Microarrays

Binarization of Microarray Data Based on a Mixture Model

Zhou, X., Wang, X., and Dougherty, E. R., Molecular Cancer Therapeutics, Vol. 2, No. 7, 679-684, 2003

Identifying Genes Involved in Cyclic Processes by Combining Gene Expression Analysis and Prior Knowledge

Zhao, W., Serpedin, E., and Dougherty, E. R., EURASIP Journal of Bioinformatics and Systems Biology, Vol. 2009, Article ID 683463, 9 pages, doi:10.1155/2009/683463, 2009

Missing Value Estimation using Linear and Nonlinear Regression with Bayesian Gene Selection

Zhou, X., Wang, X., and Dougherty, E. R., Bioinformatics, Vol. 19, No. 17, 2302-2307, November, 2003

Noise Factor Analysis for cDNA Microarrays

Balagurunathan, Y., Wang, N., Dougherty, E. R., Nguyen, D. V., Chen, Y., Bittner, M. L., Trent, J. M., and Carroll, R. J., Biomedical Optics, Vol. 9, No. 4, 663-845, 2004

Normalization Benefits Microarray-Based Classification

Hua, J., Balagurunathan, Y. Chen, Y., Lowey, J., Bittner, M., Xiong, Z., Suh, E., and Dougherty, E. R., EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2006, 2006

Ratio Statistics of Gene Expression Levels and Applications to Microarray Data Analysis

Chen, Y., Kamat, V., Dougherty, E. R., Bittner, M. L., Meltzer, P. S., and Trent, J. M., Bioinformatics, Vol.18, No.9, 1207-1215, 2002

Ratio-Based Decisions and the Quantitative Analysis of cDNA Microarray Images

Chen, Y., Dougherty, E. R., and Bittner, M. L., Journal Of Biomedical Optics, Vol. 2, No. 4, 364–374, 1997

RNAi Microarray Analysis in Cultured Mammalian Cells

Mousses, S., Caplen, N. J., Cornelison, R., Weaver, D., Basik, M., Hautaniemi, S., Elkahloun, A. G., Lotufo, R. A., Choudary, A., Dougherty, E. R., Suh, E., and Kallioniemi, O., Genome Research, Vol. 13, 2341-2347, October, 2003

Simulation of cDNA Microarrays via a Parameterized Random Signal Model

Balagurunathan, Y., Dougherty, E. R., Chen, Y., Bittner, M. L., and Trent, J. M., Biomedical Optics, Vol. 7, No. 3, 507-523, 2002

SNiPer-HD: Improved Genotype Calling Accuracy by an Expectation-Maximization Algorithm for High-Density SNP Arrays

Hua, J., Craig, D. W., Brun, M., Webster, J., Zismann, V., Tembe, W., Joshipura, K., Huentelman, M. J., Dougherty, E. R., and Stephan, D. A., Bioinformatics, Vol. 23, 57-63, January, 2007

The Effect of Microarray Image Compression on Expression-Based Classification

Xu, Q., Hua, J., Xiong, Z., Bittner, M. L., and Dougherty, E. R., Signal, Image and Video Processing, doi: 10.1007/s11760-008-0059-2, May, 2008

Which is Better for cDNA-Microarray-Based Classification: Ratios or Direct Intensities

Attoor, S., Dougherty, E. R., Chen, Y., Bittner, M. L., and Trent, J. M., Bioinformatics, Vol. 20, No. 16, 2513-2520, November, 2004