2015-02-27T00:00:002015hiHMM: Bayesian non-parametric joint inference of chromatin state maps.26061751Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang JThe New England journal of medicineComprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 2015 Jun 25; 372(26):2481-98.N Engl J Med2015-06-10T00:00:002015Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.Authorship 4425825435373Yang HW, Kim TM, Song SS, Menon L, Jiang X, Huang W, Black PM, Park PJ, Carroll RS, Johnson MDOncogeneA small subunit processome protein promotes cancer by altering translation. Oncogene. 2015 Aug 20; 34(34):4471-81.Oncogene2014-12-01T00:00:002014A small subunit processome protein promotes cancer by altering translation.Authorship 829208625636411Kann M, Ettou S, Jung YL, Lenz MO, Taglienti ME, Park PJ, Schermer B, Benzing T, Kreidberg JAJournal of the American Society of Nephrology : JASNGenome-Wide Analysis of Wilms' Tumor 1-Controlled Gene Expression in Podocytes Reveals Key Regulatory Mechanisms. J Am Soc Nephrol. 2015 Sep; 26(9):2097-104.J Am Soc Nephrol2015-01-30T00:00:002015Genome-Wide Analysis of Wilms' Tumor 1-Controlled Gene Expression in Podocytes Reveals Key Regulatory Mechanisms.Authorship 83286026Authorship 83286116Authorship 83286217Authorship 8328635Authorship 8328647Authorship 832865826335049Lee S, Seo CH, Alver BH, Lee S, Park PJBMC bioinformaticsEMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering. BMC Bioinformatics. 2015 Sep 03; 16:278.BMC Bioinformatics2015-09-03T00:00:002015EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.26399828De Los Angeles A, Ferrari F, Xi R, Fujiwara Y, Benvenisty N, Deng H, Hochedlinger K, Jaenisch R, Lee S, Leitch HG, Lensch MW, Lujan E, Pei D, Rossant J, Wernig M, Park PJ, Daley GQNatureHallmarks of pluripotency. Nature. 2015 Sep 24; 525(7570):469-78.Nature2015-09-24T00:00:002015Hallmarks of pluripotency.26210357Nam JY, Kim NK, Kim SC, Joung JG, Xi R, Lee S, Park PJ, Park WYBriefings in bioinformaticsEvaluation of somatic copy number estimation tools for whole-exome sequencing data. Brief Bioinform. 2016 Mar; 17(2):185-92.Brief Bioinform2015-07-25T00:00:002015Evaluation of somatic copy number estimation tools for whole-exome sequencing data.26399835De Los Angeles A, Ferrari F, Fujiwara Y, Mathieu R, Lee S, Lee S, Tu HC, Ross S, Chou S, Nguyen M, Wu Z, Theunissen TW, Powell BE, Imsoonthornruksa S, Chen J, Borkent M, Krupalnik V, Lujan E, Wernig M, Hanna JH, Hochedlinger K, Pei D, Jaenisch R, Deng H, Orkin SH, Park PJ, Daley GQNatureFailure to replicate the STAP cell phenomenon. Nature. 2015 Sep 24; 525(7570):E6-9.Nature2015-09-24T00:00:002015Failure to replicate the STAP cell phenomenon.26373279Kim J, Lee IH, Cho HJ, Park CK, Jung YS, Kim Y, Nam SH, Kim BS, Johnson MD, Kong DS, Seol HJ, Lee JI, Joo KM, Yoon Y, Park WY, Lee J, Park PJ, Nam DHCancer cellSpatiotemporal Evolution of the Primary Glioblastoma Genome. Cancer Cell. 2015 Sep 14; 28(3):318-28.Cancer Cell2015-09-14T00:00:002015Spatiotemporal Evolution of the Primary Glioblastoma Genome.26430121Lodato MA, Woodworth MB, Lee S, Evrony GD, Mehta BK, Karger A, Lee S, Chittenden TW, D'Gama AM, Cai X, Luquette LJ, Lee E, Park PJ, Walsh CAScience (New York, N.Y.)Somatic mutation in single human neurons tracks developmental and transcriptional history. Science. 2015 Oct 02; 350(6256):94-98.Science2015-10-02T00:00:002015Somatic mutation in single human neurons tracks developmental and transcriptional history.Authorship 9072430Authorship 83892213Authorship 842797826437032Jung H, Lee D, Lee J, Park D, Kim YJ, Park WY, Hong D, Park PJ, Lee ENature geneticsIntron retention is a widespread mechanism of tumor-suppressor inactivation. Nat Genet. 2015 Nov; 47(11):1242-8.Nat Genet2015-10-05T00:00:002015Intron retention is a widespread mechanism of tumor-suppressor inactivation.Authorship 503222Authorship 8500841426501951Choi J, Lee S, Mallard W, Clement K, Tagliazucchi GM, Lim H, Choi IY, Ferrari F, Tsankov AM, Pop R, Lee G, Rinn JL, Meissner A, Park PJ, Hochedlinger KNature biotechnologyA comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat Biotechnol. 2015 Nov; 33(11):1173-81.Nat Biotechnol2015-10-26T00:00:002015A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs.Authorship 8506761226575630Bersani F, Lee E, Kharchenko PV, Xu AW, Liu M, Xega K, MacKenzie OC, Brannigan BW, Wittner BS, Jung H, Ramaswamy S, Park PJ, Maheswaran S, Ting DT, Haber DAProceedings of the National Academy of Sciences of the United States of AmericaPericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer. Proc Natl Acad Sci U S A. 2015 Dec 08; 112(49):15148-53.Proc Natl Acad Sci U S A2015-11-02T00:00:002015Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer.Authorship 8527903326659182Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F, Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger KNatureThe histone chaperone CAF-1 safeguards somatic cell identity. Nature. 