Roger P Wise

Research Geneticist (Plants)

Corn Insect & Crop Genetics Research Unit

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Research Geneticist (Plants) 2213 Pammel Drive 4201 ATRB Iowa State University Ames, Iowa 50011-1101 515-294-9756 515-294-9359 (FAX)

     

Research is focused on the high-throughput functional analysis of important agronomic genes in cereal crops. We use a variety of interdisciplinary approaches, including plant and microbial genetics, molecular biology, plant pathology, and bioinformatics & computational biology. 

 

Additional Links

• Wise Lab

 

• Publications

  • (Clicking on the reprint icon will take you to the publication reprint.)
  • Transcriptome-based host epistasis and pathogen co-expression in barley-powdery mildew interactions -(Pre-print Publication)
    Velasquez-Zapata, V., Smith, S., Priyanka, S., Chapman, A.E., Wise, R.P. 2023. Transcriptome-based host epistasis and pathogen co-expression in barley-powdery mildew interactions. Genetics. https://doi.org/10.1101/2023.09.18.558274.
    
  • Bioinformatic analysis of yeast two-hybrid next-generation interaction screen data -(Book / Chapter)
    Velásquez-Zapata, V., Elmore, J.M., Wise, R.P. 2023. Bioinformatic analysis of yeast two-hybrid next-generation interaction screen data. In: Mukhtar, S., editor. Protein-Protein Interactions, Methods and Protocols. Methods in Molecular Biology. 2690:223-239. https://doi.org/10.1007/978-1-0716-3327-4_19.
    
  • Next-generation yeast two-hybrid screening to discover protein-protein interactions -(Book / Chapter)
    Elmore, J.M., Velásquez-Zapata, V., Wise, R.P. 2023. Next-generation yeast two-hybrid screening to discover protein-protein interactions. In: Mukhtar, S.,editor. Protein-Protein Interactions, Methods and Protocols. Methods in Molecular Biology. 2690:205-222. https://doi.org/10.1007/978-1-0716-3327-4_19.
    
  • Powdery mildew effectors AVRA1 and BEC1016 target the ER J-domain protein HvERdj3B required for immunity in barley-(Pre-print Publication)
    
    
  • An interolog-based barley interactome as an integration framework for immune signaling -(Peer Reviewed Journal)
    Velasquez-Zapata, V., Elmore, J., Fuerst, G.S., Wise, R.P. 2022. An interolog-based barley interactome as an integration framework for immune signaling. Genetics. 221(2). Article iyac056. https://doi.org/10.1093/genetics/iyac056.
    
  • Role of crop genetic diversity on pathogen impact: The tale of two pathogens -(Peer Reviewed Journal)
    Wlezien, E.B., Peters, N.T., Wise, R., Boury, N. 2022. Role of crop genetic diversity on pathogen impact: The tale of two pathogens. CourseSource. https://doi.org/10.24918/cs.2022.14.
    
  • SGT1-specific domain mutations impair interactions with the barley MLA6 immune receptor in association with loss of NLR protein -(Peer Reviewed Journal)
    Chapman, A.V., Elmore, J., McReynolds, M., Walley, J., Wise, R.P. 2021. SGT1-specific domain mutations impair interactions with the barley MLA6 immune receptor in association with loss of NLR protein. Molecular Plant-Microbe Interactions. 35(3):274-289. https://doi.org/10.1094/MPMI-08-21-0217-R.
    
  • Multi-layered characterization of the barley interactome links MLA immune receptor signaling with defense gene expression -(Proceedings)
    Velasquez-Zapata, V., Elmore, M.J., Fuerst, G.S., Wise, R.P. 2021. Multi-layered characterization of the barley interactome links MLA immune receptor signaling with defense gene expression. International Congress on Molecular Plant-Microbe Interactions. 34. https://doi.org/10.1094/MPMI-34-9-S2.1.
    
  • Disruption of barley immunity to powdery mildew by an in-frame Lys-Leu deletion in the essential protein SGT1 -(Proceedings)
    Chapman, A.E., Hunt, M., Surana, P., Velasquez-Zapata, V., Xu, W., Fuerst, G.S., Wise, R.P. 2021. Disruption of barley immunity to powdery mildew by an in-frame Lys-Leu deletion in the essential protein SGT1. Meeting Proceedings. 34. https://doi.org/10.1094/MPMI-34-7-S1.1.
    
  • FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences -(Peer Reviewed Journal)
    Banerjee, S., Bhandary, P., Woodhouse, M.H., Sen, T.Z., Wise, R.P., Andorf, C.M. 2021. FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. BMC Bioinformatics. 22. Article 205. https://doi.org/10.1186/s12859-021-04120-9.
    
  • Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor -(Peer Reviewed Journal)
    Velasquez-Zapata, V., Elmore, M.J., Banerjee, S., Dorman, K., Wise, R.P. 2021. Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor. PLoS Computational Biology. 17(4). Article e1008890. https://doi.org/10.1371/journal.pcbi.1008890.
    
  • Constructing Zea mays genes from RNA-Seq expression data using FINDER - a fully automated gene annotator-(Abstract Only)
    Banerjee, S., Bhandary, P., Woodhouse, M.H., Sen, T.Z., Wise, R.P., Andorf, C.M. 2021. Constructing Zea mays genes from RNA-Seq expression data using FINDER - a fully automated gene annotator. Maize Annual Meetings. 41.
    
  • FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences -(Pre-print Publication)
    Banerjee, S., Bhandary, P., Woodhouse, M.H., Sen, T.Z., Wise, R.P., Andorf, C.M. 2021. FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. bioRxiv. https://doi.org/10.1101/2021.02.04.429837.
    
  • Disruption of barley immunity to powdery mildew by an in-frame Lys-Leu deletion in the essential protein SGT1 -(Peer Reviewed Journal)
    Chapman, A.V., Hunt, M., Surana, P., Velasquez-Zapata, V., Xu, W., Fuerst, G.S., Wise, R.P. 2020. Disruption of barley immunity to powdery mildew by an in-frame Lys-Leu deletion in the essential protein SGT1. Genetics. 217(2). https://doi.org/10.1093/genetics/iyaa026.
    
  • NGPINT: a next-generation protein-protein interaction software -(Peer Reviewed Journal)
    Banerjee, S., Velasquez-Zapata, V., Fuerst, G.S., Elmore, J.M., Wise, R.P. 2020. NGPINT: a next-generation protein-protein interaction software. Briefings in Bioinformatics. 22(4). https://doi.org/10.1093/bib/bbaa351.
    
  • Small RNA discovery in the interaction between barley and the powdery mildew pathogen -(Peer Reviewed Journal)
    Hunt, M., Banerjee, S., Surana, P., Liu, M., Fuerst, G.S., Mathioni, S., Meyers, B.C., Nettleton, D., Wise, R.P. 2019. Small RNA discovery in the interaction between barley and the powdery mildew pathogen. Biomed Central(BMC)Genomics. 20. https://doi.org/10.1186/s12864-019-5947-z.
    
