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Fan J, Lee HO, Lee S, Ryu DE, Lee S, Xue C, Kim SJ, Kim K, Barkas N, Park PJ, Park WY, Kharchenko PV. Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data. Genome Res. 2018 Jun 13. PMID: 29898899.
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Dou Y, Gold HD, Luquette LJ, Park PJ. Detecting Somatic Mutations in Normal Cells. Trends Genet. 2018 Jul; 34(7):545-557. PMID: 29731376.
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Bailey 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 L. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 Apr 05; 173(2):371-385.e18. PMID: 29625053.
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Sherman MA, Barton AR, Lodato MA, Vitzthum C, Coulter ME, Walsh CA, Park PJ. PaSD-qc: quality control for single cell whole-genome sequencing data using power spectral density estimation. Nucleic Acids Res. 2018 Feb 28; 46(4):e20. PMID: 29186545.
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Lodato 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 CA. Aging and neurodegeneration are associated with increased mutations in single human neurons. Science. 2018 02 02; 359(6375):555-559. PMID: 29217584.
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Dekker 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 S. Corrigendum: The 4D nucleome project. Nature. 2017 12 14; 552(7684):278. PMID: 29168505.
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Shin 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 WY. Prevalence and detection of low-allele-fraction variants in clinical cancer samples. Nat Commun. 2017 Nov 09; 8(1):1377. PMID: 29123093.
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Kang H, Jung YL, McElroy KA, Zee BM, Wallace HA, Woolnough JL, Park PJ, Kuroda MI. Bivalent complexes of PRC1 with orthologs of BRD4 and MOZ/MORF target developmental genes in Drosophila. Genes Dev. 2017 10 01; 31(19):1988-2002. PMID: 29070704.
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Dekker 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 S. The 4D nucleome project. Nature. 2017 09 13; 549(7671):219-226. PMID: 28905911.
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Chen 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 WT. VEGF amplifies transcription through ETS1 acetylation to enable angiogenesis. Nat Commun. 2017 08 29; 8(1):383. PMID: 28851877.
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Kim 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 J. Clinical Application of Targeted Deep Sequencing in Solid-Cancer Patients and Utility for Biomarker-Selected Clinical Trials. Oncologist. 2017 Oct; 22(10):1169-1177. PMID: 28701572.
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Lee S, Lee S, Ouellette S, Park WY, Lee EA, Park PJ. NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types. Nucleic Acids Res. 2017 Jun 20; 45(11):e103. PMID: 28369524.
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Cortes-Ciriano I, Lee S, Park WY, Kim TM, Park PJ. A molecular portrait of microsatellite instability across multiple cancers. Nat Commun. 2017 Jun 06; 8:15180. PMID: 28585546.
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Zhang 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 CJ. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell. 2017 06 12; 31(6):820-832.e3. PMID: 28528867.
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Lu 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 KL. Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer. Cancer Res. 2017 07 01; 77(13):3502-3512. PMID: 28512244.
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Lee 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 YS. Clonal History and Genetic Predictors of Transformation Into Small-Cell Carcinomas From Lung Adenocarcinomas. J Clin Oncol. 2017 Sep 10; 35(26):3065-3074. PMID: 28498782.
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McConnell 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 FM. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science. 2017 Apr 28; 356(6336). PMID: 28450582.
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Choi 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 K. DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cell Stem Cell. 2017 05 04; 20(5):706-719.e7. PMID: 28366588.
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Shetty A, Kallgren SP, Demel C, Maier KC, Spatt D, Alver BH, Cramer P, Park PJ, Winston F. Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation. Mol Cell. 2017 Apr 06; 66(1):77-88.e5. PMID: 28366642.
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Alver BH, Kim KH, Lu P, Wang X, Manchester HE, Wang W, Haswell JR, Park PJ, Roberts CW. The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers. Nat Commun. 2017 Mar 06; 8:14648. PMID: 28262751.
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McElroy KA, Jung YL, Zee BM, Wang CI, Park PJ, Kuroda MI. 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. PMID: 28064188.
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Mathur R, Alver BH, San Roman AK, Wilson BG, Wang X, Agoston AT, Park PJ, Shivdasani RA, Roberts CW. ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice. Nat Genet. 2017 Feb; 49(2):296-302. PMID: 27941798.
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Wang 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 CW. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Nat Genet. 2017 Feb; 49(2):289-295. PMID: 27941797.
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Saini 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 DA. The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts. PLoS Genet. 2016 10; 12(10):e1006385. PMID: 27788131.
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Kavanaugh MJ, So JD, Park PJ, Davis KL. Validation 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. PMID: 27391204.
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Day DS, Zhang B, Stevens SM, Ferrari F, Larschan EN, Park PJ, Pu WT. Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types. Genome Biol. 2016 06 03; 17(1):120. PMID: 27259512; PMCID: PMC4893286.
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Xi R, Lee S, Xia Y, Kim TM, Park PJ. Copy 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. PMID: 27260798.
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Tica J, Lee E, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EE, Park PJ, Stütz AM, Korbel JO. Next-generation sequencing-based detection of germline L1-mediated transductions. BMC Genomics. 2016 05 10; 17:342. PMID: 27161561; PMCID: PMC4862182.
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Mieczkowski J, Cook A, Bowman SK, Mueller B, Alver BH, Kundu S, Deaton AM, Urban JA, Larschan E, Park PJ, Kingston RE, Tolstorukov MY. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Nat Commun. 2016 May 06; 7:11485. PMID: 27151365; PMCID: PMC4859066.
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Yang 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 PJ. Analyzing Somatic Genome Rearrangements in Human Cancers by Using Whole-Exome Sequencing. Am J Hum Genet. 2016 05 05; 98(5):843-856. PMID: 27153396.
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Chen 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 CJ. Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Rep. 2016 Mar 15; 14(10):2476-89. PMID: 26947078; PMCID: PMC4794376.
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Evrony GD, Lee E, Park PJ, Walsh CA. Resolving rates of mutation in the brain using single-neuron genomics. Elife. 2016 Feb 22; 5. PMID: 26901440; PMCID: PMC4805530.
