Publications

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2016
X. Yang, Srivastava, R., Howell, S. H., and Bassham, D. C., Activation of autophagy by unfolded proteins during endoplasmic reticulum stress., Plant J, vol. 85, no. 1, pp. 83-95, 2016.
S. Nian Char, Neelakandan, A. K., Nahampun, H., Frame, B., Main, M., Spalding, M. H., Becraft, P. W., Meyers, B. C., Walbot, V., Wang, K., and Yang, B., An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize., Plant Biotechnol J, 2016.
D. J. Klionsky, Abdelmohsen, K., Abe, A., Abedin, M. Joynal, Abeliovich, H., Arozena, A. Acevedo, Adachi, H., Adams, C. M., Adams, P. D., and Adeli, K., Guidelines for the use and interpretation of assays for monitoring autophagy, Autophagy, vol. 12, no. 1, pp. 1-222, 2016.
J. W. Walley, Sartor, R. C., Shen, Z., Schmitz, R. J., Wu, K. J., Urich, M. A., Nery, J. R., Smith, L. G., Schnable, J. C., and Ecker, J. R., Integration of omic networks in a developmental atlas of maize, Science, vol. 353, no. 6301, pp. 814-818, 2016.
B. C. Gontarek, Neelakandan, A. K., Wu, H., and Becraft, P. W., NKD Transcription Factors are Central Regulators of Maize Endosperm Development, The Plant Cell, p. tpc. 00609.2016, 2016.
M. Qi, 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., A Small Cysteine-Rich Protein from the Asian Soybean Rust Fungus, Phakopsora pachyrhizi, Suppresses Plant Immunity, PLoS Pathog, vol. 12, no. 9, p. e1005827, 2016.
M. N. Ngaki, Wang, B., Sahu, B. B., Srivastava, S. K., Farooqi, M. S., Kambakam, S., Swaminathan, S., and Bhattacharyya, M. K., Tanscriptomic 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, vol. 11, no. 10, p. e0163106, 2016.
2015
M. S. Hillwig, Chiozza, M., Casteel, C. L., Lau, S. T., Hohenstein, J., Hernandez, E., Jander, G., and MacIntosh, G. C., Abscisic acid deficiency increases defence responses against Myzus persicae in Arabidopsis, Mol Plant PatholMol Plant PatholMolecular Plant Pathology, 2015.
H. Tang, Zhang, X., Miao, C., Zhang, J., Ming, R., Schnable, J. C., Schnable, P. S., Lyons, E., and Lu, J., ALLMAPS: robust scaffold ordering based on multiple maps, Genome BiolGenome BiolGenome biology, vol. 16, p. 3, 2015.
N. Kitaoka, Lu, X., Yang, B., and Peters, R. J., The application of synthetic biology to elucidation of plant mono-, sesqui-, and diterpenoid metabolism, Mol PlantMol PlantMolecular Plant, vol. 8, pp. 6-16, 2015.
F. Jiang, An, C., Bao, Y., Zhao, X., Jernigan, R. L., Lithio, A., Nettleton, D., Li, L., Wurtele, E. S., Nolan, L. K., Lu, C., and Li, G., ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli, Infect ImmunInfect ImmunInfect Immun, vol. 83, pp. 3545-54, 2015.
N. N. Boersma, Dohleman, F. G., Miguez, F. E., and Heaton, E. A., Autumnal leaf senescence in Miscanthus x giganteus and leaf [N] differ by stand age, J Exp BotJ Exp BotJournal of experimental botany, vol. 66, pp. 4395-401, 2015.
Y. Matsuba, Zi, J., Jones, A. D., Peters, R. J., and Pichersky, E., Biosynthesis of the diterpenoid lycosantalonol via nerylneryl diphosphate in Solanum lycopersicum, PLoS OnePLoS ONEPLoS ONE, vol. 10, p. e0119302, 2015.
