| Year |
Citation |
Score |
| 2021 |
Roberts 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, et al. Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. Science Advances. 7. PMID 34144992 DOI: 10.1126/sciadv.abg5285 |
0.443 |
|
| 2020 |
Reim NI, Chuang J, Jain D, Alver BH, Park PJ, Winston F. The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae. Nucleic Acids Research. PMID 32941642 DOI: 10.1093/Nar/Gkaa745 |
0.366 |
|
| 2020 |
Ettou S, Jung YL, Miyoshi T, Jain D, Hiratsuka K, Schumacher V, Taglienti ME, Morizane R, Park PJ, Kreidberg JA. Epigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury. Science Advances. 6: eabb5460. PMID 32754639 DOI: 10.1126/Sciadv.Abb5460 |
0.302 |
|
| 2020 |
Chu C, Zhao B, Park PJ, Lee EA. Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data. Current Protocols in Human Genetics. 107: e102. PMID 32662945 DOI: 10.1002/Cphg.102 |
0.328 |
|
| 2020 |
Goldman 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, ... ... Park PJ, et al. A user guide for the online exploration and visualization of PCAWG data. Nature Communications. 11: 3400. PMID 32636365 DOI: 10.1038/S41467-020-16785-6 |
0.35 |
|
| 2020 |
Yun JW, Yang L, Park HY, Lee CW, Cha H, Shin HT, Noh KW, Choi YL, Park WY, Park PJ. Dysregulation of cancer genes by recurrent intergenic fusions. Genome Biology. 21: 166. PMID 32631391 DOI: 10.1186/S13059-020-02076-2 |
0.303 |
|
| 2020 |
Huang 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 CA. Parallel RNA and DNA analysis after deep sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain. Proceedings of the National Academy of Sciences of the United States of America. PMID 32522880 DOI: 10.1073/Pnas.2006163117 |
0.3 |
|
| 2020 |
Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, Park PJ. Publisher Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nature Genetics. PMID 32404988 DOI: 10.1038/S41588-020-0634-1 |
0.324 |
|
| 2020 |
Touat 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, ... ... Park PJ, et al. Mechanisms and therapeutic implications of hypermutation in gliomas. Nature. 580: 517-523. PMID 32322066 DOI: 10.1038/S41586-020-2209-9 |
0.315 |
|
| 2020 |
Wang S, Lee S, Chu C, Jain D, Kerpedjiev P, Nelson GM, Walsh JM, Alver BH, Park PJ. HiNT: a computational method for detecting copy number variations and translocations from Hi-C data. Genome Biology. 21: 73. PMID 32293513 DOI: 10.1186/S13059-020-01986-5 |
0.31 |
|
| 2020 |
Miller 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, ... ... Park PJ, et al. Genomics of MPNST (GeM) Consortium: Rationale and Study Design for Multi-Omic Characterization of NF1-Associated and Sporadic MPNSTs. Genes. 11. PMID 32252413 DOI: 10.3390/Genes11040387 |
0.323 |
|
| 2020 |
Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, Park PJ. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nature Genetics. PMID 32025003 DOI: 10.1038/S41588-019-0576-7 |
0.375 |
|
| 2020 |
Rodriguez-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, ... Park PJ, et al. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics. PMID 32024998 DOI: 10.1038/S41588-019-0562-0 |
0.371 |
|
| 2020 |
Sieverling 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, et al. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nature Communications. 11: 733. PMID 32024817 DOI: 10.1038/S41467-019-13824-9 |
0.37 |
|
| 2020 |
Dou Y, Kwon M, Rodin RE, Cortés-Ciriano I, Doan R, Luquette LJ, Galor A, Bohrson C, Walsh CA, Park PJ. Accurate detection of mosaic variants in sequencing data without matched controls. Nature Biotechnology. PMID 31907404 DOI: 10.1038/S41587-019-0368-8 |
0.325 |
|
| 2020 |
Touat M, Li YY, Boynton AN, Spurr LF, Iorgulescu B, Bohrson CL, Cortes-Ciriano I, Geduldig JE, Pelton K, Lim-Fat MJ, Pal S, Ramkissoon SH, Dubois F, Bellamy C, Currimjee N, ... ... Park PJ, et al. Abstract 5705: Mechanisms and therapeutic implications of hypermutation in gliomas Cancer Research. 80: 5705-5705. DOI: 10.1158/1538-7445.Am2020-5705 |
0.326 |
|
| 2019 |
Zhang 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, ... Park PJ, et al. Global impact of somatic structural variation on the DNA methylome of human cancers. Genome Biology. 20: 209. PMID 31610796 DOI: 10.1186/S13059-019-1818-9 |
0.392 |
|
| 2019 |
Luquette LJ, Bohrson CL, Sherman MA, Park PJ. Identification of somatic mutations in single cell DNA-seq using a spatial model of allelic imbalance. Nature Communications. 10: 3908. PMID 31467286 DOI: 10.1038/S41467-019-11857-8 |