  • Convergent evolution of effector protease recognition by Arabidopsis and barley -(Peer Reviewed Journal)
    Carter, M., Helm, M., Chapman, A., Wan, E., Restrepo Sierra, A., Innes, R., Bogdanove, A., Wise, R.P. 2019. Convergent evolution of effector protease recognition by Arabidopsis and barley. Molecular Plant-Microbe Interactions. 32(5):550-565. https://doi.org/10.1094/MPMI-07-18-0202-FI.
    
  • A confounding effect of bacterial titer in a type III delivery-based assay of eukaryotic effector function -(Research Technical Update)
    Carter, M., Bogdanove, A., Innes, R., Wise, R.P. 2018. A confounding effect of bacterial titer in a type III delivery-based assay of eukaryotic effector function. Molecular Plant-Microbe Interactions. 31(11):1115-1116. https://doi.org/10.1094/MPMI-05-18-0128-LE.
    
  • DiffSLc: A graph centrality method to detect essential proteins of a protein-protein interaction network-(Peer Reviewed Journal)
    Mistry, D., Wise, R.P., Dickerson, J. 2017. DiffSLc: A graph centrality method to detect essential proteins of a protein-protein interaction network. PLoS One. https://doi.org/10.1371/journal.pone.0187091.
    
  • A genomic view of biotic stress resistance -(Book / Chapter)
    Elmore, J.M., Perovic, D., Ordon, F., Schweizer, P., Wise, R.P. 2018. A genomic view of biotic stress resistance. In: Stein, N., Muehlbauer, G., editors. The Barley Genome. Cham, Switzerland: Springer International. p. 233-257. https://doi.org/10.1007/978-3-319-92528-8_14.
    
  • Inter-chromosomal transfer of immune regulation during infection of barley with the powdery mildew pathogen-(Peer Reviewed Journal)
    Surana, P., Xu, R., Fuerst, G.S., Chapman, A., Nettleton, D., Wise, R.P. 2017. Inter-chromosomal transfer of immune regulation during infection of barley with the powdery mildew pathogen. Genes, Genomes, and Genomics. https://doi.org/10.1534/g3.117.300125.
    
  • Allelic barley MLA immune receptors recognize sequence-unrelated avirulence effectors of the powdery mildew pathogen-(Peer Reviewed Journal)
    Lu, X., Kracher, B., Saur, I., Bauer, S., Ellwood, S.R., Wise, R.P., Yaeno, T., Maekawa, T., Schulze-Lefert, P. 2016. Allelic barley MLA immune receptors recognize sequence-unrelated avirulence effectors of the powdery mildew pathogen. Proceedings of the National Academy of Sciences. 113(42):e6486-6495. doi:10.1073/pnas.1612947113.
    
  • iTAG Barley: A grade 7-12 curriculum to explore inheritance of traits and genes using Oregon Wolfe Barley-(Book / Chapter)
    McGhee, L., Hayes, N., Schuck, R., Maffin, L., Hall, G., Hubband, T., Whigham, E., Fuerst, G.S., Wise, R.P. 2016. iTAG Barley: A grade 7-12 curriculum to explore inheritance of traits and genes using Oregon Wolfe Barley. iTunes. Available: https://itunes.apple.com/us/book/itag-barley-grade-7-12-curriculum/id1110510488?mt=11 & https://itunes.apple.com/us/book/itag-barley-grade-7-12-curriculum/id1108586855?mt=11.
    
  • Genes and small RNA transcripts exhibit dosage-dependent expression pattern in maize copy-number alterations-(Peer Reviewed Journal)
    Zuo, T., Zhang, J., Lithio, A., Dash, S., Weber, D., Wise, R.P., Nettleton, D., Peterson, T. 2016. Genes and small RNA transcripts exhibit dosage-dependent expression pattern in maize copy-number alterations. Genetics. 203(1):1177-1190. doi: 10.1534/genetics.116.188235.
    
  • Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome-(Peer Reviewed Journal)
    Munoz-Amatriain, M., Lonardi, S., Luo, M., Madishetty, K., Svensson, J., Moscou, M., Wanamaker, S., Jiang, T., Kleinhofs, A., Muehlbauer, G., Wise, R.P., Stein, N., Ma, Y., Rodriguez, E., Kudrna, D., Bartos, J., Bhat, P., Chao, S., Condamine, P., Heinen, S., Resnik, J., Wing, R., Witt, H., Alpert, M., Beccuti, M., Bozdag, S., Cordero, F., Mirebrahim, H., Ounit, R., Wu, Y., You, F., Zheng, J., Dolezel, J., Grimwood, J., Schmutz, J., Duma, D., Altschmied, L., Blake, T., Bregitzer, P.P., Cooper, L., Dilbirligi, M., Falk, A., Feiz, L., Graner, A., Gustafson, P., Hayes, P., Lemaux, P., Mammadov, J., Close, T. 2015. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant Journal. 84(1):216-227. doi: 10.1111/tpj.12959.
    
  • The knottin-like Blufensin family regulates genes involved in nuclear import and the secretory pathway in barley-powdery mildew interactions-(Peer Reviewed Journal)
    Xu, W., Meng, Y., Surana, P., Fuerst, G.S., Nettleton, D., Wise, R.P. 2015. The knottin-like Blufensin family regulates genes involved in nuclear import and the secretory pathway in barley-powdery mildew interactions. Frontiers in Plant Science. 6:409. DOI:10.3389/fpls.2015.00409.
    
  • Broadly conserved fungal effector BEC1019 suppresses host cell death and enhances pathogen virulence in powdery mildew of barley (Hordeum vulgare L.)-(Peer Reviewed Journal)
    Whigham, E., Qi, S., Mistry, D., Surana, P., Xu, R., Fuerst, G.S., Pliego, C., Bindschedler, L., Spanu, P., Dickerson, J., Innes, R.W., Nettleton, D., Bogdanove, A.J., Wise, R.P. 2015. Broadly conserved fungal effector BEC1019 suppresses host cell death and enhances pathogen virulence in powdery mildew of barley (Hordeum vulgare L.). Molecular Plant-Microbe Interactions. 28(9): 968-983. DOI: http://dx.doi.org/10.1094/MPMI-02-15-0027-FI.
    
  • The miR9863 family regulates distinct Mla alleles in barley to attenuate NLR receptor-triggered disease resistance and cell-death signaling-(Peer Reviewed Journal)
    Liu, J., Cheng, X., Liu, D., Xu, W., Wise, R.P., Shen, Q. 2014. The miR9863 family regulates distinct Mla alleles in barley to attenuate NLR receptor-triggered disease resistance and cell-death signaling. PLoS Genetics. 10(12):e1004755. DOI:10.1371/journal.pgen.1004755.
    
  • Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene-(Peer Reviewed Journal)
    Cernadas, R.A., Doyle, E.L., Nino-Liu, D., Wilkins, K.E., Bancroft, T., Wang, L., Schmidt, C., Caldo, R., Yang, B., White, F.F., Nettleton, D., Wise, R.P., Bogdanove, A. 2014. Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene. PLoS Pathogens. DOI: 10.1371/journal.ppat.1003972.
    