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Lee JK, Choi YL, Kwon M, Park PJ. Mechanisms and Consequences of Cancer Genome Instability: Lessons from Genome Sequencing Studies. Annu Rev Pathol. 2016 05 23; 11:283-312. PMID: 26907526.
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Ordulu Z, Nucci MR, Dal Cin P, Hollowell ML, Otis CN, Hornick JL, Park PJ, Kim TM, Quade BJ, Morton CC. Intravenous leiomyomatosis: an unusual intermediate between benign and malignant uterine smooth muscle tumors. Mod Pathol. 2016 05; 29(5):500-10. PMID: 26892441.
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De 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 GQ. Corrigendum: Failure to replicate the STAP cell phenomenon. Nature. 2016 Mar 17; 531(7594):400. PMID: 26675720.
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De 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 GQ. Corrigendum: Hallmarks of pluripotency. Nature. 2016 Mar 17; 531(7594):400. PMID: 26675727.
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Cheloufi 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 K. The histone chaperone CAF-1 safeguards somatic cell identity. Nature. 2015 Dec 10; 528(7581):218-24. PMID: 26659182.
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Binanay 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 GS. Building Sustainable Capacity for Cardiovascular Care at a Public Hospital in Western Kenya. J Am Coll Cardiol. 2015 Dec 08; 66(22):2550-60. PMID: 26653630.
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Bersani 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 DA. Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer. Proc Natl Acad Sci U S A. 2015 Dec 08; 112(49):15148-53. PMID: 26575630; PMCID: PMC4679016.
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Choi 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 K. A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat Biotechnol. 2015 Nov; 33(11):1173-81. PMID: 26501951; PMCID: PMC4847940.
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Jung H, Lee D, Lee J, Park D, Kim YJ, Park WY, Hong D, Park PJ, Lee E. Intron retention is a widespread mechanism of tumor-suppressor inactivation. Nat Genet. 2015 Nov; 47(11):1242-8. PMID: 26437032.
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Lodato 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 CA. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science. 2015 Oct 02; 350(6256):94-98. PMID: 26430121; PMCID: PMC4664477 [Available on 10/02/16].
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De 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 GQ. Failure to replicate the STAP cell phenomenon. Nature. 2015 Sep 24; 525(7570):E6-9. PMID: 26399835.
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De 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 GQ. Hallmarks of pluripotency. Nature. 2015 Sep 24; 525(7570):469-78. PMID: 26399828.
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Kim 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 DH. Spatiotemporal Evolution of the Primary Glioblastoma Genome. Cancer Cell. 2015 Sep 14; 28(3):318-28. PMID: 26373279.
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Lee S, Seo CH, Alver BH, Lee S, Park PJ. EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering. BMC Bioinformatics. 2015 Sep 03; 16:278. PMID: 26335049; PMCID: PMC4559005.
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Nam JY, Kim NK, Kim SC, Joung JG, Xi R, Lee S, Park PJ, Park WY. Evaluation of somatic copy number estimation tools for whole-exome sequencing data. Brief Bioinform. 2016 Mar; 17(2):185-92. PMID: 26210357.
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Brat 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 J. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 2015 Jun 25; 372(26):2481-98. PMID: 26061751.
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Kang H, McElroy KA, Jung YL, Alekseyenko AA, Zee BM, Park PJ, Kuroda MI. Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila. Genes Dev. 2015 Jun 01; 29(11):1136-50. PMID: 26063573; PMCID: PMC4470282.
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Sohn KA, Ho JW, Djordjevic D, Jeong HH, Park PJ, Kim JH. hiHMM: Bayesian non-parametric joint inference of chromatin state maps. Bioinformatics. 2015 Jul 01; 31(13):2066-74. PMID: 25725496; PMCID: PMC4481846.
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Li H, Zhang X, Park P, Liu W, Chang J, Liao Z, Frank S, Li Y, Poenisch F, Mohan R, Gillin M, Zhu R. Robust optimization in intensity-modulated proton therapy to account for anatomy changes in lung cancer patients. Radiother Oncol. 2015 Mar; 114(3):367-72. PMID: 25708992; PMCID: PMC4400219.
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Park RW, Kim TM, Kasif S, Park PJ. Identification of rare germline copy number variations over-represented in five human cancer types. Mol Cancer. 2015 Feb 03; 14:25. PMID: 25644941; PMCID: PMC4381456.
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Kann M, Ettou S, Jung YL, Lenz MO, Taglienti ME, Park PJ, Schermer B, Benzing T, Kreidberg JA. Genome-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. PMID: 25636411; PMCID: PMC4552122.
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Biagioli 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 IS. Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation. Hum Mol Genet. 2015 May 01; 24(9):2442-57. PMID: 25574027; PMCID: PMC4383859.
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Evrony GD, Lee E, Mehta BK, Benjamini Y, Johnson RM, Cai X, Yang L, Haseley P, Lehmann HS, Park PJ, Walsh CA. Cell lineage analysis in human brain using endogenous retroelements. Neuron. 2015 Jan 07; 85(1):49-59. PMID: 25569347.
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Jung YL, Kang H, Park PJ, Kuroda MI. Correspondence of Drosophila polycomb group proteins with broad H3K27me3 silent domains. Fly (Austin). 2015; 9(4):178-82. PMID: 26940990; PMCID: PMC4862425 [Available on 03/03/17].
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Merlo P, Frost B, Peng S, Yang YJ, Park PJ, Feany M. p53 prevents neurodegeneration by regulating synaptic genes. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):18055-60. PMID: 25453105; PMCID: PMC4273405.
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Yang HW, Kim TM, Song SS, Menon L, Jiang X, Huang W, Black PM, Park PJ, Carroll RS, Johnson MD. A small subunit processome protein promotes cancer by altering translation. Oncogene. 2015 Aug 20; 34(34):4471-81. PMID: 25435373.
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Xing Z, Lin A, Li C, Liang K, Wang S, Liu Y, Park PK, Qin L, Wei Y, Hawke DH, Hung MC, Lin C, Yang L. lncRNA directs cooperative epigenetic regulation downstream of chemokine signals. Cell. 2014 Nov 20; 159(5):1110-1125. PMID: 25416949; PMCID: PMC4266991.