2015 Dec 10; 528(7581):218-24.Nature2015-12-10T00:00:002015The histone chaperone CAF-1 safeguards somatic cell identity.Authorship 5361612Authorship 863232325207565Li H, Liu W, Park P, Matney J, Liao Z, Chang J, Zhang X, Li Y, Zhu RXJournal of applied clinical medical physicsEvaluation of the systematic error in using 3D dose calculation in scanning beam proton therapy for lung cancer. J Appl Clin Med Phys. 2014 Sep 08; 15(5):4810.J Appl Clin Med Phys2014-09-08T00:00:002014Evaluation of the systematic error in using 3D dose calculation in scanning beam proton therapy for lung cancer.26907526Lee JK, Choi YL, Kwon M, Park PJAnnual review of pathologyMechanisms and Consequences of Cancer Genome Instability: Lessons from Genome Sequencing Studies. Annu Rev Pathol. 2016 05 23; 11:283-312.Annu Rev Pathol2016-02-22T00:00:002016Mechanisms and Consequences of Cancer Genome Instability: Lessons from Genome Sequencing Studies.Authorship 8723303Authorship 87166728Authorship 8723513Authorship 87183226Authorship 8719571625708992Li H, Zhang X, Park P, Liu W, Chang J, Liao Z, Frank S, Li Y, Poenisch F, Mohan R, Gillin M, Zhu RRadiotherapy and oncology : journal of the European Society for Therapeutic Radiology and OncologyRobust optimization in intensity-modulated proton therapy to account for anatomy changes in lung cancer patients. Radiother Oncol. 2015 Mar; 114(3):367-72.Radiother Oncol2015-02-20T00:00:002015Robust optimization in intensity-modulated proton therapy to account for anatomy changes in lung cancer patients.26675727De Los Angeles A, Ferrari F, Xi R, Fujiwara Y, Benvenisty N, Deng H, Hochedlinger K, Jaenisch R, Lee S, Leitch HG, Lensch MW, Lujan E, Pei D, Rossant J, Wernig M, Park PJ, Daley GQNatureCorrigendum: Hallmarks of pluripotency. Nature. 2016 Mar 17; 531(7594):400.Nature2015-12-16T00:00:002015Corrigendum: Hallmarks of pluripotency.26901440Evrony GD, Lee E, Park PJ, Walsh CAeLifeResolving rates of mutation in the brain using single-neuron genomics. Elife. 2016 Feb 22; 5.Elife2016-02-22T00:00:002016Resolving rates of mutation in the brain using single-neuron genomics.26675720De Los Angeles A, Ferrari F, Fujiwara Y, Mathieu R, Lee S, Lee S, Tu HC, Ross S, Chou S, Nguyen M, Wu Z, Theunissen TW, Powell BE, Imsoonthornruksa S, Chen J, Borkent M, Krupalnik V, Lujan E, Wernig M, Hanna JH, Hochedlinger K, Pei D, Jaenisch R, Deng H, Orkin SH, Park PJ, Daley GQNatureCorrigendum: Failure to replicate the STAP cell phenomenon. Nature. 2016 Mar 17; 531(7594):400.Nature2015-12-16T00:00:002015Corrigendum: Failure to replicate the STAP cell phenomenon.26947078Chen F, Zhang Y, Senbabaoglu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond JA, Muzny D, Kang H, Lee J, Tamboli P, Reuter V, Shelley CS, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, Hakimi AA, Wheeler DA, Creighton CJCell reportsMultilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Rep. 2016 Mar 15; 14(10):2476-89.Cell Rep2016-03-03T00:00:002016Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma.Authorship 877820326940990Jung YL, Kang H, Park PJ, Kuroda MIFlyCorrespondence of Drosophila polycomb group proteins with broad H3K27me3 silent domains. Fly (Austin). 2015; 9(4):178-82.Fly (Austin)2015-01-01T00:00:002015Correspondence of Drosophila polycomb group proteins with broad H3K27me3 silent domains.Authorship 878805726892441Ordulu Z, Nucci MR, Dal Cin P, Hollowell ML, Otis CN, Hornick JL, Park PJ, Kim TM, Quade BJ, Morton CCModern pathology : an official journal of the United States and Canadian Academy of Pathology, IncIntravenous leiomyomatosis: an unusual intermediate between benign and malignant uterine smooth muscle tumors. Mod Pathol. 2016 05; 29(5):500-10.Mod Pathol2016-02-19T00:00:002016Intravenous leiomyomatosis: an unusual intermediate between benign and malignant uterine smooth muscle tumors.Authorship 8799991027151365Mieczkowski J, Cook A, Bowman SK, Mueller B, Alver BH, Kundu S, Deaton AM, Urban JA, Larschan E, Park PJ, Kingston RE, Tolstorukov MYNature communicationsMNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Nat Commun. 2016 05 06; 7:11485.Nat Commun2016-05-06T00:00:002016MNase titration reveals differences between nucleosome occupancy and chromatin accessibility.Authorship 45690911Authorship 88210517Authorship 8822784Authorship 882333827161561Tica J, Lee E, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EE, Park PJ, Stütz AM, Korbel JOBMC genomicsNext-generation sequencing-based detection of germline L1-mediated transductions. BMC Genomics. 2016 05 10; 17:342.BMC Genomics2016-05-10T00:00:002016Next-generation sequencing-based detection of germline L1-mediated transductions.27153396Yang L, Lee MS, Lu H, Oh DY, Kim YJ, Park D, Park G, Ren X, Bristow CA, Haseley PS, Lee S, Pantazi A, Kucherlapati R, Park WY, Scott KL, Choi YL, Park PJAmerican journal of human geneticsAnalyzing Somatic Genome Rearrangements in Human Cancers by Using Whole-Exome Sequencing. Am J Hum Genet. 