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Research Areas

Genomic Ecology of Global Change: Publications

Jeong, H., Arif, B., Caetano-Anolles, G., Kim, K. M., & Nasir, A. (2019). Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation. Scientific Reports, 9(1), [5953]. https://doi.org/10.1038/s41598-019-42227-5

Fu, P., Xie, Y., Weng, Q., Myint, S., Meacham-Hensold, K., & Bernacchi, C. (2019). A physical model-based method for retrieving urban land surface temperatures under cloudy conditions. Remote Sensing of Environment, 230, [111191]. https://doi.org/10.1016/j.rse.2019.05.010

Zhang, Q., Demejia, E., Luna-Vital, D., Tao, T., Chandrasekaran, S., Chatham, L., ... Kumar, D. (2019). Relationship of phenolic composition of selected purple maize (Zea mays L.) genotypes with their anti-inflammatory, anti-adipogenic and anti-diabetic potential. Food Chemistry, 289, 739-750. https://doi.org/10.1016/j.foodchem.2019.03.116

Zhu, P., Zhuang, Q., Archontoulis, S. V., Bernacchi, C., & Müller, C. (2019). Dissecting the nonlinear response of maize yield to high temperature stress with model-data integration. Global change biology, 25(7), 2470-2484. https://doi.org/10.1111/gcb.14632

Li, Y., Guan, K., Schnitkey, G. D., Delucia, E. H., & Peng, B. (2019). Excessive rainfall leads to maize yield loss of a comparable magnitude to extreme drought in the United States. Global change biology, 25(7), 2325-2337. https://doi.org/10.1111/gcb.14628

Delucia, E. H., Chen, S., Guan, K., Peng, B., Li, Y., Gomez-casanovas, N., ... Ort, D. R. (2019). Are we approaching a water ceiling to maize yields in the United States? Ecosphere, 10(6), [e02773]. https://doi.org/10.1002/ecs2.2019.10.issue-6

Wang, Z., Dien, B. S., Rausch, K. D., Tumbleson, M. E., & Singh, V. (2019). Improving ethanol yields with deacetylated and two-stage pretreated corn stover and sugarcane bagasse by blending commercial xylose-fermenting and wild type Saccharomyces yeast. Bioresource Technology, 103-109. https://doi.org/10.1016/j.biortech.2019.02.123

Lichiheb, N., Myles, L. T., Personne, E., Heuer, M., Buban, M., Nelson, A. J., ... Bernacchi, C. (2019). Implementation of the effect of urease inhibitor on ammonia emissions following urea-based fertilizer application at a Zea mays field in central Illinois: A study with SURFATM-NH 3 model. Agricultural and Forest Meteorology, 269-270, 78-87. https://doi.org/10.1016/j.agrformet.2019.02.005

Li, Q., Singh, V., Demejia, E., & Somavat, P. (2019). Effect of sulfur dioxide and lactic acid in steeping water on the extraction of anthocyanins and bioactives from purple corn pericarp. Cereal Chemistry, 96(3), 575-589. https://doi.org/10.1002/cche.10157

Cheng, M. H., Huang, H., Dien, B. S., & Singh, V. (2019). The costs of sugar production from different feedstocks and processing technologies. Biofuels, Bioproducts and Biorefining, 13(3), 723-739. https://doi.org/10.1002/bbb.1976

Zhuang, W., Chen, H., Yang, M., Wang, J., Pandey, M. K., Zhang, C., ... Varshney, R. K. (2019). The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature Genetics, 51(5), 865-876. https://doi.org/10.1038/s41588-019-0402-2

Higuti, V. A. H., Velasquez, A. E. B., Magalhaes, D. V., Becker, M., & Chowdhary, G. (2019). Under canopy light detection and ranging-based autonomous navigation. Journal of Field Robotics, 36(3), 547-567. https://doi.org/10.1002/rob.21852

Berenbaum, M. R. (2019). Speaking of gender bias. Proceedings of the National Academy of Sciences of the United States of America, 116(17), 8086-8088. https://doi.org/10.1073/pnas.1904750116

Caetano-Anollés, D., Nasir, A., Kim, K. M., & Caetano-Anolles, G. (2019). Testing Empirical Support for Evolutionary Models that Root the Tree of Life. Journal of Molecular Evolution, 87(2-3), 131-142. https://doi.org/10.1007/s00239-019-09891-7

Li, S., Courbet, G., Ourry, A., & Ainsworth, E. A. (2019). Elevated Ozone Concentration Reduces Photosynthetic Carbon Gain but Does Not Alter Leaf Structural Traits, Nutrient Composition or Biomass in Switchgrass. Plants, 8(4), 85. https://doi.org/10.3390/plants8040085

