Publications

2017
  • Deng, X.G., Zhu, T., Peng, X.J., Xi, D.H., Guo, H., Yin, Y., Zhang, D.W. and Lin, H.H., 2016. Role of brassinosteroid signaling in modulating Tobacco mosaic virus resistance in Nicotiana benthamiana. Scientific reports, 6: 20579.
  • Deng, Y., Srivastava, R., Quilichini, T.D., Dong, H., Bao, Y., Horner, H.T. and Howell, S.H., 2016. IRE1, a component of the unfolded protein response signaling pathway, protects pollen development in Arabidopsis from heat stress. The Plant Journal, 88(2), pp.193-204.
  • Dinkins, R.D., Nagabhyru, P., Graham, M.A., Boykin, D. and Schardl, C.L., 2017. Transcriptome response of Lolium arundinaceum to its fungal endophyte Epichloë coenophiala. New Phytologist, 213(1), pp.324-337.
  • Do Canto, J., Studer, B. and Lubberstedt, T., 2016. Overcoming self-incompatibility in grasses: a pathway to hybrid breeding. Theoretical and Applied Genetics, 129(10), pp.1815-1829.
  • Dumortier, J., Kauffman, N. and Hayes, D.J., 2016. Production and Spatial Distribution of Switchgrass and Miscanthus in the United States under Uncertainty and Sunk Cost. Working Paper-Center for Agricultural and Rural Development, Iowa State University, (16-WP 568).
  • Duvick, J., Standage, D.S., Merchant, N. and Brendel, V.P., 2016. xGDBvm: A Web GUI-driven workflow for annotating eukaryotic genomes in the cloud. The Plant Cell, pp.tpc-00933.
  • EL-Manzalawy, Y., Dobbs, D. and Honavar, V.G., 2017. In Silico Prediction of Linear B-Cell Epitopes on Proteins. Prediction of Protein Secondary Structure, pp.255-264.
2016
  • Feng, X., and Hayes, D., 2016. Diversifying systemic risk in agriculture. Agricultural Finance Review, 76(4), pp.512-531.
  • Ge, L., Yu, J., Wang, H., Luth, D., Bai, G., Wang, K. and Chen, R., 2016. Increasing seed size and quality by manipulating BIG SEEDS1 in legume species. Proceedings of the National Academy of Sciences, 113(44), pp. 12414-12419.
  • Gelli, M., Mitchell, S.E., Liu, K., Clemente, T.E., Weeks, D.P., Zhang, C., Holding, D.R. and Dweikat, I.M., 2016. Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum. BMC Plant Biology, 16(1), p.16.
  • Gontarek, B.C., Neelakandan, A.K., Wu, H. and Becraft, P.W., 2016. NKD Transcription Factors Are Central Regulators of Maize Endosperm Development. The Plant Cell, pp.tpc-00609.
  • Hart, C.E., Lence, S.H., Hayes, D.J. and Jin, N., 2016. Price mean reversion, seasonality, and options markets. American Journal of Agricultural Economics, 98(3), pp.707-725.
  • Howard, R., Beavis, W.D. and Carriquiry, A., 2016. Evaluation of a Computational Diagnostic for Epistasis in Plant Breeding Populations. bioRxiv, p.044453.
  • Hu, S., Lübberstedt, T., Zhao, G. and Lee, M., 2016. QTL mapping of low-temperature germination ability in the maize IBM Syn4 RIL population. PloS one, 11(3), p.e0152795.
  • Huang, H., Antony,G., Li, T., Liu, B., Obasa, K., Yang, B. and White, F.F. 2016, The broad recessive resistance gene xa5 of rice is a virulence effector-dependent quantitative trait for bacterial blight. Plant Journal. 86 (2), 186-194.
  • Huber, S.C., Li, K., Nelson, R., Ulanov, A., DeMuro, C.M. and Baxter, I., 2016. Canopy position has a profound effect on soybean seed composition. PeerJ, 4, p.e2452.
