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For: Lai WR, Johnson MD, Kucherlapati R, Park PJ. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 2005;21:3763-70. [PMID: 16081473 PMCID: PMC2819184 DOI: 10.1093/bioinformatics/bti611] [Citation(s) in RCA: 297] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
251
Alibés A, Morrissey ER, Cañada A, Rueda OM, Casado D, Yankilevich P, Díaz-Uriarte R. Asterias: a parallelized web-based suite for the analysis of expression and aCGH data. Cancer Inform 2007;3:1-9. [PMID: 19455230 PMCID: PMC2675829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
252
Hu J, Gao JB, Cao Y, Bottinger E, Zhang W. Exploiting noise in array CGH data to improve detection of DNA copy number change. Nucleic Acids Res 2007;35:e35. [PMID: 17272296 PMCID: PMC1994778 DOI: 10.1093/nar/gkl730] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
253
Oosting J, Lips EH, van Eijk R, Eilers PHC, Szuhai K, Wijmenga C, Morreau H, van Wezel T. High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays. Genome Res 2007;17:368-76. [PMID: 17267813 PMCID: PMC1800928 DOI: 10.1101/gr.5686107] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
254
Venkatraman ES, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 2007;23:657-63. [PMID: 17234643 DOI: 10.1093/bioinformatics/btl646] [Citation(s) in RCA: 681] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
255
Alibés A, Morrissey ER, Cañada A, Rueda OM, Casado D, Yankilevich P, Díaz-Uriarte R. Asterias: A Parallelized Web-based Suite for the Analysis of Expression and aCGH Data. Cancer Inform 2007. [DOI: 10.1177/117693510700300007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
256
Juric D, Bredel C, Sikic BI, Bredel M. Integrated high-resolution genome-wide analysis of gene dosage and gene expression in human brain tumors. Methods Mol Biol 2007;377:187-202. [PMID: 17634618 DOI: 10.1007/978-1-59745-390-5_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
257
Vauhkonen H, Vauhkonen M, Sajantila A, Sipponen P, Knuutila S. Characterizing genetically stable and unstable gastric cancers by microsatellites and array comparative genomic hybridization. ACTA ACUST UNITED AC 2006;170:133-9. [PMID: 17011984 DOI: 10.1016/j.cancergencyto.2006.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2005] [Revised: 05/24/2006] [Accepted: 06/01/2006] [Indexed: 01/02/2023]
258
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;66:10815-23. [PMID: 17090523 DOI: 10.1158/0008-5472.can-06-1408] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
259
Ribeiro FR, Henrique R, Hektoen M, Berg M, Jerónimo C, Teixeira MR, Lothe RA. Comparison of chromosomal and array-based comparative genomic hybridization for the detection of genomic imbalances in primary prostate carcinomas. Mol Cancer 2006;5:33. [PMID: 16952311 PMCID: PMC1570364 DOI: 10.1186/1476-4598-5-33] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Accepted: 09/04/2006] [Indexed: 12/31/2022]  Open
260
Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F, Haden K, Li J, Shaw CA, Belmont J, Cheung SW, Shen RM, Barker DL, Gunderson KL. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res 2006;16:1136-48. [PMID: 16899659 PMCID: PMC1557768 DOI: 10.1101/gr.5402306] [Citation(s) in RCA: 401] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
261
McGhee SA, McCabe ERB. Genome-wide testing: genomic medicine: commentary on the article by Bar-Shira et al. on page 353. Pediatr Res 2006;60:243-4. [PMID: 16923947 DOI: 10.1203/01.pdr.0000233116.85413.cd] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
262
Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ, Weber BL, Maris JM, Grant GR. STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genes Dev 2006;16:1149-58. [PMID: 16899652 PMCID: PMC1557772 DOI: 10.1101/gr.5076506] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
263
Pounds S, Cheng C. Robust estimation of the false discovery rate. Bioinformatics 2006;22:1979-87. [PMID: 16777905 DOI: 10.1093/bioinformatics/btl328] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
264
Le Caignec C, Spits C, Sermon K, De Rycke M, Thienpont B, Debrock S, Staessen C, Moreau Y, Fryns JP, Van Steirteghem A, Liebaers I, Vermeesch JR. Single-cell chromosomal imbalances detection by array CGH. Nucleic Acids Res 2006;34:e68. [PMID: 16698960 PMCID: PMC3303179 DOI: 10.1093/nar/gkl336] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
265
Han W, Han MR, Kang JJ, Bae JY, Lee JH, Bae YJ, Lee JE, Shin HJ, Hwang KT, Hwang SE, Kim SW, Noh DY. Genomic alterations identified by array comparative genomic hybridization as prognostic markers in tamoxifen-treated estrogen receptor-positive breast cancer. BMC Cancer 2006;6:92. [PMID: 16608533 PMCID: PMC1459182 DOI: 10.1186/1471-2407-6-92] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 04/12/2006] [Indexed: 01/08/2023]  Open
266
Marioni JC, Thorne NP, Tavaré S. BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data. Bioinformatics 2006;22:1144-6. [PMID: 16533818 DOI: 10.1093/bioinformatics/btl089] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
267
Huang J, Wei W, Chen J, Zhang J, Liu G, Di X, Mei R, Ishikawa S, Aburatani H, Jones KW, Shapero MH. CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays. BMC Bioinformatics 2006;7:83. [PMID: 16504045 PMCID: PMC1402331 DOI: 10.1186/1471-2105-7-83] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2005] [Accepted: 02/21/2006] [Indexed: 12/13/2022]  Open
268
van den IJssel P, Tijssen M, Chin SF, Eijk P, Carvalho B, Hopmans E, Holstege H, Bangarusamy DK, Jonkers J, Meijer GA, Caldas C, Ylstra B. Human and mouse oligonucleotide-based array CGH. Nucleic Acids Res 2005;33:e192. [PMID: 16361265 PMCID: PMC1316119 DOI: 10.1093/nar/gni191] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
269
Willenbrock H, Fridlyand J. A comparison study: applying segmentation to array CGH data for downstream analyses. ACTA ACUST UNITED AC 2005;21:4084-91. [PMID: 16159913 DOI: 10.1093/bioinformatics/bti677] [Citation(s) in RCA: 210] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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