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References for PMC Articles for PubMed (Select 20529894)


Applying unmixing to gene expression data for tumor phylogeny inference.

Schwartz R, Shackney SE.

BMC Bioinformatics. 2010 Jan 20;11:42. doi: 10.1186/1471-2105-11-42.


Inferring tumor progression from genomic heterogeneity.

Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S, Zetterberg A, Hicks J, Wigler M.

Genome Res. 2010 Jan;20(1):68-80. doi: 10.1101/gr.099622.109. Epub 2009 Nov 10.


Quantifying cancer progression with conjunctive Bayesian networks.

Gerstung M, Baudis M, Moch H, Beerenwinkel N.

Bioinformatics. 2009 Nov 1;25(21):2809-15. doi: 10.1093/bioinformatics/btp505. Epub 2009 Aug 19.


HER2 status and benefit from adjuvant trastuzumab in breast cancer.

Paik S, Kim C, Wolmark N.

N Engl J Med. 2008 Mar 27;358(13):1409-11. doi: 10.1056/NEJMc0801440. No abstract available.


A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

Lamy P, Andersen CL, Dyrskjot L, Torring N, Wiuf C.

BMC Bioinformatics. 2007 Nov 9;8:434.


Reconstructing tumor phylogenies from heterogeneous single-cell data.

Pennington G, Smith CA, Shackney S, Schwartz R.

J Bioinform Comput Biol. 2007 Apr;5(2a):407-27.


Why is cancer drug discovery so difficult?

Kamb A, Wee S, Lengauer C.

Nat Rev Drug Discov. 2007 Feb;6(2):115-20. Epub 2006 Dec 8.


Linking oncogenic pathways with therapeutic opportunities.

Bild AH, Potti A, Nevins JR.

Nat Rev Cancer. 2006 Sep;6(9):735-41. Epub 2006 Aug 17. Review.


Distance-based clustering of CGH data.

Liu J, Mohammed J, Carter J, Ranka S, Kahveci T, Baudis M.

Bioinformatics. 2006 Aug 15;22(16):1971-8. Epub 2006 May 16.


Analyzing patterns of staining in immunohistochemical studies: application to a study of prostate cancer recurrence.

Etzioni R, Hawley S, Billheimer D, True LD, Knudsen B.

Cancer Epidemiol Biomarkers Prev. 2005 May;14(5):1040-6.


Mtreemix: a software package for learning and using mixture models of mutagenetic trees.

Beerenwinkel N, Rahnenführer J, Kaiser R, Hoffmann D, Selbig J, Lengauer T.

Bioinformatics. 2005 May 1;21(9):2106-7. Epub 2005 Jan 18.


Circular binary segmentation for the analysis of array-based DNA copy number data.

Olshen AB, Venkatraman ES, Lucito R, Wigler M.

Biostatistics. 2004 Oct;5(4):557-72.


Intracellular patterns of Her-2/neu, ras, and ploidy abnormalities in primary human breast cancers predict postoperative clinical disease-free survival.

Shackney SE, Smith CA, Pollice A, Brown K, Day R, Julian T, Silverman JF.

Clin Cancer Res. 2004 May 1;10(9):3042-52.


Breast cancer classification and prognosis based on gene expression profiles from a population-based study.

Sotiriou C, Neo SY, McShane LM, Korn EL, Long PM, Jazaeri A, Martiat P, Fox SB, Harris AL, Liu ET.

Proc Natl Acad Sci U S A. 2003 Sep 2;100(18):10393-8. Epub 2003 Aug 13.


Repeated observation of breast tumor subtypes in independent gene expression data sets.

Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou CM, Lønning PE, Brown PO, Børresen-Dale AL, Botstein D.

Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8418-23. Epub 2003 Jun 26.


Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications.

Sørlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Lønning PE, Børresen-Dale AL.

Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10869-74.


Multivariate analyses of genomic imbalances in solid tumors reveal distinct and converging pathways of karyotypic evolution.

Höglund M, Gisselsson D, Mandahl N, Johansson B, Mertens F, Mitelman F, Säll T.

Genes Chromosomes Cancer. 2001 Jun;31(2):156-71.


Molecular portraits of human breast tumours.

Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lønning PE, Børresen-Dale AL, Brown PO, Botstein D.

Nature. 2000 Aug 17;406(6797):747-52.


Learning the parts of objects by non-negative matrix factorization.

Lee DD, Seung HS.

Nature. 1999 Oct 21;401(6755):788-91.

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