V. Lionetti, Giancaspro, A., Fabri, E., Giove, S. L., Reem, N., Zabotina, O. A., Blanco, A., Gadaleta, A., and Bellincampi, D., Cell wall traits as potential resources to improve resistance of durum wheat against Fusarium graminearum, BMC Plant BiolBMC Plant Biol, vol. 15, p. 6, 2015.
W. A. Miller, Jackson, J., and Feng, Y., Cis- and trans-regulation of luteovirus gene expression by the 3' end of the viral genome, Virus ResVirus ResVirus Res, vol. 206, pp. 37-45, 2015.
Y. Wang, Stessman, D. J., and Spalding, M. H., The CO2 concentrating mechanism and photosynthetic carbon assimilation in limiting CO2 : how Chlamydomonas works against the gradient, Plant JPlant J, vol. 82, pp. 429-48, 2015.
G. Pogorelko, Juvale, P. S., Rutter, W. B., Hewezi, T., Hussey, R., Davis, E. L., Mitchum, M. G., and Baum, T. J., A cyst nematode effector binds to diverse plant proteins, increases nematode susceptibility and affects root morphology., Mol Plant Pathol, 2015.
T. Hewezi, Juvale, P. S., Piya, S., Maier, T. R., Rambani, A., Rice, J. H., Mitchum, M. G., Davis, E. L., Hussey, R. S., and Baum, T. J., The cyst nematode effector protein 10A07 targets and recruits host posttranslational machinery to mediate its nuclear trafficking and to promote parasitism in Arabidopsis, Plant CellPlant CellThe Plant Cell, vol. 27, pp. 891-907, 2015.
E. Smirnova, Firth, A. E., Miller, W. A., Scheidecker, D., Brault, V., Reinbold, C., Rakotondrafara, A. M., Chung, B. Y., and Ziegler-Graff, V., Discovery of a Small Non-AUG-Initiated ORF in Poleroviruses and Luteoviruses That Is Required for Long-Distance Movement, PLoS PathogPLoS PathogPLoS Pathog, vol. 11, p. e1004868, 2015.
A. M. Thompson, Yu, J., Timmermans, M. C., Schnable, P., Crants, J. C., Scanlon, M. J., and Muehlbauer, G. J., Diversity of maize shoot apical meristem architecture and its relationship to plant morphology, G3 (Bethesda)G3 (Bethesda), vol. 5, pp. 819-27, 2015.
Y. Feng, Yin, Y., and Fei, S., Down-regulation of BdBRI1, a putative brassinosteroid receptor gene produces a dwarf phenotype with enhanced drought tolerance in Brachypodium distachyon, Plant SciPlant Sci, vol. 234, pp. 163-73, 2015.
J. B. Noon, Hewezi, T. A., Maier, T. R., Simmons, C., Wei, J. Z., Wu, G., Llaca, V., Deschamps, S., Davis, E., Mitchum, M., Hussey, R. S., and Baum, T. J., Eighteen new candidate effectors of the phytonematode Heterodera glycines produced specifically in the secretory esophageal gland cells during parasitism, PhytopathologyPhytopathologyPhytopathology, 2015.
X. Lu, Hershey, D. M., Wang, L., Bogdanove, A. J., and Peters, R. J., An ent-kaurene-derived diterpenoid virulence factor from Xanthomonas oryzae pv. oryzicola, New PhytolNew Phytol, vol. 206, pp. 295-302, 2015.
G. Riesberg, Bigelow, T. A., Stessman, D. J., Spalding, M. H., Yao, L., Wang, T., and Xu, J., Erratum: Flow rate and duty cycle effects in lysis of Chlamydomonas reinhardtii using high-energy pulsed focused ultrasound [J. Acoust. Soc. Am. 135(6), 3632-3638 (2014)], J Acoust Soc AmJ Acoust Soc Am, vol. 137, p. 513, 2015.