Conlan, B., Birch, R., Kelso, C., Holland, S., De Souza, A. P., Long, S. P., ... Whitney, S. M. (2019). BSD2 is a Rubisco-specific assembly chaperone, forms intermediary hetero-oligomeric complexes, and is nonlimiting to growth in tobacco. Plant Cell and Environment, 42(4), 1287-1301. https://doi.org/10.1111/pce.13473

Argueso, C. T., Assmann, S. M., Birnbaum, K. D., Chen, S., Dinneny, J. R., Doherty, C. J., ... Williams, C. M. (2019). Directions for research and training in plant omics: Big Questions and Big Data. Plant Direct, 3(4), [e00133]. https://doi.org/10.1002/pld3.133

Wedow, J. M., Yendrek, C. R., Mello, T. R., Creste, S., Martinez, C. A., & Ainsworth, E. (2019). Metabolite and transcript profiling of Guinea grass (Panicum maximum Jacq) response to elevated [CO 2 ] and temperature Metabolomics, 15(4), [51]. https://doi.org/10.1007/s11306-019-1511-8

Leakey, A., Ferguson, J. N., Pignon, C. P., Wu, A., Jin, Z., Hammer, G. L., & Lobell, D. B. (2019). Water Use Efficiency as a Constraint and Target for Improving the Resilience and Productivity of C 3 and C 4 Crops Annual Review of Plant Biology, 70, 781-808. https://doi.org/10.1146/annurev-arplant-042817-040305

Berenbaum, M. R. (2019). Out of Order. American Entomologist, 65(1), 3-5. https://doi.org/10.1093/ae/tmz012

Baek, Y. S., Goodrich, L. V., Brown, P. J., James, B. T., Moose, S. P., Lambert, K. N., & Riechers, D. E. (2019). Transcriptome profiling and genome-wide association studies reveal Gsts and other defense genes involved in multiple signaling pathways induced by herbicide safener in grain sorghum. Frontiers in Plant Science, 10, [192]. https://doi.org/10.3389/fpls.2019.00192

Juneja, A., Zhang, G., Jin, Y-S., & Singh, V. (2019). Bioprocessing and technoeconomic feasibility analysis of simultaneous production of D-psicose and ethanol using engineered yeast strain KAM-2GD. Bioresource Technology, 275, 27-34. https://doi.org/10.1016/j.biortech.2018.12.025

Valluru, R., Gazave, E. E., Fernandes, S. B., Ferguson, J. N., Lozano, R., Hirannaiah, P., ... Bandillo, N. (2019). Deleterious mutation burden and its association with complex traits in sorghum (Sorghum bicolor). Genetics, 211(3), 1075-1087. https://doi.org/10.1534/genetics.118.301742

Cheng, M. H., Dien, B. S., & Singh, V. (2019). Economics of plant oil recovery: A review. Biocatalysis and Agricultural Biotechnology, 18, [101056]. https://doi.org/10.1016/j.bcab.2019.101056

Kumar, D., & Singh, V. (2019). Improving dry-fractionated corn fermentation by supplementation of corn germ meal and pasta mill feed from agro-food industries. Cereal Chemistry, 96(2), 243-251. https://doi.org/10.1002/cche.10114

Köhler, I. H., Huber, S. C., Bernacchi, C., & Baxter, I. R. (2019). Increased temperatures may safeguard the nutritional quality of crops under future elevated CO 2 concentrations Plant Journal, 97(5), 872-886. https://doi.org/10.1111/tpj.14166

Pereira, I. S., do Nascimento, H. E. M., Vicari, M. B., Disney, M., Delucia, E. H., Domingues, T., ... Hofhansl, F. (2019). Performance of laser-based electronic devices for structural analysis of Amazonian terra-firme forests. Remote Sensing, 11(5), [510]. https://doi.org/10.3390/rs11050510

Jaiswal, D., De Souza, A. P., Larsen, S., LeBauer, D. S., Miguez, F. E., Sparovek, G., ... Long, S. P. (2019). Reply to: Brazilian ethanol expansion subject to limitations. Nature Climate Change, 9(3), 211-212. https://doi.org/10.1038/s41558-019-0423-y

Juneja, A., Sharma, N., Cusick, R., & Singh, V. (2019). Techno-economic feasibility of phosphorus recovery as a coproduct from corn wet milling plants. Cereal Chemistry, 96(2), 380-390. https://doi.org/10.1002/cche.10139