0.326 |
|
| 2019 |
Oberlick 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, ... ... Park PJ, et al. Small-Molecule and CRISPR Screening Converge to Reveal Receptor Tyrosine Kinase Dependencies in Pediatric Rhabdoid Tumors. Cell Reports. 28: 2331-2344.e8. PMID 31461650 DOI: 10.1016/J.Celrep.2019.07.021 |
0.344 |
|
| 2019 |
Yang L, Wang S, Lee JJ, Lee S, Lee E, Shinbrot E, Wheeler DA, Kucherlapati R, Park PJ. An enhanced genetic model of colorectal cancer progression history. Genome Biology. 20: 168. PMID 31416464 DOI: 10.1186/S13059-019-1782-4 |
0.331 |
|
| 2019 |
Lee 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, et al. Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma. Cell. PMID 31155235 DOI: 10.1016/J.Cell.2019.05.013 |
0.317 |
|
| 2019 |
Wang X, Wang S, Troisi EC, Howard TP, Haswell JR, Wolf BK, Hawk WH, Ramos P, Oberlick EM, Tzvetkov EP, Vazquez F, Hahn WC, Park PJ, Roberts CWM. BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors. Nature Communications. 10: 1881. PMID 31015438 DOI: 10.1038/S41467-019-09891-7 |
0.323 |
|
| 2019 |
Gulhan DC, Lee JJ, Melloni GEM, Cortés-Ciriano I, Park PJ. Detecting the mutational signature of homologous recombination deficiency in clinical samples. Nature Genetics. PMID 30988514 DOI: 10.1038/S41588-019-0390-2 |
0.331 |
|
| 2019 |
Bohrson 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 PJ. Linked-read analysis identifies mutations in single-cell DNA-sequencing data. Nature Genetics. PMID 30886424 DOI: 10.1038/S41588-019-0366-2 |
0.316 |
|
| 2019 |
Howard 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, ... ... Park PJ, et al. MDM2 and MDM4 are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors. Cancer Research. PMID 30755442 DOI: 10.1158/0008-5472.Can-18-3066 |
0.327 |
|
| 2019 |
Wang 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, ... ... Park PJ, et al. A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA. Genome Research. PMID 30670628 DOI: 10.1101/Gr.239053.118 |
0.324 |
|
| 2018 |
Zhang 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, ... Park PJ, et al. A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases. Cell Reports. 24: 515-527. PMID 29996110 DOI: 10.1016/J.Celrep.2018.06.025 |
0.395 |
|
| 2018 |
Holm 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, et al. The BabySeq project: implementing genomic sequencing in newborns. Bmc Pediatrics. 18: 225. PMID 29986673 DOI: 10.1186/S12887-018-1200-1 |
0.316 |
|
| 2018 |
Zhang L, Ettou S, Khalid M, Taglienti M, Jain D, Jung YL, Seager C, Liu Y, Ng KH, Park PJ, Kreidberg JA. Eed, a member of the Polycomb group, is required for nephron differentiation and the maintenance of nephron progenitor cells. Development (Cambridge, England). PMID 29945864 DOI: 10.1242/Dev.157149 |
0.324 |
|
| 2018 |
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 Research. PMID 29898899 DOI: 10.1101/Gr.228080.117 |
0.362 |
|
| 2018 |
Dou Y, Gold HD, Luquette LJ, Park PJ. Detecting Somatic Mutations in Normal Cells. Trends in Genetics : Tig. PMID 29731376 DOI: 10.1016/J.Tig.2018.04.003 |
0.318 |
|
| 2018 |
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, ... ... Park PJ, et al. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 173: 371-385.e18. PMID 29625053 DOI: 10.1016/J.Cell.2018.02.060 |
0.35 |
|
| 2017 |
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 Research. PMID 29186545 DOI: 10.1093/Nar/Gkx1195 |
0.346 |
|
| 2017 |
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, ... ... Park PJ, et al. Prevalence and detection of low-allele-fraction variants in clinical cancer samples. Nature Communications. 8: 1377. PMID 29123093 DOI: 10.1038/S41467-017-01470-Y |
0.306 |
|
| 2017 |
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 & Development. PMID 29070704 DOI: 10.1101/Gad.305987.117 |
0.327 |
|
| 2017 |
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. 549: 219-226. PMID 28905911 DOI: 10.1038/Nature23884 |
0.333 |
|
| 2017 |
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, et al. Clinical Application of Targeted Deep Sequencing in Solid-Cancer Patients; Utility of Targeted Deep Sequencing for Biomarker-Selected Clinical Trial. The Oncologist. PMID 28701572 DOI: 10.1634/Theoncologist.2017-0020 |
0.311 |
|
| 2017 |
Cortes-Ciriano I, Lee S, Park WY, Kim TM, Park PJ. A molecular portrait of microsatellite instability across multiple cancers. Nature Communications. 8: 15180. PMID 28585546 DOI: 10.1038/Ncomms15180 |
