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Items: 1 to 20 of 104

1.

Decoding the fine-scale structure of a breast cancer genome and transcriptome.

Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Murnane J, Brebner JH, Bajsarowicz K, Paris PL, Tao Q, Kowbel D, Lapuk A, Shagin DA, Shagina IA, Gray JW, Cheng JF, de Jong PJ, Pevzner P, Collins C.

Genome Res. 2006 Mar;16(3):394-404. Epub 2006 Feb 3.

2.

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome.

Hampton OA, Den Hollander P, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, Gibbs RA, Lee AV, Milosavljevic A.

Genome Res. 2009 Feb;19(2):167-77. doi: 10.1101/gr.080259.108. Epub 2008 Dec 3.

3.

End-sequence profiling: sequence-based analysis of aberrant genomes.

Volik S, Zhao S, Chin K, Brebner JH, Herndon DR, Tao Q, Kowbel D, Huang G, Lapuk A, Kuo WL, Magrane G, De Jong P, Gray JW, Collins C.

Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7696-701. Epub 2003 Jun 4.

4.

A sequence-based survey of the complex structural organization of tumor genomes.

Raphael BJ, Volik S, Yu P, Wu C, Huang G, Linardopoulou EV, Trask BJ, Waldman F, Costello J, Pienta KJ, Mills GB, Bajsarowicz K, Kobayashi Y, Sridharan S, Paris PL, Tao Q, Aerni SJ, Brown RP, Bashir A, Gray JW, Cheng JF, de Jong P, Nefedov M, Ried T, Padilla-Nash HM, Collins CC.

Genome Biol. 2008;9(3):R59. doi: 10.1186/gb-2008-9-3-r59. Epub 2008 Mar 25.

5.

Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution.

Bignell GR, Santarius T, Pole JC, Butler AP, Perry J, Pleasance E, Greenman C, Menzies A, Taylor S, Edkins S, Campbell P, Quail M, Plumb B, Matthews L, McLay K, Edwards PA, Rogers J, Wooster R, Futreal PA, Stratton MR.

Genome Res. 2007 Sep;17(9):1296-303. Epub 2007 Aug 3.

6.

Reconstructing tumor genome architectures.

Raphael BJ, Volik S, Collins C, Pevzner PA.

Bioinformatics. 2003 Oct;19 Suppl 2:ii162-71.

PMID:
14534186
7.

Semaphorin-plexin signalling genes associated with human breast tumourigenesis.

Gabrovska PN, Smith RA, Tiang T, Weinstein SR, Haupt LM, Griffiths LR.

Gene. 2011 Dec 10;489(2):63-9. doi: 10.1016/j.gene.2011.08.024. Epub 2011 Sep 2.

PMID:
21925246
8.

Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes.

Schulte I, Batty EM, Pole JC, Blood KA, Mo S, Cooke SL, Ng C, Howe KL, Chin SF, Brenton JD, Caldas C, Howarth KD, Edwards PA.

BMC Genomics. 2012 Dec 22;13:719. doi: 10.1186/1471-2164-13-719.

9.

Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array.

Jung SH, Shin SH, Yim SH, Choi HS, Lee SH, Chung YJ.

Exp Mol Med. 2009 Jul 31;41(7):462-70. doi: 10.3858/emm.2009.41.7.051.

10.

Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer.

Bashir A, Volik S, Collins C, Bafna V, Raphael BJ.

PLoS Comput Biol. 2008 Apr 25;4(4):e1000051. doi: 10.1371/journal.pcbi.1000051.

11.

Novel gene rearrangements in transformed breast cells identified by high-resolution breakpoint analysis of chromosomal aberrations.

Unger K, Wienberg J, Riches A, Hieber L, Walch A, Brown A, O'Brien PC, Briscoe C, Gray L, Rodriguez E, Jackl G, Knijnenburg J, Tallini G, Ferguson-Smith M, Zitzelsberger H.

Endocr Relat Cancer. 2010 Jan 29;17(1):87-98. doi: 10.1677/ERC-09-0065. Print 2010 Mar.

12.

Epigenetic mapping and functional analysis in a breast cancer metastasis model using whole-genome promoter tiling microarrays.

Rodenhiser DI, Andrews J, Kennette W, Sadikovic B, Mendlowitz A, Tuck AB, Chambers AF.

Breast Cancer Res. 2008;10(4):R62. doi: 10.1186/bcr2121. Epub 2008 Jul 18.

13.

Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer.

Kloth JN, Oosting J, van Wezel T, Szuhai K, Knijnenburg J, Gorter A, Kenter GG, Fleuren GJ, Jordanova ES.

BMC Genomics. 2007 Feb 20;8:53.

14.

Chromosome 8 BAC array comparative genomic hybridization and expression analysis identify amplification and overexpression of TRMT12 in breast cancer.

Rodriguez V, Chen Y, Elkahloun A, Dutra A, Pak E, Chandrasekharappa S.

Genes Chromosomes Cancer. 2007 Jul;46(7):694-707.

PMID:
17440925
15.

Combined cDNA array comparative genomic hybridization and serial analysis of gene expression analysis of breast tumor progression.

Yao J, Weremowicz S, Feng B, Gentleman RC, Marks JR, Gelman R, Brennan C, Polyak K.

Cancer Res. 2006 Apr 15;66(8):4065-78.

16.

Genetic profiling of chromosome 1 in breast cancer: mapping of regions of gains and losses and identification of candidate genes on 1q.

Orsetti B, Nugoli M, Cervera N, Lasorsa L, Chuchana P, Rougé C, Ursule L, Nguyen C, Bibeau F, Rodriguez C, Theillet C.

Br J Cancer. 2006 Nov 20;95(10):1439-47. Epub 2006 Oct 24.

17.

Reconstructing tumor amplisomes.

Raphael BJ, Pevzner PA.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i265-73.

PMID:
15262808
18.

nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing.

McPherson A, Wu C, Wyatt AW, Shah S, Collins C, Sahinalp SC.

Genome Res. 2012 Nov;22(11):2250-61. doi: 10.1101/gr.136572.111. Epub 2012 Jun 28.

19.

Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics.

Jönsson G, Staaf J, Vallon-Christersson J, Ringnér M, Holm K, Hegardt C, Gunnarsson H, Fagerholm R, Strand C, Agnarsson BA, Kilpivaara O, Luts L, Heikkilä P, Aittomäki K, Blomqvist C, Loman N, Malmström P, Olsson H, Johannsson OT, Arason A, Nevanlinna H, Barkardottir RB, Borg A.

Breast Cancer Res. 2010;12(3):R42. doi: 10.1186/bcr2596. Epub 2010 Jun 24.

20.

Comprehensive characterization of the DNA amplification at 13q34 in human breast cancer reveals TFDP1 and CUL4A as likely candidate target genes.

Melchor L, Saucedo-Cuevas LP, Muñoz-Repeto I, Rodríguez-Pinilla SM, Honrado E, Campoverde A, Palacios J, Nathanson KL, García MJ, Benítez J.

Breast Cancer Res. 2009;11(6):R86. doi: 10.1186/bcr2456. Epub 2009 Dec 8.

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