2016 05 05; 98(5):843-856.Am J Hum Genet2016-05-05T00:00:002016Analyzing Somatic Genome Rearrangements in Human Cancers by Using Whole-Exome Sequencing.Authorship 5334843Authorship 885863627259512Day DS, Zhang B, Stevens SM, Ferrari F, Larschan EN, Park PJ, Pu WTGenome biologyComprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types. Genome Biol. 2016 06 03; 17(1):120.Genome Biol2016-06-03T00:00:002016Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types.Authorship 6438046Fellow or Post Doc0Full Professor4Instructor5Other FacultyLJL11JoeLuquetteJoe Luquette, Ph.D.67475Luquette, JoeResearch Fellow in Biomedical InformaticsAuthorship 673206Authorship 990087Authorship 894833527260798Xi R, Lee S, Xia Y, Kim TM, Park PJNucleic acids researchCopy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants. Nucleic Acids Res. 2016 07 27; 44(13):6274-86.Nucleic Acids Res2016-06-03T00:00:002016Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants.Authorship 5129765Authorship 56052230Authorship 57290482021-01-31WALSH, CHRISTOPHER A.2015-05-011/2-Somatic mosaicism and autism spectrum disorderU01MH1068832009-05-31PARK, PETER J2003-06-01Statistical and Computational Studies of Microarray DataK25GM0678252012-06-30PARK, PETER J2009-09-22Statistical methods for estimation of copy number from next-generation sequencingRC1HG0054822018-03-31PARK, PETER J2014-04-01Linking sequence and copy number variation to eye diseases by regulatory genomicsR01EY0242302012-08-31PARK, PETER J2007-09-25Integrative Analysis of Multiple Genomic Data SetsR01GM0827982012-02-29DALEY, GEORGE Q2009-09-30Comparative phenotypic, functional, and molecular analysis of ESC and iPSCRC2HL1028152023-08-31PARK, PETER J2000-07-01Training in Bioinformatics and Integrative GenomicsT32HG0022952019-05-31PARK, PETER J2015-06-01Visual Analysis of Genomic and Clinical Data from Large Patient CohortsU01CA1989352025-08-31PARK, PETER J2015-09-074D Nucleome Network Data Coordination and Integration CenterU01CA200059Principal InvestigatorPrincipal InvestigatorCo-Principal InvestigatorPrincipal InvestigatorPrincipal InvestigatorPrincipal InvestigatorPrincipal InvestigatorPrincipal InvestigatorPrincipal InvestigatorAuthorship 928132322022339Tolstorukov MY, Kharchenko PV, Park PJEpigenomicsAnalysis of primary structure of chromatin with next-generation sequencing. Epigenomics. 2010 Apr; 2(2):187-197.Epigenomics2010-04-01T00:00:002010Analysis of primary structure of chromatin with next-generation sequencing.Authorship 440833Authorship 47066911Authorship 513407Authorship 9344401327788131Saini N, Roberts SA, Klimczak LJ, Chan K, Grimm SA, Dai S, Fargo DC, Boyer JC, Kaufmann WK, Taylor JA, Lee E, Cortes-Ciriano I, Park PJ, Schurman SH, Malc EP, Mieczkowski PA, Gordenin DAPLoS geneticsThe Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts. PLoS Genet. 2016 10; 12(10):e1006385.PLoS Genet2016-10-27T00:00:002016The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.Authorship 9411917Authorship 9428331727941797Wang X, Lee RS, Alver BH, Haswell JR, Wang S, Mieczkowski J, Drier Y, Gillespie SM, Archer TC, Wu JN, Tzvetkov EP, Troisi EC, Pomeroy SL, Biegel JA, Tolstorukov MY, Bernstein BE, Park PJ, Roberts CWNature geneticsSMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Nat Genet. 2017 Feb; 49(2):289-295.Nat Genet2016-12-12T00:00:002016SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation.27941798Mathur R, Alver BH, San Roman AK, Wilson BG, Wang X, Agoston AT, Park PJ, Shivdasani RA, Roberts CWNature geneticsARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice. Nat Genet. 2017 Feb; 49(2):296-302.Nat Genet2016-12-12T00:00:002016ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice.Authorship 9491705Authorship 9500002028064188McElroy KA, Jung YL, Zee BM, Wang CI, Park PJ, Kuroda MIG3 (Bethesda, Md.)upSET, the Drosophila homologue of SET3, Is Required for Viability and the Proper Balance of Active and Repressive Chromatin Marks. G3 (Bethesda). 2017 02 09; 7(2):625-635.G3 (Bethesda)2017-02-09T00:00:002017upSET, the Drosophila homologue of SET3, Is Required for Viability and the Proper Balance of Active and Repressive Chromatin Marks.26653630Binanay CA, Akwanalo CO, Aruasa W, Barasa FA, Corey GR, Crowe S, Esamai F, Einterz R, Foster MC, Gardner A, Kibosia J, Kimaiyo S, Koech M, Korir B, Lawrence JE, Lukas S, Manji I, Maritim P, Ogaro F, Park P, Pastakia SD, Sugut W, Vedanthan R, Yanoh R, Velazquez EJ, Bloomfield GSJournal of the American College of CardiologyBuilding Sustainable Capacity for Cardiovascular Care at a Public Hospital in Western Kenya. J Am Coll Cardiol. 2015 Dec 08; 66(22):2550-60.J Am Coll Cardiol2015-12-08T00:00:002015Building Sustainable Capacity for Cardiovascular Care at a Public Hospital in Western Kenya.Authorship 95726815Authorship 956328325960695Pihlajamäki J, Lerin C, Kaminska D, Venesmaa S, 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 MECell metabolismResponse to Brosch et al. Cell Metab. 2012 Mar 07; 15(3):267-269.Cell Metab2012-03-07T00:00:002012Response to Brosch et al.27391204Kavanaugh MJ, So JD, Park PJ, Davis KLTelemedicine journal and e-health : the official journal of the American Telemedicine AssociationValidation of the Intensive Care Unit Early Warning Dashboard: Quality Improvement Utilizing a Retrospective Case-Control Evaluation. Telemed J E Health. 