MICROARRAY ANALYSIS & PROTEOMICS

Falk CT, Finch SJ, Kim W, Mukhopadhyay ND, Gong B, Hinrichs A, Li X, Liu X, Malhotra A, Mehta T, Page G, Rao S, Saccone N, Shete S, Yang Y, Yu R, Zhao JH, Zhou X. Data mining of RNA expression and DNA genotype data: presentation group 5 contributions to Genetic Analysis Workshop 15. Genet Epidemiol. (2007) 31 Suppl 1:S43-50.

Wu X, Wang J, Cui X, Maianu L, Rhees B, Rosinski J, So WV, Willi SM, Osier MV, Hill HS, Page GP, Allison DB, Martin M, Garvey WT. The effect of insulin on expression of genes and biochemical pathways in human skeletal muscle. Endocrine. (2007) Feb;31(1):5-17.

Ye J, Cui X, Loraine A, Bynum K, Kim NC, White G, De Luca M, Garfinkel MD, Lu X, Ruden DM. Methods for nutrigenomics and longevity studies in Drosophila: effects of diets high in sucrose, palmitic acid, soy, or beef. Methods Mol Biol. (2007);371:111-41.

Brand JP, Chen L, Cui X, Bartolucci AA, Page GP, Kim K, Barnes S, Srinivasasainagendra V, Beasley MT, Allison DB. An adaptive alpha spending algorithm improves the power of statistical inference in microarray data analysis. Bioinformation. (2007) Apr 10;1(10):384-9.

Laudencia-Chingcuanco DL, Stamova BS, Lazo GR, Cui X, Anderson OD. Analysis of the wheat endosperm transcriptome. J Appl Genet. (2006);47(4):287-302.

Misirlioglu M, Page GP, Sagirkaya H, Kaya A, Parrish JJ, First NL, Memili E. Dynamics of global transcriptome in bovine matured oocytes and preimplantation embryos. Proc Natl Acad Sci USA. (2006) Dec 12;103(50):18905-10.

Mukherjee S, Frolova N, Sadlonova A, Novak Z, Steg A, Page GP, Welch DR, Lobo-Ruppert SM, Ruppert JM, Johnson MR, Frost AR. Hedgehog signaling and response to cyclopamine differ in epithelial and stromal cells in benign breast and breast cancer. Cancer Biol Ther. (2006) Jun;5(6):674-83.

Bailey SM, Robinson G, Pinner A, Chamlee L, Ulasova E, Pompilius M, Page GP, Chhieng D, Jhala N, Landar A, Kharbanda KK, Ballinger S, Darley-Usmar V. S-adenosylmethionine prevents chronic alcohol-induced mitochondrial dysfunction in the rat liver. Am J Physiol Gastrointest Liver Physiol. (2006) Nov;291(5):G857-67.

Wei H, Persson S, Mehta T, Srinivasasainagendra V, Chen L, Page GP, Somerville C, Loraine A. Transcriptional coordination of the metabolic network in Arabidopsis. Plant Physiol. (2006) Oct;142(2):762-74.

Mehta TS, Zakharkin SO, Gadbury GL, Allison DB. Epistemological issues in omics and high-dimensional biology: give the people what they want. Physiol Genomics. (2006) Dec 13;28(1):24-32.

Zakharkin SO, Kim K, Bartolucci AA, Page GP, Allison DB. Optimal allocation of replicates for measurement evaluation studies. Genomics Proteomics Bioinformatics. (2006) Aug;4(3):196-202.

Higami Y, Barger JL, Page GP, Allison DB, Smith SR, Prolla TA, Weindruch R. Energy restriction lowers the expression of genes linked to inflammation, the cytoskeleton, the extracellular matrix, and angiogenesis in mouse adipose tissue. J Nutr. (2006) Feb;136(2):343-52.

Xiangqin Cui, Jason Affourtit, Keith R. Shockley, Yong Woo, and Gary A. Churchill. (2006). Inheritance Patterns of Transcript Levels in F1 Hybrid Mice. Genetics, 174:627-637

Cui, X. and A. E. Loraine (2006). Global Correlation Analysis Between Redundant Probe Sets Using A Large Collection Of Arabidopsis Ath1 Expression Profiling Data. CSB 2006 Proceedings of the LSS Computational Systems Bioinformatics Conference. Stanford, CA, August, 223-226

Page, G. P., Edwards, J. W., Yelisetti, P., Wang, J., Trivedi, P., & Allison, D. B. (2006). The PowerAtlas: A Power and Sample Size Atlas for Microarray Experimental Design and Research. BMC Bioinformatics, 7:84.