  • Mla- and Rom1-mediated control of microRNA398 and chloroplast copper/zinc superoxide dismutase regulates cell death in response to the barley powdery mildew fungus-(Peer Reviewed Journal)
    Xu, W., Meng, Y., Wise, R.P. 2014. Mla- and Rom1-mediated control of microRNA398 and chloroplast copper/zinc superoxide dismutase regulates cell death in response to the barley powdery mildew fungus. New Phytologist. 201(4):1396-1412.
    
  • iTAG Barley: A 9-12 curriculum to explore inheritance of traits and genes using Oregon Wolfe barley-(Book / Chapter)
    Hayes, N., Maffin, L., McGhee, L., Hall, G., Hubbard, T., Whigham, E., Wise, R.P. 2013. iTAG Barley: A 9-12 curriculum to explore inheritance of traits and genes using Oregon Wolfe barley. iTunes. Available: https://itunes.apple.com/us/book/itag-barley/id715260619?mt=11.
    
  • Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)-(Peer Reviewed Journal)
    Mascher, M., Muehlbauer, G.J., Rokhsar, D.S., Chapman, J., Schmutz, J., Barry, K., Munoz-Amatriain, M., Close, T.J., Wise, R.P., Schulman, A.H., Himmelbach, A., Mayer, K.F., Scholz, U., Poland, J.A., Stein, N., Waugh, R. 2013. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant Journal. DOI: 10.1111/tpj.12319.
    
  • 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.
    
  • Host-Induced gene silencing in barley powdery mildew reveals a class of ribonuclease-like effectors-(Peer Reviewed Journal)
    Pliego, C., Nowara, D., Bonciani, G., Gheorghe, D., Xu, R., Surana, P., Whigham, E., Nettleton, D., Bogdanove, A., Wise, R.P., Schweizer, P., Bindschedler, L., Spanu, P. 2013. Host-Induced gene silencing in barley powdery mildew reveals a class of ribonuclease-like effectors. Molecular Plant-Microbe Interactions. 26(6):633-642.
    
  • Flor revisited (again): eQTL and mutational analysis of NB-LRR mediated immunity to powdery mildew in barley-(Peer Reviewed Journal)
    Wise, R.P., Surana, P., Fuerst, G.S., Xu, R., Mistry, D., Dickerson, J., Nettleton, D. 2014. Flor revisited (again): eQTL and mutational analysis of NB-LRR mediated immunity to powdery mildew in barley. Journal of Integrative Agriculture. 13(2):237-243.
    
  • A physical, genetic and functional sequence assembly of the barley genome-(Peer Reviewed Journal)
    Mayer, K., Waugh, R., Langridge, P., Close, T.J., Wise, R.P., Graner, A., Matsumoto, T., Sato, K., Schulman, A., Muehlbaueer, G.J., Stein, N., Ariyadasa, R., Schulte, D., Poursarebani, N., Zhou, R., Steuernagel, B., Mascher, M., Scholz, U., Shi, B., Madishetty, K., Svensson, J.T., Bhat, P., Moscou, M., Resnik, J., Hedley, P., Liu, H., Morris, J., Frenkel, Z., Korol, A., Berges, H., Taudien, S., Felder, M., Groth, M., Platzer, M., Himmelbach, A., Lonardi, S., Duma, D., Alpert, M., Cordero, F., Beccuti, M., Ciardo, G., Ma, Y., Wanamaker, S., Cattonaro, F., Vendramin, V., Scalabrin, S., Radovic, S., Wing, R., Morgante, M., Nussbaumer, T., Gundlach, H., Martis, M., Poland, J.A., Spannagl, M., Pfeifer, M., Moisy, C., Tanskanen, J., Zuccolo, A., Russell, J., Druka, A., Marshall, D., Bayer, M., Sampath, D., Febrer, M., Caccamo, M., Tanaka, T., Platzer, M., Fincher, G., Schmutzer, T. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature. 491:711-716.
    
  • TEnest 2.0: Computational annotation and visualization of nested transposable elements-(Book / Chapter)
    Kronmiller, B.A., Wise, R.P. 2013. TEnest 2.0: Computational annotation and visualization of nested transposable elements. In: Peterson, T., editor. Methods in Molecular Biology. New York, NY: Springer. p. 305-320.
    
  • HvWRKY10, HvWRKY19, and HvWRKY28 positively regulate Mla-triggered immunity and basal defense to barley powdery mildew-(Peer Reviewed Journal)
    Meng, Y., Wise, R.P. 2012. HvWRKY10, HvWRKY19, and HvWRKY28 positively regulate Mla-triggered immunity and basal defense to barley powdery mildew. Molecular Plant-Microbe Interactions. DOI:10.1094/MPMI-04-12-0082-R.
    
  • The hordeum toolbox - the barley CAP genotype and phenotype resource-(Peer Reviewed Journal)
    Blake, V.C., Kling, J.G., Hayes, P.M., Jannink, J., Jillella, S.R., Lee, J., Matthews, D.E., Chao, S., Close, T.J., Muehlbauer, G.J., Smith, K.P., Wise, R.P., Dickerson, J.A. 2012. The hordeum toolbox - the barley CAP genotype and phenotype resource. The Plant Genome. DOI: 10.385/plantgenome2012.03.0002.
    
  • 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.
    
  • iTAG Barley: A 9-12 classroom module to explore gene expression and segregation using Oregon Wolfe Barley-(Book / Chapter)
    Maffin, L., Hall, G., Hubbard, T., Whigham, E., Wise, R.P. 2012. iTAG Barley: A 9-12 classroom module to explore gene expression and segregation using Oregon Wolfe Barley. American Society of Plant Biologists. http://c.ymcdn.com/sites/my.aspb.org/resource/group/a9372bf4-9ae4-4d0b-ad0c-595c9dfc3543/itag_v20_march_2013.pdf.
    
  • PLEXdb: Gene expression resources for plants and plant pathogens-(Peer Reviewed Journal)
    Dash, S., Van Hemert, J., Hong, L., Wise, R.P., Dickerson, J.A. 2011. PLEXdb: Gene expression resources for plants and plant pathogens. Nucleic Acids Research. 40(D1):D1194-D1201.
    
  • Rf8-mediated T-urf13 transcript accumulation coincides with a pentatricopeptide repeat cluster on maize chromosome 2L-(Peer Reviewed Journal)
    Meyer, J.M., Pei, D., Wise, R.P. 2011. Rf8-mediated T-urf13 transcript accumulation coincides with a pentatricopeptide repeat cluster on maize chromosome 2L. The Plant Genome. 4(3):283-299.
    
  • 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.
    
