Statistical Methods for Agricultural Genomics

This research that we propose supports 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 as such our motivation and rationale for a computational genomics research and education program is to provide methods and education that can be utilized across numerous areas of genomics (animal, microbe, and plant). Additionally, we anticipate that much of what we develop will be adaptable to other quantifications of genomic activity.

References:

• M.A. Black and R.W. Doerge. 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.
• B. Munneke. 2001. Null Model Methods for Clustering of Gene Expression Data Ph.D. Dissertation. Department of Statistics, Purdue University, West Lafayette, IN. USA
• B.A. Craig, O. Vitek, M.A. Black, M. Tanurdzic, R.W. Doerge. 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.
• R.W. Doerge. 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nature Reviews Genetics 3:43-52.
• M.A. Black. 2002. Statistical Issues in the Design and Analysis of Spotted Microarray Experiments. Department of Statistics, Purdue University, West Lafayette, IN. USA.
• M. Black and R.W. Doerge. 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.
• B.A. Craig, M.A. Black, and R.W. Doerge. 2003. Gene Expression Data: The technology and statistical analysis. JABES 8(1):1-28.
• Kontoyiannis and J. Zhang. 2002. Arbitrary source models and Bayesian codebooks in rate-distortion theory. IEEE Transactions on Information Theory 48: 2276-2290.
• Dembo and I. Kontoyiannis. 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.
• M. Wayne and L. McIntyre. 2002. Combining Mapping and Arraying: A novel approach to candidate gene identification. PNAS 99: 14903-14906
• D.E. Moody, Z. Zou, and L. McIntyre. 2002. Cross-species hybridization of pig RNA to human nylon microarrays. BMC Genomics 3:27.
• D.B. Moody, Fadlia, A. Singh, S. Shah, and L. McIntyre. 2002. Quantitative Comparison of Image Analysis Software. DNA Press p. 155-166. eds G. Kamberova and S. Shah.
• O. Abiola, et al., 2003. The nature and identification of quantitative trait loci: a community's view. Nature Genetics Reviews. 4:911-916.
• A.Singh, L. McIntyre, and L. Sherman. 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.
• B. Lahner, J. Gong, M. Mahmoudian, E. Smith, K. Abid, E. Rogers, M. Guerinot, J. Harper, J. Ward, L. McIntyre, J. Schroeder, D. Salt 2003. Genomic scale profiling of nutrient and trace elements in Arabidopsis thaliana. Nature Biotechnology 21 (10):1215-1221.
• Bodgan M., J.K. Ghosh, R.W. Doerge. 2004. Modifying the Schwarz Bayesian Information Citerion to locate multiple interacting quantitative trait loci. Genetics. 167:989-999.
• Munneke, K.A. Schlauch, W. Beavis and R.W. Doerge. 2004. Permutation and convex hull based confidence measures applied to gene expression data. Genetics (accepted).
• H. Jiang. 2004. Testing Groups of Genes for Differential Expression. Department of Statistics, Purdue University, West Lafayette, IN. USA
• A.M. Pirttila, L. M. McIntyre, G. A., Payne and C. P. Woloshuk. 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(6): 647-656.
• J.H.F. Pedra, L. M. McIntyre, M.E. Scharf and B. Pittendrigh. 2004 Genome-wide transcription profile of field and laboratory selected DDT resistant Drosophila PNAS 101(18):7034-7039.
• L. Hong, A K. Singh, L. M. McIntyre and A. Sherman. 2004. Differential gene expression in response to hydrogen peroxide and the putative PerR regulon of Synechocystis sp. Strain PCC 6803 J. of Bacteriology 186 (11): 3331-3345.
• S.V. Nuzhdin, M.L. Wayne, K.L. Harmon, and L.M. McIntyre. 2004 Common pattern of evolution of gene expression level and protein sequence in Drosophila. Molecular Biology and Evolution 21(7):1308-17.
• M. Wayne, Y.-J. Pan, S. V. Nuzhdin and L. M. McIntyre. 2004 Additivity and trans-acting effects on gene expression in male Drosophila simulans. Genetics (in press).
• 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).