Bai, J., Sun, F., Wang, M., Su, L., Li, R., & Caetano-Anolles, G. (2019). Correction to: Genome-wide analysis of the MYB-CC gene family of maize (Genetica, (2019), 147, 1, (1-9), 10.1007/s10709-018-0042-y). Genetica, 147(1). https://doi.org/10.1007/s10709-018-0045-8

Bai, J., Sun, F., Wang, M., Su, L., Li, R., & Caetano-Anolles, G. (2019). Genome-wide analysis of the MYB-CC gene family of maize. Genetica, 147(1). https://doi.org/10.1007/s10709-018-0042-y

Krichels, A., Delucia, E. H., Sanford, R. A., Chee-Sanford, J., & Yang, W. (2019). Historical soil drainage mediates the response of soil greenhouse gas emissions to intense precipitation events. Biogeochemistry, 142(3), 425-442. https://doi.org/10.1007/s10533-019-00544-x

Kolbe, A. R., Studer, A. J., Cornejo, O. E., & Cousins, A. B. (2019). Insights from transcriptome profiling on the non-photosynthetic and stomatal signaling response of maize carbonic anhydrase mutants to low CO 2BMC genomics, 20(1), [138]. https://doi.org/10.1186/s12864-019-5522-7

Yang, X., Song, J., Todd, J., Peng, Z., Paudel, D., Luo, Z., ... Wang, J. (2019). Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a ‘sweet’ crop with ‘bitter’ genomes. Plant Biotechnology Journal, 17(2), 488-498. https://doi.org/10.1111/pbi.12992

Wang, Y., Hua, X., Xu, J., Chen, Z., Fan, T., Zeng, Z., ... Zhang, J. (2019). Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum. BMC genomics, 20(1), [5437]. https://doi.org/10.1186/s12864-019-5437-3

Joshi, G., & Chowdhary, G. (2019). Adaptive Control using Gaussian-Process with Model Reference Generative Network. In 2018 IEEE Conference on Decision and Control, CDC 2018 (pp. 237-243). [8619431] (Proceedings of the IEEE Conference on Decision and Control; Vol. 2018-December). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CDC.2018.8619431

Maske, H., & Chowdhary, G. (2019). Likelihood Rate Based Estimation of Nonstationary Markov Models. In 2018 IEEE Conference on Decision and Control, CDC 2018 (pp. 4759-4766). [8619316] (Proceedings of the IEEE Conference on Decision and Control; Vol. 2018-December). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CDC.2018.8619316

Jin, Z., Pagilla, P. R., Maske, H., & Chowdhary, G. (2019). Methods for Blended Shared Control of Hydraulic Excavators with Learning and Prediction. In 2018 IEEE Conference on Decision and Control, CDC 2018 (pp. 1973-1978). [8619826] (Proceedings of the IEEE Conference on Decision and Control; Vol. 2018-December). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CDC.2018.8619826

Jin, Z., Pagilla, P., Maske, H., & Chowdhary, G. (2019). Blended Shared Control with Subgoal Adjustment. In Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018 (pp. 2724-2729). [8616461] (Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/SMC.2018.00465

Shen, Y. H., Yang, F. Y., Lu, B. G., Zhao, W. W., Jiang, T., Feng, L., ... Ming, R. R. (2019). Exploring the differential mechanisms of carotenoid biosynthesis in the yellow peel and red flesh of papaya. BMC genomics, 20(1), [49]. https://doi.org/10.1186/s12864-018-5388-0

Nelson, A. J., Lichiheb, N., Koloutsou-Vakakis, S., Rood, M. J., Heuer, M., Myles, L. T., ... Bernacchi, C. (2019). Ammonia flux measurements above a corn canopy using relaxed eddy accumulation and a flux gradient system. Agricultural and Forest Meteorology, 264, 104-113. https://doi.org/10.1016/j.agrformet.2018.10.003

Berenbaum, M. R. (2019). Proceedings of the national academy of sciences—its evolution and adaptation. Proceedings of the National Academy of Sciences of the United States of America, 116(3), 704-706. https://doi.org/10.1073/pnas.1821201116

South, P. F., Cavanagh, A. P., Liu, H. W., & Ort, D. R. (2019). Synthetic glycolate metabolism pathways stimulate crop growth and productivity in the field. Science, 363(6422), [eaat9077]. https://doi.org/10.1126/science.aat9077