  • Irani, S., Knapp, A.D., Lubberstedt, T., Frei, U. and Askari, E., 2016. Increasing Seed Viability of Maize Haploid Inducing Lines by Genetic and Non-Genetic Approaches. Crop Science, 56(4), pp.1940-1947.
  • Jacobs, K.L., Li, Z. and Hayes, D.J., 2016. Forward Contracting by Iowa Corn Producers: Connecting Hedging with Price Movements. Agricultural Policy Review. Fall 2016
  • Jeffrey, B., Kuzhiyil, N., de Leon, N. and Lübberstedt, T., 2016. Genetic and Quantitative Trait Locus Analysis for Bio-Oil Compounds after Fast Pyrolysis in Maize Cobs. PloS One, 11(1), p.e0145845.
  • Ji, Z.Y., Ji, C.H., Liu, B., Zou, L.F., Chen, G.Y. and Yang, B. 2016, Interfering TAL effectors of Xanthomonas oryzae neutralize R-gene-mediated plant disease resistance. Nature Communications. DOI: 10.1038/ncomms13435.
  • Jiao, Y., Young, C.W., Yang, S., Oren, S., Ceylan, H., Kim, S., Gopalakrishnan, K., Taylor, P.C. and Dong, L., 2016. Wearable Graphene Sensors With Microfluidic Liquid Metal Wiring for Structural Health Monitoring and Human Body Motion Sensing. IEEE Sensors Journal, 16(22), pp.7870-7875.
  • Juvale, P.S., Wagner, R.L. and Spalding, M.H., 2016. Opportunistic proteolytic processing of carbonic anhydrase 1 from Chlamydomonas in Arabidopsis reveals a novel route for protein maturation. Journal of experimental botany, 67(8), pp.2339-2351.
  • Kim, B. and Beavis, W.D., 2016. Numericware i: Identical in state matrix calculator. bioRxiv, p.075267.
  • Kim, B., Beavis, W.D. and Léon, J., 2016. Numericware N: Numerator Relationship Matrix Calculator. Journal of Heredity, p.esw057.
  • Kim, S.Y., Bender, K.W., Walker, B.J., Zielinski, R.E., Spalding, M.H., Ort, D.R. and Huber, S.C., 2016. The plastid casein kinase 2 phosphorylates Rubisco activase at the Thr-78 site but is not essential for regulation of Rubisco activation state. Frontiers in Plant Science, 7, 404.
  • Li, L., Briskine, R., Schaefer, R., Schnable, P.S., Myers, C.L., Flagel, L.E., Springer, N.M. and Muehlbauer, G.J., 2016. Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias. BMC Genomics, 17(1), p.875.
  • Li, T., Liu, B., Chen, C.Y. and Yang, B. 2016, TALEN-mediated homologous recombination produces site-directed DNA base change and herbicide-resistant rice. Journal of Genetics and Genomics. 43 (5), 297-305.
  • Lin, M., Zhang, D., Liu, S., Zhang, G., Yu, J., Fritz, A.K. and Bai, G., 2016. Genome-wide association analysis on pre-harvest sprouting resistance and grain color in US winter wheat. BMC Genomics, 17(1), p.794.
  • Liu, J.X. and Howell, S.H., 2016. Managing the protein folding demands in the endoplasmic reticulum of plants. New Phytologist, 211(2), pp.418-428.
  • Liu, M., Li, S., Swaminathan, S., Sahu, B.B., Leandro, L.F., Cardinal, A.J., Bhattacharyya, M.K., Song, Q., Walker, D.R. and Cianzio, S.R., 2016. Identification of a soybean rust resistance gene in PI 567104B. Theoretical and Applied Genetics, 129(5), pp.863-877.
  • Liu, Z., Wang, Y., Ren, J., Mei, M., Frei, U.K., Trampe, B. and Lubberstedt, T., 2016. Maize Doubled Haploids. Plant Breeding Reviews, 40, p.123.
