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Items: 1 to 20 of 104

1.

Robust unmixing of tumor states in array comparative genomic hybridization data.

Tolliver D, Tsourakakis C, Subramanian A, Shackney S, Schwartz R.

Bioinformatics. 2010 Jun 15;26(12):i106-14. doi: 10.1093/bioinformatics/btq213.

2.

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.

3.

Inference of tumor phylogenies from genomic assays on heterogeneous samples.

Subramanian A, Shackney S, Schwartz R.

J Biomed Biotechnol. 2012;2012:797812. doi: 10.1155/2012/797812. Epub 2012 May 13.

4.

Smoothing waves in array CGH tumor profiles.

van de Wiel MA, Brosens R, Eilers PH, Kumps C, Meijer GA, Menten B, Sistermans E, Speleman F, Timmerman ME, Ylstra B.

Bioinformatics. 2009 May 1;25(9):1099-104. doi: 10.1093/bioinformatics/btp132. Epub 2009 Mar 10.

PMID:
19276148
5.

A simplicial complex-based approach to unmixing tumor progression data.

Roman T, Nayyeri A, Fasy BT, Schwartz R.

BMC Bioinformatics. 2015 Aug 12;16:254. doi: 10.1186/s12859-015-0694-x.

6.

Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.

Barutcuoglu Z, Airoldi EM, Dumeaux V, Schapire RE, Troyanskaya OG.

Bioinformatics. 2009 May 15;25(10):1307-13. doi: 10.1093/bioinformatics/btn585. Epub 2008 Dec 3.

7.

Challenges in array comparative genomic hybridization for the analysis of cancer samples.

Nowak NJ, Miecznikowski J, Moore SR, Gaile D, Bobadilla D, Smith DD, Kernstine K, Forman SJ, Mhawech-Fauceglia P, Reid M, Stoler D, Loree T, Rigual N, Sullivan M, Weiss LM, Hicks D, Slovak ML.

Genet Med. 2007 Sep;9(9):585-95.

PMID:
17873646
8.

Estimation of tumor heterogeneity using CGH array data.

Wang K, Li J, Li S, Bolund L, Wiuf C.

BMC Bioinformatics. 2009 Jan 9;10:12. doi: 10.1186/1471-2105-10-12.

9.

Medoidshift clustering applied to genomic bulk tumor data.

Roman T, Xie L, Schwartz R.

BMC Genomics. 2016 Jan 11;17 Suppl 1:6. doi: 10.1186/s12864-015-2302-x.

10.

Waved aCGH: to smooth or not to smooth.

LeprĂȘtre F, Villenet C, Quief S, Nibourel O, Jacquemin C, Troussard X, Jardin F, Gibson F, Kerckaert JP, Roumier C, Figeac M.

Nucleic Acids Res. 2010 Apr;38(7):e94. doi: 10.1093/nar/gkp1215. Epub 2010 Jan 13.

11.

Stationary wavelet packet transform and dependent laplacian bivariate shrinkage estimator for array-CGH data smoothing.

Nguyen N, Huang H, Oraintara S, Vo A.

J Comput Biol. 2010 Feb;17(2):139-52. doi: 10.1089/cmb.2009.0013.

PMID:
20078226
12.

Accurate detection of aneuploidies in array CGH and gene expression microarray data.

Myers CL, Dunham MJ, Kung SY, Troyanskaya OG.

Bioinformatics. 2004 Dec 12;20(18):3533-43. Epub 2004 Jul 29.

PMID:
15284100
13.

CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations.

van Houte BP, Binsl TW, Hettling H, Pirovano W, Heringa J.

BMC Genomics. 2009 Aug 26;10:401. doi: 10.1186/1471-2164-10-401.

14.

A very fast and accurate method for calling aberrations in array-CGH data.

Benelli M, Marseglia G, Nannetti G, Paravidino R, Zara F, Bricarelli FD, Torricelli F, Magi A.

Biostatistics. 2010 Jul;11(3):515-8. doi: 10.1093/biostatistics/kxq008. Epub 2010 Mar 5.

PMID:
20207682
15.

Robust smooth segmentation approach for array CGH data analysis.

Huang J, Gusnanto A, O'Sullivan K, Staaf J, Borg A, Pawitan Y.

Bioinformatics. 2007 Sep 15;23(18):2463-9. Epub 2007 Jul 27.

PMID:
17660206
16.

LSAMP, a novel candidate tumor suppressor gene in human osteosarcomas, identified by array comparative genomic hybridization.

Kresse SH, Ohnstad HO, Paulsen EB, Bjerkehagen B, Szuhai K, Serra M, Schaefer KL, Myklebost O, Meza-Zepeda LA.

Genes Chromosomes Cancer. 2009 Aug;48(8):679-93. doi: 10.1002/gcc.20675.

PMID:
19441093
17.

A Systems Biology Interpretation of Array Comparative Genomic Hybridization (aCGH) Data through Phylogenetics.

Abunimer AN, Salazar J, Noursi DP, Abu-Asab MS.

OMICS. 2016 Mar;20(3):169-79. doi: 10.1089/omi.2015.0184.

18.

Algorithms for calling gains and losses in array CGH data.

Wang P.

Methods Mol Biol. 2009;556:99-116. doi: 10.1007/978-1-60327-192-9_8.

PMID:
19488874
19.

Comparative genomic hybridization by representational oligonucleotide microarray analysis.

Lucito R, Byrnes J.

Methods Mol Biol. 2009;556:33-46. doi: 10.1007/978-1-60327-192-9_4.

PMID:
19488870
20.

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

Auer H, Newsom DL, Nowak NJ, McHugh KM, Singh S, Yu CY, Yang Y, Wenger GD, Gastier-Foster JM, Kornacker K.

BMC Genomics. 2007 Apr 30;8:111.

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