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Selected Research Publication Research partially supported by the National Cancer Institute, American Cancer Society, National Institute of Environmental Health Sciences, and National Science Foundation. High-dimensional data: bioinformatics, genomics Nguyen, D.V. and Rocke, D.M. (2002). Classification of acute leukemia based on DNA microarray gene expressions using partial least squares. In Lin, S.M and Johnson, K.F. (eds), Methods of Microarray Data Analysis. Kluwer Academic Publishers, Dordrecht, 109-124 Article PDF   Book @ Amazon   Nguyen, D.V. and Rocke, D.M. (2002). Tumor classification by partial least squares using microarray gene expression data. Bioinformatics, 18, 39-50. Article PDF   Suppl. Figs. PDF   Sample SAS Codes TEXT   Errata TEXT   Nguyen, D.V. and Rocke, D.M. (2002). Multi-class cancer classification via partial least squares using gene expression profiles. Bioinformatics, 18, 1216-1226. Article PDF   Suppl. Figs. PDF   Suppl. Appendix PDF   Nguyen, D.V. and Rocke, D.M. (2002). Partial least squares proportional hazard regression for application to DNA microarray survival data. Bioinformatics, 18, 1625-1632. Article PDF   Suppl. Figs. PDF   Suppl. Appendix PDF  Sample SAS Codes TEXT   Nguyen, D.V., Arpat, A.B., Wang, N. and Carroll, R.J. (2002). DNA microarray experiments: biological and technological aspects. Biometrics, 58, 701-717. Article PDF1   Article PDF2   Color Figs. PDF   Suppl. Figs. PDF   Nguyen, D.V., Wang, N. and Carroll, R.J. (2004). Evaluation of misssing value estimation for microarray data. Journal of Data Science, 2, 347-370. Article PDF   Suppl. Figs. PDF   Algorithms PDF   Matlab Codes TEXT   Nguyen, D.V. and Rocke, D.M. (2004). On partial least squares dimension reduction for microarray-based classification: a simulation study. Computational Statistics and Data Analysis, 46, 407-425. Article PDF   Suppl. Figs. PDF Nguyen, D.V. (2004). On estimating the proportion of true null hypotheses for false discovery rate controlling procedures in exploratory DNA microarray studies. Computational Statistics and Data Analysis, 47, 611-637. Article PDF   Suppl. Web Page   Davidson, L.A., Nguyen, D.V. Hokanson, R.M., Callaway, E.S., Isett, R.B., Turner, N.D., Dougherty, E.R., Wang, N., Lupton, J.R., Carroll, R.J. and Chapkin, R.S. (2004). Chemopreventive n-3 polyunsaturated fatty acids reprogram genetic signatures during colon cancer initiation and progression in the rat. Cancer Research, 64, 6797-6804. Article PDF   Suppl. Web Page   Braga-Neto, U., Hashimoto, R., Dougherty, E.R., Nguyen, D.V. and Carroll, R.J. (2004). Is cross-validation better than resubstitution for ranking genes? Bioinformatics, 20, 253-258. Article PDF   Balagurunathan, Y., Wang, N., Dougherty E.R., Nguyen, D.V., Chen, Y., Bittner, M.L., Trent, J.M. and Carroll, R.J. (2004). Noise factor analysis for cDNA microarrays. Journal of Biomedical Optics, 9, 663-678. Article PDF   A related article PDF   Malgorzata, G., Nguyen, D.V., Attor, S.N., Dougherty, E.R., Turner, N.D., Bancroft, L.K., Chapkin, R.S., Lupton, J.R. and Carroll, R.J. (2005). Comparing automatic and manual image processing in FLARE assay analysis for colon carcinogenesis. Statistical Applications in Genetics and Molecular Biology, 4, article 5. (p.1-18) Article PDF   Nguyen, D.V. (2005). Partial least squares dimension reduction for microarray gene expression data with a censored response. Mathematical Biosciences, 193, 119-137. Article PDF   Nguyen, D.V. (2005). A unified computational framework to compare direct and sequential false discovery rate algorithms for exploratory DNA microarray studies. Journal of Data Science, 3, 331-352. Article PDF   Nguyen, D.V., Liu, H. and Senturk, D. (2007). A general FDR-based computational framework for sample size planning in microarray studies, In Pham, T., Yan, H., and Crane, D. (eds), Advanced Computational Methods for Biocomputing and Bioimaging. Nova Science Publishers, New York, p.55-69. Article PDF   Book @ Nova Publisher   Nguyen, D.V., Senturk, D., Harvey, D.J. and Li, S.