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For: Nilsson B, Johansson M, Al-Shahrour F, Carpenter AE, Ebert BL. Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. ACTA ACUST UNITED AC 2009;25:1078-9. [PMID: 19228802 DOI: 10.1093/bioinformatics/btp091] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
1
Ajore R, Niroula A, Pertesi M, Cafaro C, Thodberg M, Went M, Bao EL, Duran-Lozano L, Lopez de Lapuente Portilla A, Olafsdottir T, Ugidos-Damboriena N, Magnusson O, Samur M, Lareau CA, Halldorsson GH, Thorleifsson G, Norddahl GL, Gunnarsdottir K, Försti A, Goldschmidt H, Hemminki K, van Rhee F, Kimber S, Sperling AS, Kaiser M, Anderson K, Jonsdottir I, Munshi N, Rafnar T, Waage A, Weinhold N, Thorsteinsdottir U, Sankaran VG, Stefansson K, Houlston R, Nilsson B. Functional dissection of inherited non-coding variation influencing multiple myeloma risk. Nat Commun 2022;13:151. [PMID: 35013207 PMCID: PMC8748989 DOI: 10.1038/s41467-021-27666-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/02/2021] [Indexed: 12/16/2022]  Open
2
Girimurugan SB, Liu Y, Lung PY, Vera DL, Dennis JH, Bass HW, Zhang J. iSeg: an efficient algorithm for segmentation of genomic and epigenomic data. BMC Bioinformatics 2018;19:131. [PMID: 29642840 PMCID: PMC5896135 DOI: 10.1186/s12859-018-2140-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/26/2018] [Indexed: 11/16/2022]  Open
3
Ajore R, Raiser D, McConkey M, Jöud M, Boidol B, Mar B, Saksena G, Weinstock DM, Armstrong S, Ellis SR, Ebert BL, Nilsson B. Deletion of ribosomal protein genes is a common vulnerability in human cancer, especially in concert with TP53 mutations. EMBO Mol Med 2017;9:498-507. [PMID: 28264936 PMCID: PMC5376749 DOI: 10.15252/emmm.201606660] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
4
Hugerth LW, Larsson J, Alneberg J, Lindh MV, Legrand C, Pinhassi J, Andersson AF. Metagenome-assembled genomes uncover a global brackish microbiome. Genome Biol 2015;16:279. [PMID: 26667648 PMCID: PMC4699468 DOI: 10.1186/s13059-015-0834-7] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/12/2015] [Indexed: 02/03/2023]  Open
5
Anjum S, Morganella S, D'Angelo F, Iavarone A, Ceccarelli M. VEGAWES: variational segmentation on whole exome sequencing for copy number detection. BMC Bioinformatics 2015;16:315. [PMID: 26416038 PMCID: PMC4587906 DOI: 10.1186/s12859-015-0748-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/16/2015] [Indexed: 11/10/2022]  Open
6
Zhou X, Yang C, Wan X, Zhao H, Yu W. Multisample aCGH data analysis via total variation and spectral regularization. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013;10:230-235. [PMID: 23702561 PMCID: PMC3715577 DOI: 10.1109/tcbb.2012.166] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
7
Seifert M, Gohr A, Strickert M, Grosse I. Parsimonious higher-order hidden Markov models for improved array-CGH analysis with applications to Arabidopsis thaliana. PLoS Comput Biol 2012;8:e1002286. [PMID: 22253580 PMCID: PMC3257270 DOI: 10.1371/journal.pcbi.1002286] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 10/11/2011] [Indexed: 12/19/2022]  Open
8
Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting. PLoS One 2011;6:e20090. [PMID: 21750698 PMCID: PMC3130029 DOI: 10.1371/journal.pone.0020090] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 04/25/2011] [Indexed: 11/19/2022]  Open
9
Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol 2011;12:R41. [PMID: 21527027 PMCID: PMC3218867 DOI: 10.1186/gb-2011-12-4-r41] [Citation(s) in RCA: 2474] [Impact Index Per Article: 176.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 02/14/2011] [Accepted: 04/28/2011] [Indexed: 12/18/2022]  Open
10
Wang S, Wang Y, Xie Y, Xiao G. A novel approach to DNA copy number data segmentation. J Bioinform Comput Biol 2011;9:131-48. [PMID: 21328710 PMCID: PMC3084615 DOI: 10.1142/s0219720011005343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 11/02/2010] [Accepted: 11/04/2010] [Indexed: 11/18/2022]
11
Lamy P, Wiuf C, Ørntoft TF, Andersen CL. Rseg—an R package to optimize segmentation of SNP array data. Bioinformatics 2010;27:419-20. [DOI: 10.1093/bioinformatics/btq668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
12
Morganella S, Cerulo L, Viglietto G, Ceccarelli M. VEGA: variational segmentation for copy number detection. ACTA ACUST UNITED AC 2010;26:3020-7. [PMID: 20959380 DOI: 10.1093/bioinformatics/btq586] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
13
Ivakhno S, Tavaré S. CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data. ACTA ACUST UNITED AC 2010;26:1395-402. [PMID: 20403815 DOI: 10.1093/bioinformatics/btq145] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
14
SNP array analysis in hematologic malignancies: avoiding false discoveries. Blood 2010;115:4157-61. [PMID: 20304806 DOI: 10.1182/blood-2009-11-203182] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
15
Zhang Q, Ding L, Larson DE, Koboldt DC, McLellan MD, Chen K, Shi X, Kraja A, Mardis ER, Wilson RK, Borecki IB, Province MA. CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. ACTA ACUST UNITED AC 2009;26:464-9. [PMID: 20031968 DOI: 10.1093/bioinformatics/btp708] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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