  • Lukman, R., Afifuddin, A. and Lübberstedt, T., 2016. Tracing the signature of Peronosclerospora maydis in maize seeds. Australasian Plant Pathology, 45(1), pp.73-82.
  • Martin, K., Singh, J., Hill, J.H., Whitham, S.A. and Cannon, S.B., 2016. Dynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean (Phaseolus vulgaris L.). BMC Genomics, 17(1), p.613.
  • McCabe, C.E., Singh, A.K., Leandro, L.F., Cianzio, S.R. and Graham, M.A., 2016. Identifying new sources of resistance to Brown Stem Rot in Soybean. Crop Science, 56(5), pp.2287-2296.
  • Mei, Y., Zhang, C., Kernodle, B.M., Hill, J.H. and Whitham, S.A., 2016. A Foxtail mosaic virus vector for virus-induced gene silencing in maize. Plant physiology, 171(2), pp.760-772.
  • Nahampun, H.N., López-Arredondo, D., Xu, X., Herrera-Estrella, L. and Wang, K., 2016. Assessment of ptxD gene as an alternative selectable marker for Agrobacterium-mediated maize transformation. Plant cell reports, 35(5), pp.1121-1132.
  • Ngaki, M.N., Wang, B., Sahu, B.B., Srivastava, S.K., Farooqi, M.S., Kambakam, S., Swaminathan, S. and Bhattacharyya, M.K., 2016. Transcriptomic Study of the Soybean-Fusarium virguliforme Interaction Revealed a Novel Ankyrin-Repeat Containing Defense Gene, Expression of Whose during Infection Led to Enhanced Resistance to the Fungal Pathogen in Transgenic Soybean Plants. PloS One, 11(10), p.e0163106.
  • Nolan, T., Liu, S., Guo, H., Li, L., Schnable, P. and Yin, Y., 2017. Identification of Brassinosteroid Target Genes by Chromatin Immunoprecipitation Followed by High-Throughput Sequencing (ChIP-seq) and RNA-Sequencing. Brassinosteroids: Methods and Protocols, pp.63-79.
  • Noon, J.B. and Baum, T.J., 2016. Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients. BMC Evolutionary Biology, 16(1), p.74.
  • Noon, J.B., Qi, M., Sill, D.N., Muppirala, U., Eves‐van den Akker, S., Maier, T.R., Dobbs, D., Mitchum, M.G., Hewezi, T. and Baum, T.J., 2016. A Plasmodium‐like virulence effector of the soybean cyst nematode suppresses plant innate immunity. New Phytologist, 212(2), pp.444-460.
  • Pauli, D., Chapman, S.C., Bart, R., Topp, C.N., Lawrence-Dill, C.J., Poland, J. and Gore, M.A., 2016. The quest for understanding phenotypic variation via integrated approaches in the field environment. Plant Physiology, 172(2), pp.622-634.
  • Pogorelko, G., Juvale, P.S., Rutter, W.B., Hewezi, T., Hussey, R., Davis, E.L., Mitchum, M.G. and Baum, T.J., 2016. A cyst nematode effector binds to diverse plant proteins, increases nematode susceptibility and affects root morphology. Molecular Plant Pathology, 17(6), pp.832-844.
  • Qi, M., Link, T.I., Müller, M., Hirschburger, D., Pudake, R.N., Pedley, K.F., Braun, E., Voegele, R.T., Baum, T.J. and Whitham, S.A., 2016. A small cysteine-rich protein from the Asian soybean rust fungus, Phakopsora pachyrhizi, suppresses plant immunity. PLoS Pathogens, 12(9), p.e1005827.
  • Richard, C., Osiru, D.S., Mwala, M.S. and Lubberstedt, T., 2016. Genetic diversity and heterotic grouping of the core set of southern African and temperate maize (Zea mays L) Inbred lines using SNP markers. Maydica, 61(1).