Clark, L. V., Dwiyanti, M. S., Anzoua, K. G., Brummer, J. E., Ghimire, B. K., Głowacka, K., ... Sacks, E. J. (2019). Biomass yield in a genetically diverse Miscanthus sinensis germplasm panel evaluated at five locations revealed individuals with exceptional potential. GCB Bioenergy. https://doi.org/10.1111/gcbb.12606

Wolz, K. J., & Delucia, E. H. (2019). Black walnut alley cropping is economically competitive with row crops in the Midwest USA. Ecological Applications, 29(1), [e01829]. https://doi.org/10.1002/eap.1829

Pignon, C. P., Lundgren, M. R., Osborne, C. P., & Long, S. P. (2019). Bundle sheath chloroplast volume can house sufficient Rubisco to avoid limiting C4 photosynthesis during chilling. Journal of experimental botany, 70(1), 357-365. https://doi.org/10.1093/jxb/ery345

Shi, Y., Xu, H., Shen, Q., Lin, J., Wang, Y., Hua, X., ... Zhang, J. (2019). Comparative Analysis of SUS Gene Family between Saccharum officinarum and Saccharum spontaneum. Tropical Plant Biology. https://doi.org/10.1007/s12042-019-09230-6

Ma, P., Yuan, Y., Shen, Q., Jiang, Q., Hua, X., Zhang, Q., ... Zhang, J. (2019). Evolution and Expression Analysis of Starch Synthase Gene Families in Saccharum spontaneum. Tropical Plant Biology. https://doi.org/10.1007/s12042-019-09225-3

Wang, J., Li, Y., Zhu, F., Ming, R. R., & Chen, L. (2019). Genome-Wide Analysis of Nitrate Transporter (NRT/NPF) Family in Sugarcane Saccharum spontaneum L. Tropical Plant Biology. https://doi.org/10.1007/s12042-019-09220-8

Clark, L. V., Dwiyanti, M. S., Anzoua, K. G., Brummer, J. E., Ghimire, B. K., Głowacka, K., ... Sacks, E. J. (2019). Genome-wide association and genomic prediction for biomass yield in a genetically diverse Miscanthus sinensis germplasm panel phenotyped at five locations in Asia and North America. GCB Bioenergy. https://doi.org/10.1111/gcbb.12620

Taylor, S. H., & Long, S. P. (2019). Phenotyping photosynthesis on the limit - a critical examination of RACiR. The New phytologist, 221(2), 621-624. https://doi.org/10.1111/nph.15382

Kromdijk, J., Głowacka, K., & Long, S. P. (2019). Predicting light-induced stomatal movements based on the redox state of plastoquinone: theory and validation. Photosynthesis research. https://doi.org/10.1007/s11120-019-00632-x

Ainsworth, E., Lemonnier, P., & Wedow, J. M. (2019). The influence of rising tropospheric carbon dioxide and ozone on plant productivity. Plant Biology. https://doi.org/10.1111/plb.12973

Dong, H., Clark, L. V., Lipka, A. E., Brummer, J. E., Głowacka, K., Hall, M. C., ... Sacks, E. J. (2019). Winter hardiness of Miscanthus (III): Genome-wide association and genomic prediction for overwintering ability in Miscanthus sinensis. GCB Bioenergy. https://doi.org/10.1111/gcbb.12615

Kumar, D., Hager, A-S., Sun, A., Debyser, W., Javier Guagliano, B., & Singh, V. (2019). Improving Fermentation Rate during Use of Corn Grits in Beverage Alcohol Production. Beverages, 5(1). https://doi.org/10.3390/beverages5010005

McAllister, W., Osipychev, D., Chowdhary, G., & Davis, A. (2018). Multi-Agent Planning for Coordinated Robotic Weed Killing. In 2018 IEEE/RSJ International Conference on Intelligent Robots and Systems, IROS 2018 (pp. 7955-7960). [8593429] (IEEE International Conference on Intelligent Robots and Systems). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/IROS.2018.8593429

Dien, B. S., Mitchell, R. B., Bowman, M. J., Jin, V. L., Quarterman, J., Schmer, M. R., ... Slininger, P. J. (2018). Bioconversion of pelletized big bluestem, switchgrass, and low-diversity grass mixtures into sugars and bioethanol. Frontiers in Energy Research, 6(DEC), [129]. https://doi.org/10.3389/fenrg.2018.00129

Bush, D. S., Siegel, J. P., & Berenbaum, M. R. (2018). Accelerated Development and Toxin Tolerance of the Navel Orangeworm Amyelois transitella (Lepidoptera: Pyralidae) in the Presence of Aspergillus flavus. Journal of Chemical Ecology, 44(12), 1170-1177. https://doi.org/10.1007/s10886-018-1027-0