  • Targeting of the rice transcriptome by TAL effectors of Xanthomonas oryzae -(Book / Chapter)
    Nino-Liu, D.O., Bancroft, T., Rajaram, M.L., Moscou, M., Caldo, R., Schmidt, C., Dorman, K., Yang, B., Patil, P., Szurek, B., Koebnik, R., Van Sluys, M., Leach, J.E., Salzberg, S.L., White, F.F., Nettleton, D., Wise, R.P., Bogdanove, A.J. 2017. Targeting of the rice transcriptome by TAL effectors of Xanthomonas oryzae. In: Wolpert, T., Shiraishi T., Collmer A., Akimitsu K., and Glazebrook J., editors. Genome-Enabled Analysis of Plant-Pathogen Interactions. St. Paul, Minnesota: American Phytopathological Society Press. p.193-206. https://doi.org/10.1094/9780890544983.021.
    
  • 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.
    
  • 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.
    
  • 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 18:355-366.
    
  • CONTRIBUTION OF GENETIC DIVERSITY TO TYPE I ERRORS IN SHORT-OLIGONUCLEOTIDE MICROARRAY ANALYSIS-(Peer Reviewed Journal)
    Kirst, M., Caldo, R., Casati, P., Tanimoto, G., Walbot, V., Wise, R.P., Buckler Iv, E.S. 2006. Contribution of genetic diversity to type 1 errors in short-oligonucleotide microarray analysis. Plant Biotechnology Journal. 4:489-498.
    
  • Stage-specific Suppression of Basal Defense Discriminates Barley Plants Containing Fast- and Delayed-acting Mla Powdery Mildew Resistance Alleles-(Peer Reviewed Journal)
    Caldo, R.A., Nettleton, D., Peng, J., Wise, R.P. 2006. Stage-specific Suppression of Basal Defense Discriminates Barley Plants Containing Fast- and Delayed-acting Mla Powdery Mildew Resistance Alleles. Molecular Plant-Microbe Interactions. 19(9):939-947.
    
  • ESTIMATING THE NUMBER OF TRUE NULL HYPOTHESES FROM A HISTOGRAM OF P-VALUES-(Peer Reviewed Journal)
    Nettleton, D., Hwang, G., Caldo, R.A., Wise, R.P. 2006. Estimating the number of true null hypotheses from a histogram of p-values. Journal of Agricultural, Biological, and Environmental Statistics. 11:337-356.
    
  • BarleyBase/PLEXdb: A Unified Expression Profiling Database for Plants and Plant Pathogens-(Book / Chapter)
    Wise, R.P., Caldo, R.A., Hong, L., Shen, L., Dickerson, J.A. 2007. BarleyBase/PLEXdb: A Unified Expression Profiling Database for Plants and Plant Pathogens. In: David Edwards editor. Plant Bioinformatics: Methods and Protocols. Secaucus, N.J. Springer. p. 347-363.
    
  • UPSTREAM OPEN READING FRAMES OF THE BARLEY MLA13 POWDERY MILDEW RESISTANCE GENE FUNCTION COOPERATIVELY TO DOWN-REGULATE TRANSLATION-(Peer Reviewed Journal)
    Halterman, D.A., Wise, R.P. 2006. Upstream open reading frames of the barley Mla13 powdery mildew resistance gene function cooperatively to down-regulate translation. Molecular Plant Pathology. 7:167-176.
    
  • AN ATLAS OF GENE EXPRESSION FROM SEED TO SEED THROUGH BARLEY DEVELOPMENT-(Peer Reviewed Journal)
    Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, N., Schreiber, A., Wise, R.P., Close, T., Kleinhofs, A. 2006. An atlas of gene expression from seed to seed through barley development. Functional and Integrative Genomics. 6(3):202-211.
    
  • INTERPLAY OF GENE-SPECIFIC DISEASE RESISTANCE, BASAL DEFENSE, AND THE SUPPRESSION OF HOST RESPONSES TO BARLEY POWDERY MILDEW-(Book / Chapter)
    Caldo, R.A., Nettleton, D., Wise, R.P. 2006. Interplay of gene-specific disease resistance, basal defense, and the suppression of host responses to barley powdery mildew. In: Sanchez, F., Quinto, C., Lopez-Lara, I., Geiger, O., editors. Biology of Plant Microbe Interactions. St. Paul, MN: International Society of Molecular Plant-Microbe Interactions. Vol. 5, p. 620-624.
    
  • BARLEYBASE/WHEATPLEX: THE TRITICEAE HUB OF PLEXDB PLANT EXPRESSION DATABASE-(Proceedings)
    Wise, R.P., Shen, L., Gong, J., Xin, J., Caldo, R., Nettleton, D., Dickerson, J. 2005. BarleyBase/WheatPLEX: The triticeae hub of PLEXdb plant expression database. International Triticeae Mapping Initiative Workshop. Available: http://wheat.pw.usda.gov/ITMI/ITMI2005/Wise_BarleyBase/.
    
  • INTERPLAY OF GENE-SPECIFIC DISEASE RESISTANCE, BASAL DEFENSE, AND THE SUPPRESSION OF HOST-RESPONSES-(Proceedings)
    Caldo, R.A., Nettleton, D., Wise, R.P. 2005. Interplay of gene-specific disease resistance, basal defense, and the suppression of host-responses. 2005 Society for In Vitro Biology Proceedings. PS1.
    
  • AFFYMETRIX MAIZE PILOT EXPRESSION ARRAY-(Proceedings)
    Williams, A., Caldo, R., Hanna, D., McLean, L., Tanimoto, G., Wise, R.P. 2005. Affymetrix maize pilot expression array. Plant and Animal Genome XIII Conference Proceedings. P897.
    
  • BARLEYBASE - PUTTING LARGE-SCALE PLANT EXPRESSION PROFILING DATA INTO A FUNCTIONAL GENOMICS CONTEXT-(Proceedings)
    Shen, L., Gong, J., Caldo, R.A., Nettleton, D., Cook, D., Wise, R.P., Dickerson, J.A. 2005. BarleyBase - Putting large-scale plant expression profiling data into a functional genomics context. Plant and Animal Genome XIII Conference Proceedings. P878.
    
  • INDUCTION OF BASAL DEFENSE DIFFERENTIATES RAPID AND DELAYED HOST-SPECIFIC BARLEY RESISTANCE TO POWDERY MILDEW-(Proceedings)
    Caldo, R.A., Nettleton, D., Wise, R.P. 2005. Induction of basal defense differentiates rapid and delayed host-specific barley resistance to powdery mildew. Plant and Animal Genome XIII Conference Proceedings. P665.
    
  • MULTIPLE UPSTREAM OPEN READING FRAMES OF THE BARLEY MLA13 POWDERY MILDEW RESISTANCE GENE COLLECTIVELY DOWN-REGULATE TRANSLATION-(Proceedings)
    Halterman, D.A., Wise, R.P. 2005. Multiple Upstream Open Reading Frames Of The Barley Mla13 Powdery Mildew Resistance Gene Collectively Down-Regulate Translation. XIII Plant and Animal Genome Conference Proceedings. p. P729.
    