B. E. Floyd, Morriss, S. C., MacIntosh, G. C., and Bassham, D. C., Evidence for autophagy-dependent pathways of rRNA turnover in Arabidopsis., Autophagy, vol. 11, no. 12, pp. 2199-212, 2015.
L. A. Royce, Yoon, J. M., Chen, Y., Rickenbach, E., Shanks, J. V., and Jarboe, L. R., Evolution for exogenous octanoic acid tolerance improves carboxylic acid production and membrane integrity, Metab EngMetab EngMetab Eng, vol. 29, pp. 180-8, 2015.
X. Li, Scanlon, M. J., and Yu, J., Evolutionary patterns of DNA base composition and correlation to polymorphisms in DNA repair systems, Nucleic Acids ResNucleic Acids ResNucleic Acids Research, vol. 43, pp. 3614-25, 2015.
H. Gao, Wang, Y., Fei, X., Wright, D. A., and Spalding, M. H., Expression activation and functional analysis of HLA3, a putative inorganic carbon transporter in Chlamydomonas reinhardtii, Plant JPlant J, vol. 82, pp. 1-11, 2015.
H. N. Nahampun, Bosworth, B., Cunnick, J., Mogler, M., and Wang, K., Expression of H3N2 nucleoprotein in maize seeds and immunogenicity in mice, Plant Cell RepPlant Cell RepPlant cell reports, vol. 34, pp. 969-80, 2015.
M. Pautler, Eveland, A. L., LaRue, T., Yang, F., Weeks, R., Lunde, C., Je, B. I., Meeley, R., Komatsu, M., Vollbrecht, E., Sakai, H., and Jackson, D., FASCIATED EAR4 encodes a bZIP transcription factor that regulates shoot meristem size in maize, Plant CellPlant CellThe Plant Cell, vol. 27, pp. 104-20, 2015.
A. E. Lipka, Kandianis, C. B., Hudson, M. E., Yu, J., Drnevich, J., Bradbury, P. J., and Gore, M. A., From association to prediction: statistical methods for the dissection and selection of complex traits in plants, Curr Opin Plant BiolCurr Opin Plant Biol, vol. 24, pp. 110-8, 2015.
Z. Xu, Peters, R. J., Weirather, J., Luo, H., Liao, B., Zhang, X., Zhu, Y., Ji, A., Zhang, B., Hu, S., Au, K. F., Song, J., and Chen, S., Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis, Plant JPlant J, vol. 82, pp. 951-61, 2015.
G. Cui, Duan, L., Jin, B., Qian, J., Xue, Z., Shen, G., Snyder, J. H., Song, J., Chen, S., Huang, L., Peters, R. J., and Qi, X., Functional divergence of diterpene syntheses in the medicinal plant Salvia miltiorrhiza Bunge, Plant PhysiolPlant PhysiolPlant Physiology, 2015.
J. Zhou, Peng, Z., Long, J., Sosso, D., Liu, B., Eom, J. S., Huang, S., Liu, S., C. Cruz, V., Frommer, W. B., White, F. F., and Yang, B., Gene targeting by the TAL effector PthXo2 reveals cryptic resistance gene for bacterial blight of rice, Plant JPlant J, vol. 82, pp. 632-43, 2015.
G. Hu, Koh, J., Yoo, M. J., Chen, S., and Wendel, J. F., Gene-expression novelty in allopolyploid cotton: a proteomic perspective, GeneticsGeneticsGenetics, vol. 200, pp. 91-104, 2015.
A. Adeyanju, Little, C., Yu, J., and Tesso, T., Genome-Wide Association Study on Resistance to Stalk Rot Diseases in Grain Sorghum, G3 (Bethesda)G3 (Bethesda), vol. 5, pp. 1165-75, 2015.