0.379 |
|
| 2017 |
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, ... Park PJ, et al. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell. PMID 28528867 DOI: 10.1016/J.Ccell.2017.04.013 |
0.336 |
|
| 2017 |
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 P, et al. Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer. Cancer Research. PMID 28512244 DOI: 10.1158/0008-5472.Can-16-2745 |
0.324 |
|
| 2017 |
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, ... ... Park PJ, et al. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science (New York, N.Y.). 356. PMID 28450582 DOI: 10.1126/Science.Aal1641 |
0.307 |
|
| 2017 |
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 Research. PMID 28369524 DOI: 10.1093/Nar/Gkx193 |
0.317 |
|
| 2017 |
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. Molecular Cell. PMID 28366642 DOI: 10.1016/J.Molcel.2017.02.023 |
0.309 |
|
| 2017 |
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. Nature Communications. 8: 14648. PMID 28262751 DOI: 10.1038/Ncomms14648 |
0.355 |
|
| 2017 |
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, Md.). PMID 28064188 DOI: 10.1534/G3.116.037788 |
0.36 |
|
| 2017 |
Mathur R, Alver BH, Roman AKS, Wilson BG, Wang X, Agoston AT, Park P, Shivdasani R, Roberts CW. Abstract LB-286: ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice Cancer Research. 77. DOI: 10.1158/1538-7445.Am2017-Lb-286 |
0.362 |
|
| 2017 |
Wang X, Lee R, Alver B, Haswell J, Wang S, Troisi E, Bernstein B, Park P, Roberts C. Abstract LB-096: SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation Cancer Research. 77. DOI: 10.1158/1538-7445.Am2017-Lb-096 |
0.375 |
|
| 2016 |
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. Nature Genetics. PMID 27941798 DOI: 10.1038/Ng.3744 |
0.363 |
|
| 2016 |
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, ... ... Park PJ, et al. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Nature Genetics. PMID 27941797 DOI: 10.1038/Ng.3746 |
0.343 |
|
| 2016 |
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 Research. PMID 27260798 DOI: 10.1093/Nar/Gkw491 |
0.377 |
|
| 2016 |
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. 17: 342. PMID 27161561 DOI: 10.1186/S12864-016-2670-X |
0.319 |
|
| 2016 |
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, ... Park PJ, et al. Analyzing Somatic Genome Rearrangements in Human Cancers by Using Whole-Exome Sequencing. American Journal of Human Genetics. 98: 843-856. PMID 27153396 DOI: 10.1016/J.Ajhg.2016.03.017 |
0.41 |
|
| 2016 |
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. Nature Communications. 7: 11485. PMID 27151365 DOI: 10.1038/Ncomms11485 |
0.31 |
|
| 2016 |
Chen F, Zhang Y, Şenbabaoğlu 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, ... ... Park PJ, et al. Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Reports. PMID 26947078 DOI: 10.1016/J.Celrep.2016.02.024 |
0.346 |
|
| 2016 |
Lee JK, Choi YL, Kwon M, Park PJ. Mechanisms and Consequences of Cancer Genome Instability: Lessons from Genome Sequencing Studies. Annual Review of Pathology. PMID 26907526 DOI: 10.1146/Annurev-Pathol-012615-044446 |
0.37 |
|
| 2016 |
Evrony GD, Lee E, Park PJ, Walsh CA. Resolving rates of mutation in the brain using single-neuron genomics. Elife. 5. PMID 26901440 DOI: 10.7554/Elife.12966 |
0.317 |
|
| 2016 |
Davoli T, Uno H, Xu A, Mengwasser K, Sack L, Park PJ, Elledge SJ. Abstract SY10-01: How aneuploidy drives cancer Cancer Research. 76. DOI: 10.1158/1538-7445.Am2016-Sy10-01 |
0.349 |
|
| 2015 |
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, ... ... Park PJ, et al. The histone chaperone CAF-1 safeguards somatic cell identity. Nature. 528: 218-224. PMID 26659182 DOI: 10.1038/Nature15749 |
0.337 |
|
| 2015 |
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. Proceedings of the National Academy of Sciences of the United States of America. PMID 26575630 DOI: 10.1073/Pnas.1518008112 |
0.355 |
|
| 2015 |
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. Nature Biotechnology. PMID 26501951 DOI: 10.1038/Nbt.3388 |
0.305 |
|
| 2015 |
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. Nature Genetics. PMID 26437032 DOI: 10.1038/Ng.3414 |
0.369 |
|
| 2015 |
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. 16: 278. PMID 26335049 DOI: 10.1186/S12859-015-0704-Z |
0.302 |
|
| 2015 |
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. Briefings in Bioinformatics. PMID 26210357 DOI: 10.1093/Bib/Bbv055 |