  • SEQUENCING A 1.3 MB CONTIG SPANNING THE RF1 FERTILITY RESTORER LOCUS AS A PROTOTYPE TO ASSESS COMPLEX-GENOME COVERAGE STRATEGIES-(Proceedings)
    Kronmiller, B., Gobelman Werner, K.S., Wise, R.P. 2005. Sequencing a 1.3 Mb contig spanning the rf1 fertility restorer locus as a prototype to assess complex-genome coverage strategies. 47th Annual Maize Genetics Conference Abstracts. P184.
    
  • BARLEYBASE - AN EXPRESSION PROFILING DATABASE FOR PLANT GENOMICS-(Peer Reviewed Journal)
    Shen, L., Gong, J., Caldo, R.A., Nettleton, D., Cook, D., Wise, R.P., Dickerson, J.A. 2005. Barleybase - an expression profiling database for plant genomics. Nucleic Acids Research. 33:D614-D618.
    
  • FLOR REVISITED: SYSTEMS BIOLOGY IN BARLEY-POWDERY MILDEW INTERACTIONS-(Proceedings)
    Wise, R.P., Caldo, R.A., Halterman, D.A., Nettleton, D.A. 2004. Flor revisited: Systems biology in barley-powdery mildew interactions. Cereal Rusts and Mildews Conference European and Mediterranean Proceedings. Abstract 1.14, Cereal Rusts and Powdery Mildews Bulletin.
    
  • INTERACTION-DEPENDENT GENE EXPRESSION IN MLA-SPECIFIED RESPONSE TO BARLEY POWDERY MILDEW-(Peer Reviewed Journal)
    Caldo, R.A., Nettleton, D.A., Wise, R.P. 2004. Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. The Plant Cell. 16:2514-2528.
    
  • SYSTEMS BIOLOGY IN BARLEY POWDERY MILDEW INTERACTIONS-(Proceedings)
    
    
  • COMPARATIVE ANALYSIS OF A ONE-MEGABASE SEQUENCE SPANNING THE MAIZE RF1 FERTILITY RESTORER WITH THE RICE GENOME-(Proceedings)
    Kronmiller, B., Gobelman Werner, K.S., Wise, R.P. 2004. Comparative analysis of a one-megabase sequence spanning the maize rf1 fertility restorer with the rice genome. Proceedings of Keystone Symposia "Comparative Genomics of Plants." p. 117.
    
  • A SINGLE AMINO ACID SUBSTITUTION IN THE SIXTH LEUCINE-RICH REPEAT OF BARLEY MLA6 AND MLA13 ALLEVIATES DEPENDENCE ON RAR1 FOR DISEASE RESISTANCE SIGNALING-(Proceedings)
    Halterman, D.A., Wise, R.P. 2004. A single amino acid substitution in the sixth leucine-rich repeat of barley Mla6 and Mla13 alleviates dependence on Rar1 for disease resistance signaling. Plant and Animal Genome Conference Proceedings. XII Conference. p. 858.
    
  • PARALLEL GENE EXPRESSION ANALYSIS IN CEREAL DEVELOPMENT-(Proceedings)
    Druka, A., Muehlbauer, G., Caldo, R., Wise, R.P., Close, T., Kleinhofs, A., Graner, A., Schulman, A., Langridge, P., Sato, K., Hayes, P., Marshall, D., Waugh, R. 2004. Parallel gene expression analysis in cereal development. Plant and Animal Genome XII Conference. p. 783.
    
  • BARLEYBASE - AN EXPRESSION PROFILING DATABASE FOR CEREAL GENOMICS-(Proceedings)
    Tang, X., Gong, J., Xin, J., Lishuang, S., Turner, S., Caldo, R., Nettleton, D., Wise, R.P., Dickerson, J. 2004. BarleyBase - An expression profiling database for cereal genomics. Plant and Animal Genome XII Conference. p. 944.
    
  • COMPARATIVE ANALYSIS OF A ONE-MEGABASE SEQUENCE SPANNING THE MAIZE RF1 FERTILITY RESTORER WITH THE RICE GENOME-(Abstract Only)
    Kronmiller, B., Gobelman Werner, K.S., Wise, R.P. 2004. Comparative analysis of a one-megabase sequence spanning the maize Rf1 fertility restorer with the rice genome. 46th Maize Genetics Conference. p. 112.
    
  • PARALLEL EXPRESSION PROFILING OF GENE-FOR-GENE-SPECIFIED RESPONSES IN BARLEY-POWDERY MILDEW INTERACTIONS-(Proceedings)
    Wise, R.P., Caldo, R.A., Nettleton, D.A. 2004. Parallel expression profiling of gene-for-gene-specified responses in barley-powdery mildew interactions.Plant and Animal Genome XII Conference. p. W33.
    
  • DECIPHERING RAR1 SIGNALING SPECIFICITY IN BARLEY/POWDERY MILDEW INTERACTIONS-(Proceedings)
    Halterman, D.A., Wise, R.P. 2004. Deciphering Rar1 signaling specificity in barley/powdery mildew interactions. Plant and Animal Genome Conference Proceedings. XII Conference. p. W199.
    
  • PROBE-LEVEL ANALYSIS OF GENE-FOR-GENE-SPECIFIED RESPONSES IN BARLEY-POWDERY MILDEW INTERACTIONS-(Proceedings)
    Wise, R.P., Caldo, R.A., Nettleton, D.S., Dickerson, J.A. 2004. Probe-level analysis of gene-for-gene-specified responses in barley-powdery mildew interactions. Plant and Animal Genome Conference Proceedings. XII Conference. p. W264.
    
  • PHYSICAL MAPPING OF NEW LRK AND TAK RECEPTOR-LIKE KINASE GENE CLUSTERS IN BARLEY-(Proceedings)
    Hu, P., Wise, R.P. 2004. Physical mapping of new Lrk and Tak receptor-like kinase gene clusters in barley. Plant and Animal Genome Conference Proceedings. XII Conference. p. 857.
    
  • INTERPLAY OF NON-SPECIFIC AND SPECIFIC MODULATION PATTERNS OF BARLEY TRANSCRIPTIONAL RESPONSES DURING POWDERY MILDEW INFECTION-(Proceedings)
    Caldo, R.A., Nettleton, D., Wise, R.P. 2004. Interplay of non-specific and specific modulation patterns of barley transcriptional responses during powdery mildew infection. Plant and Animal Genome Conference Proceedings. XII Conference. p. 793.
    
  • A SINGLE AMINO ACID SUBSTITUTION IN THE SIXTH LEUCINE-RICH REPEAT OF BARLEY MLA6 AND MLA13 ALLEVIATES DEPENDENCE ON RAR1 FOR DISEASE RESISTANCE SIGNALING-(Peer Reviewed Journal)
    Halterman, D.A., Wise, R.P. 2004. A single amino acid substitution in the sixth leucine-rich repeat of barley MLA6 and MLA13 alleviates dependence on RAR1 for disease resistance signaling. Plant Journal. 38:215-226.
    