S. N. Char, Unger-Wallace, E., Frame, B., Briggs, S. A., Main, M., Spalding, M. H., Vollbrecht, E., Wang, K., and Yang, B., Heritable site-specific mutagenesis using TALENs in maize, Plant Biotechnol JPlant Biotechnol JPlant Biotechnol J, vol. 13, pp. 1002-10, 2015.
S. Takuno, Ralph, P., Swarts, K., Elshire, R. J., Glaubitz, J. C., Buckler, E. S., Hufford, M. B., and Ross-Ibarra, J., Independent Molecular Basis of Convergent Highland Adaptation in Maize, GeneticsGeneticsGenetics, vol. 200, pp. 1297-312, 2015.
A. M. Boutanaev, Moses, T., Zi, J., Nelson, D. R., Mugford, S. T., Peters, R. J., and Osbourn, A., Investigation of terpene diversification across multiple sequenced plant genomes, Proc Natl Acad Sci U S AProc Natl Acad Sci U S AProc Natl Acad Sci U S A, vol. 112, pp. E81-8, 2015.
A. T. Klein, Yagnik, G. B., Hohenstein, J. D., Ji, Z., Zi, J., Reichert, M. D., MacIntosh, G. C., Yang, B., Peters, R. J., Vela, J., and Lee, Y. J., Investigation of the Chemical Interface in the Soybean-Aphid and Rice-Bacteria Interactions Using MALDI-Mass Spectrometry Imaging, Anal ChemAnal ChemAnal Chem, vol. 87, pp. 5294-301, 2015.
L. Li, Hill-Skinner, S., Liu, S., Beuchle, D., Tang, H. M., Yeh, C. T., Nettleton, D., and Schnable, P. S., The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase, Plant JPlant J, vol. 81, pp. 493-504, 2015.
B. Frame, Warnberg, K., Main, M., and Wang, K., Maize (Zea mays L.), Methods Mol BiolMethods Mol Biol, vol. 1223, pp. 101-17, 2015.
Y. Fu, Yoon, J. M., Jarboe, L., and Shanks, J. V., Metabolic flux analysis of Escherichia coli MG1655 under octanoic acid (C8) stress, Appl Microbiol BiotechnolAppl Microbiol BiotechnolAppl Microbiol Biotechnol, vol. 99, pp. 4397-408, 2015.
C. Noutsos, Perera, A. M., Nikolau, B. J., Seaver, S. M., and Ware, D. H., Metabolomic Profiling of the Nectars of Aquilegia pubescens and A. Canadensis, PLoS OnePLoS ONEPLoS ONE, vol. 10, p. e0124501, 2015.
D. C. Bassham, Methods for analysis of autophagy in plants, MethodsMethods, vol. 75, pp. 181-8, 2015.
R. Almasi, Miller, W. A., and Ziegler-Graff, V., Mild and severe cereal yellow dwarf viruses differ in silencing suppressor efficiency of the P0 protein, Virus ResVirus ResVirus Res, vol. 208, pp. 199-206, 2015.
L. W. Sumner, Lei, Z., Nikolau, B. J., and Saito, K., Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects, Nat Prod RepNatural product reports, vol. 32, pp. 212-29, 2015.
H. S. Vu, Roston, R., Shiva, S., Hur, M., Wurtele, E. S., Wang, X., Shah, J., and Welti, R., Modifications of membrane lipids in response to wounding of Arabidopsis thaliana leaves, Plant Signal BehavPlant Signal Behav, 2015.
A. D. Feenstra, Hansen, R. L., and Lee, Y. J., Multi-matrix, dual polarity, tandem mass spectrometry imaging strategy applied to a germinated maize seed: toward mass spectrometry imaging of an untargeted metabolome, AnalystAnalystAnalyst, 2015.
L. F. Li, Liu, B., Olsen, K. M., and Wendel, J. F., Multiple rounds of ancient and recent hybridizations have occurred within the Aegilops-Triticum complex, New PhytolNew Phytol, vol. 208, pp. 11-2, 2015.

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