0.35 |
|
| 2015 |
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 & Development. 29: 1136-50. PMID 26063573 DOI: 10.1101/Gad.260562.115 |
0.329 |
|
| 2015 |
Sohn KA, Ho JW, Djordjevic D, Jeong HH, Park PJ, Kim JH. hiHMM: Bayesian non-parametric joint inference of chromatin state maps. Bioinformatics (Oxford, England). 31: 2066-74. PMID 25725496 DOI: 10.1093/Bioinformatics/Btv117 |
0.338 |
|
| 2015 |
Park RW, Kim TM, Kasif S, Park PJ. Identification of rare germline copy number variations over-represented in five human cancer types. Molecular Cancer. 14: 25. PMID 25644941 DOI: 10.1186/S12943-015-0292-6 |
0.333 |
|
| 2015 |
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. Journal of the American Society of Nephrology : Jasn. PMID 25636411 DOI: 10.1681/Asn.2014090940 |
0.367 |
|
| 2015 |
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, et al. Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation. Human Molecular Genetics. 24: 2442-57. PMID 25574027 DOI: 10.1093/Hmg/Ddv006 |
0.35 |
|
| 2014 |
Kim TM, Park PJ. A genome-wide view of microsatellite instability: old stories of cancer mutations revisited with new sequencing technologies. Cancer Research. 74: 6377-82. PMID 25371413 DOI: 10.1158/0008-5472.Can-14-1225 |
0.382 |
|
| 2014 |
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, ... Park PJ, et al. Characterization of HPV and host genome interactions in primary head and neck cancers. Proceedings of the National Academy of Sciences of the United States of America. 111: 15544-9. PMID 25313082 DOI: 10.1073/Pnas.1416074111 |
0.314 |
|
| 2014 |
Streit M, Lex A, Gratzl S, Partl C, Schmalstieg D, Pfister H, Park PJ, Gehlenborg N. Guided visual exploration of genomic stratifications in cancer. Nature Methods. 11: 884-5. PMID 25166867 DOI: 10.1038/Nmeth.3088 |
0.346 |
|
| 2014 |
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, ... Park PJ, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/Nature13415 |
0.368 |
|
| 2014 |
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, ... ... Park PJ, et al. Comparative analysis of the transcriptome across distant species. Nature. 512: 445-8. PMID 25164755 DOI: 10.1038/Nature13424 |
0.341 |
|
| 2014 |
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. Nature Communications. 5: 4719. PMID 25158628 DOI: 10.1038/Ncomms5719 |
0.326 |
|
| 2014 |
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, ... Park PJ, et al. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 26: 319-30. PMID 25155756 DOI: 10.1016/J.Ccr.2014.07.014 |
0.375 |
|
| 2014 |
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 Research. 42: e74. PMID 24598259 DOI: 10.1093/Nar/Gku178 |
0.329 |
|
| 2014 |
Ferrari F, Alekseyenko AA, Park PJ, Kuroda MI. Transcriptional control of a whole chromosome: emerging models for dosage compensation. Nature Structural & Molecular Biology. 21: 118-25. PMID 24500429 DOI: 10.1038/Nsmb.2763 |
0.32 |
|
| 2014 |
Marinov GK, Kundaje A, Park PJ, Wold BJ. Large-scale quality analysis of published ChIP-seq data. G3 (Bethesda, Md.). 4: 209-23. PMID 24347632 DOI: 10.1534/G3.113.008680 |
0.308 |
|
| 2014 |
Ferrari F, Apostolou E, Park PJ, Hochedlinger K. Rearranging the chromatin for pluripotency. Cell Cycle (Georgetown, Tex.). 13: 167-8. PMID 24241209 DOI: 10.4161/Cc.27028 |
0.389 |
|
| 2014 |
Davoli T, Xu W, Park P, Elledge SJ. Abstract SY36-03: How aneuploidy drives tumorigenesis Cancer Research. 74. DOI: 10.1158/1538-7445.Am2014-Sy36-03 |
0.357 |
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| 2014 |
Davoli T, Xu AW, Mengwasser KE, Sack LM, Yoon JC, Park PJ, Elledge SJ. Abstract 2404: Cumulative dosage effect of TSGs and OGs drives aneuploidy patterns in cancer Cancer Research. 74: 2404-2404. DOI: 10.1158/1538-7445.Am2014-2404 |
0.344 |
|
| 2014 |
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. Erratum: Diverse mechanisms of somatic structural variations in human cancer genomes (Cell (2013) 153 (919-929)) Cell. 157. DOI: 10.1016/J.Cell.2014.05.020 |
0.339 |
|
| 2013 |
Kim TM, Laird PW, Park PJ. The landscape of microsatellite instability in colorectal and endometrial cancer genomes. Cell. 155: 858-68. PMID 24209623 DOI: 10.1016/J.Cell.2013.10.015 |
0.394 |
|
| 2013 |
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 Reports. 5: 629-36. PMID 24183666 DOI: 10.1016/J.Celrep.2013.09.037 |
0.332 |
|
| 2013 |
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. 155: 948-62. PMID 24183448 DOI: 10.1016/J.Cell.2013.10.011 |
