Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies.

Nilsson B, Håkansson P, Johansson M, Nelander S, Fioretos T.

Genome Biol. 2007;8(5):R74.

PMID: 17488501 [PubMed - indexed for MEDLINE]

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Fast model-based protein homology detection without alignment.

Hochreiter S, Heusel M, Obermayer K.

Bioinformatics. 2007 Jul 15;23(14):1728-36. Epub 2007 May 8.

PMID: 17488755 [PubMed - indexed for MEDLINE]

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Genome Expression Pathway Analysis Tool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context.

Weniger M, Engelmann JC, Schultz J.

BMC Bioinformatics. 2007 Jun 2;8:179.

PMID: 17543125 [PubMed - indexed for MEDLINE]

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Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme.

Su LJ, Chang CW, Wu YC, Chen KC, Lin CJ, Liang SC, Lin CH, Whang-Peng J, Hsu SL, Chen CH, Huang CY.

BMC Genomics. 2007 Jun 1;8:140.

PMID: 17540040 [PubMed - indexed for MEDLINE]

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Integrated high-resolution genome-wide analysis of gene dosage and gene expression in human brain tumors.

Juric D, Bredel C, Sikic BI, Bredel M.

Methods Mol Biol. 2007;377:187-202. Review.

PMID: 17634618 [PubMed - indexed for MEDLINE]

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Improving gene set analysis of microarray data by SAM-GS.

Dinu I, Potter JD, Mueller T, Liu Q, Adewale AJ, Jhangri GS, Einecke G, Famulski KS, Halloran P, Yasui Y.

BMC Bioinformatics. 2007 Jul 5;8:242.

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Visualization-based cancer microarray data classification analysis.

Mramor M, Leban G, Demsar J, Zupan B.

Bioinformatics. 2007 Aug 15;23(16):2147-54. Epub 2007 Jun 22.

PMID: 17586552 [PubMed - indexed for MEDLINE]

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Microarray analysis of gliomas reveals chromosomal position-associated gene expression patterns and identifies potential immunotherapy targets.

Persson O, Krogh M, Saal LH, Englund E, Liu J, Parsons R, Mandahl N, Borg A, Widegren B, Salford LG.

J Neurooncol. 2007 Oct;85(1):11-24. Epub 2007 Jul 17.

PMID: 17634744 [PubMed - indexed for MEDLINE]

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Statistical methods in cardiac gene expression profiling: from image to function.

Kong SW.

Methods Mol Biol. 2007;366:75-105.

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STOP: searching for transcription factor motifs using gene expression.

Hertzberg L, Izraeli S, Domany E.

Bioinformatics. 2007 Jul 15;23(14):1737-43. Epub 2007 May 8.

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Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data.

Hulshizer R, Blalock EM.

BMC Bioinformatics. 2007 Jul 5;8:240.

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Improved classification accuracy in 1- and 2-dimensional NMR metabolomics data using the variance stabilising generalised logarithm transformation.

Parsons HM, Ludwig C, Günther UL, Viant MR.

BMC Bioinformatics. 2007 Jul 2;8:234.

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Transposable elements in human cancers by genome-wide EST alignment.

Kim DS, Huh JW, Kim HS.

Genes Genet Syst. 2007 Apr;82(2):145-56.

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Incorporation of gene ontology annotations to enhance microarray data analysis.

Ochs MF, Peterson AJ, Kossenkov A, Bidaut G.

Methods Mol Biol. 2007;377:243-54. Review.

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Molecular networks in microarray analysis.

Sivachenko AY, Yuryev A, Daraselia N, Mazo I.

J Bioinform Comput Biol. 2007 Apr;5(2B):429-56. Review.

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Exploiting sample variability to enhance multivariate analysis of microarray data.

Möller-Levet CS, West CM, Miller CJ.

Bioinformatics. 2007 Oct 15;23(20):2733-40. Epub 2007 Sep 7.

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Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.

Ferragina P, Giancarlo R, Greco V, Manzini G, Valiente G.

BMC Bioinformatics. 2007 Jul 13;8:252.

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A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data.

Thomas R, Paredes CJ, Mehrotra S, Hatzimanikatis V, Papoutsakis ET.

BMC Bioinformatics. 2007 Jun 29;8:228.

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Classification of heterogeneous microarray data by maximum entropy kernel.

Fujibuchi W, Kato T.

BMC Bioinformatics. 2007 Jul 26;8:267.

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Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.

Huttenhower C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA.

BMC Bioinformatics. 2007 Jul 12;8:250.

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