Ruiz-Vera, U. M., Siebers, M. H., Jaiswal, D., Ort, D. R., & Bernacchi, C. (2018). Canopy warming accelerates development in soybean and maize, offsetting the delay in soybean reproductive development by elevated CO 2 concentrations Plant Cell and Environment, 41(12), 2806-2820. https://doi.org/10.1111/pce.13410

Pradyawong, S., Juneja, A., Bilal Sadiq, M., Noomhorm, A., & Singh, V. (2018). Comparison of cassava starch with corn as a feedstock for bioethanol production. Energies, 11(12), [3476]. https://doi.org/10.3390/en11123476

Zhang, J., Zhang, X., Tang, H., Zhang, Q., Hua, X., Ma, X., ... Ming, R. R. (2018). Erratum to: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. (Nature Genetics, (2018), 50, 11, (1565-1573), 10.1038/s41588-018-0237-2). Nature Genetics, 50(12). https://doi.org/10.1038/s41588-018-0293-7

Kurambhatti, C. V., Kumar, D., Rausch, K. D., Tumbleson, M. E., & Singh, V. (2018). Increasing ethanol yield through fiber conversion in corn dry grind process. Bioresource Technology, 270, 742-745. https://doi.org/10.1016/j.biortech.2018.09.120

South, P. F., Cavanagh, A. P., Lopez-Calcagno, P. E., Raines, C. A., & Ort, D. R. (2018). Optimizing photorespiration for improved crop productivity. Journal of Integrative Plant Biology, 60(12), 1217-1230. https://doi.org/10.1111/jipb.12709

Xu, H., Yu, Q., Shi, Y., Hua, X., Tang, H., Yang, L., ... Zhang, J. (2018). PGD: Pineapple Genomics Database. Horticulture Research, 5(1), [66]. https://doi.org/10.1038/s41438-018-0078-2

Głowacka, K., Kromdijk, J., Kucera, K., Xie, J., Cavanagh, A. P., Leonelli, L., ... Long, S. P. (2018). Photosystem II Subunit S overexpression increases the efficiency of water use in a field-grown crop. Nature communications, 9(1), [868]. https://doi.org/10.1038/s41467-018-03231-x

Tran, D., Do, H. M., Sheng, W., Bai, H., & Chowdhary, G. (2018). Real-time detection of distracted driving based on deep learning. IET Intelligent Transport Systems, 12(10), 1210-1219. https://doi.org/10.1049/iet-its.2018.5172

Singh, R., Jones, T., Wai, C. M., Jifon, J., Nagai, C., Ming, R. R., & Yu, Q. (2018). Transcriptomic analysis of transgressive segregants revealed the central role of photosynthetic capacity and efficiency in biomass accumulation in sugarcane. Scientific Reports, 8(1), [4415]. https://doi.org/10.1038/s41598-018-22798-5

Colson, P., Levasseur, A., Scola, B. L., Sharma, V., Nasir, A., Pontarotti, P., ... Raoult, D. (2018). Ancestrality and mosaicism of giant viruses supporting the definition of the fourth TRUC of microbes. Frontiers in Microbiology, 9(NOV), [2668]. https://doi.org/10.3389/fmicb.2018.02668

Hu, W., Hua, X., Zhang, Q., Wang, J., Shen, Q., Zhang, X., ... Zhang, J. (2018). New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics. BMC Plant Biology, 18(1), [270]. https://doi.org/10.1186/s12870-018-1495-y

Zhang, J., Zhang, X., Tang, H., Zhang, Q., Hua, X., Ma, X., ... Ming, R. R. (2018). Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nature Genetics, 50(11), 1565-1573. https://doi.org/10.1038/s41588-018-0237-2

Wong, M. J., Liao, L. H., & Berenbaum, M. R. (2018). Biphasic concentration-dependent interaction between imidacloprid and dietary phytochemicals in honey bees (Apis mellifera). PloS one, 13(11), [e0206625]. https://doi.org/10.1371/journal.pone.0206625

Seong, K. M., Coates, B. S., Berenbaum, M. R., Clark, J. M., & Pittendrigh, B. R. (2018). Comparative CYP-omic analysis between the DDT-susceptible and -resistant Drosophila melanogaster strains 91-C and 91-R. Pest Management Science, 74(11), 2530-2543. https://doi.org/10.1002/ps.4936

Kurambhatti, C. V., Kumar, D., Rausch, K. D., Tumbleson, M. E., & Singh, V. (2018). Ethanol production from corn fiber separated after liquefaction in the dry grind process. Energies, 11(11), [2921]. https://doi.org/10.3390/en11112921