  • Salas, E.N., Shu, J., Cserhati, M.F., Weeks, D.P. and Ladunga, I., 2016. Pluralistic and stochastic gene regulation: examples, models and consistent theory. Nucleic Acids Research, p.gkw042.
  • Shen, R., Ying, K., Wang, Z. and Schnable, P.S., 2016, March. Algorithm for DNA copy number variation detection with read depth and paramorphism information. In: 2016 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), (pp. 869-873). IEEE.
  • Smelser, A., Gardner, C., Blanco, M., Lübberstedt, T. and Frei, U., 2016. Germplasm enhancement of maize: a look into haploid induction and chromosomal doubling of haploids from temperate‐adapted tropical sources. Plant Breeding, 135(5), pp.593-597.
  • Smith, S., Lence, S., Hayes, D., Alston, J. and Corona, E., 2016. Elements of Intellectual Property Protection in Plant Breeding and Biotechnology: Interactions and Outcomes. Crop Science, 56(4), pp.1401-1411.
  • Srivistava, R., Zalisko, B.E., Keenan, R.J. and Howell, S.H., 2016. The GET system inserts the tail-anchored SYP72 protein into endoplasmic reticulum membranes. Plant Physiology, pp.pp-00928.
  • Standage, D.S., Berens, A.J., Glastad, K.M., Severin, A.J., Brendel, V.P. and Toth, A.L., 2016. Genome, transcriptome, and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect. Molecular Ecology, 25(8), pp.1769-1784.
  • Suza, W.P., Gibson, P., Edema, R., Akromah, R., Sibiya, J., Madakadze, R. and Lamkey, K.R., 2016. Plant breeding capacity building in Africa. Nature Climate Change, 6(11), pp.976-976.
  • Swaminathan, S., Abeysekara, N.S., Liu, M., Cianzio, S.R. and Bhattacharyya, M.K., 2016. Quantitative trait loci underlying host responses of soybean to Fusarium virguliforme toxins that cause foliar sudden death syndrome. Theoretical and Applied Genetics, 129(3), pp.495-506.
  • Wang, K., Yang, B, 2016. A High-efficiency CRISPR Platform for Maize Improvement.  Information System for Biotechnology News Report, October/November, 2016.  www.isb.vt.edu
  • Wang, M., Dzievit, M., Chen, Z., Morris, J.B., Norris, J., Barkley, N.A., Tonnis, B., Pederson, G.A. and Yu, J., 2016. Genetic diversity and population structure of castor (Ricinus communis L.) germplasm within the US collection assessed with EST-SSR markers. Genome, doi: 10.1139/gen-2016-0116.
  • Wang, Q., Hong, W. and Dong, L., 2016. Graphene “microdrums” on a freestanding perforated thin membrane for high sensitivity MEMS pressure sensors. Nanoscale, 8(14), pp.7663-7671.
  • Wang, Y., Liu, L., Wang, Q., Han, W., Lu, M. and Dong, L., 2016. Strain-tunable plasmonic crystal using elevated nanodisks with polarization-dependent characteristics. Applied Physics Letters, 108(7), p.071110.
  • Weeks, D.P., Spalding, M.H. and Yang, B., 2016. Use of designer nucleases for targeted gene and genome editing in plants. Plant Biotechnology Journal, 14(2), pp.483-495.
  • Whitham, S.A. and Hajimorad, M.R., 2016. Plant genetic resistance to viruses. In: Current Research Topics in Plant Virology (pp. 87-111). Springer International Publishing.
  • Whitham, S.A., Lincoln, L.M., Chowda‐Reddy, R.V., Dittman, J.D., O’Rourke, J.A. and Graham, M.A., 2016. Virus‐Induced Gene Silencing and Transient Gene Expression in Soybean (Glycine max) Using Bean Pod Mottle Virus Infectious Clones. Current Protocols in Plant Biology, pp.263-283.
  • Whitham, S.A., Qi, M., Innes, R.W., Ma, W., Lopes-Caitar, V. and Hewezi, T., 2016. Molecular Soybean-Pathogen Interactions. Annual Review of Phytopathology, 54, pp.443-468.