David B. Allison, Xiangqin Cui, Grier P. Page, Mahyar Sabripour, (2006). Microarray data analysis: from disarray to consolidation and consensus. NATURE REVIEWS GENETICS, 7(1), 55-65.

Kim K, Page GP, Beasley TM, Barnes S, Scheirer KE, Allison DB. (2006). A proposed metric for assessing the measurement quality of individual microarrays. BMC Bioinformatics, 2006 7:35.

Edwards, J. W., Page, G. P., Gadbury, G., Heo, M., Kayo, T., Weindruch, R., & Allison, D. B. (2005). Empirical Bayes (EB) Estimation of Gene-Specific Effects in Microarray Research. Functional & Integrative Genomics, 5, 32-39.

Garge NR, Page GP, Sprague AP, Gorman BS, Allison DB. (2005). Reproducible clusters from microarray research: whither? BMC Bioinformatics, Jul 15;6 Suppl 2:S10.

Zakharkin SO, Kim K, Mehta T, Chen L, Barnes S, Scheirer KE, Parrish RS, Allison DB, Page GP. (2005). Sources of variation in Affymetrix microarray experiments. BMC Bioinformatics, 6: 214.

Cui XQ, Hwang TG, Qui J, Blades J, Churchill GA. (2005). Improved statistical tests for differential gene expression by shrinking variance component estimates. Biostatistics, 6(1), 59-75.

Trivedi P, Edwards JE, Wang J, Gadbury GL, Srinivasasainagendra V, Zakharkin SO, Kim K, Mehta T, Brand JPL, Patki A, Page GP, Allison B. (2005). HDBStat!: A platform-independent software suite for statistical analysis of high dimensional biology data. BMC Bioinformatics, 6:86 (6 April 2005).

Beasley TM, Holt JK, Allison DB, (2005). Comparison of linear weighting schemes for perfect match and mismatch gene expression levels from microarray data. American Journal of Pharmacogenomics, 5(3):197-205.

Volk AA, Rivera AL,Page GP, Salazaar-Gonzales JF, Nettelbeck DM, and Curiel DM. (2005). Employment of microarray analysis to characterize biologic differences associated with tropism-modified adenoviral vectors: utilization of non-native cellular entry pathways. Cancer Gene Therapy, 12, 162–174.

Allison DB, Page GP, Beasley TM, Edward JE. (2005). DNA Microarrays and Related Genomics Techniques: Design, Analysis, and Interpretation of Experiments. ISBN-10: 0824754611, ISBN-13: 978-0824754617.

Barnes, S. & Allison, D. B. (2004). Excitement and realities in microarray analysis of the biological effects of polyphenols. Pharmaceutical Biology, 42, 94-101.

Beasley TM, Page GP, Brand JPL, Gadbury GL, Mountz JD, Allison DB (2004). Chebyshev's Inequality for Non-parametric Testing with Small N and alpha in microarray research. Journal of the Royal Statistical Society (Series C): Applied Statistics, 53, Part 1, 95-108.

Gadbury GL, Page GP, Edwards JW, Kayo T, Prolla TA, Weindruch R, Permana PA, Mountz J, Allison DB. (2004). Power and sample size estimation in high dimensional biology. Statistical Methods in Medical Research, 13 (4), 325-338.

Ginos MA, Page GP, Michalowicz BS, Patel KJ, Volker SE, Pambuccian SE, Ondrey FG, Adams GL, Gaffney PM. (2004). Identification of a gene expression signature associated with recurrent disease in squamous cell carcinoma of the head and neck. Cancer Research, 64(1), 55-63.

Higami Y, Pugh TD, Page GP, Allison DB, Prolla TA, Weindruch R. (2004). Adipose tissue energy metabolism: altered gene expression profile of mice subjected to long-term caloric restriction. FASEB, 18(2), 415-427.

Lobenhofer EK, Cui XQ, Bennett L, Cable PL, Churchill GA, Afshari CA. (2004). Exploration of Low Dose Estrogen Effects: Identification of No Observed Transcriptional Effect Level (NOTEL). Toxicologic Pathology, 32(4), 482-492.