Calla, B., MacLean, M., Liao, L. H., Dhanjal, I., Tittiger, C., Blomquist, G. J., & Berenbaum, M. R. (2018). Functional characterization of CYP4G11—a highly conserved enzyme in the western honey bee Apis mellifera. Insect Molecular Biology, 27(5), 661-674. https://doi.org/10.1111/imb.12516

Liu, M., Chowdhary, G., Castra Da Silva, B., Liu, S. Y., & How, J. P. (2018). Gaussian Processes for Learning and Control: A Tutorial with Examples. IEEE Control Systems, 38(5), 53-86. [8467518]. https://doi.org/10.1109/MCS.2018.2851010

Kayacan, E., Young, S. N., Peschel, J. M., & Chowdhary, G. (2018). High-precision control of tracked field robots in the presence of unknown traction coefficients. Journal of Field Robotics, 35(7), 1050-1062. https://doi.org/10.1002/rob.21794

Emberson, L. D., Pleijel, H., Ainsworth, E., van den Berg, M., Ren, W., Osborne, S., ... Van Dingenen, R. (2018). Ozone effects on crops and consideration in crop models. European Journal of Agronomy, 100, 19-34. https://doi.org/10.1016/j.eja.2018.06.002

Caetano-Anolles, G., Nasir, A., Kim, K. M., & Caetano-Anollés, D. (2018). Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions. Evolutionary Bioinformatics, 14. https://doi.org/10.1177/1176934318805101

Sharma, A., Song, J., Lin, Q., Singh, R., Ramos, N., Wang, K., ... Yu, Q. (2018). Comparative analysis of homologous sequences of saccharum officinarum and saccharum spontaneum reveals independent polyploidization events. Frontiers in Plant Science, 9, [1414]. https://doi.org/10.3389/fpls.2018.01414

Koç, I., Yuksel, I., & Caetano-Anolles, G. (2018). Metabolite-centric reporter pathway and tripartite network analysis of Arabidopsis under cold stress. Frontiers in Bioengineering and Biotechnology, 6(SEP), [121]. https://doi.org/10.3389/fbioe.2018.00121

Deng, Y., Hsiang, T., Li, S., Lin, L., Wang, Q., Chen, Q., ... Ming, R. R. (2018). Comparison of the mitochondrial genome sequences of six Annulohypoxylon stygium isolates suggests short fragment insertions as a potential factor leading to larger genomic size. Frontiers in Microbiology, 9(SEP), [2079]. https://doi.org/10.3389/fmicb.2018.02079

Joshi, G., & Chowdhary, G. (2018). Cross-Domain Transfer in Reinforcement Learning Using Target Apprentice. In 2018 IEEE International Conference on Robotics and Automation, ICRA 2018 (pp. 7525-7532). [8462977] (Proceedings - IEEE International Conference on Robotics and Automation). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ICRA.2018.8462977

Maske, H., Kieson, E., Chowdhary, G., & Abramson, C. (2018). Learning Task-Based Instructional Policy for Excavator-Like Robots. In 2018 IEEE International Conference on Robotics and Automation, ICRA 2018 (pp. 1962-1969). [8462923] (Proceedings - IEEE International Conference on Robotics and Automation). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ICRA.2018.8462923

Bishop, K. A., Lemonnier, P., Quebedeaux, J. C., Montes, C. M., Leakey, A., & Ainsworth, E. (2018). Similar photosynthetic response to elevated carbon dioxide concentration in species with different phloem loading strategies. Photosynthesis research, 137(3), 453-464. https://doi.org/10.1007/s11120-018-0524-x

Quindlen, J. F., Topcu, U., Chowdhary, G., & How, J. P. (2018). Active Sampling for Closed-Loop Statistical Verification of Uncertain Nonlinear Systems. In 2018 Annual American Control Conference, ACC 2018 (pp. 6259-6265). [8431662] (Proceedings of the American Control Conference; Vol. 2018-June). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.23919/ACC.2018.8431662

Quindlen, J. F., Topcu, U., Chowdhary, G., & How, J. P. (2018). Closed-Loop Statistical Verification of Stochastic Nonlinear Systems Subject to Parametric Uncertainties. In 2018 Annual American Control Conference, ACC 2018 (Vol. 2018-June, pp. 5460-5466). [8431742] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.23919/ACC.2018.8431742

Maske, H., Kingravi, H. A., & Chowdhary, G. (2018). Sensor Selection via Observability Analysis in Feature Space. In 2018 Annual American Control Conference, ACC 2018 (pp. 1058-1064). [8431625] (Proceedings of the American Control Conference; Vol. 2018-June). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.23919/ACC.2018.8431625