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Kim TM, Park PJ. A 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. PMID: 25371413; PMCID: PMC4233171.
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Parfenov 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 R. Characterization 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. PMID: 25313082; PMCID: PMC4217452.
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Li H, Liu W, Park P, Matney J, Liao Z, Chang J, Zhang X, Li Y, Zhu RX. Evaluation 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. PMID: 25207565; PMCID: PMC4161985.
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Streit M, Lex A, Gratzl S, Partl C, Schmalstieg D, Pfister H, Park PJ, Gehlenborg N. Guided visual exploration of genomic stratifications in cancer. Nat Methods. 2014 Sep; 11(9):884-885. PMID: 25166867; PMCID: PMC4196637.
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Ho 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 PJ. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52. PMID: 25164756.
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Gerstein 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 R. Comparative analysis of the transcriptome across distant species. Nature. 2014 Aug 28; 512(7515):445-8. PMID: 25164755.
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West JA, Cook A, Alver BH, Stadtfeld M, Deaton AM, Hochedlinger K, Park PJ, Tolstorukov MY, Kingston RE. Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming. Nat Commun. 2014 Aug 27; 5:4719. PMID: 25158628; PMCID: PMC4217530.
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Davis 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 CJ. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 2014 Sep 08; 26(3):319-330. PMID: 25155756; PMCID: PMC4160352.
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Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen GH, Kuroda MI, Park PJ. Impact of sequencing depth in ChIP-seq experiments. Nucleic Acids Res. 2014 May; 42(9):e74. PMID: 24598259; PMCID: PMC4027199.
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Marinov GK, Kundaje A, Park PJ, Wold BJ. Large-scale quality analysis of published ChIP-seq data. G3 (Bethesda). 2014 Feb 19; 4(2):209-23. PMID: 24347632; PMCID: PMC3931556.
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Ferrari F, Alekseyenko AA, Park PJ, Kuroda MI. Transcriptional control of a whole chromosome: emerging models for dosage compensation. Nat Struct Mol Biol. 2014 Feb; 21(2):118-25. PMID: 24500429; PMCID: PMC4342042.
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Ferrari F, Apostolou E, Park PJ, Hochedlinger K. Rearranging the chromatin for pluripotency. Cell Cycle. 2014; 13(2):167-8. PMID: 24241209; PMCID: PMC3906226.
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Kim TM, Laird PW, Park PJ. The landscape of microsatellite instability in colorectal and endometrial cancer genomes. Cell. 2013 Nov 07; 155(4):858-68. PMID: 24209623; PMCID: PMC3871995.
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Ferrari F, Plachetka A, Alekseyenko AA, Jung YL, Ozsolak F, Kharchenko PV, Park PJ, Kuroda MI. "Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts. Cell Rep. 2013 Nov 14; 5(3):629-36. PMID: 24183666; PMCID: PMC3852897.
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Davoli T, Xu AW, Mengwasser KE, Sack LM, Yoon JC, Park PJ, Elledge SJ. Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell. 2013 Nov 07; 155(4):948-62. PMID: 24183448; PMCID: PMC3891052.
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Ajay AK, Kim TM, Ramirez-Gonzalez V, Park PJ, Frank DA, Vaidya VS. A bioinformatics approach identifies signal transducer and activator of transcription-3 and checkpoint kinase 1 as upstream regulators of kidney injury molecule-1 after kidney injury. J Am Soc Nephrol. 2014 Jan; 25(1):105-18. PMID: 24158981; PMCID: PMC3871775.
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DeGennaro CM, Alver BH, Marguerat S, Stepanova E, Davis CP, Bähler J, Park PJ, Winston F. Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast. Mol Cell Biol. 2013 Dec; 33(24):4779-92. PMID: 24100010.
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Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct; 45(10):1113-20. PMID: 24071849; PMCID: PMC3919969.
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Gokcumen O, Tischler V, Tica J, Zhu Q, Iskow RC, Lee E, Fritz MH, Langdon A, Stütz AM, Pavlidis P, Benes V, Mills RE, Park PJ, Lee C, Korbel JO. Primate genome architecture influences structural variation mechanisms and functional consequences. Proc Natl Acad Sci U S A. 2013 Sep 24; 110(39):15764-9. PMID: 24014587; PMCID: PMC3785719.
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Soruco MM, Chery J, Bishop EP, Siggers T, Tolstorukov MY, Leydon AR, Sugden AU, Goebel K, Feng J, Xia P, Vedenko A, Bulyk ML, Park PJ, Larschan E. The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation. Genes Dev. 2013 Jul 15; 27(14):1551-6. PMID: 23873939; PMCID: PMC3731544.
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Majumdar S, Gong EM, Di Vizio D, Dreyfuss J, Degraff DJ, Hager MH, Park PJ, Bellmunt J, Matusik RJ, Rosenberg JE, Adam RM. Loss of Sh3gl2/endophilin A1 is a common event in urothelial carcinoma that promotes malignant behavior. Neoplasia. 2013 Jul; 15(7):749-60. PMID: 23814487; PMCID: PMC3689238.
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Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 Jul 04; 499(7456):43-9. PMID: 23792563; PMCID: PMC3771322.
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Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE. Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters. Mol Cell Biol. 2013 Aug; 33(16):3274-85. PMID: 23775117; PMCID: PMC3753906.
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Tolstorukov MY, Sansam CG, Lu P, Koellhoffer EC, Helming KC, Alver BH, Tillman EJ, Evans JA, Wilson BG, Park PJ, Roberts CW. Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters. Proc Natl Acad Sci U S A. 2013 Jun 18; 110(25):10165-70. PMID: 23723349; PMCID: PMC3690861.
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Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, Kharchenko PV, Park PJ, Hochedlinger K. Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell. 2013 Jun 06; 12(6):699-712. PMID: 23665121; PMCID: PMC3725985.
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Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh CH, Zhang C, Ren X, Protopopov A, Chin L, Kucherlapati R, Lee C, Park PJ. Diverse mechanisms of somatic structural variations in human cancer genomes. Cell. 2013 May 09; 153(4):919-29. PMID: 23663786; PMCID: PMC3704973.
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Kandoth 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 DA. Integrated genomic characterization of endometrial carcinoma. Nature. 2013 May 02; 497(7447):67-73. PMID: 23636398; PMCID: PMC3704730.