  • A NEW RESOURCE FOR CEREAL GENOMICS: 22K BARLEY GENECHIP COMES OF AGE-(Peer Reviewed Journal)
    Close, T., Wanamaker, S., Caldo, R., Turner, S., Ashlock, D., Dickerson, J., Wing, R., Muehlbauer, G., Kleinhofs, A., Wise, R.P. 2004. A new resource for cereal genomics: 22k barley genechip comes of age. Plant Physiology. 134:960-968.
    
  • A SINGLE AMINO ACID SUBSTITUTION IN THE SIXTH LEUCINE-RICH REPEAT OF BARLEY MLA ALLEVIATES DEPENDENCE ON RAR1 FOR DISEASE RESISTANCE SIGNALING-(Proceedings)
    HALTERMAN, D.A., WISE, R.P. A SINGLE AMINO ACID SUBSTITUTION IN THE SIXTH LEUCINE-RICH REPEAT OF BARLEY MLA ALLEVIATES DEPENDENCE ON RAR1 FOR DISEASE RESISTANCE SIGNALING. AVAILABLE FROM: http://www.apsnet.org/meetings/2003/abstracts/a03ma232.htm. AMERICAN PHYTOPATHOLOGICAL SOCIETY ANNUAL MEETING. 2003. Phytopathology 93:S32 Publication no. P-2003-0232-AMA.
    
  • A SINGLE AMINO ACID SUBSTITUTION IN THE SIXTH LEUCINE-RICH REPEAT OF BARLEY MLA ALLEVIATES DEPENDENCE ON RAR1 FOR DISEASE RESISTANCE SIGNALING-(Proceedings)
    HALTERMAN, D.A., WISE, R.P. A SINGLE AMINO ACID SUBSTITUTION IN THE SIXTH LEUCINE-RICH REPEAT OF BARLEY MLA ALLEVIATES DEPENDENCE ON RAR1 FOR DISEASE RESISTANCE SIGNALING. AVAILABLE FROM: http://abstracts.aspb.org/pb2003/public/P49/1386.html. AMERICAN SOCIETY OF PLANT BIOLOGISTS ANNUAL MEETING. 2003. Poster 821 Session 49; Plant Pathogen/Symbiont Interactions.
    
  • PARALLEL EXPRESSION PROFILING OF GENE-FOR-GENE-SPECIFIED RESPONSES IN BARLEY-POWDERY MILDEW INTERACTIONS-(Proceedings)
    CALDO, R., NETTLETON, D., TURNER, S., DICKERSON, J., WISE, R.P. PARALLEL EXPRESSION PROFILING OF GENE-FOR-GENE-SPECIFIED RESPONSES IN BARLEY-POWDERY MILDEW INTERACTIONS. AVAILABLE FROM: http://www.ispmb2003.com/. PLANT MOLECULAR BIOLOGY INTERNATIONAL CONFERENCE PROCEEDINGS. 2003. Poster S21-51.
    
  • COMPREHENSIVE TRANSCRIPTIONAL PROFILING OF BARLEY-POWDERY MILDEW INTERACTIONS USING AFFYMETRIX GENECHIPS-(Proceedings)
    CALDO, R., NETTLETON, D., TURNER, S., ASHLOCK, D., DICKERSON, J., WISE, R.P. COMPREHENSIVE TRANSCRIPTIONAL PROFILING OF BARLEY-POWDERY MILDEW INTERACTIONS USING AFFYMETRIX GENECHIPS. AVAILABLE FROM: http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=658. KEYSTONE SYMPOSIA. 2003.
    
  • POWDERY MILDEW INDUCED MLA MRNAS ARE ALTERNATIVELY SPLICED AND CONTAIN UPSTREAM OPEN READING FRAMES THAT CUMULATIVELY DOWN-REGULATE TRANSLATION-(Proceedings)
    HALTERMAN, D.A., WISE, R.P. POWDERY MILDEW INDUCED MLA MRNAS ARE ALTERNATIVELY SPLICED AND CONTAIN UPSTREAM OPEN READING FRAMES THAT CUMULATIVELY DOWN-REGULATE TRANSLATION. AVAILABLE FROM: http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=658. KEYSTONE SYMPOSIA. 2003.
    
  • MLA RESISTANCE SPECIFICITIES ARE NOT LINEAR DESCENDANTS OF A COMMON ANCESTOR, BUT EVOLVED SEPARATELY SUBSEQUENT TO GENE DUPLICATION-(Proceedings)
    HALTERMAN, D.A., WISE, R.P. MLA RESISTANCE SPECIFICITIES ARE NOT LINEAR DESCENDANTS OF A COMMON ANCESTOR, BUT EVOLVED SEPARATELY SUBSEQUENT TO GENE DUPLICATION. AVAILABLE FROM: http://www.intl-pag.org/11/abstracts/P7b_P828_XI.html. PLANT AND ANIMAL GENOME CONFERENCE PROCEEDINGS. 2003. ABSTRACT NO. P828.
    
  • POWDERY MILDEW INDUCED MLA MRNAS ARE ALTERNATIVELY SPLICED AND CONTAIN UPSTREAM OPEN READING FRAMES THAT CUMULATIVELY DOWN REGULATE TRANSLATION-(Proceedings)
    HALTERMAN, D.A., WEI, F., WISE, R.P. POWDERY MILDEW INDUCED MLA MRNAS ARE ALTERNATIVELY SPLICED AND CONTAIN UPSTREAM OPEN READING FRAMES THAT CUMULATIVELY DOWN REGULATE TRANSLATION. AVAILABLE FROM: http://www.intl-pag.org/11/abstracts/P7b_P827_XI.html. PLANT AND ANIMAL GENOME CONFERENCE PROCEEDINGS. 2003. ABSTRACT NO. P827.
    
  • PARALLEL EXPRESSION ANALYSIS USING BARLEY MICROARRAYS-(Abstract Only)
    Wise, R.P., Caldo, R.A., Turner, S., Ashlock, D., Dickerson, J. 2003. Parallel expression analysis using barley microarrays. Plant and Animal Genome Conference Proceedings. XI Conference. p. W50.
    
  • EVOLUTIONARY ORGANIZATION OF THE MLA LOCUS IN THE POACEAE-(Abstract Only)
    Turner, S., Wise, R.P. 2003. Evolutionary organization of the Mla locus in the poaceae. Plant and Animal Genome Conference Proceedings. XI Conference. p. 351.
    
  • GENOME-WIDE PHYSICAL MAPPING OF PATHOGEN-RESPONSE GENES IN BARLEY-(Abstract Only)
    Hu, P., Wise, R.P. 2003. Genome-wide physical mapping of pathogen-response genes in barley. Plant and Animal Genome Conference Proceedings. XI Conference. p. 403.
    