0.37 |
|
| 2013 |
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. Molecular and Cellular Biology. 33: 4779-92. PMID 24100010 DOI: 10.1128/Mcb.01068-13 |
0.333 |
|
| 2013 |
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. Proceedings of the National Academy of Sciences of the United States of America. 110: 15764-9. PMID 24014587 DOI: 10.1073/Pnas.1305904110 |
0.372 |
|
| 2013 |
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 & Development. 27: 1551-6. PMID 23873939 DOI: 10.1101/Gad.214585.113 |
0.333 |
|
| 2013 |
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 (New York, N.Y.). 15: 749-60. PMID 23814487 DOI: 10.1593/Neo.121956 |
0.328 |
|
| 2013 |
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. Molecular and Cellular Biology. 33: 3274-85. PMID 23775117 DOI: 10.1128/Mcb.00275-13 |
0.32 |
|
| 2013 |
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. Proceedings of the National Academy of Sciences of the United States of America. 110: 10165-70. PMID 23723349 DOI: 10.1073/Pnas.1302209110 |
0.334 |
|
| 2013 |
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. 12: 699-712. PMID 23665121 DOI: 10.1016/J.Stem.2013.04.013 |
0.361 |
|
| 2013 |
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. 153: 919-29. PMID 23663786 DOI: 10.1016/J.Cell.2013.04.010 |
0.381 |
|
| 2013 |
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 & Development. 27: 853-8. PMID 23630075 DOI: 10.1101/Gad.215426.113 |
0.323 |
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| 2013 |
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 Research. 23: 917-27. PMID 23547170 DOI: 10.1101/Gr.149674.112 |
0.333 |
|
| 2013 |
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. The Journal of Clinical Investigation. 123: 727-39. PMID 23321669 DOI: 10.1172/Jci64535 |
0.384 |
|
| 2013 |
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 Research. 23: 217-27. PMID 23132910 DOI: 10.1101/Gr.140301.112 |
0.396 |
|
| 2013 |
Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE. Identification of regions in the HOX cluster that can confer repression in a Polycomb-dependent manner Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P86 |
0.303 |
|
| 2013 |
Majumdar S, Gong E, Vizio DD, Dreyfuss J, DeGraff D, Hager M, Park P, Bellmunt J, Matusik R, Rosenberg J, Adam R. Abstract 4066: Loss of Sh3gl2/endophilin A1 is an early event in urothelial carcinoma that regulates malignant behavior. Cancer Research. 73: 4066-4066. DOI: 10.1158/1538-7445.Am2013-4066 |
0.366 |
|
| 2012 |
Lex A, Streit M, Schulz HJ, Partl C, Schmalstieg D, Park PJ, Gehlenborg N. StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization. Computer Graphics Forum : Journal of the European Association For Computer Graphics. 31: 1175-1184. PMID 27942089 DOI: 10.1111/J.1467-8659.2012.03110.X |
0.346 |
|
| 2012 |
Xi R, Lee S, Park PJ. A survey of copy-number variation detection tools based on high-throughput sequencing data. Current Protocols in Human Genetics / Editorial Board, Jonathan L. Haines ... [Et Al.]. Unit7.19. PMID 23074071 DOI: 10.1002/0471142905.Hg0719S75 |
0.33 |
|
| 2012 |
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, et al. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. Plos Genetics. 8: e1002954. PMID 23028361 DOI: 10.1371/Journal.Pgen.1002954 |
0.378 |
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| 2012 |
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, ... Park PJ, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/Gr.136184.111 |
0.321 |
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| 2012 |
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 Genetics. 8: e1002830. PMID 22844249 DOI: 10.1371/Journal.Pgen.1002830 |
0.35 |
|
| 2012 |
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. Molecular Cell. 47: 596-607. PMID 22795134 DOI: 10.1016/J.Molcel.2012.06.011 |
0.348 |
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| 2012 |
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, ... Park PJ, et al. Nature and function of insulator protein binding sites in the Drosophila genome. Genome Research. 22: 2188-98. PMID 22767387 DOI: 10.1101/Gr.138156.112 |
0.351 |
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| 2012 |
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, et al. Landscape of somatic retrotransposition in human cancers. Science (New York, N.Y.). 337: 967-71. PMID 22745252 DOI: 10.1126/Science.1222077 |