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Ferrari F, Jung YL, Kharchenko PV, Plachetka A, Alekseyenko AA, Kuroda MI, Park PJ. Comment on "Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters". Science. 2013 Apr 19; 340(6130):273. PMID: 23599463; PMCID: PMC3665607.
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Alekseyenko AA, Ellison CE, Gorchakov AA, Zhou Q, Kaiser VB, Toda N, Walton Z, Peng S, Park PJ, Bachtrog D, Kuroda MI. Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila. Genes Dev. 2013 Apr 15; 27(8):853-8. PMID: 23630075; PMCID: PMC3650223.
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Zhang B, Day DS, Ho JW, Song L, Cao J, Christodoulou D, Seidman JG, Crawford GE, Park PJ, Pu WT. A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. Genome Res. 2013 Jun; 23(6):917-27. PMID: 23547170; PMCID: PMC3668360.
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Ho 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 W. The 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. PMID: 24303302.
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Gehlenborg N, Noble MS, Getz G, Chin L, Park PJ. Nozzle: a report generation toolkit for data analysis pipelines. Bioinformatics. 2013 Apr 15; 29(8):1089-91. PMID: 23419376; PMCID: PMC3624805.
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Tzatsos A, Paskaleva P, Ferrari F, Deshpande V, Stoykova S, Contino G, Wong KK, Lan F, Trojer P, Park PJ, Bardeesy N. KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs. J Clin Invest. 2013 Feb; 123(2):727-39. PMID: 23321669; PMCID: PMC3561797.
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McClay J, Park P, Marr SD, Langford LH. The HL7 standards-based model of emergency care information. Stud Health Technol Inform. 2013; 192:1180. PMID: 23920954.
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Kim TM, Xi R, Luquette LJ, Park RW, Johnson MD, Park PJ. Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Res. 2013 Feb; 23(2):217-27. PMID: 23132910; PMCID: PMC3561863.
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Evrony GD, Cai X, Lee E, Hills LB, Elhosary PC, Lehmann HS, Parker JJ, Atabay KD, Gilmore EC, Poduri A, Park PJ, Walsh CA. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell. 2012 Oct 26; 151(3):483-96. PMID: 23101622; PMCID: PMC3567441.
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Tan X, Hu L, Luquette LJ, Gao G, Liu Y, Qu H, Xi R, Lu ZJ, Park PJ, Elledge SJ. Systematic identification of synergistic drug pairs targeting HIV. Nat Biotechnol. 2012 Nov; 30(11):1125-30. PMID: 23064238; PMCID: PMC3494743.
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Xi R, Lee S, Park PJ. A survey of copy-number variation detection tools based on high-throughput sequencing data. Curr Protoc Hum Genet. 2012 Oct; Chapter 7:Unit7.19. PMID: 23074071.
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Riddle NC, Jung YL, Gu T, Alekseyenko AA, Asker D, Gui H, Kharchenko PV, Minoda A, Plachetka A, Schwartz YB, Tolstorukov MY, Kuroda MI, Pirrotta V, Karpen GH, Park PJ, Elgin SC. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genet. 2012 Sep; 8(9):e1002954. PMID: 23028361; PMCID: PMC3447959.
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An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
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Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31. PMID: 22955991; PMCID: PMC3431496.
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Larschan E, Soruco MM, Lee OK, Peng S, Bishop E, Chery J, Goebel K, Feng J, Park PJ, Kuroda MI. Identification of chromatin-associated regulators of MSL complex targeting in Drosophila dosage compensation. PLoS Genet. 2012; 8(7):e1002830. PMID: 22844249; PMCID: PMC3405997.
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Tolstorukov MY, Goldman JA, Gilbert C, Ogryzko V, Kingston RE, Park PJ. Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. Mol Cell. 2012 Aug 24; 47(4):596-607. PMID: 22795134; PMCID: PMC3708478.
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Schwartz YB, Linder-Basso D, Kharchenko PV, Tolstorukov MY, Kim M, Li HB, Gorchakov AA, Minoda A, Shanower G, Alekseyenko AA, Riddle NC, Jung YL, Gu T, Plachetka A, Elgin SC, Kuroda MI, Park PJ, Savitsky M, Karpen GH, Pirrotta V. Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res. 2012 Nov; 22(11):2188-98. PMID: 22767387; PMCID: PMC3483548.
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Jiang X, Xing H, Kim TM, Jung Y, Huang W, Yang HW, Song S, Park PJ, Carroll RS, Johnson MD. Numb regulates glioma stem cell fate and growth by altering epidermal growth factor receptor and Skp1-Cullin-F-box ubiquitin ligase activity. Stem Cells. 2012 Jul; 30(7):1313-26. PMID: 22553175; PMCID: PMC3963835.
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Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ. Landscape of somatic retrotransposition in human cancers. Science. 2012 Aug 24; 337(6097):967-71. PMID: 22745252; PMCID: PMC3656569.
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Kim YJ, Lee HJ, Kim TM, Eisinger-Mathason TS, Zhang AY, Schmidt B, Karl DL, Nakazawa MS, Park PJ, Simon MC, Yoon SS. Overcoming evasive resistance from vascular endothelial growth factor a inhibition in sarcomas by genetic or pharmacologic targeting of hypoxia-inducible factor 1a. Int J Cancer. 2013 Jan 01; 132(1):29-41. PMID: 22684860; PMCID: PMC3677782.
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Saikumar J, Hoffmann D, Kim TM, Gonzalez VR, Zhang Q, Goering PL, Brown RP, Bijol V, Park PJ, Waikar SS, Vaidya VS. Expression, circulation, and excretion profile of microRNA-21, -155, and -18a following acute kidney injury. Toxicol Sci. 2012 Oct; 129(2):256-67. PMID: 22705808; PMCID: PMC3499041.
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Reis BY, Olson KL, Tian L, Bohn RL, Brownstein JS, Park PJ, Cziraky MJ, Wilson MD, Mandl KD. A pharmacoepidemiological network model for drug safety surveillance: statins and rhabdomyolysis. Drug Saf. 2012 May 01; 35(5):395-406. PMID: 22506565.
