Genomic Applications

Chemopreventive n-3 Polyunsaturated Fatty Acids Reprogram Genetic Signatures During Colon Cancer Initiation and Progression in the Rat

Davidson, L. A., Nguyen, D. V., Hokanson, R. M., Callaway, E. S., Isett, R., Turner, N. D., Dougherty, E. R., Lupton, J. R., Carroll, R. J., and Chapkin, R. S., Cancer Research, Vol. 64, 6797-6804, September, 2004

Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study

Zhao, W, Agyepong, K., Serpedin, E., and Dougherty, E. R., EURASIP Jounral on Bioinformatics and Systems Biology, Vol. 2008, Article ID 769293, 8 pages, doi: 10.1155/2008/769293, June, 2008

Gene Expression Profiles in Hereditary Breast Cancer

Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M., Bittner, M., Simon, R., Meltzer, P., Gusterson, B., Esteller, M., Kallioniemi, O. P., Wilfond, B., Borg, A., Trent, J., Raffeld, M., Yakhini, Z., Ben-Dor, A., Dougherty, E. R., Kononen, J., Bubendorf, L., Fehrle, W., Pittaluga, S., Gruvberger, S., Loman, N., Johannsson, O., Olsson, H., Sauter, G., New England Journal of Medicine, Vol. 344, No. 8, 539-548, 2001

Gene Expression Profiling Identifies Strong Feature Genes that Classify de novo CD5+ and CD5 Diffuse Large B-cell Lymphoma and Mantle Cell Lymphoma

Kobayashi, T., Yamaguchi, M., Kim, S., Morikawa, J., Ueno, S., Suh, E., Dougherty, E. R., Shmulevich, I., Shiku, H., and Zhang, W., Cancer Research, Vol. 63, 60-66, 2003

Genomic Profiles and Predictive Biological Networks in Oxidant-Induced Atherogenesis

Johnson, C. D., Balagurunathan, Y., Lu, K. P., Tadesse, M., Falahatpisheh, M. H., Balagurunathan, Y., Carroll, R. A., Dougherty, E. R., Afshari, C. A., and Ramos, K. S., Physiological Genomics, Vol. 13, 263-275, 2003

Identification of Combination Gene Sets for Glioma Classification

Kim, S., Dougherty, E. R., Shmulevich, I., Hess, K. R., Hamilton, S. R., Trent, J. M., Fuller, G. N., and Zhang, W., Molecular Cancer Therapeutics, Vol. 1, No. 13, 1229-1236, 2002

Identification of Signature Genes by Microarray for Acute Myeloid Leukemia Without Maturation (FAB-M1) and AML with t(15;17)(q22;q12)(PML/RARa)

Morikawa, J., Li, H., Kim, S., Nishii, K., Ueno, S., Suh, E., Dougherty, E. R., Shmulevich, I., Shiku, H., Zhang, W., and Kobayashi, T., International Journal of Oncology, Vol. 23, No. 3, 617- 625, 2003

Insight Into Redox-regulatory Gene Networks in Vascular Cells

Johnson, C. D., Balagurunathan, Y., Dougherty, E. R., Afshari, C. A., He, Q., and Ramos, K. S., Bioinformation, Vol. 1, No. 10, 379-383, April, 2007

Molecular Classification of Cutaneous Malignant Melanoma by Gene Expression Profiling

Bittner, M., Meltzer, P. S. J., Chen, Y. D., Jiang, Y., Seftor, E., Hendrix, M., Radmacher, M., Simon, R., Yakhini, Z., Ben-Dor, A., Sampas, N., Dougherty, E. R., Wang, E. L., Marincola, F., Gooden, C., Lueders, J., Glatfelter, A., Pollock, P. C. A., Carpten, J., Gillanders, E., Leja, D., Dietrich, K., Beaudry, C.,Berens, M., Alberts, D., Sondak, V., Hayward, N., Trent, J., Nature, Vol. 406, No. 6795, 536-540, August, 2000

The Role of Signal-processing Concepts in Genomics and Proteomics

Vaidyanathan. P. P., and Byung-Jun Yoon, Journal of the Franklin Institute (invited paper), Special Issue on Genomics, Vol. 341, 111-135, 2004

Unraveling Gene-Gene Interactions Regulated by Ligands of the Aril Hydrocarbon Receptor

Johnson, C. D., Balagurunathan, Y., Tadesse, M. G., Falahatpisheh, Marcel Brun, M. H., Walker, M. K., Dougherty, E. R., and Ramos, K. S., Environmental Health Perspectives, Vol. 112, No. 4, 403-412, March 2004