Staley, J. T., & Caetano-Anolles, G. (2018). Archaea-First and the Co-Evolutionary Diversification of Domains of Life. BioEssays, 40(8), [1800036]. https://doi.org/10.1002/bies.201800036

Wang, Z., Dien, B. S., Rausch, K. D., Tumbleson, M. E., & Singh, V. (2018). Fermentation of undetoxified sugarcane bagasse hydrolyzates using a two stage hydrothermal and mechanical refining pretreatment. Bioresource Technology, 261, 313-321. https://doi.org/10.1016/j.biortech.2018.04.018

Johnson, R. M., Harpur, B. A., Dogantzis, K. A., Zayed, A., & Berenbaum, M. R. (2018). Genomic footprint of evolution of eusociality in bees: floral food use and CYPome “blooms”. Insectes Sociaux, 65(3), 445-454. https://doi.org/10.1007/s00040-018-0631-x

Mills, G., Sharps, K., Simpson, D., Pleijel, H., Broberg, M., Uddling, J., ... Van Dingenen, R. (2018). Ozone pollution will compromise efforts to increase global wheat production. Global change biology, 24(8), 3560-3574. https://doi.org/10.1111/gcb.14157

Alkhalifah, N., Campbell, D. A., Falcon, C. M., Gardiner, J. M., Miller, N. D., Romay, M. C., ... Lawrence-Dill, C. J. (2018). Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets. BMC Research Notes, 11(1), [452]. https://doi.org/10.1186/s13104-018-3508-1

Wadlington, W. H., & Ming, R. R. (Accepted/In press). Development of an X-specific marker and identification of YY individuals in spinach. Theoretical And Applied Genetics, 1-8. https://doi.org/10.1007/s00122-018-3127-1

Liu, J., Chatham, L., Aryal, R., Yu, Q., & Ming, R. R. (2018). Differential methylation and expression of HUA1 ortholog in three sex types of papaya. Plant Science, 272, 99-106. https://doi.org/10.1016/j.plantsci.2018.04.001

Zhu, X., Liang, C., Masters, M. D., Kantola, I. B., & Delucia, E. H. (2018). The impacts of four potential bioenergy crops on soil carbon dynamics as shown by biomarker analyses and DRIFT spectroscopy. GCB Bioenergy, 10(7), 489-500. https://doi.org/10.1111/gcbb.12520

Varala, K., Marshall-Colon, A., Cirrone, J., Brooks, M. D., Pasquino, A. V., Léran, S., ... Coruzzi, G. M. (2018). Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. Proceedings of the National Academy of Sciences of the United States of America, 115(25), 6494-6499. https://doi.org/10.1073/pnas.1721487115

Berenbaum, M. R. (2018). Cinema-tick experience. American Entomologist, 64(2), 67-70. https://doi.org/10.1093/ae/tmy023

Calla, B., Maclean, M., Liao, L., Dhanjal, I., Tittiger, C., Blomquist, G. J., & Berenbaum, M. R. (2018). Functional characterization of CYP4G11—a highly conserved enzyme in the western honey bee Apis mellifera. Insect Molecular Biology. https://doi.org/10.1111/imb.12516

Wu, J., Wang, Y., Xu, J., Korban, S. S., Fei, Z., Tao, S., ... Zhang, S. (2018). Diversification and independent domestication of Asian and European pears. Genome biology, 19(1), [77]. https://doi.org/10.1186/s13059-018-1452-y

Kolbe, A. R., Brutnell, T. P., Cousins, A. B., & Studer, A. J. (2018). Carbonic anhydrase mutants in zea mays have altered stomatal responses to environmental signals. Plant physiology, 177(3), 980-989. https://doi.org/10.1104/pp.18.00176

Beerling, D. J., Leake, J. R., Long, S. P., Scholes, J. D., Ton, J., Nelson, P. N., ... Hansen, J. (2018). Erratum: Farming with crops and rocks to address global climate, food and soil security (Nature Plants (2018), DOI: 10.1038/s41477-018-0108-y). Nature Plants, 4(6). https://doi.org/10.1038/s41477-018-0162-5

Demkovich, M. R., Siegel, J. P., Walse, S. S., & Berenbaum, M. R. (2018). Impact of agricultural adjuvants on the toxicity of the diamide insecticides chlorantraniliprole and flubendiamide on different life stages of the navel orangeworm (Amyelois transitella). Journal of Pest Science, 91(3), 1127-1136. https://doi.org/10.1007/s10340-018-0959-z