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Alekseyenko AA, Ho JW, Peng S, Gelbart M, Tolstorukov MY, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E, Gu T, Minoda A, Riddle NC, Schwartz YB, Elgin SC, Karpen GH, Pirrotta V, Kuroda MI, Park PJ. Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genet. 2012; 8(4):e1002646. PMID: 22570616; PMCID: PMC3343056.
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Balakrishnan A, Stearns AT, Park PJ, Dreyfuss JM, Ashley SW, Rhoads DB, Tavakkolizadeh A. Upregulation of proapoptotic microRNA mir-125a after massive small bowel resection in rats. Ann Surg. 2012 Apr; 255(4):747-53. PMID: 22418008; PMCID: PMC4116096.
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Lachke SA, Ho JW, Kryukov GV, O'Connell DJ, Aboukhalil A, Bulyk ML, Park PJ, Maas RL. iSyTE: integrated Systems Tool for Eye gene discovery. Invest Ophthalmol Vis Sci. 2012 Mar; 53(3):1617-27. PMID: 22323457.
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Pihlajamäki 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 ME. Response to Brosch et al. Cell Metab. 2012 Mar 07; 15(3):267-269. PMID: 25960695.
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Stadtfeld M, Apostolou E, Ferrari F, Choi J, Walsh RM, Chen T, Ooi SS, Kim SY, Bestor TH, Shioda T, Park PJ, Hochedlinger K. Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nat Genet. 2012 Mar 04; 44(4):398-405, S1-2. PMID: 22387999.
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Hodge JC, Kim TM, Dreyfuss JM, Somasundaram P, Christacos NC, Rousselle M, Quade BJ, Park PJ, Stewart EA, Morton CC. Expression profiling of uterine leiomyomata cytogenetic subgroups reveals distinct signatures in matched myometrium: transcriptional profilingof the t(12;14) and evidence in support of predisposing genetic heterogeneity. Hum Mol Genet. 2012 May 15; 21(10):2312-29. PMID: 22343407; PMCID: PMC3335314.
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O'Connell DJ, Ho JW, Mammoto T, Turbe-Doan A, O'Connell JT, Haseley PS, Koo S, Kamiya N, Ingber DE, Park PJ, Maas RL. A Wnt-bmp feedback circuit controls intertissue signaling dynamics in tooth organogenesis. Sci Signal. 2012 Jan 10; 5(206):ra4. PMID: 22234613.
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Yang HW, Kim TM, Song SS, Shrinath N, Park R, Kalamarides M, Park PJ, Black PM, Carroll RS, Johnson MD. Alternative splicing of CHEK2 and codeletion with NF2 promote chromosomal instability in meningioma. Neoplasia. 2012 Jan; 14(1):20-8. PMID: 22355270; PMCID: PMC3281938.
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Kharchenko PV, Xi R, Park PJ. Evidence for dosage compensation between the X chromosome and autosomes in mammals. Nat Genet. 2011 Nov 28; 43(12):1167-9; author reply 1171-2. PMID: 22120048.
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Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, Johnson MD, Muzny DM, Wheeler DA, Gibbs RA, Kucherlapati R, Park PJ. Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Natl Acad Sci U S A. 2011 Nov 15; 108(46):E1128-36. PMID: 22065754; PMCID: PMC3219132.
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Kim TM, Ramírez V, Barrera-Chimal J, Bobadilla NA, Park PJ, Vaidya VS. Gene expression analysis reveals the cell cycle and kinetochore genes participating in ischemia reperfusion injury and early development in kidney. PLoS One. 2011; 6(9):e25679. PMID: 21980527; PMCID: PMC3181346.
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Zacharek SJ, Fillmore CM, Lau AN, Gludish DW, Chou A, Ho JW, Zamponi R, Gazit R, Bock C, Jäger N, Smith ZD, Kim TM, Saunders AH, Wong J, Lee JH, Roach RR, Rossi DJ, Meissner A, Gimelbrant AA, Park PJ, Kim CF. Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci. Cell Stem Cell. 2011 Sep 02; 9(3):272-81. PMID: 21885022.
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Pihlajamäki J, Lerin C, Itkonen P, Boes T, Floss T, Schroeder J, Dearie F, Crunkhorn S, Burak F, Jimenez-Chillaron JC, Kuulasmaa T, Miettinen P, Park PJ, Nasser I, Zhao Z, Zhang Z, Xu Y, Wurst W, Ren H, Morris AJ, Stamm S, Goldfine AB, Laakso M, Patti ME. Expression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis. Cell Metab. 2011 Aug 03; 14(2):208-18. PMID: 21803291; PMCID: PMC3167228.
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Tolstorukov MY, Volfovsky N, Stephens RM, Park PJ. Impact of chromatin structure on sequence variability in the human genome. Nat Struct Mol Biol. 2011 Apr; 18(4):510-5. PMID: 21399641; PMCID: PMC3188321.
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Kim TM, Huang W, Park R, Park PJ, Johnson MD. A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs. Cancer Res. 2011 May 01; 71(9):3387-99. PMID: 21385897; PMCID: PMC3085663.
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Larschan E, Bishop EP, Kharchenko PV, Core LJ, Lis JT, Park PJ, Kuroda MI. X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature. 2011 Mar 03; 471(7336):115-8. PMID: 21368835; PMCID: PMC3076316.
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Ho JW, Bishop E, Karchenko PV, Nègre N, White KP, Park PJ. ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics. 2011 Feb 28; 12:134. PMID: 21356108; PMCID: PMC3053263.
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Xi R, Kim TM, Park PJ. Detecting structural variations in the human genome using next generation sequencing. Brief Funct Genomics. 2010 Dec; 9(5-6):405-15. PMID: 21216738; PMCID: PMC3080742.
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Kim TM, Park PJ. Advances in analysis of transcriptional regulatory networks. Wiley Interdiscip Rev Syst Biol Med. 2011 Jan-Feb; 3(1):21-35. PMID: 21069662.
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Gritt A, Park P. The workhouse populations of Lancashire in 1881. Local Popul Stud. 2011; (86):37-65. PMID: 21796861.
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Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011 Mar 24; 471(7339):480-5. PMID: 21179089; PMCID: PMC3109908.