0.389 |
|
| 2012 |
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, ... Park PJ, et al. Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. Plos Genetics. 8: e1002646. PMID 22570616 DOI: 10.1371/Journal.Pgen.1002646 |
0.356 |
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| 2012 |
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 (New York, N.Y.). 14: 20-8. PMID 22355270 DOI: 10.1593/Neo.111574 |
0.309 |
|
| 2012 |
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. Investigative Ophthalmology & Visual Science. 53: 1617-27. PMID 22323457 DOI: 10.1167/Iovs.11-8839 |
0.347 |
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| 2012 |
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. Science Signaling. 5: ra4. PMID 22234613 DOI: 10.1126/Scisignal.2002414 |
0.31 |
|
| 2012 |
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, et al. Analysis of somatic retrotransposition in human cancers Bmc Proceedings. 6. DOI: 10.1186/1753-6561-6-S6-O23 |
0.338 |
|
| 2012 |
Park PJ, Chase I, Bell MA. Phenotypic plasticity of the threespine stickleback Gasterosteus aculeatus telencephalon in response to experience in captivity Current Zoology. 58: 189-210. DOI: 10.1093/Czoolo/58.1.189 |
0.459 |
|
| 2011 |
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. Proceedings of the National Academy of Sciences of the United States of America. 108: E1128-36. PMID 22065754 DOI: 10.1073/Pnas.1110574108 |
0.356 |
|
| 2011 |
Tolstorukov MY, Volfovsky N, Stephens RM, Park PJ. Impact of chromatin structure on sequence variability in the human genome. Nature Structural & Molecular Biology. 18: 510-5. PMID 21399641 DOI: 10.1038/Nsmb.2012 |
0.344 |
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| 2011 |
Kim TM, Huang W, Park R, Park PJ, Johnson MD. A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs. Cancer Research. 71: 3387-99. PMID 21385897 DOI: 10.1158/0008-5472.Can-10-4117 |
0.324 |
|
| 2011 |
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. 471: 115-8. PMID 21368835 DOI: 10.1038/Nature09757 |
0.355 |
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| 2011 |
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. 12: 134. PMID 21356108 DOI: 10.1186/1471-2164-12-134 |
0.343 |
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| 2011 |
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, ... Park PJ, et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 471: 480-5. PMID 21179089 DOI: 10.1038/Nature09725 |
0.393 |
|
| 2011 |
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, et al. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Research. 21: 147-63. PMID 21177972 DOI: 10.1101/Gr.110098.110 |
0.378 |
|
| 2011 |
Kim TM, Park PJ. Advances in analysis of transcriptional regulatory networks. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 3: 21-35. PMID 21069662 DOI: 10.1002/Wsbm.105 |
0.331 |
|
| 2010 |
Tolstorukov MY, Kharchenko PV, Park PJ. Analysis of primary structure of chromatin with next-generation sequencing. Epigenomics. 2: 187-197. PMID 22022339 DOI: 10.2217/Epi.09.48 |
0.347 |
|
| 2010 |
Xi R, Kim TM, Park PJ. Detecting structural variations in the human genome using next generation sequencing. Briefings in Functional Genomics. 9: 405-15. PMID 21216738 DOI: 10.1093/Bfgp/Elq025 |
0.324 |
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| 2010 |
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, ... Park PJ, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374 |
0.382 |
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| 2010 |
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, et al. Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway. Nature Medicine. 16: 1429-33. PMID 21076395 DOI: 10.1038/Nm.2251 |
0.318 |
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| 2010 |
Kim TM, Luquette LJ, Xi R, Park PJ. rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. Bmc Bioinformatics. 11: 432. PMID 20718989 DOI: 10.1186/1471-2105-11-432 |
0.368 |
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| 2010 |
Day DS, Luquette LJ, Park PJ, Kharchenko PV. Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biology. 11: R69. PMID 20584328 DOI: 10.1186/Gb-2010-11-6-R69 |
0.314 |
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| 2010 |
Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJ. CpG islands recruit a histone H3 lysine 36 demethylase. Molecular Cell. 38: 179-90. PMID 20417597 DOI: 10.1016/J.Molcel.2010.04.009 |