2017 02; 23(2):88-95.Telemed J E Health2016-07-08T00:00:002016Validation of the Intensive Care Unit Early Warning Dashboard: Quality Improvement Utilizing a Retrospective Case-Control Evaluation.11897023Kuruvilla FG, Park PJ, Schreiber SLGenome biologyVector algebra in the analysis of genome-wide expression data. Genome Biol. 2002; 3(3):RESEARCH0011.Genome Biol2002-02-13T00:00:002002Vector algebra in the analysis of genome-wide expression data.Authorship 966924828262751Alver BH, Kim KH, Lu P, Wang X, Manchester HE, Wang W, Haswell JR, Park PJ, Roberts CWNature communicationsThe SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers. Nat Commun. 2017 03 06; 8:14648.Nat Commun2017-03-06T00:00:002017The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers.16547173Alekseyenko AA, Larschan E, Lai WR, Park PJ, Kuroda MIGenes & developmentHigh-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. Genes Dev. 2006 Apr 01; 20(7):848-57.Genes Dev2006-03-17T00:00:002006High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome.16603191Yoon SS, Segal NH, Park PJ, Detwiller KY, Fernando NT, Ryeom SW, Brennan MF, Singer SThe Journal of surgical researchAngiogenic profile of soft tissue sarcomas based on analysis of circulating factors and microarray gene expression. J Surg Res. 2006 Oct; 135(2):282-90.J Surg Res2006-10-01T00:00:002006Angiogenic profile of soft tissue sarcomas based on analysis of circulating factors and microarray gene expression.11262969Park PJ, Pagano M, Bonetti MPacific Symposium on Biocomputing. Pacific Symposium on BiocomputingA nonparametric scoring algorithm for identifying informative genes from microarray data. Pac Symp Biocomput. 2001; 52-63.Pac Symp Biocomput2001-01-01T00:00:002001A nonparametric scoring algorithm for identifying informative genes from microarray data.DCG18DogaGulhanDoga C Gulhan, Ph.D.157365Gulhan, DogaMember of the Faculty of MedicineAuthorship 97571416Authorship 9751748Authorship 976469628369524Lee S, Lee S, Ouellette S, Park WY, Lee EA, Park PJNucleic acids researchNGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types. Nucleic Acids Res. 2017 Jun 20; 45(11):e103.Nucleic Acids Res2017-06-20T00:00:002017NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.28366588Choi J, Clement K, Huebner AJ, Webster J, Rose CM, Brumbaugh J, Walsh RM, Lee S, Savol A, Etchegaray JP, Gu H, Boyle P, Elling U, Mostoslavsky R, Sadreyev R, Park PJ, Gygi SP, Meissner A, Hochedlinger KCell stem cellDUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cell Stem Cell. 2017 05 04; 20(5):706-719.e7.Cell Stem Cell2017-03-30T00:00:002017DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells.28366642Shetty A, Kallgren SP, Demel C, Maier KC, Spatt D, Alver BH, Cramer P, Park PJ, Winston FMolecular cellSpt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation. Mol Cell. 2017 Apr 06; 66(1):77-88.e5.Mol Cell2017-03-30T00:00:002017Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation.16081473Lai WR, Johnson MD, Kucherlapati R, Park PJBioinformatics (Oxford, England)Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics. 2005 Oct 01; 21(19):3763-70.Bioinformatics2005-08-04T00:00:002005Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data.16823376Kuo 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 TKNature biotechnologyA sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol. 2006 Jul; 24(7):832-40.Nat Biotechnol2006-07-02T00:00:002006A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies.20633552Balakrishnan A, Stearns AT, Park PJ, Dreyfuss JM, Ashley SW, Rhoads DB, Tavakkolizadeh AExperimental cell researchMicroRNA mir-16 is anti-proliferative in enterocytes and exhibits diurnal rhythmicity in intestinal crypts. Exp Cell Res. 2010 Dec 10; 316(20):3512-21.Exp Cell Res2010-07-13T00:00:002010MicroRNA mir-16 is anti-proliferative in enterocytes and exhibits diurnal rhythmicity in intestinal crypts.21177972Riddle 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 GHGenome researchPlasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res. 2011 Feb; 21(2):147-63.Genome Res2010-12-22T00:00:002010Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin.28498782Lee JK, Lee J, Kim S, Kim S, Youk J, Park S, An Y, Keam B, Kim DW, Heo DS, Kim YT, Kim JS, Kim SH, Lee JS, Lee SH, Park K, Ku JL, Jeon YK, Chung DH, Park PJ, Kim J, Kim TM, Ju YSJournal of clinical oncology : official journal of the American Society of Clinical OncologyClonal History and Genetic Predictors of Transformation Into Small-Cell Carcinomas From Lung Adenocarcinomas. J Clin Oncol. 