  • Whitis, N.R., Xue, C., Sashital, D.G. and Carver, R.J., 2016. Control of CRISPR Priming and Interference Activities by a Cascade-Activated Switch. The FASEB Journal, 30(1 Supplement), pp.571-3.
  • Wolt, J.D., Wang, K. and Yang, B. 2016, The Regulatory Status of Genome-edited Crops. Plant. Biotechnol. J., 14, 510-518.
  • Wolt, J.D., Wang, K., Sashital, D. and Lawrence-Dill, C.J., 2016. Achieving Plant CRISPR Targeting that Limits Off-Target Effects. The Plant Genome, 9(3).
  • Wolt, J.D., Yang, B., Wang, K. and Spalding, M.H., 2016. Regulatory aspects of genome-edited crops. In Vitro Cellular & Developmental Biology-Plant, 52(4), pp.349-353.
  • Xu, Z., Jiang, H., Sahu, B.B., Kambakam, S., Singh, P., Wang, X., Wang, Q., Bhattacharyya, M.K. and Dong, L., 2016. Humidity assay for studying plant-pathogen interactions in miniature controlled discrete humidity environments with good throughput. Biomicrofluidics, 10(3), p.034108.
  • Xu, Z., Wang, X., Weber, R.J., Kumar, R. and Dong, L., 2016, October. Microfluidic eletrophoretic ion nutrient sensor. In: SENSORS, 2016 IEEE (pp. 1-3). IEEE.
  • Xue, C., Whitis, N.R. and Sashital, D.G., 2016. Conformational Control of Cascade Interference and Priming Activities in CRISPR Immunity. Molecular Cell, 64(4), pp.826-834.
  • Xue, L.C., Rodrigues, J.P., Dobbs, D., Honavar, V. and Bonvin, A.M., 2016. Template-based protein–protein docking exploiting pairwise interfacial residue restraints. Briefings in Bioinformatics, p.bbw027.
  • Yang, X., Srivastava, R., Howell, S.H. and Bassham, D.C., 2016. Activation of autophagy by unfolded proteins during endoplasmic reticulum stress. The Plant Journal, 85(1), pp.83-95.
  • Yu X., Li X., Guo T., Zhu C., Wu Y., Mitchell S.E., Roozeboom K.L., Wang D., Wang M.L., Pederson G.A., Tesso T.T., Schnable P.S., Bernardo R., and Yu, J., 2016. Genomic prediction contributing to a promising global strategy to turbocharge gene banks. Nature Plants, 2, p.16150.
  • Zhang, D.W., Yuan, S., Xu, F., Zhu, F., Yuan, M., Ye, H.X., Guo, H.Q., Lv, X., Yin, Y. and Lin, H.H., 2016. Light intensity affects chlorophyll synthesis during greening process by metabolite signal from mitochondrial alternative oxidase in Arabidopsis. Plant, Cell & Environment, 39(1), pp.12-25.
  • Zhang, K., Zhou, L., Brady, M., Xu, F., Yu, J. and Wang, D., 2016. Fast analysis of high heating value and elemental compositions of sorghum biomass using near-infrared spectroscopy. Energy, 118, pp.1353-1360.
  • Zhao, J., Mantilla Perez, M.B., Hu, J. and Salas Fernandez, M.G., 2016. Genome-Wide Association Study for Nine Plant Architecture Traits in Sorghum. The Plant Genome, 9(2). doi: 10.3835/plantgenome2015.06.0044
  • Zheng, F., Du, X., Chou, T.H., Robertson, A.P., Edward, W.Y., VanVeller, B. and Martin, R.J., 2016. (S)-5-ethynyl-anabasine, a novel compound, is a more potent agonist than other nicotine alkaloids on the nematode Asu-ACR-16 receptor. International Journal for Parasitology: Drugs and Drug Resistance, 7, pp.12-22.
2015
2014
2013 and Before