0.304 |
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| 2010 |
Park PJ, Bell MA. Variation of telencephalon morphology of the threespine stickleback (Gasterosteus aculeatus) in relation to inferred ecology. Journal of Evolutionary Biology. 23: 1261-77. PMID 20406344 DOI: 10.1111/J.1420-9101.2010.01987.X |
0.458 |
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| 2010 |
Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE. A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell. 140: 99-110. PMID 20085705 DOI: 10.1016/J.Cell.2009.12.022 |
0.315 |
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| 2010 |
Xi R, Luquette J, Hadjipanayis A, Kim T, Park PJ. BIC-seq: a fast algorithm for detection of copy number alterations based on high-throughput sequencing data Genome Biology. 11: 1-1. DOI: 10.1186/Gb-2010-11-S1-O10 |
0.365 |
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| 2010 |
Gorchakov AA, Alekseyenko AA, Kharchenko PV, Park PJ, Kuroda MI. Dosage compensation in drosophila: Sequence-specific initiation and sequence-independent spreading of MSL complex to the active genes on the male X chromosome Russian Journal of Genetics. 46: 1263-1266. DOI: 10.1134/S1022795410100303 |
0.354 |
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| 2009 |
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 & Development. 23: 2266-71. PMID 19797766 DOI: 10.1101/Gad.1840409 |
0.345 |
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| 2009 |
Park PJ. ChIP-Seq: advantages and challenges of a maturing technology Nature Reviews Genetics. 10: 669-680. PMID 19736561 DOI: 10.1038/Nrg2641 |
0.348 |
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| 2009 |
Dreyfuss JM, Johnson MD, Park PJ. Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers. Molecular Cancer. 8: 71. PMID 19732454 DOI: 10.1186/1476-4598-8-71 |
0.314 |
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| 2009 |
Gelbart ME, Larschan E, Peng S, Park PJ, Kuroda MI. Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation. Nature Structural & Molecular Biology. 16: 825-32. PMID 19648925 DOI: 10.1038/Nsmb.1644 |
0.311 |
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| 2009 |
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. 48: 865-85. PMID 19603527 DOI: 10.1002/Gcc.20692 |
0.331 |
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| 2009 |
Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ. Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Research. 19: 967-77. PMID 19246569 DOI: 10.1101/Gr.084830.108 |
0.322 |
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| 2009 |
Bell MA, Stewart JD, Park PJ. The world's oldest fossil threespine stickleback fish Copeia. 256-265. DOI: 10.1643/Cg-08-059 |
0.454 |
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| 2009 |
Nomakuchi S, Park PJ, Bell MA. Correlation between exploration activity and use of social information in three-spined sticklebacks Behavioral Ecology. 20: 340-345. DOI: 10.1093/Beheco/Arp001 |
0.456 |
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| 2008 |
Park PJ. Epigenetics meets next-generation sequencing Epigenetics. 3: 318-321. PMID 19098449 DOI: 10.4161/Epi.3.6.7249 |
0.338 |
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| 2008 |
Park PJ. Experimental design and data analysis for array comparative genomic hybridization. Cancer Investigation. 26: 923-928. PMID 19034774 DOI: 10.1080/07357900801993432 |
0.352 |
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| 2008 |
Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nature Biotechnology. 26: 1351-9. PMID 19029915 DOI: 10.1038/Nbt.1508 |
0.32 |
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| 2008 |
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. Nature Structural & Molecular Biology. 15: 1318-25. PMID 19029895 DOI: 10.1038/Nsmb.1520 |
0.319 |
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| 2008 |
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. 134: 599-609. PMID 18724933 DOI: 10.1016/J.Cell.2008.06.033 |
0.349 |
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| 2008 |
Kharchenko PV, Woo CJ, Tolstorukov MY, Kingston RE, Park PJ. Nucleosome positioning in human HOX gene clusters. Genome Research. 18: 1554-61. PMID 18723689 DOI: 10.1101/Gr.075952.107 |
0.37 |
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| 2008 |
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. Developmental Cell. 14: 798-809. PMID 18477461 DOI: 10.1016/J.Devcel.2008.04.002 |