2017 Sep 10; 35(26):3065-3074.J Clin Oncol2017-05-12T00:00:002017Clonal History and Genetic Predictors of Transformation Into Small-Cell Carcinomas From Lung Adenocarcinomas.12620102Blackshaw S, Kuo WP, Park PJ, Tsujikawa M, Gunnersen JM, Scott HS, Boon WM, Tan SS, Cepko CLGenome biologyMicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues. Genome Biol. 2003; 4(3):R17.Genome Biol2003-02-18T00:00:002003MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues.17090523Liu 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 MDCancer researchA 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.Cancer Res2006-11-06T00:00:002006A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma.Authorship 98206115Authorship 9819692028512244Lu H, Villafane N, Dogruluk T, Grzeskowiak CL, Kong K, Tsang YH, Zagorodna O, Pantazi A, Yang L, Neill NJ, Kim YW, Creighton CJ, Verhaak RG, Mills GB, Park PJ, Kucherlapati R, Scott KLCancer researchEngineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer. Cancer Res. 2017 07 01; 77(13):3502-3512.Cancer Res2017-05-16T00:00:002017Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer.Authorship 9842523728528867Zhang Y, Kwok-Shing Ng P, Kucherlapati M, Chen F, Liu Y, Tsang YH, de Velasco G, Jeong KJ, Akbani R, Hadjipanayis A, Pantazi A, Bristow CA, Lee E, Mahadeshwar HS, Tang J, Zhang J, Yang L, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Westbrook TF, Shelley CS, Choueiri TK, Ittmann M, Van Waes C, Weinstein JN, Liang H, Henske EP, Godwin AK, Park PJ, Kucherlapati R, Scott KL, Mills GB, Kwiatkowski DJ, Creighton CJCancer cellA Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell. 2017 06 12; 31(6):820-832.e3.Cancer Cell2017-05-18T00:00:002017A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations.16204180Hamada FN, Park PJ, Gordadze PR, Kuroda MIGenes & developmentGlobal regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster. Genes Dev. 2005 Oct 01; 19(19):2289-94.Genes Dev2005-10-01T00:00:002005Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster.Authorship 986955528585546Cortes-Ciriano I, Lee S, Park WY, Kim TM, Park PJNature communicationsA molecular portrait of microsatellite instability across multiple cancers. Nat Commun. 2017 06 06; 8:15180.Nat Commun2017-06-06T00:00:002017A molecular portrait of microsatellite instability across multiple cancers.17936709Larschan E, Alekseyenko AA, Gortchakov AA, Peng S, Li B, Yang P, Workman JL, Park PJ, Kuroda MIMolecular cellMSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism. Mol Cell. 2007 Oct 12; 28(1):121-33.Mol Cell2007-10-12T00:00:002007MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism.17560690Baskerville KA, Kent C, Personett D, Lai WR, Park PJ, Coleman P, McKinney MNeurobiology of agingAging elevates metabolic gene expression in brain cholinergic neurons. Neurobiol Aging. 2008 Dec; 29(12):1874-93.Neurobiol Aging2007-06-11T00:00:002007Aging elevates metabolic gene expression in brain cholinergic neurons.28450582McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FMScience (New York, N.Y.)Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science. 2017 04 28; 356(6336).Science2017-04-27T00:00:002017Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network.18724933Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee OK, Kharchenko P, McGrath SD, Wang CI, Mardis ER, Park PJ, Kuroda MICellA sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell. 2008 Aug 22; 134(4):599-609.Cell2008-08-22T00:00:002008A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome.22705808Saikumar J, Hoffmann D, Kim TM, Gonzalez VR, Zhang Q, Goering PL, Brown RP, Bijol V, Park PJ, Waikar SS, Vaidya VSToxicological sciences : an official journal of the Society of ToxicologyExpression, circulation, and excretion profile of microRNA-21, -155, and -18a following acute kidney injury. Toxicol Sci. 2012 Oct; 129(2):256-67.Toxicol Sci2012-06-15T00:00:002012Expression, circulation, and excretion profile of microRNA-21, -155, and -18a following acute kidney injury.22767387Schwartz 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 VGenome researchNature and function of insulator protein binding sites in the Drosophila genome. Genome Res. 2012 Nov; 22(11):2188-98.Genome Res2012-07-05T00:00:002012Nature and function of insulator protein binding sites in the Drosophila genome.22795134Tolstorukov MY, Goldman JA, Gilbert C, Ogryzko V, Kingston RE, Park PJMolecular cellHistone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. Mol Cell. 2012 Aug 24; 47(4):596-607.Mol Cell2012-07-12T00:00:002012Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells.21385897Kim TM, Huang W, Park R, Park PJ, Johnson MDCancer researchA developmental taxonomy of glioblastoma defined and maintained by MicroRNAs. Cancer Res. 2011 May 01; 71(9):3387-99.Cancer Res2011-03-08T00:00:002011A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs.14568979Koopman LA, Kopcow HD, Rybalov B, Boyson JE, Orange JS, Schatz F, Masch R, Lockwood CJ, Schachter AD, Park PJ, Strominger JLThe Journal of experimental medicineHuman decidual natural killer cells are a unique NK cell subset with immunomodulatory potential. J Exp Med. 2003 Oct 20; 198(8):1201-12.J Exp Med2003-10-20T00:00:002003Human decidual natural killer cells are a unique NK cell subset with immunomodulatory potential.15345054Kim RD, Park PJGenome biologyImproving identification of differentially expressed genes in microarray studies using information from public databases. Genome Biol. 2004; 5(9):R70.Genome Biol2004-08-26T00:00:002004Improving identification of differentially expressed genes in microarray studies using information from public databases.Authorship 997097928701572Kim ST, Kim KM, Kim NKD, Park JO, Ahn S, Yun JW, Kim KT, Park SH, Park PJ, Kim HC, Sohn TS, Choi DI, Cho JH, Heo JS, Kwon W, Lee H, Min BH, Hong SN, Park YS, Lim HY, Kang WK, Park WY, Lee JThe oncologistClinical Application of Targeted Deep Sequencing in Solid-Cancer Patients and Utility for Biomarker-Selected Clinical Trials. Oncologist. 