Statistical Methods for Agricultural Genomics

This research supported current methodological needs requiring accurate tools for assessing gene expression data and modeling complex traits in agricultural genomics. We expect these needs to continue evolving as they have in the past, and our research programs continue to address these topics.

Publications supported by this project:

• Black, M.A. and Doerge, R.W. 2001. Calculation of the minimum number of replicate spots required for detection of significant gene expression fold changes for cDNA microarrays. Proceedings of Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken, pp 144-158.
• Munneke, B., 2001. Null Model Methods for Clustering of Gene Expression Data Ph.D. Dissertation. Department of Statistics, Purdue University, West Lafayette, IN. USA
• Craig, B.A., Vitek, O., Black, M.A., Tanurdzic, M., Doerge, R.W. 2001. Designing microarray experiments: chips, dips, flips, and skips. Proceedings of Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken, pp 159-182.
• Doerge, R.W. 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nature Reviews Genetics 3:43-52.
• Black, M.A. 2002. Statistical Issues in the Design and Analysis of Spotted Microarray Experiments. Department of Statistics, Purdue University, West Lafayette, IN. USA.
• Black, M. and Doerge, R.W. 2002. Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments. Bioinformatics 18(12):1609-1616.
• Craig, B.A., Black, M.A. and Doerge, R.W. 2003. Gene Expression Data: The technology and statistical analysis. JABES 8(1):1-28.
• Kontoyiannis, I. and Zhang, J. 2002. Arbitrary source models and Bayesian codebooks in rate-distortion theory. IEEE Transactions on Information Theory 48: 2276-2290.
• Dembo and Kontoyiannis, I. 2002. Source coding, large deviations, and approximate pattern matching. Invited paper in the special issue of the IEEE Transactions on Information Theory on Shannon Theory, dedicated to A.D. Wyner, 48:1590-1615.
• Wayne, M. and McIntyre, L.M. 2002. Combining Mapping and Arraying: A novel approach to candidate gene identification. PNAS 99: 14903-14906
• Moody,D.E., Zou, Z. and McIntyre, L.M. 2002. Cross-species hybridization of pig RNA to human nylon microarrays. BMC Genomics 3:27.
• Moody, D.B., Fadlia, Singh, A., Shah, S. and McIntyre,L.M. 2002. Quantitative Comparison of Image Analysis Software. DNA Press p. 155-166. eds G. Kamberova and S. Shah.
• Abiola, O. et al., 2003. The nature and identification of quantitative trait loci: a community's view. Nature Genetics Reviews. 4:911-916.
• Singh, A., McIntyre, L.M. and Sherman, L. 2003. Microarray Analysis of the Genome-wide Response to Iron Deficiency and Iron Reconstitution in the Cyanobacterium Synechocystis sp. PCC 6803 Plant Physiology 132 (4): 1825-1839.
• Lahner, B., Gong, J., Mahmoudian, M., Smith, E., Abid, K., Rogers, E., Guerinot, M., Harper, J., Ward, J., McIntyre, L.M., Schroeder, J., Salt, D. 2003. Genomic scale profiling of nutrient and trace elements in Arabidopsis thaliana. Nature Biotechnology 21 (10):1215-1221.
• Bodgan M., Ghosh, J.K., Doerge, R.W. 2004. Modifying the Schwarz Bayesian Information Citerion to locate multiple interacting quantitative trait loci. Genetics. 167:989-999.
• Munneke, K., Schlauch, A., Beavis, W. and Doerge, R.W. 2005. Permutation and convex hull based confidence measures applied to gene expression data. Genetics 170:2003-2011.
• Jiang, H. 2004. Testing Groups of Genes for Differential Expression. Department of Statistics, Purdue University, West Lafayette, IN. USA
• Pirttila, A.M., McIntyre, L.M., Payne, G.A. and Woloshuk, C.P. 2004. Comparison of expression profiles associate gene tags with fumonisin biosynthesis in wild type and fcc1 mutant of Fusarium verticillioides 2 Fungal Genetics and Biology 41: 647-656.
• Pedra, J.H.F., McIntyre, L.M., Scharf, M.E. and Pittendrigh, B., 2004 Genome-wide transcription profile of field and laboratory selected DDT resistant Drosophila PNAS 101:7034-7039.
• Hong, L., Singh, A.K., McIntyre, L.M. and Sherman, A. 2004. Differential gene expression in response to hydrogen peroxide and the putative PerR regulon of Synechocystis sp. Strain PCC 6803 J. of Bacteriology 186: 3331-3345.
• Nuzhdin, S.V., Wayne, M.L., Harmon, K.L. and McIntyre, L.M. 2004 Common pattern of evolution of gene expression level and protein sequence in Drosophila. Molecular Biology and Evolution 21:1308-17.
• Wayne, M., Pan, Y.-J., Nuzhdin, S.V. and McIntyre, L.M. 2004. Additivity and trans-acting effects on gene expression in male Drosophila simulans. Genetics 168:1413-1420.
• K. Bradley, M.B. Boulware, H. Jiang, R.W. Doerge, and R.L. Meisel. 2004. Sexual experience generates distinct patterns of gene expression in the nucleus accumbens and dorsal striatum of female syrian hamsters. Genes, Brain, and Behavior. (in press).