Bioinformatics - 2006

Haas, D. W., Geraghty, D. E., Andersen, J., Mar, J., Motsinger, A. A., D’Aquila, R. T., … Landay, A. (2006). Immunogenetics of CD4 Lymphocyte Count Recovery during Antiretroviral Therapy: An AIDS Clinical Trials Group Study. The Journal of Infectious Diseases, 194(8), 1098–1107. https://doi.org/10.1086/507313

Ritchie, M. D., Haas, D. W., Motsinger, A. A., Donahue, J. P., Erdem, H., Raffanti, S., … Sterling, T. R. (2006). Drug Transporter and Metabolizing Enzyme Gene Variants and Nonnucleoside Reverse-Transcriptase Inhibitor Hepatotoxicity. Clinical Infectious Diseases, 43(6), 779–782. https://doi.org/10.1086/507101

Brassat, D., Motsinger, A. A., Caillier, S. J., Erlich, H. A., Walker, K., Steiner, L. L., … Ritchie, M. D. (2006). Multifactor dimensionality reduction reveals gene–gene interactions associated with multiple sclerosis susceptibility in African Americans. Genes & Immunity, 7(4), 310–315. https://doi.org/10.1038/sj.gene.6364299

Motsinger, A. A., Dudek, S. M., Hahn, L. W., & Ritchie, M. D. (2006). Comparison of Neural Network Optimization Approaches for Studies of Human Genetics. In F. Rothlauf (Ed.), Applications of Evolutionary Computing. EvoWorkshops 2006 (pp. 103–114). https://doi.org/10.1007/11732242_10

Motsinger, A. A., & Ritchie, M. D. (2006). The effect of reduction in cross-validation intervals on the performance of multifactor dimensionality reduction. Genetic Epidemiology, 30(6), 546–555. https://doi.org/10.1002/gepi.20166

Yu, J., Pressoir, G., Briggs, W. H., Vroh Bi, I., Yamasaki, M., Doebley, J. F., … Buckler, E. S. (2006). A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics, 38(2), 203–208. https://doi.org/10.1038/ng1702

Tetko, I. V., Solov'ev, V. P., Antonov, A. V., Yao, X., Doucet, J. P., Fan, B., … Varnek, A. (2006). Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure−Property Relationship Studies of Metal Complexation with Ionophores. Journal of Chemical Information and Modeling, 46(2), 808–819. https://doi.org/10.1021/ci0504216

Vanholme, B., Mitreva, M., Van Criekinge, W., Logghe, M., Bird, D., McCarter, J. P., & Gheysen, G. (2006). Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii. Parasitology Research, 98(5), 414–424. https://doi.org/10.1007/s00436-005-0029-3

Reif, D. M., & Moore, J. H. (2006). Visual analysis of statistical results from microarray studies of human breast cancer. Oncology Reports, c, 1043–1047. Retrieved from http://europepmc.org/abstract/med/16525698

Reif, D. M., & Libraries, V. U. (2006). Integrated analysis of genetic and proteomic data. Retrieved from http://europepmc.org/theses/ETH/7299

Reif, D., & Moore, J. (2006). Visual analysis of statistical results from microarray studies of human breast cancer. Oncol Rep, 4(4), 1043–1047. https://doi.org/10.3892/or.15.4.1043

Motsinger, A. A., Reif, D. M., Dudek, S. M., & Ritchie, M. D. (2006). Understanding the evolutionary process of grammatical evolution neural networks for feature selection in genetic epidemiology. Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06, 263–270. https://doi.org/10.1109/CIBCB.2006.330945

McKinney, B. A., Reif, D. M., Ritchie, M. D., & Moore, J. H. (2006). Machine Learning for Detecting Gene-Gene Interactions. Applied Bioinformatics, 5(2), 77–88. https://doi.org/10.2165/00822942-200605020-00002

Feature selection using a random forests classifier for the integrated analysis of multiple data types. (2006). Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06, 171–178. https://doi.org/10.1109/CIBCB.2006.330987

McKinney, B. A., Reif, D. M., Rock, M. T., Edwards, K. M., Kingsmore, S. F., Moore, J. H., & JE, C., Jr. (2006). Cytokine expression patterns associated with systemic adverse events following smallpox immunization. Journal of Infectious Diseases, 194(4), 444–453. https://doi.org/10.1086/505503

Starmer, J., Stomp, A., Vouk, M., & Bitzer, D. (2006). Predicting Shine-Dalgarno sequence locations exposes genome annotation errors. PLOS COMPUTATIONAL BIOLOGY, 2(5), 454–466. https://doi.org/10.1371/journal.pcbi.0020057

Jackson, M., Watt, A. J., Gautier, P., Gilchrist, D., Driehaus, J., Graham, G. J., … Forrester, L. M. (2006). A murine specific expansion of the Rhox cluster involved in embryonic stem cell biology is under natural selection. BMC Genomics, 7.

Waterman, J. T., Bird, D. M. K., & Opperman, C. H. (2006). A method for isolation of Pasteuria penetrans endospores for bioassay and genomic studies. Journal of Nematology, 38(1), 165–167. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-34248330929&partnerID=MN8TOARS

Snyder, D. W., Opperman, C. H., & Bird, D. M. K. (2006). A method for generating Meloidogyne incognita males. Journal of Nematology, 38(2), 192–194. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-33750134280&partnerID=MN8TOARS

McCarter, J. P., Bird, D. M., & Mitreva, M. (2006). Nematode gene sequences: Update for December 2005. Journal of Nematology, 37(4), 417–421.

Bird, D. M., Blaxter, M. L., McCarter, J. P., Mitreva, M., Sternberg, P. W., & Thomas, W. K. (2006). A white paper on nematode comparative genomics. Journal of Nematology, 37(4), 408–416.