2017 10; 22(10):1169-1177.Oncologist2017-07-12T00:00:002017Clinical Application of Targeted Deep Sequencing in Solid-Cancer Patients and Utility for Biomarker-Selected Clinical Trials.18172325Claus EB, Park PJ, Carroll R, Chan J, Black PMCancer researchSpecific genes expressed in association with progesterone receptors in meningioma. Cancer Res. 2008 Jan 01; 68(1):314-22.Cancer Res2008-01-01T00:00:002008Specific genes expressed in association with progesterone receptors in meningioma.20663215Peng S, Kuroda MI, Park PJBMC bioinformaticsQuantized correlation coefficient for measuring reproducibility of ChIP-chip data. BMC Bioinformatics. 2010 Jul 27; 11:399.BMC Bioinformatics2010-07-27T00:00:002010Quantized correlation coefficient for measuring reproducibility of ChIP-chip data.21980527Kim TM, Ramírez V, Barrera-Chimal J, Bobadilla NA, Park PJ, Vaidya VSPloS oneGene 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.PLoS One2011-09-28T00:00:002011Gene expression analysis reveals the cell cycle and kinetochore genes participating in ischemia reperfusion injury and early development in kidney.Authorship 9997093721179089Kharchenko 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 PJNatureComprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011 Mar 24; 471(7339):480-5.Nature2010-12-22T00:00:002010Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.21254570Gorchakov AA, Alekseenko AA, Kharchenko PV, Park P, Kuroda MGenetika[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.Genetika2010-10-01T00:00:002010[Dosage compensation in drosophila: sequence-specific initiation and sequence-independent spreading of MSL complex to the active genes on the male X chromosome].22387999Stadtfeld M, Apostolou E, Ferrari F, Choi J, Walsh RM, Chen T, Ooi SS, Kim SY, Bestor TH, Shioda T, Park PJ, Hochedlinger KNature geneticsAscorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nat Genet. 2012 Mar 04; 44(4):398-405, S1-2.Nat Genet2012-03-04T00:00:002012Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells.20584328Day DS, Luquette LJ, Park PJ, Kharchenko PVGenome biologyEstimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol. 2010; 11(6):R69.Genome Biol2010-06-28T00:00:002010Estimating enrichment of repetitive elements from high-throughput sequence data.21216738Xi R, Kim TM, Park PJBriefings in functional genomicsDetecting structural variations in the human genome using next generation sequencing. Brief Funct Genomics. 2010 Dec; 9(5-6):405-15.Brief Funct Genomics2011-01-06T00:00:002011Detecting structural variations in the human genome using next generation sequencing.22355270Yang HW, Kim TM, Song SS, Shrinath N, Park R, Kalamarides M, Park PJ, Black PM, Carroll RS, Johnson MDNeoplasia (New York, N.Y.)Alternative splicing of CHEK2 and codeletion with NF2 promote chromosomal instability in meningioma. Neoplasia. 2012 Jan; 14(1):20-8.Neoplasia2012-01-01T00:00:002012Alternative splicing of CHEK2 and codeletion with NF2 promote chromosomal instability in meningioma.Authorship 100572119Authorship 1003078728851877Chen J, Fu Y, Day DS, Sun Y, Wang S, Liang X, Gu F, Zhang F, Stevens SM, Zhou P, Li K, Zhang Y, Lin RZ, Smith LEH, Zhang J, Sun K, Melero-Martin JM, Han Z, Park PJ, Zhang B, Pu WTNature communicationsVEGF amplifies transcription through ETS1 acetylation to enable angiogenesis. Nat Commun. 2017 08 29; 8(1):383.Nat Commun2017-08-29T00:00:002017VEGF amplifies transcription through ETS1 acetylation to enable angiogenesis.25416949Xing Z, Lin A, Li C, Liang K, Wang S, Liu Y, Park PK, Qin L, Wei Y, Hawke DH, Hung MC, Lin C, Yang LCelllncRNA directs cooperative epigenetic regulation downstream of chemokine signals. Cell. 2014 Nov 20; 159(5):1110-1125.Cell2014-11-13T00:00:002014lncRNA directs cooperative epigenetic regulation downstream of chemokine signals.21177974Roy 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 MScience (New York, N.Y.)Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97.Science2010-12-22T00:00:002010Identification of functional elements and regulatory circuits by Drosophila modENCODE.Authorship 1011182928905911Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong SNatureThe 4D nucleome project. Nature. 2017 09 13; 549(7671):219-226.Nature2017-09-13T00:00:002017The 4D nucleome project.23132910Kim TM, Xi R, Luquette LJ, Park RW, Johnson MD, Park PJGenome researchFunctional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Res. 2013 Feb; 23(2):217-27.Genome Res2012-11-06T00:00:002012Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes.12169539Park PJ, Tian L, Kohane ISBioinformatics (Oxford, England)Linking gene expression data with patient survival times using partial least squares. Bioinformatics. 