0.346 |
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| 2008 |
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. Nature Genetics. 40: 794-9. PMID 18454149 DOI: 10.1038/Ng.126 |
0.319 |
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| 2008 |
Lee H, Kong SW, Park PJ. Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes. Bioinformatics (Oxford, England). 24: 889-96. PMID 18263644 DOI: 10.1093/Bioinformatics/Btn034 |
0.379 |
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| 2008 |
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. 111: 3200-3210. PMID 18184868 DOI: 10.1182/Blood-2007-10-119099 |
0.338 |
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| 2008 |
Claus EB, Park PJ, Carroll R, Chan J, Black PM. Specific genes expressed in association with progesterone receptors in meningioma. Cancer Research. 68: 314-22. PMID 18172325 DOI: 10.1158/0008-5472.Can-07-1796 |
0.309 |
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| 2007 |
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. Molecular Cell. 28: 121-33. PMID 17936709 DOI: 10.1016/J.Molcel.2007.08.011 |
0.342 |
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| 2007 |
Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ. Normalization and experimental design for ChIP-chip data. Bmc Bioinformatics. 8: 219. PMID 17592629 DOI: 10.1186/1471-2105-8-219 |
0.31 |
|
| 2007 |
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. Cytogenetic and Genome Research. 116: 1-11. PMID 17268171 DOI: 10.1159/000097411 |
0.334 |
|
| 2006 |
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 Harbor Symposia On Quantitative Biology. 71: 385-94. PMID 17381321 DOI: 10.1101/Sqb.2006.71.026 |
0.333 |
|
| 2006 |
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, et al. A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma. Cancer Research. 66: 10815-23. PMID 17090523 DOI: 10.1158/0008-5472.Can-06-1408 |
0.392 |
|
| 2006 |
Kong SW, Pu WT, Park PJ. A multivariate approach for integrating genome-wide expression data and biological knowledge Bioinformatics. 22: 2373-2380. PMID 16877751 DOI: 10.1093/Bioinformatics/Btl401 |
0.33 |
|
| 2006 |
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, ... ... Park P, et al. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nature Biotechnology. 24: 832-40. PMID 16823376 DOI: 10.1038/Nbt1217 |
0.326 |
|
| 2006 |
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. The Journal of Surgical Research. 135: 282-90. PMID 16603191 DOI: 10.1016/J.Jss.2006.01.023 |
0.304 |
|
| 2006 |
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 & Development. 20: 848-57. PMID 16547173 DOI: 10.1101/Gad.1400206 |
0.374 |
|
| 2005 |
Hamada FN, Park PJ, Gordadze PR, Kuroda MI. Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster. Genes & Development. 19: 2289-94. PMID 16204180 DOI: 10.1101/Gad.1343705 |
0.316 |
|
| 2005 |
Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies Proceedings of the National Academy of Sciences of the United States of America. 102: 13544-13549. PMID 16174746 DOI: 10.1073/Pnas.0506577102 |
0.33 |
|
| 2005 |
Lai WR, Johnson MD, Kucherlapati R, Park PJ. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics (Oxford, England). 21: 3763-70. PMID 16081473 DOI: 10.1093/Bioinformatics/Bti611 |
0.333 |
|
| 2004 |
Hwang KB, Kong SW, Greenberg SA, Park PJ. Combining gene expression data from different generations of oligonucleotide arrays Bmc Bioinformatics. 5: 159-159. PMID 15504239 DOI: 10.1186/1471-2105-5-159 |
0.365 |
|
| 2004 |
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. Journal of Biotechnology. 112: 225-45. PMID 15313001 DOI: 10.1016/J.Jbiotec.2004.05.006 |
0.318 |
|
| 2003 |
Kuo WP, Whipple ME, Jenssen TK, Todd R, Epstein JB, Ohno-Machado L, Sonis ST, Park PJ. Microarrays and clinical dentistry Journal of the American Dental Association. 134: 456-462. PMID 12733779 DOI: 10.14219/Jada.Archive.2003.0195 |
0.356 |
|
| 2002 |
Park PJ, Butte AJ, Kohane IS. Comparing expression profiles of genes with similar promoter regions. Bioinformatics (Oxford, England). 18: 1576-84. PMID 12490441 DOI: 10.1093/Bioinformatics/18.12.1576 |
0.32 |
|
| 2002 |
Kuruvilla FG, Park PJ, Schreiber SL. Vector algebra in the analysis of genome-wide expression data. Genome Biology. 3: RESEARCH0011. PMID 11897023 DOI: 10.1186/Gb-2002-3-3-Research0011 |
0.333 |
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