  • ELUCIDATION OF THE INCOMPATIBLE AND COMPATIBLE BARLEY-POWDERY MILDEW INTERACTIONS USING AFFYMETRIX GENECHIPS: A MICROARRAY REPRESENTATION OF THE QUADRATIC CHECK-(Abstract Only)
    Caldo, R.A., Wise, R.P. 2003. Elucidation of the incompatible and compatible barley-powdery mildew interactions using affymetrix genechips: a microarray representation of the quadratic check. Plant and Animal Genome Conference Proceedings. XI Conference. p. 758.
    
  • POWDERY MILDEW INDUCED MLA MRNAS ARE ALTERNATIVELY SPLICED AND CONTAIN UPSTREAM OPEN READING FRAMES-(Peer Reviewed Journal)
    Halterman, D.A., Wei, F., Wise, R.P. 2003. Powdery mildew induced Mla mRNAs are alternatively spliced and contain upstream open reading frames. Plant Physiology. 131(2):558-567.
    
  • ALTERNATIVE TRANSCRIPTION INITIATION SITES AND POLYADENYLATION SITES ARE RECRUITED DURING MU SUPPRESSION AT THE RF2A LOCUS OF MAIZE-(Peer Reviewed Journal)
    Cui, X., Hsia, A., Liu, F., Ashlock, D.A., Wise, R.P., Schnable, P.S. 2003. Alternative transcription initiation sites and polyadenylation sites are recruited during Mu suppression at the rf2a locus of maize. Genetics. 163:685-698.
    
  • NUCLEAR-MEDIATED MITOCHONDRIAL GENE REGULATION AND MALE FERTILITY IN HIGHER PLANTS: LIGHT AT THE END OF THE TUNNEL?-(Review Article)
    Wise, R.P., Pring, D.R. 2002. Nuclear-mediated mitochondrial gene regulation and male fertility in higher plants: light at the end of the tunnel? Proceedings of the National Academy of Sciences. 99:10240-10242.
    
  • RDS AND RIH MEDIATE HYPERSENSITIVE CELL DEATH INDEPENDENT OF GENE-FOR-GENE RESISTANCE TO THE OAT CROWN RUST PATHOGEN, PUCCINIA CORONATA F. SP. AVENAE-(Government Publication)
    
    
  • RESISTANCE GENE-(Patent Application)
    Wise, R.P., Schulze-Lefert, P., Zhou, F., Kurth, J., Halterman, D.A., Wei, F., Elliot, C. 2002. Resistance gene. Patent Application. U.S. Patent 10/148,351.
    
  • GENOME DYNAMICS AND EVOLUTION OF THE MLA (POWDERY MILDEW) RESISTANCE LOCUS IN BARLEY-(Peer Reviewed Journal)
    
    
  • RECOGNITION SPECIFICITY AND POST-TRANSCRIPTIONAL REGULATION OF MLA (POWDERY MILDEW) RESISTANCE ALLELES IN BARLEY-(Abstract Only)
    
    
  • FUNCTIONAL ANALYSIS AND MOLECULAR EVOLUTION OF THE MLA PLANT-DEFENSE COMPLEX-(Abstract Only)
    
    
  • NUCLEAR-DIRECTED MODIFICATION OF MITOCHONDRIAL TRANSCRIPTS IN CMS-T MAIZE-(Abstract Only)
    
    
  • VECTOR-BASED HOMOLOGY ANALYSIS OF DATA SETS FROM DIVERSE TAXA FOR A TRITICEAE MICROARRAY-(Abstract Only)
    
    
  • THE GENE-RICH MLA-REGION CONTAINS DIFFERENTIALLY EXPRESSED, DEFENSE GENE FAMILIES INTERSPERSED WITH NESTED RETROTRANSPOSONS-(Abstract Only)
    
    
  • RDS AND RIH MEDIATE HYPERSENSITIVE CELL DEATH INDEPENDENT OF GENE-FOR-GENE RESISTANCE TO THE OAT CROWN RUST PATHOGEN, PUCCINIA CORONATA F. SP. AVENAE-(Peer Reviewed Journal)
    
    
  • EVOLUTION OF A PLANT-DEFENSE GENE CLUSTER-(Abstract Only)
    
    
  • CHARACTERIZATION OF MLA-MEDIATED POWDERY MILDEW RESISTANCE IN BARLEY-(Abstract Only)
    
    
  • THE MLA6 COILED-COIL, NBS-LRR PROTEIN CONFERS AVRMLA6-DEPENDENT RESISTANCE SPECIFICITY TO BLUMERIA GRAMINIS F. SP. HORDEI IN BARLEY AND WHEAT-(Abstract Only)
    
    
  • THE MLA6 COILED-COIL, NBS-LRR PROTEIN CONFERS AVRMLA6-DEPENDENT RESISTANCE SPECIFICITY TO BLLUMERIA GRAMINIS F. SP. HORDEI IN BARLEY AND WHEAT-(Peer Reviewed Journal)
    
    
  • CELL-AUTONOMOUS EXPRESSION OF BALEY MLA1 CONFERS RACE--SPECIFIC RESISTANCE TO THE POWDRY MILDEW FUNGUS VIA A RAR1 INDEPENDENT SIGNALING PATHWAY-(Peer Reviewed Journal)
    
    
  • SEQUENCE ANALYSIS OF THE 270-KB MLA-SPANNING REGION REVEALS COUPLED DEFENSE GENE FAMILIES-(Abstract Only)
    
    
  • DISEASE RESISTANCE: WHATS BREWING IN BARLEY GENOMICS-(Review Article)
    
    
  • RAPD-DERIVED MARKERS FLANKING THE MLA RESISTANCE GENE CLUSTER IN BARLEY-(Peer Reviewed Journal)
    
    
  • FUNCTIONAL ANALYSIS OF MLA-MEDIATED POWDERY MILDEW RESISTANCE IN BARLEY-(Abstract Only)
    
    
  • UNRAVELING THE MAIZE RF1 GENOMIC REGION-(Abstract Only)
    
    
  • AN ANCHORED AFLP AND RETROTRANSPOSON-BASED MAP OF DIPLOID AVENA-(Peer Reviewed Journal)
    
    
  • THE MLA CLUSTER OF BARLEY IS ASSOCIATED WITH THREE INTERSPERSED FAMILIES OF NBS-LRR TYPE RESISTANCE GENES-(Abstract Only)
    
    
  • A BACTERIAL ARTIFICIAL CHROMOSOME LIBRARY FOR BARLEY (HORDEUM VULGARE L.) AND THE IDENTIFICATION OF CLONES CONTAINING PUTATIVE RESISTANCE GENES-(Peer Reviewed Journal)
    
    
  • THE MLA (POWDERY MILDEW) RESISTANCE CLUSTER IS ASSOCIATED WITH THREE NBS- LRR GENE FAMILIES AND SUPPRESSED RECOMBINATION WITHIN A 240-KB DNA INTERVAL ON CHROMOSOME 5S (1HS) OF BARLEY-(Peer Reviewed Journal)
    
    
  • CHROMOSOME LANDING AND SEQUENCE ANALYSIS OF THE MLA RESISTANCE GENE CLUSTERIN BARLEY-(Abstract Only)
    