2002; 18 Suppl 1:S120-7.Bioinformatics2002-01-01T00:00:002002Linking gene expression data with patient survival times using partial least squares.14728197Kuo WP, Mendez E, Chen C, Whipple ME, Farell G, Agoff N, Park PJAMIA ... Annual Symposium proceedings. AMIA SymposiumFunctional relationships between gene pairs in oral squamous cell carcinoma. AMIA Annu Symp Proc. 2003; 371-5.AMIA Annu Symp Proc2003-01-01T00:00:002003Functional relationships between gene pairs in oral squamous cell carcinoma.16581510Namekawa SH, Park PJ, Zhang LF, Shima JE, McCarrey JR, Griswold MD, Lee JTCurrent biology : CBPostmeiotic sex chromatin in the male germline of mice. Curr Biol. 2006 Apr 04; 16(7):660-7.Curr Biol2006-04-04T00:00:002006Postmeiotic sex chromatin in the male germline of mice.19034774Park PJCancer investigationExperimental design and data analysis for array comparative genomic hybridization. Cancer Invest. 2008 Nov; 26(9):923-8.Cancer Invest2008-11-01T00:00:002008Experimental design and data analysis for array comparative genomic hybridization.19420357McKinney-Freeman SL, Naveiras O, Yates F, Loewer S, Philitas M, Curran M, Park PJ, Daley GQBloodSurface antigen phenotypes of hematopoietic stem cells from embryos and murine embryonic stem cells. Blood. 2009 Jul 09; 114(2):268-78.Blood2009-05-06T00:00:002009Surface antigen phenotypes of hematopoietic stem cells from embryos and murine embryonic stem cells.19736561Park PJNature reviews. GeneticsChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009 Oct; 10(10):669-80.Nat Rev Genet2009-09-08T00:00:002009ChIP-seq: advantages and challenges of a maturing technology.Authorship 1020878729070704Kang H, Jung YL, McElroy KA, Zee BM, Wallace HA, Woolnough JL, Park PJ, Kuroda MIGenes & developmentBivalent complexes of PRC1 with orthologs of BRD4 and MOZ/MORF target developmental genes in Drosophila. Genes Dev. 2017 10 01; 31(19):1988-2002.Genes Dev2017-10-01T00:00:002017Bivalent complexes of PRC1 with orthologs of BRD4 and MOZ/MORF target developmental genes in Drosophila.21124451Gurumurthy 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 NNatureThe Lkb1 metabolic sensor maintains haematopoietic stem cell survival. Nature. 2010 Dec 02; 468(7324):659-63.Nature2010-12-02T00:00:002010The Lkb1 metabolic sensor maintains haematopoietic stem cell survival.22234613O'Connell DJ, Ho JW, Mammoto T, Turbe-Doan A, O'Connell JT, Haseley PS, Koo S, Kamiya N, Ingber DE, Park PJ, Maas RLScience signalingA Wnt-bmp feedback circuit controls intertissue signaling dynamics in tooth organogenesis. Sci Signal. 2012 Jan 10; 5(206):ra4.Sci Signal2012-01-10T00:00:002012A Wnt-bmp feedback circuit controls intertissue signaling dynamics in tooth organogenesis.Authorship 10244923029123093Shin HT, Choi YL, Yun JW, Kim NKD, Kim SY, Jeon HJ, Nam JY, Lee C, Ryu D, Kim SC, Park K, Lee E, Bae JS, Son DS, Joung JG, Lee J, Kim ST, Ahn MJ, Lee SH, Ahn JS, Lee WY, Oh BY, Park YH, Lee JE, Lee KH, Kim HC, Kim KM, Im YH, Park K, Park PJ, Park WYNature communicationsPrevalence and detection of low-allele-fraction variants in clinical cancer samples. Nat Commun. 2017 11 09; 8(1):1377.Nat Commun2017-11-09T00:00:002017Prevalence and detection of low-allele-fraction variants in clinical cancer samples.17381321Larschan E, Alekseyenko AA, Lai WR, Park PJ, Kuroda MICold Spring Harbor symposia on quantitative biologyMSL complex associates with clusters of actively transcribed genes along the Drosophila male X chromosome. Cold Spring Harb Symp Quant Biol. 2006; 71:385-94.Cold Spring Harb Symp Quant Biol2006-01-01T00:00:002006MSL complex associates with clusters of actively transcribed genes along the Drosophila male X chromosome.Authorship 1027903929168505Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong SNatureCorrigendum: The 4D nucleome project. Nature. 2017 12 14; 552(7684):278.Nature2017-11-22T00:00:002017Corrigendum: The 4D nucleome project.20417597Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJMolecular cellCpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell. 2010 Apr 23; 38(2):179-90.Mol Cell2010-04-23T00:00:002010CpG islands recruit a histone H3 lysine 36 demethylase.21131980Egelhofer 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 JDNature structural & molecular biologyAn assessment of histone-modification antibody quality. Nat Struct Mol Biol. 2011 Jan; 18(1):91-3.Nat Struct Mol Biol2010-12-05T00:00:002010An assessment of histone-modification antibody quality.21368835Larschan E, Bishop EP, Kharchenko PV, Core LJ, Lis JT, Park PJ, Kuroda MINatureX chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature. 2011 Mar 03; 471(7336):115-8.Nature2011-03-03T00:00:002011X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila.21803291Pihlajamäki 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 MECell metabolismExpression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis. Cell Metab. 2011 Aug 03; 14(2):208-18.Cell Metab2011-08-03T00:00:002011Expression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis.10 Shattuck StHMS Department of Biomedical InformaticsCountway Library, Rm 31810 Shattuck StBoston02115MAAuthorship 1029541729186545Sherman MA, Barton AR, Lodato MA, Vitzthum C, Coulter ME, Walsh CA, Park PJNucleic acids researchPaSD-qc: quality control for single cell whole-genome sequencing data using power spectral density estimation. Nucleic Acids Res. 2018 02 28; 46(4):e20.Nucleic Acids Res2018-02-28T00:00:002018PaSD-qc: quality control for single cell whole-genome sequencing data using power spectral density estimation.23321669Tzatsos A, Paskaleva P, Ferrari F, Deshpande V, Stoykova S, Contino G, Wong KK, Lan F, Trojer P, Park PJ, Bardeesy NThe Journal of clinical investigationKDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs. J Clin Invest. 