Dabney Group Papers

Karpievitch YV, Polpitiya AD, Anderson GA, Smith RD, Dabney AR. (2009) Mass spectrometry-based proteomics: Biological and technological aspects. Submitted.

Karpievitch YV, Hill EG, Leclerc AP, Dabney AR, Almeida JS. (2009) An introspective comparison of Random Forest-based classifiers on the analysis of cluster-correlated data by way of RF++. PLoS ONE, 4(9):e7087.

Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, Smith RD, Dabney AR. (2009) Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition. Bioinformatics, 25:2573-2580. [DAnTE]

Karpievitch YV, Stanley J, Taverner T, Huang J, Adkins JN, Ansong C, Heffron F, Metz TO, Qian W-J, Yoon H, Smith RD, Dabney AR. (2009) A statistical framework for protein quantitation in bottom-up MS-based proteomics. Bioinformatics, 25:2028-2034. [DAnTE]

Petuyk VA, Jaitly N, Moore RJ, Ding J, Metz TO, Tang K, Monroe ME, Tolmachev AV, Adkins JN, Belov ME, Dabney AR, Qian W-J, Camp II DG, Smith RD. (2008) Elimination of systematic mass measurement errors in liquid chromatography - mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content. Analytical Chemistry, 80:693-706.

Dabney AR and Storey JD. (2007) Optimality-driven nearest centroid classification from genomic data. PLoS One, 2(10):e1002.

Dabney AR and Storey JD. (2007) Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships. Genome Biology, 8:R44. [Software] [Manual]

Dabney AR and Storey JD. (2007) A new approach to intensity-dependent normalization of two-channel microarrays. Biostatistics, 8:128-138. [Software] [Manual]

Dabney AR and Storey JD. (2006) A reanalysis of a published Affymetrix GeneChip control dataset. Genome Biology, 7:401.

Leek JT, Monsen EC, Dabney AR, and Storey JD. (2006) EDGE: Point-and-click software for the extraction and analysis of differential gene expression. Bioinformatics, 22:507-508. [Software]

Dabney AR. (2006) ClaNC: Point-and-click software for classifying microarrays to nearest centroids. Bioinformatics, 22:122-123. [Linux/Mac] [Windows] [Manual]

Dabney AR. (2005) Classification of microarrays to nearest centroids. Bioinformatics, 21:4148-4154. [Linux/Mac] [Windows] [Manual]

Dabney AR and Wakefield JC. (2005) Issues in the mapping of two diseases. Statistical Methods in Medical Research, 14:83-112.