Mehta T, Tanik M, Allison DB (2004). Towards Sound Epistemological Foundation of Statistical Methods for High-Dimensional Biology. Nature Genetics, 36(9) 943-947.

Page GP, Edwards JW, Barnes S, Weindruch R, Allison DB. (2004). A design and statistical perspective on microarray gene expression studies in nutrition: the need for playful creativity and scientific hard-mindedness. Nutrition, 19(11-12), 997-1000.

Sadlonova A, Novak Z, Johnson MR, Bowe DB, Gault SR, Page, GP, Thottassery JV, Welch DR, Frost AR (2004). Breast fibroblasts modulate epithelial cell proliferation in three-dimensional in vitro co-culture. Breast Cancer Research, 7, R46-R59.

Yang, D, Zakharkin, SO, Page GP, Brand, JPL, Edwards, JW, Bartoculli, AA, Allison, DB (2004). Applications of Bayesian Statistical Methods in Microarray Data Analysis. American Journal of Pharmacogenomics, 4(1), 53-62.

Zhang, H., Hyde, K, Page, GP, Brand, JPL, Zhou, J, Allison, DB, Hsu, H, Mountz, JD (2004). Novel tumor necrosis factor α-regulated genes in rheumatoid arthritis. Arthritis and Rheumatism, 50(2), 420-431.

Kim H, Page GP, Barnes S. (2004). Proteomics and mass spectrometry in nutrition research. Nutrition, 20(1), 155-165.

Venkatraman A, Landar A, Davis AJ, Chamlee L, Sanderson T, Kim H, Page G, Pompilius M, Ballinger S, Darley-Usmar V, Bailey SM. (2004). Modification of the mitochondrial proteome in response to the stress of ethanol-dependent hepatotoxicity. Journal of Biological Chemistry, 279, 21, 22092-22101

Venkatraman A, Landar A, Davis AJ, Ulasova E, Page G, Murphy MP, Darley-Usmar V, Bailey SM. (2004). Oxidative modification of hepatic mitochondria protein thiols: effect of chronic alcohol consumption. Am J Physiol Gastrointest Liver Physiology, 286(4):G521-7.

Gadbury, G. L., Page, G. P., Heo, M., Mountz, J. D., Allison, D. B. (2003). Randomization Tests for Small Samples: An Application for Genetic Expression Data. Journal of the Royal Statistical Society: Series C (Applied Statistics), 365-76

Allison, D. B., Coffey, C. S. (2002). Two Stage Testing in Microarray Analysis: What is Gained?. Journal of Gerontology: Biological Sciences, 57, B189-B192.

Allison, D. B., Gadbury, G., Heo, M., Fernandez, J., Lee, C-K., Prolla, T. A., Weindruch, R. (2002). A mixture model approach for the analysis of microarray gene expression data. Computational Statistics & Data Analysis, 39, 1–20.

Lee, C. K., Allison, D. B., Brand, J. P. L., Weindruch, R., Prolla, T. A. (2002). Transcriptional profiles associated with aging and middle age-onset caloric restriction in mouse hearts. PNAS, 99, 14988-14993.

Allison, D. B. (2002). Statistical Methods For Microarray Research For Drug Target Identification. Proceedings of the American Statistical Association, Biopharmaceutical Section, Alexandria, VA: American Statistical Association. [ PDF ]

Cheung, K-H, White, K., Hager, J., Gerstein, M., Reinke, V., Nelson, K., Masiar, P., Srivastava, R., Li, Y., Li, J., Zhao, H., Li, J., Allison, D. B., Snyder, M., Miller, P., Williams, K. (2002). YMD: A microarray database for large-scale gene expression analysis.The American Medical Informatics Association (AMIA) Symposium, San Antonio, Texas [ PDF ]

Zhang, Z., Page, G. P., Zhang, H. (2001).  Fishing Expedition - A Supervised Approach to Extract Patterns from a Compendium of Expression Profiles. Methods of Microarray Data Analysis: Papers from CAMDA 2001.

Zhang, Z., Page, G. P., Zhang, H. (2000). Applying Classification Separability Analysis to Microarray Data. Methods of Microarray Data Analysis: Papers from CAMDA 2000.