    
  • PHYSICAL MAPPING AND CHARACTERIZATION OF YACS DERIVED FROM THE MLA- RESISTANCE GENE REGION IN BARLEY-(Abstract Only)
    
    
  • MITOCHONDRIAL TRANSCRIPT PROCESSING AND RESTORATION OF MALE FERTILITY IN T-CYTOPLASM MAIZE-(Review Article)
    
    
  • MOLECULAR MARKER LINKAGE MAPS IN DIPLOID AND HEXAPLOID OAT (AVENA SP.)-(Book / Chapter)
    
    
  • THE MOECULAR BASIS OF CYTOPLASMIC MALE STERILITY AND FERTILITY RESTORATION-(Review Article)
    
    
  • THE GENETICS, PATHOLOGY AND MOLECULAR BIOLOGY OF T-CYTOPLASM MALE STERILITY IN MAIZE (REVIEW)-(Review Article)
    
    
  • SUPPRESSION OF RF2-MU ALLELES-(Abstract Only)
    
    
  • MITOCHONDRIAL ALDEHYDE DEHYDROGENASE ACTIVITY IS REQUIRED FOR MALE FERTILITY IN MAIZE-(Abstract Only)
    
    
  • DISSECTING A RESISTANCE LOCUS WITH MULTIPLE SPECIFICITIES TO PUCCINIA CORONATA AND ESTABLISHING A SATURATED AFLP MAP IN DIPLOID AVENA-(Abstract Only)
    
    
  • HIGH RESOLUTION MAPPING ADJACENT TO THE PC71 CROWN-RUST RESISTANCE LOCUS INHEXAPLOID OAT-(Peer Reviewed Journal)
    
    
  • NUCLEAR GENES MEDIATING PROCESSING OF MITOCHONDRIAL TRANSCRIPTS AND RESTORATION OF POLLEN FERTILITY IN T. CYTOPLASM, MALE-STERILE MAIZE-(Abstract Only)
    
    
  • RF8 AND RF* MEDIATE UNIQUE T-URF13-TRANSCRIPT ACCUMULATION, REVEALING A MITOCHONDRIAL CONSENSUS SEQUENCE ASSOCIATED WITH RNA PROCESSING AND RESTORATION OF POLLEN FERTILITY IN T-CYTOPLASM MAIZE-(Peer Reviewed Journal)
    
    
  • BIOCHEMICAL CHARACTERIZATION OF THE RF2 PROTEIN REQUIRED FOR THE RESTORATION OF FERTILITY TO CMST-(Abstract Only)
    
    
  • UNLINKED RF GENES MEDIATE UNIQUE T-URFL3 TRANSCRIPT ACCUMULATION, REVEALINGA MITOCHONDRIAL CONSENSUS SEQUENCE ASSOCIATED WITH RNA PROCESSING-(Abstract Only)
    
    
  • AFLP MAPPING OF THE PCA CROWN-RUST RESISTANCE-GENE CLUSTER IN DIPLOID-(Abstract Only)
    
    
  • GENETIC AND PHYSICAL ANALYSIS OF THE MLA RESISTANCE GENE CLUSTER IN BARLEY-(Abstract Only)
    
    
  • THE RF2 NUCLEAR RESTORER GENE OF MALE-STERILE, T-CYTOPLASM MAIZE ENCODES A PUTATIVE ALDEHYDE DEHYDOGENASE-(Peer Reviewed Journal)
    
    
  • MUTATOR-INDUCED MUTANTS OF THE RF1 NUCLEAR RESTORER OF T-CYTOPLASM MALE- STERILE MAIZE ALTER T-URF13 MITOCHONDRIAL TRANSCRIPTION-(Abstract Only)
    
    
  • MOLECULAR ISOLATION AND ANALYSIS OF THE RF2 NUCLEAR RESTORER GENE OF THE MALE-STERILE, T CYTOPLASM OF MAIZE-(Abstract Only)
    
    
  • MUTATOR-INDUCED MUTATIONS OF THE RF1 NUCLEAR FERTILITY RESTORER OF T-CYTOPLASM MAIZE ALTER THE ACCUMULATION OF T-URF13 MITOCHONDRIAL TRANSCRIPTS-(Peer Reviewed Journal)
    
    
  • RF8, A SECOND NUCLEAR GENE THAT ALTERS T-URF13 MITOCHONDRIAL-TRANSCRIPT ACCUMULATION AND RESTORES POLLEN FERTILITY IN T-CYTOPLASM MAIZE-(Abstract Only)
    
    
  • THE RF2 NUCLEAR RESTORER OF MALE-STERILE, T-CYTOPLASM MAIZE ENCODES AN ALDEHYDE DEHYDROGENASE-(Abstract Only)
    
    
  • COMPLEMENTARY GENES FOR CROWN RUST RESISTANCE IN CULTIVATED OAT-(Peer Reviewed Journal)
    
    
  • PHYSICAL ANALYSIS OF RECOMBINATION EVENTS ADJACENT TO THE MLA LOCUS ON BARLEY CHROMOSOME 1H-(Peer Reviewed Journal)
    
    
  • RECOMBINATION WITHIN A 5 CM REGION IN DIPLOID AVENA REVEALS MULTIPLE SPECIFICITIES CONFERRING RESISTANCE TO PUCCINIA CORONATA-(Peer Reviewed Journal)
    
    
  • CROWN RUST RESISTANCE IN HEXAPLOID OAT DETERMINED BY TWO COMPLEMENTARY LOCI-(Abstract Only)
    
    
  • VARIATION IN THE RATIO OF PHYSICAL TO GENETIC DISTANCE AND MICROSYNTENY WITH RICE BACS IN INTERVALS ADJACENT TO THE MLA LOCUS ON CHROMOSOME 1H IN BARLEY-(Abstract Only)
    
    
  • COMPARATIVE MAPPING OF HOMOEOLOGOUS GROUP 1 REGIONS AND GENES FOR RESISTANCE TO OBLIGATE BIOTROPHS IN AVENA, HORDEUM, AND ZEA MAYS-(Peer Reviewed Journal)
    
    
  • MOLECULAR ISOLATION AND ANALYSIS OF NUCLEAR RESTORER GENES FOR THE MALE- STERILE T CYTOPLASM-(Abstract Only)
    
    
  • THE RF2 NUCLEAR RESTORER OF MALE-STERILE T CYTOPLASM ENCODES AN ALDEHYDE DEHYDROGENASE-(Abstract Only)
    
    

 

• Projects

  Temporal Control of Immunity to Powdery Mildew in Barley Cooperative Agreement (A)   Accession Number:438180

  Regulatory Networks in Cereal Host-Fungal Pathogen Interactions In-House Appropriated (D)   Accession Number:443549

  Temporal Control of Immunity to Powdery Mildew in Barley Interagency Reimbursable Agreement (I)   Accession Number:438250

 

• ARS News Articles

  USDA's Agricultural Research Service Announces Scientist of the Year and Other Awards