Publications (Clicking on the reprint icon will take you to the publication reprint.)

Prospects for advancing defense to cereal rusts through genetical genomics - (Peer Reviewed Journal)

Ballini, E., Lauter, N.C., Wise, R.P. 2013. Prospects for advancing defense to cereal rusts through genetical genomics. Frontiers in Plant Science. 4:117 DOI: 10.3389/fpls.2013.00117.

Differential regulation of host mRNA translation during obligate pathogen-plant interactions - (Peer Reviewed Journal)

Moeller, J.R., Moscou, M.J., Bancroft, T., Skadsen, R.W., Wise, R.P., Whitham, S.A. 2012. Differential regulation of host mRNA translation during obligate pathogen-plant interactions. Molecular Biosystems. 8:2153-2165.

Quantitative and qualitative stem rust resistance factors in barley are associated with transcriptional suppression of defense regulons - (Peer Reviewed Journal)

Moscou, M.J., Lauter, N.C., Steffenson, B., Wise, R.P. 2011. Quantitative and qualitative stem rust resistance factors in barley are associated with transcriptional suppression of defense regulons. PLoS Genetics. 7(7):DOI: 10.1371/journal.pgen.1002208.

Quantitative and temporal definition of the Mla transcriptional regulon during barley-powdery mildew interactions - (Peer Reviewed Journal)

Moscou, M.J., Lauter, N.C., Caldo, R.A., Nettleton, D., Wise, R.P. 2011. Quantitative and temporal definition of the Mla transcriptional regulon during barley-powdery mildew interactions. Molecular Plant-Microbe Interactions. 24(6):694-705.

Regulators of Innate Immunity in Cereal-fungal Interactions - (Book / Chapter)

Wise, R.P., Meng, Y., Moscou, M.J., Xu, W. 2010. Regulators of Innate Immunity in Cereal-fungal Interactions. In: Antoun, H., Avis, T., Brisson, L., Prevost, D., Trepanier, M., editors. Biology of Plant-Microbe Interactions. St. Paul, MN: International Society for Molecular Plant-Microbe Interactions. p. 1-7.

An Empirical Method for Establishing Positional Confidence Intervals Tailored for Composite Interval Mapping of QTL - (Peer Reviewed Journal)

Crossett, A., Lauter, N.C., Love, T.M. 2010. An Empirical Method for Establishing Positional Confidence Intervals Tailored for Composite Interval Mapping of QTL. PLoS One. 5:e9039.

Comparative Transcriptional Profiling Established the Awn as the Major Photosynthetic Organ of the Barley Spike while the Lemma and the Palea Primarily Protect the Seed     - (Peer Reviewed Journal)

Abebe, T., Wise, R.P., Skadsen, R.W. 2009. Comparative Transcriptional Profiling Established the Awn as the Major Photosynthetic Organ of the Barley Spike while the Lemma and the Palea Primarily Protect the Seed. The Plant Genome. 2(3):247-259.

Drought Response in the Spikes of Barley: Gene Expression in the Lemma, Palea, Awn, and Seed     - (Peer Reviewed Journal)

Abebe, T., Melmaiee, K., Berg, V., Wise, R.P. 2009. Drought Response in the Spikes of Barley: Gene Expression in the Lemma, Palea, Awn, and Seed. Functional and Integrative Genomics. 10(2):191-205.

Strategies for the Production of Maize-derived Pharmaceuticals using Cytoplasmic Male Sterile Lines: in vitro Tissue Culture/Transformation and Field Breeding Approaches     - (Peer Reviewed Journal)

Wang, K., Frame, B., Xu, X., Moeller, L., Lamkey, K., Wise, R.P. 2009. Strategies for the Production of Maize-derived Pharmaceuticals using Cytoplasmic Male Sterile Lines: in vitro Tissue Culture/Transformation and Field Breeding Approaches. Maydica. 54(1):199-210.

A Single Molecule Scaffold for the Maize Genome     - (Peer Reviewed Journal)

Zhou, S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M.R., Churas, C., Pasternak, S., Forrest, D.K., Wise, R.P., Ware, D., Wing, R., Waterman, M., Livny, M., Schwartz, D.C. 2009. A Single Molecule Scaffold for the Maize Genome. PLoS Genetics. 5(11):1-14.

Transcript-based Cloning of RRP46, a Regulator of rRNA Processing and R-Gene-Independent Cell Death in Barley–Powdery Mildew Interactions     - (Peer Reviewed Journal)

Xi, L., Moscou, M.J., Meng, Y., Xu, W., Caldo, R.A., Shaver, M., Nettleton, D., Wise, R.P. 2009. Transcript-based Cloning of RRP46, a Regulator of rRNA Processing and R-Gene-Independent Cell Death in Barley–Powdery Mildew Interactions. The Plant Cell. 21(10):3280-3295.

Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-associated Region of Maize     - (Peer Reviewed Journal)

Kronmiller, B.A., Wise, R.P. 2009. Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-associated Region of Maize. Plant Physiology. doi: 10.1104. p. 109.143370. 151(2):483-495.

Comparative Transcriptomics in the Triticeae     - (Peer Reviewed Journal)

Schreiber, A.W., Sutton, T., Caldo, R.A., Kalashyan, E., Lovell, B., Mayo, G., Muehlbauer, G.J., Druka, A., Waugh, R., Wise, R.P., Langridge, P., Baumann, U. 2009. Comparative Transcriptomics in the Triticeae. BioMed Central (BMC) Genetics. 10:285.

Genomics of Biotic Interactions in the Triticeae     - (Book / Chapter)

Wise, R.P., Lauter, N.C., Szabo, L.J., Schweizer, P. 2009. Genomics of Biotic Interactions in the Triticeae. In: Feuillet, C., Muehlbauer, G., editors. Genetics and Genomics of the Triticeae. New York, NY: Springer. p. 559-589.

Towards Systems Genetic Analyses in Barley: Integration of Phenotypic, Expression and Genotype Data into GeneNetwork     - (Peer Reviewed Journal)

Druka, A., Druka, I., Centeno, A.G., Li, H., Sun, Z., Thomas, W.T., Bonar, N., Steffenson, B.J., Ullrich, S.E., Kleinhofs, A., Wise, R.P., Close, T.J., Potokina, E., Luo, Z., Wagner, C., Schweizer, G.F., Marshall, D.F., Kearsey, M.J., Williams, R.W., Waugh, R. 2008. Towards Systems Genetic Analyses in Barley: Integration of Phenotypic, Expression and Genotype Data into GeneNetwork. BioMed Central (BMC) Genetics. 9:73.

Blufensin1 Negatively Impacts Basal Defense in Response to Barley Powdery Mildew     - (Peer Reviewed Journal)

Meng, Y., Moscou, M., Wise, R.P. 2008. Blufensin1 Negatively Impacts Basal Defense in Response to Barley Powdery Mildew. Plant Physiology. 149(1):271-285.

Functional Contribution of Chorismate Synthase, Anthranilate Synthase, and Chorismate Mutase to Penetration Resistance in Barley-Powdery Mildew Interactions     - (Peer Reviewed Journal)

Hu, P., Meng, Y., Wise, R.P. 2009. Functional Contribution of Chorismate Synthase, Anthranilate Synthase, and Chorismate Mutase to Penetration Resistance in Barley-Powdery Mildew Interactions. Molecular Plant-Microbe Interactions. 22(3):311-320.

The International Barley Sequencing Consortium — At the Threshold of Efficient Access to the Barley Genome     - (Peer Reviewed Journal)

Schulte, D., Close, T.J., Graner, A., Langridge, P., Matsumoto, T., Muehlbauer, G., Sato, K., Schulman, A.H., Waugh, R., Wise, R.P., Stein, N. 2009. The International Barley Sequencing Consortium — At the Threshold of Efficient Access to the Barley Genome. Plant Physiology. 149(1):142-147.

Quantitative Genetic Dissection of Shoot Architecture Traits in Maize: Towards a Functional Genomics Approach - (Peer Reviewed Journal)

Lauter, N.C., Moscou, M.J., Habiger, J., Moose, S.P. 2008. Quantitative Genetic Dissection of Shoot Architecture Traits in Maize: Towards a Functional Genomics Approach. The Plant Genome. 01(02):99-110.

Tissue Dependent Limited Pleiotropy Affects Gene Expression in Barley     - (Peer Reviewed Journal)

Potokina, E., Druka, A., Luo, Z., Moscou, M., Wise, R.P., Waugh, R., Kearsey, M. 2008. Tissue Dependent Limited Pleiotropy Affects Gene Expression in Barley. Plant Journal. 56(2):287-296. DOI: 10.1111/j.1365-313X.2008.03601.x. Available: http://www3.interscience.wiley.com/cgi-bin/fulltext/120696653/HTMLSTART.

Exploiting Regulatory Variation to Identify Genes Underlying Quantitative Resistance to the Wheat Stem Rust Pathogen Puccinia graminis f. sp. tritici in Barley     - (Peer Reviewed Journal)

Druka, A., Potokina, E., Luo, Z., Bonar, N., Druka, I., Zhang, L., Marshall, D.F., Steffenson, B.J., Close, T.J., Wise, R.P., Kleinhofs, A., Williams, R.W., Kearsey, M.J., Waugh, R. 2008. Exploiting Regulatory Variation to Identify Genes Underlying Quantitative Resistance to the Wheat Stem Rust Pathogen Puccinia graminis f. sp. tritici in Barley. Theoretical and Applied Genetics. 117(2):261-272. Available: http://www.springerlink.com/content/x16mlth1489u8161/fulltext.html.