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Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SC, Karpen GH. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res. 2011 Feb; 21(2):147-63. PMID: 21177972; PMCID: PMC3032919.
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Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97. PMID: 21177974.
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Anchan RM, Quaas P, Gerami-Naini B, Bartake H, Griffin A, Zhou Y, Day D, Eaton JL, George LL, Naber C, Turbe-Doan A, Park PJ, Hornstein MD, Maas RL. Amniocytes can serve a dual function as a source of iPS cells and feeder layers. Hum Mol Genet. 2011 Mar 01; 20(5):962-74. PMID: 21156717; PMCID: PMC3033187.
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Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SC, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD. An assessment of histone-modification antibody quality. Nat Struct Mol Biol. 2011 Jan; 18(1):91-3. PMID: 21131980.
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Gurumurthy S, Xie SZ, Alagesan B, Kim J, Yusuf RZ, Saez B, Tzatsos A, Ozsolak F, Milos P, Ferrari F, Park PJ, Shirihai OS, Scadden DT, Bardeesy N. The Lkb1 metabolic sensor maintains haematopoietic stem cell survival. Nature. 2010 Dec 02; 468(7324):659-63. PMID: 21124451; PMCID: PMC3037591.
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Jagani Z, Mora-Blanco EL, Sansam CG, McKenna ES, Wilson B, Chen D, Klekota J, Tamayo P, Nguyen PT, Tolstorukov M, Park PJ, Cho YJ, Hsiao K, Buonamici S, Pomeroy SL, Mesirov JP, Ruffner H, Bouwmeester T, Luchansky SJ, Murtie J, Kelleher JF, Warmuth M, Sellers WR, Roberts CW, Dorsch M. Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway. Nat Med. 2010 Dec; 16(12):1429-33. PMID: 21076395; PMCID: PMC3859448.
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Yoon SS, Duda DG, Karl DL, Kim TM, Kambadakone AR, Chen YL, Rothrock C, Rosenberg AE, Nielsen GP, Kirsch DG, Choy E, Harmon DC, Hornicek FJ, Dreyfuss J, Ancukiewicz M, Sahani DV, Park PJ, Jain RK, Delaney TF. Phase II study of neoadjuvant bevacizumab and radiotherapy for resectable soft tissue sarcomas. Int J Radiat Oncol Biol Phys. 2011 Nov 15; 81(4):1081-90. PMID: 20932656; PMCID: PMC3021107.
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Gorchakov AA, Alekseenko AA, Kharchenko PV, Park P, Kuroda M. [Dosage compensation in drosophila: sequence-specific initiation and sequence-independent spreading of MSL complex to the active genes on the male X chromosome]. Genetika. 2010 Oct; 46(10):1430-4. PMID: 21254570.
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Kim TM, Luquette LJ, Xi R, Park PJ. rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. BMC Bioinformatics. 2010 Aug 18; 11:432. PMID: 20718989; PMCID: PMC2939611.
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Goutagny S, Yang HW, Zucman-Rossi J, Chan J, Dreyfuss JM, Park PJ, Black PM, Giovannini M, Carroll RS, Kalamarides M. Genomic profiling reveals alternative genetic pathways of meningioma malignant progression dependent on the underlying NF2 status. Clin Cancer Res. 2010 Aug 15; 16(16):4155-64. PMID: 20682713.
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Peng S, Kuroda MI, Park PJ. Quantized correlation coefficient for measuring reproducibility of ChIP-chip data. BMC Bioinformatics. 2010 Jul 27; 11:399. PMID: 20663215; PMCID: PMC2919519.
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Balakrishnan A, Stearns AT, Park PJ, Dreyfuss JM, Ashley SW, Rhoads DB, Tavakkolizadeh A. MicroRNA mir-16 is anti-proliferative in enterocytes and exhibits diurnal rhythmicity in intestinal crypts. Exp Cell Res. 2010 Dec 10; 316(20):3512-21. PMID: 20633552; PMCID: PMC2976799.
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Day DS, Luquette LJ, Park PJ, Kharchenko PV. Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol. 2010; 11(6):R69. PMID: 20584328; PMCID: PMC2911117.
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Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJ. CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell. 2010 Apr 23; 38(2):179-90. PMID: 20417597; PMCID: PMC3098377.
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Park PJ, Bell MA. Variation of telencephalon morphology of the threespine stickleback (Gasterosteus aculeatus) in relation to inferred ecology. J Evol Biol. 2010 Jun 01; 23(6):1261-77. PMID: 20406344.
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Tolstorukov MY, Kharchenko PV, Park PJ. Analysis of primary structure of chromatin with next-generation sequencing. Epigenomics. 2010 Apr; 2(2):187-197. PMID: 22022339.
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Kim H, Huang W, Jiang X, Pennicooke B, Park PJ, Johnson MD. Integrative genome analysis reveals an oncomir/oncogene cluster regulating glioblastoma survivorship. Proc Natl Acad Sci U S A. 2010 Feb 02; 107(5):2183-8. PMID: 20080666; PMCID: PMC2836668.
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Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE. A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell. 2010 Jan 08; 140(1):99-110. PMID: 20085705; PMCID: PMC3324942.
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Hodge JC, Park PJ, Dreyfuss JM, Assil-Kishawi I, Somasundaram P, Semere LG, Quade BJ, Lynch AM, Stewart EA, Morton CC. Identifying the molecular signature of the interstitial deletion 7q subgroup of uterine leiomyomata using a paired analysis. Genes Chromosomes Cancer. 2009 Oct; 48(10):865-85. PMID: 19603527; PMCID: PMC2778251.
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Gorchakov AA, Alekseyenko AA, Kharchenko P, Park PJ, Kuroda MI. Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X. Genes Dev. 2009 Oct 01; 23(19):2266-71. PMID: 19797766; PMCID: PMC2758747.
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Park PJ, Kong SW, Tebaldi T, Lai WR, Kasif S, Kohane IS. Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Bioinformatics. 2009 Dec 01; 25(23):3121-7. PMID: 19786482; PMCID: PMC2778339.
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Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009 Oct; 10(10):669-80. PMID: 19736561; PMCID: PMC3191340.