-C. (2008). Sample size and power in genomics studies. Submitted. Article PDF   Covariate adjusted analysis: regression and correlation Senturk, D. and Nguyen, D.V. (2006). Estimation in covariate-adjusted regression. Computational Statistics and Data Analysis, 50, 3294-3310. Article PDF   Suppl. Figs. PDF   Nguyen, D.V. and Senturk, D. (2007). Distortion diagnostics for covariate-adjusted regression: graphical techniques based on local linear modeling. Journal of Data Science, 5, 471-490. Nguyen, D.V. and Senturk, D. (2008) Multicovariate-adjusted regression models. Journal of Statistical Computation and Simulation, in-press. Article PDF   Suppl. Figs. PDF   Nguyen, D.V. and Senturk, D. (2008) Covariate-adjusted regression for longitudinal data incorporating correlation between repeated measurements. Australian and New Zealand Journal of Statistics, in-press. Article PDF   Suppl. Figs. PDF   Senturk, D. and Nguyen, D.V. (2008) Partial covariate adjusted regression. Journal of Statistical Planning and Inference, in-press. Article PDF   Nguyen, D.V., Senturk, D. and Carroll, R.J. (2008) Covariate-adjusted linear mixed effects models with an application to longitudinal data. Journal of Nonparametric Statistics, in-press. Article PDF   Senturk, D., Nguyen, D.V., Tassone, F., Hagerman, R.J., Carroll, R.J. Hagerman, P.J (2008) Covariate adjusted correlation analysis with application to FMR1 premutation female carrier data. Biometrics , in-press. Article PDF   Fragile X syndrome, Fragile X premutation, Fragile X-associated tremor/ataxia Berry-Kravis, E., Goetz, C.G., Leehey, M., Hagerman, R., Zhang, L., Li, L., Nguyen, D., Hall, D., Tartaglia, N., Cogswell, J., Tassone, F. and Hagerman, P.J. (2007). Neuropathic features in fragile X premutation carriers. American Journal of Medical Genetics, 143A, 19-26. Adams, J.S., Adams, P.E., Nguyen, D., Brunberg, J.A., Tassone, F., Zhang, W., Koldewyn, K., Rivera, S.M., Grigsby, J., Zhang, L., DeCarli, C., Hagerman, P.J. and Hagerman, R. (2007). Volumetric brain changes in females with fragile X associated tremor/ataxia syndrome (FXTAS). Neurology, 69, 851-859. Coffey, S.M., Cook, K., Tartaglia, N., Tassone, F., Nguyen, D.V., Pan, R., Bronksy, H.E., Yuhas, J., Borodyanskaya, M., Grigsby, J., Doerflinger, M., Hagerman, P.J. and Hagerman, R.J. (2008) Expanded clinical phenotype of women with the FMR1 premutation. American Journal of Medical Genetics, 146, 1009-1016. Aguilar, D.C., Sigford, K., Soontarapornchai, K., Nguyen, D.V., Adams, P.E., Yuhas, J., Hagerman, P.J. and Hagerman, R.J. (2008) A quantitative assessment of tremor and ataxia in FMR1 premutation carriers using CATSYS. American Journal of Medical Genetics, 146, 629-635. Seritan, A., Nguyen, D.V., Farias, S., Fakhri, D., Hinton, L., Grigsby, J., Bourgeois, J.A. and Hagerman, R.J. (2008) Dementia in fragile X-associated tremor/ataxia syndrome (FXTAS): comparison with alzheimer's disease. American Journal of Medical Genetics: Neuropsychiatric Genetics, in-press. Epidemiology & biomedical applications Devaraj, S., Cheung, A.T., Jialal, I., Griffen, S.C., Nguyen, D. Glaser, N. and Aoki, T. (2007) Evidence of increased inflammation and microcirculatory abnormalities in patients with type 1 diabetes and their role in microvascular complications. Diabetes, 56, 2790-2796. Sonneborn, D., Park, H.-Y., Petrik, J., Kocan, A., Palkovicova, L., Trnovec, T., Nguyen, D.V. and Hertz-Picciotto, I. (2008) Prenatal PCB exposures in Eastern Slovakia modify effects of social factors on birthweight. Paediatric and Perinatal Epidemiology, 22, 202-213. Sonneborn, D., Park, H.-Y., Babinska, K., Palkovicova, L., Trnovec, T., Nguyen, D.V. and Hertz-Picciotto, I. (2008) Serum PCB concentrations in relation to locally produced food items in Eastern Slovakia. Journal of Exposure Science and Environmental Epidemiology, in-press. Verro, P., Gorelick, P. and Nguyen, D. (2008) Aspirin plus dipyridamole versus aspirin for prevention of vascular events after stroke or TIA: a meta-analysis. Stroke, 39, 1358-1363. Chee, K. G., Nguyen, D. V., Brown, M., Gandara, D. R., Wun, T. and Lara, P. N. (2008) Positron emission tomography and improved survival in lung cancer: The Will Rogers phenomenon revisited. Archives of Internal Medicine, in-press. Conference articles, Dissertation   Nguyen, D.V. (2004). A comparison of direct and sequential false discovery rate algorithms: computational experiments for exploratory DNA microarray studes. Computing Science and Statistics, 36, pp. 1-15. Article PDF   Nguyen, D.V. and Rocke, D.M. (2001). Assessing patient survival using microarray gene expression data via partial least squares proportional hazard regression. Computing Science and Statistics, 33, 376-389. Article PDF   Full vol. PDF (697 pages)   Nguyen, D.V. (2000). Statistical analysis of gene expression data from DNA microarrays based on partial least squares and related dimension reduction methods. Ph.D dissertation, Department of Statistics, University of California, Davis, 169 pages. Available @ Digital Dissertations