2013 Feb; 123(2):727-39.J Clin Invest2013-01-16T00:00:002013KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs.Authorship 10347251629217584Lodato MA, Rodin RE, Bohrson CL, Coulter ME, Barton AR, Kwon M, Sherman MA, Vitzthum CM, Luquette LJ, Yandava CN, Yang P, Chittenden TW, Hatem NE, Ryu SC, Woodworth MB, Park PJ, Walsh CAScience (New York, N.Y.)Aging and neurodegeneration are associated with increased mutations in single human neurons. Science. 2018 02 02; 359(6375):555-559.Science2017-12-07T00:00:002017Aging and neurodegeneration are associated with increased mutations in single human neurons.22955616NatureAn integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74.Nature2012-09-06T00:00:002012An integrated encyclopedia of DNA elements in the human genome.23064238Tan X, Hu L, Luquette LJ, Gao G, Liu Y, Qu H, Xi R, Lu ZJ, Park PJ, Elledge SJNature biotechnologySystematic identification of synergistic drug pairs targeting HIV. Nat Biotechnol. 2012 Nov; 30(11):1125-30.Nat Biotechnol2012-10-14T00:00:002012Systematic identification of synergistic drug pairs targeting HIV.19786482Park PJ, Kong SW, Tebaldi T, Lai WR, Kasif S, Kohane ISBioinformatics (Oxford, England)Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Bioinformatics. 2009 Dec 01; 25(23):3121-7.Bioinformatics2009-09-28T00:00:002009Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance.20080666Kim H, Huang W, Jiang X, Pennicooke B, Park PJ, Johnson MDProceedings of the National Academy of Sciences of the United States of AmericaIntegrative genome analysis reveals an oncomir/oncogene cluster regulating glioblastoma survivorship. Proc Natl Acad Sci U S A. 2010 Feb 02; 107(5):2183-8.Proc Natl Acad Sci U S A2010-01-13T00:00:002010Integrative genome analysis reveals an oncomir/oncogene cluster regulating glioblastoma survivorship.21069662Kim TM, Park PJWiley interdisciplinary reviews. Systems biology and medicineAdvances in analysis of transcriptional regulatory networks. Wiley Interdiscip Rev Syst Biol Med. 2011 Jan-Feb; 3(1):21-35.Wiley Interdiscip Rev Syst Biol Med2011-01-01T00:00:002011Advances in analysis of transcriptional regulatory networks.19545786Yoon 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 DGInternational journal of radiation oncology, biology, physicsEfficacy 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.Int J Radiat Oncol Biol Phys2009-07-15T00:00:002009Efficacy of sunitinib and radiotherapy in genetically engineered mouse model of soft-tissue sarcoma.22343407Hodge JC, Kim TM, Dreyfuss JM, Somasundaram P, Christacos NC, Rousselle M, Quade BJ, Park PJ, Stewart EA, Morton CCHuman molecular geneticsExpression 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.Hum Mol Genet2012-02-17T00:00:002012Expression 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.23028361Riddle 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 SCPLoS geneticsEnrichment 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.PLoS Genet2012-09-20T00:00:002012Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain.12474876Kuo WP, Jenssen TK, Park PJ, Lingen MW, Hasina R, Ohno-Machado LProceedings. AMIA SymposiumGene expression levels in different stages of progression in oral squamous cell carcinoma. Proc AMIA Symp. 2002; 415-9.Proc AMIA Symp2002-01-01T00:00:002002Gene expression levels in different stages of progression in oral squamous cell carcinoma.15684227Kong SW, Hwang KB, Kim RD, Zhang BT, Greenberg SA, Kohane IS, Park PJBioinformatics (Oxford, England)CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays. Bioinformatics. 2005 May 01; 21(9):2116-7.Bioinformatics2005-01-31T00:00:002005CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays.Authorship 1003712015852401Greenberg SA, Pinkus JL, Pinkus GS, Burleson T, Sanoudou D, Tawil R, Barohn RJ, Saperstein DS, Briemberg HR, Ericsson M, Park P, Amato AAAnnals of neurologyInterferon-alpha/beta-mediated innate immune mechanisms in dermatomyositis. Ann Neurol. 2005 May; 57(5):664-78.Ann Neurol2005-05-01T00:00:002005Interferon-alpha/beta-mediated innate immune mechanisms in dermatomyositis.23074071Xi R, Lee S, Park PJCurrent protocols in human geneticsA survey of copy-number variation detection tools based on high-throughput sequencing data. Curr Protoc Hum Genet. 2012 Oct; Chapter 7:Unit7.19.Curr Protoc Hum Genet2012-10-01T00:00:002012A survey of copy-number variation detection tools based on high-throughput sequencing data.12733779Kuo WP, Whipple ME, Jenssen TK, Todd R, Epstein JB, Ohno-Machado L, Sonis ST, Park PJJournal of the American Dental Association (1939)Microarrays and clinical dentistry. J Am Dent Assoc. 2003 Apr; 134(4):456-62.J Am Dent Assoc2003-04-01T00:00:002003Microarrays and clinical dentistry.