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Dreyfuss JM, Johnson MD, Park PJ. Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers. Mol Cancer. 2009 Sep 04; 8:71. PMID: 19732454; PMCID: PMC2743637.
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Gelbart ME, Larschan E, Peng S, Park PJ, Kuroda MI. Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation. Nat Struct Mol Biol. 2009 Aug; 16(8):825-32. PMID: 19648925; PMCID: PMC2722042.
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Yoon SS, Stangenberg L, Lee YJ, Rothrock C, Dreyfuss JM, Baek KH, Waterman PR, Nielsen GP, Weissleder R, Mahmood U, Park PJ, Jacks T, Dodd RD, Fisher CJ, Ryeom S, Kirsch DG. Efficacy of sunitinib and radiotherapy in genetically engineered mouse model of soft-tissue sarcoma. Int J Radiat Oncol Biol Phys. 2009 Jul 15; 74(4):1207-16. PMID: 19545786; PMCID: PMC2733223.
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Pihlajamäki J, Boes T, Kim EY, Dearie F, Kim BW, Schroeder J, Mun E, Nasser I, Park PJ, Bianco AC, Goldfine AB, Patti ME. Thyroid hormone-related regulation of gene expression in human fatty liver. J Clin Endocrinol Metab. 2009 Sep; 94(9):3521-9. PMID: 19549744; PMCID: PMC2741713.
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Wang XP, O'Connell DJ, Lund JJ, Saadi I, Kuraguchi M, Turbe-Doan A, Cavallesco R, Kim H, Park PJ, Harada H, Kucherlapati R, Maas RL. Apc inhibition of Wnt signaling regulates supernumerary tooth formation during embryogenesis and throughout adulthood. Development. 2009 Jun; 136(11):1939-49. PMID: 19429790; PMCID: PMC2680115.
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McKinney-Freeman SL, Naveiras O, Yates F, Loewer S, Philitas M, Curran M, Park PJ, Daley GQ. Surface antigen phenotypes of hematopoietic stem cells from embryos and murine embryonic stem cells. Blood. 2009 Jul 09; 114(2):268-78. PMID: 19420357; PMCID: PMC2714203.
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Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ. Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Res. 2009 Jun; 19(6):967-77. PMID: 19246569; PMCID: PMC2694475.
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Sural TH, Peng S, Li B, Workman JL, Park PJ, Kuroda MI. The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster X chromosome. Nat Struct Mol Biol. 2008 Dec; 15(12):1318-25. PMID: 19029895; PMCID: PMC2636508.
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Park PJ. Epigenetics meets next-generation sequencing. Epigenetics. 2008 Nov; 3(6):318-21. PMID: 19098449.
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Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008 Dec; 26(12):1351-9. PMID: 19029915; PMCID: PMC2597701.
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Park PJ. Experimental design and data analysis for array comparative genomic hybridization. Cancer Invest. 2008 Nov; 26(9):923-8. PMID: 19034774.
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Dermody JL, Dreyfuss JM, Villén J, Ogundipe B, Gygi SP, Park PJ, Ponticelli AS, Moore CL, Buratowski S, Bucheli ME. Unphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation. PLoS One. 2008 Sep 26; 3(9):e3273. PMID: 18818768; PMCID: PMC2538588.
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Kharchenko PV, Woo CJ, Tolstorukov MY, Kingston RE, Park PJ. Nucleosome positioning in human HOX gene clusters. Genome Res. 2008 Oct; 18(10):1554-61. PMID: 18723689; PMCID: PMC2556261.
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Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee OK, Kharchenko P, McGrath SD, Wang CI, Mardis ER, Park PJ, Kuroda MI. A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell. 2008 Aug 22; 134(4):599-609. PMID: 18724933; PMCID: PMC2613042.
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Mueller JL, Mahadevaiah SK, Park PJ, Warburton PE, Page DC, Turner JM. The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression. Nat Genet. 2008 Jun; 40(6):794-9. PMID: 18454149; PMCID: PMC2740655.
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Orford K, Kharchenko P, Lai W, Dao MC, Worhunsky DJ, Ferro A, Janzen V, Park PJ, Scadden DT. Differential H3K4 methylation identifies developmentally poised hematopoietic genes. Dev Cell. 2008 May; 14(5):798-809. PMID: 18477461.
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Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ. nuScore: a web-interface for nucleosome positioning predictions. Bioinformatics. 2008 Jun 15; 24(12):1456-8. PMID: 18445607; PMCID: PMC3807124.
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Lai W, Choudhary V, Park PJ. CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms. Bioinformatics. 2008 Apr 01; 24(7):1014-5. PMID: 18296463; PMCID: PMC2516369.
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Lee H, Kong SW, Park PJ. Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes. Bioinformatics. 2008 Apr 01; 24(7):889-96. PMID: 18263644; PMCID: PMC2600603.
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Tun HW, Personett D, Baskerville KA, Menke DM, Jaeckle KA, Kreinest P, Edenfield B, Zubair AC, O'Neill BP, Lai WR, Park PJ, McKinney M. Pathway analysis of primary central nervous system lymphoma. Blood. 2008 Mar 15; 111(6):3200-10. PMID: 18184868; PMCID: PMC2265457.
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Claus EB, Park PJ, Carroll R, Chan J, Black PM. Specific genes expressed in association with progesterone receptors in meningioma. Cancer Res. 2008 Jan 01; 68(1):314-22. PMID: 18172325; PMCID: PMC3256746.
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Larschan E, Alekseyenko AA, Gortchakov AA, Peng S, Li B, Yang P, Workman JL, Park PJ, Kuroda MI. MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism. Mol Cell. 2007 Oct 12; 28(1):121-33. PMID: 17936709.
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Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ. Normalization and experimental design for ChIP-chip data. BMC Bioinformatics. 2007 Jun 25; 8:219. PMID: 17592629; PMCID: PMC1913544.
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Baskerville KA, Kent C, Personett D, Lai WR, Park PJ, Coleman P, McKinney M. Aging elevates metabolic gene expression in brain cholinergic neurons. Neurobiol Aging. 2008 Dec; 29(12):1874-93. PMID: 17560690.