Construction of Coexpression Networks to Explore Barley-Powdery Mildew Interactions - (Book / Chapter)

Moscou, M.J., Caldo, R.A., Lauter, N.C., Wise, R.P. 2008. Construction of Coexpression Networks to Explore Barley-Powdery Mildew Interactions. In: Lorito, M., Woo, S.L., Scala, F., editors. Biology of Plant Microbe Interactions: The Impact of "omics." Volume 6. St. Paul, MN: APS Press. p. 113-117.

Diversification of Lrk/Tak Kinase Gene Clusters is Associated with Subfunctionalization and Cultivar-specific Transcript Accumulation in Barley     - (Peer Reviewed Journal)

Hu, P., Wise, R.P. 2008. Diversification of Lrk/Tak Kinase Gene Clusters is Associated with Subfunctionalization and Cultivar-specific Transcript Accumulation in Barley. Functional and Integrative Genomics. 8:199-209. Available: http://www.springerlink.com/content/cn67678u46506857/fulltext.html.

Gene-For-Gene-Mediated Transcriptome Reprogramming in Barley-Powdery Mildew Interactions - (Abstract Only)

Moscou, M.J., Lauter, N.C., Caldo, R.A., Wise, R.P. 2007. Gene-For-Gene-Mediated Transcriptome Reprogramming in Barley-Powdery Mildew Interactions [abstract]. Annual International Plant & Animal Genome Conference. Abstract Book. p. 88.

PLEXdb: Plant and Pathogen Expression Database and Tools for Comparative and Functional Genomics Analysis - (Abstract Only)

Cannon, E.K., Dash, S., Lu, H., Nadkarni, D., Thomas, A., Lauter, N.C., Brendel, V., Wise, R.P., Dickerson, J.A. 2007. PLEXdb: Plant and Pathogen Expression Database and Tools for Comparative and Functional Genomics Analysis [abstract]. Annual International Plant & Animal Genome Conference. Abstract Book. p. 351.

Genetical Genomic Dissection of Stem Rust Infection in Barley - (Abstract Only)

Lauter, N.C., Moscou, M.J., Rodriguez, J.E., Fuerst, G.S., Steffenson, B.J., Jin, Y., Szabo, L.J., Wise, R.P. 2007. Genetical Genomic Dissection of Stem Rust Infection in Barley [abstract]. Annual International Plant & Animal Genome Conference. Book of Abstracts. p. 17.

TEnest: Automated Chronological Annotation and Visualization of Nested Plant Transposable Elements     - (Peer Reviewed Journal)

Kronmiller, B.A., Wise, R.P. 2007. TEnest: Automated Chronological Annotation and Visualization of Nested Plant Transposable Elements. Plant Physiology. 146(1):45-59.

Gene Expression Quantitative Trait Locus Analysis of 16,000 Barley Genes Reveals a Complex Pattern of Genome-wide Transcriptional Regulation - (Peer Reviewed Journal)

Potokina, E., Druka, A., Luo, Z.W., Wise, R.P., Waugh, R., Kearsey, M.J. 2008. Gene Expression Quantitative Trait Locus Analysis of 16,000 Barley Genes Reveals a Complex Pattern of Genome-wide Transcriptional Regulation. Plant Journal. 53(1):90-101.

Transcript Profiling in Host-pathogen Interactions - (Review Article)

Wise, R.P., Moscou, M.M., Whitham, S.A., Bogdanove, A.J. 2007. Transcript Profiling in Host-pathogen Interactions. Annual Review of Phytopathology. 45:329-369.

SFP Genotyping from Affymetrix Arrays is Robust but Largely Detects Cis-acting Expression Regulators     - (Peer Reviewed Journal)

Luo, Z.W., Potokina, E., Druka, A., Wise, R.P., Waugh, R., Kearsey, M.J. 2007. SFP genotyping from Affymetrix arrays is robust but largely detects cis-acting expression regulators. Genetics. 176:789-800.

High-throughput gene expression studies provide clues for how cereal crops grow     - (Government Publication)

Wise, R.P., Muehlbauer, G. 2006. High-throughput gene expression studies provide clues for how cereal crops grow. USDA-NRI Research Highlight. 3:1-2.

Mapping multiple disease resistance genes using a barley mapping population evaluated in Peru, Mexico, and the USA     - (Peer Reviewed Journal)

Rossi, C., Cuesta-Marcos, A., Vales, I., Gomez-Pando, L., Orjeda, G., Wise, R.P., Sato, K., Hori, K., Capettini, F., Vivar, H., Chen, X., Hayes, P. 2006. Mapping multiple disease resistance genes using a barley mapping population evaluated in Peru, Mexico, and the USA. Molecular Breeding. 18(4):355-366.