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Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S. Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet. 2007 Jun; 3(6):e96. PMID: 17571924; PMCID: PMC1904360.
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Vukovic B, Beheshti B, Park P, Lim G, Bayani J, Zielenska M, Squire JA. Correlating breakage-fusion-bridge events with the overall chromosomal instability and in vitro karyotype evolution in prostate cancer. Cytogenet Genome Res. 2007; 116(1-2):1-11. PMID: 17268171.
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Liu F, Park PJ, Lai W, Maher E, Chakravarti A, Durso L, Jiang X, Yu Y, Brosius A, Thomas M, Chin L, Brennan C, DePinho RA, Kohane I, Carroll RS, Black PM, Johnson MD. A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma. Cancer Res. 2006 Nov 15; 66(22):10815-23. PMID: 17090523.
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Yoon SS, Segal NH, Park PJ, Detwiller KY, Fernando NT, Ryeom SW, Brennan MF, Singer S. Angiogenic profile of soft tissue sarcomas based on analysis of circulating factors and microarray gene expression. J Surg Res. 2006 Oct; 135(2):282-90. PMID: 16603191.
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Kong SW, Pu WT, Park PJ. A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics. 2006 Oct 01; 22(19):2373-80. PMID: 16877751; PMCID: PMC2813864.
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Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol. 2006 Jul; 24(7):832-40. PMID: 16823376.
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Namekawa SH, Park PJ, Zhang LF, Shima JE, McCarrey JR, Griswold MD, Lee JT. Postmeiotic sex chromatin in the male germline of mice. Curr Biol. 2006 Apr 04; 16(7):660-7. PMID: 16581510.
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Alekseyenko AA, Larschan E, Lai WR, Park PJ, Kuroda MI. High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. Genes Dev. 2006 Apr 01; 20(7):848-57. PMID: 16547173; PMCID: PMC1472287.
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Larschan E, Alekseyenko AA, Lai WR, Park PJ, Kuroda MI. MSL complex associates with clusters of actively transcribed genes along the Drosophila male X chromosome. Cold Spring Harb Symp Quant Biol. 2006; 71:385-94. PMID: 17381321.
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Hamada FN, Park PJ, Gordadze PR, Kuroda MI. Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster. Genes Dev. 2005 Oct 01; 19(19):2289-94. PMID: 16204180; PMCID: PMC1240037.
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Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A. 2005 Sep 20; 102(38):13544-9. PMID: 16174746; PMCID: PMC1200092.
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Lai WR, Johnson MD, Kucherlapati R, Park PJ. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics. 2005 Oct 01; 21(19):3763-70. PMID: 16081473; PMCID: PMC2819184.
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Greenberg SA, Pinkus JL, Pinkus GS, Burleson T, Sanoudou D, Tawil R, Barohn RJ, Saperstein DS, Briemberg HR, Ericsson M, Park P, Amato AA. Interferon-alpha/beta-mediated innate immune mechanisms in dermatomyositis. Ann Neurol. 2005 May; 57(5):664-78. PMID: 15852401.
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Kong SW, Hwang KB, Kim RD, Zhang BT, Greenberg SA, Kohane IS, Park PJ. CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays. Bioinformatics. 2005 May 01; 21(9):2116-7. PMID: 15684227; PMCID: PMC2819168.
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Hwang KB, Kong SW, Greenberg SA, Park PJ. Combining gene expression data from different generations of oligonucleotide arrays. BMC Bioinformatics. 2004 Oct 25; 5:159. PMID: 15504239; PMCID: PMC528726.
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Park PJ, Cao YA, Lee SY, Kim JW, Chang MS, Hart R, Choi S. Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. J Biotechnol. 2004 Sep 09; 112(3):225-45. PMID: 15313001.
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Kim RD, Park PJ. Improving identification of differentially expressed genes in microarray studies using information from public databases. Genome Biol. 2004; 5(9):R70. PMID: 15345054; PMCID: PMC522877.
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Koopman LA, Kopcow HD, Rybalov B, Boyson JE, Orange JS, Schatz F, Masch R, Lockwood CJ, Schachter AD, Park PJ, Strominger JL. Human decidual natural killer cells are a unique NK cell subset with immunomodulatory potential. J Exp Med. 2003 Oct 20; 198(8):1201-12. PMID: 14568979; PMCID: PMC2194228.
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Kuo WP, Whipple ME, Jenssen TK, Todd R, Epstein JB, Ohno-Machado L, Sonis ST, Park PJ. Microarrays and clinical dentistry. J Am Dent Assoc. 2003 Apr; 134(4):456-62. PMID: 12733779.
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Blackshaw S, Kuo WP, Park PJ, Tsujikawa M, Gunnersen JM, Scott HS, Boon WM, Tan SS, Cepko CL. MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues. Genome Biol. 2003; 4(3):R17. PMID: 12620102; PMCID: PMC153457.
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Kuo WP, Mendez E, Chen C, Whipple ME, Farell G, Agoff N, Park PJ. Functional relationships between gene pairs in oral squamous cell carcinoma. AMIA Annu Symp Proc. 2003; 371-5. PMID: 14728197; PMCID: PMC1479982.
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Park PJ, Butte AJ, Kohane IS. Comparing expression profiles of genes with similar promoter regions. Bioinformatics. 2002 Dec; 18(12):1576-84. PMID: 12490441.
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Kuruvilla FG, Park PJ, Schreiber SL. Vector algebra in the analysis of genome-wide expression data. Genome Biol. 2002; 3(3):RESEARCH0011. PMID: 11897023; PMCID: PMC88809.
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Park PJ, Tian L, Kohane IS. Linking gene expression data with patient survival times using partial least squares. Bioinformatics. 2002; 18 Suppl 1:S120-7. PMID: 12169539.
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Kuo WP, Jenssen TK, Park PJ, Lingen MW, Hasina R, Ohno-Machado L. Gene expression levels in different stages of progression in oral squamous cell carcinoma. Proc AMIA Symp. 2002; 415-9. PMID: 12474876; PMCID: PMC2244435.
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Park PJ, Pagano M, Bonetti M. A nonparametric scoring algorithm for identifying informative genes from microarray data. Pac Symp Biocomput. 2001; 52-63. PMID: 11262969.