Caetano-Anollés, K., Caetano-Anollés, D., Nasir, A., Kim, K. M., & Caetano-Anolles, G. (2018). Order and polarity in character state transformation models that root the tree of life. Biochimie, 149, 135-136. https://doi.org/10.1016/j.biochi.2018.04.001

Ainsworth, E., & Lemonnier, P. (2018). Phloem function: a key to understanding and manipulating plant responses to rising atmospheric [CO2]? Current opinion in plant biology, 43, 50-56. https://doi.org/10.1016/j.pbi.2017.12.003

Kirpich, A., Ainsworth, E., Wedow, J. M., Newman, J. R. B., Michailidis, G., & McIntyre, L. M. (2018). Variable selection in omics data: A practical evaluation of small sample sizes. PloS one, 13(6), [e0197910]. https://doi.org/10.1371/journal.pone.0197910

Kumar, D., Juneja, A., & Singh, V. (2018). Fermentation technology to improve productivity in dry grind corn process for bioethanol production. Fuel Processing Technology, 173, 66-74. https://doi.org/10.1016/j.fuproc.2018.01.014

Somavat, P., Kumar, D., & Singh, V. (2018). Techno-economic feasibility analysis of blue and purple corn processing for anthocyanin extraction and ethanol production using modified dry grind process. Industrial Crops and Products, 115, 78-87. https://doi.org/10.1016/j.indcrop.2018.02.015

De Souza, A. P., & Long, S. P. (2018). Toward improving photosynthesis in cassava: Characterizing photosynthetic limitations in four current African cultivars. Food and Energy Security, 7(2), [e00130]. https://doi.org/10.1002/fes3.130

Christensen, A. J., Srinivasan, V., Hart, J. C., & Marshall-Colon, A. (2018). Use of computational modeling combined with advanced visualization to develop strategies for the design of crop ideotypes to address food security. Nutrition reviews, 76(5), 332-347. https://doi.org/10.1093/nutrit/nux076

Petronikolou, N., Hollatz, A. J., Schuler, M. A., & Nair, S. K. (2018). Loganic Acid Methyltransferase: Insights into the Specificity of Methylation on an Iridoid Glycoside. ChemBioChem, 19(8), 784-788. https://doi.org/10.1002/cbic.201700679

Seong, K. M., Coates, B. S., Berenbaum, M. R., Clark, J. M., & Pittendrigh, B. R. (2018). Comparative CYP‐omic analysis between the DDT‐susceptible and ‐resistant Drosophila melanogaster strains 91‐C and 91‐R. Pest Management Science. https://doi.org/10.1002/ps.4936

Wolz, K. J., Branham, B. E., & Delucia, E. H. (2018). Reduced nitrogen losses after conversion of row crop agriculture to alley cropping with mixed fruit and nut trees. Agriculture, Ecosystems and Environment, 258, 172-181. https://doi.org/10.1016/j.agee.2018.02.024

Berenbaum, M. (2018). Damselflies in Distress. American Entomologist, 64(1), 3-6. https://doi.org/10.1093/ae/tmy003

Meng, Z., Hu, X., Zhang, Z., Li, Z., Lin, Q., Yang, M., ... Wang, K. (2018). Chromosome Nomenclature and Cytological Characterization of Sacred Lotus. Cytogenetic and Genome Research, 153(4), 223-231. https://doi.org/10.1159/000486777

Whitaker, J., Field, J. L., Bernacchi, C., Cerri, C. E. P., Ceulemans, R., Davies, C. A., ... McNamara, N. P. (2018). Consensus, uncertainties and challenges for perennial bioenergy crops and land use. GCB Bioenergy, 10(3), 150-164. https://doi.org/10.1111/gcbb.12488

Beerling, D. J., Leake, J. R., Long, S. P., Scholes, J. D., Ton, J., Nelson, P. N., ... Hansen, J. (2018). Farming with crops and rocks to address global climate, food and soil security /631/449 /706/1143 /704/47 /704/106 perspective. Nature Plants, 4(3), 138-147. https://doi.org/10.1038/s41477-018-0108-y

Wolz, K. J., Lovell, S. T., Branham, B. E., Eddy, W. C., Keeley, K., Revord, R. S., ... Delucia, E. H. (2018). Frontiers in alley cropping: Transformative solutions for temperate agriculture. Global change biology, 24(3), 883-894. https://doi.org/10.1111/gcb.13986

Gomez-Casanovas, N., Delucia, N. J., Bernacchi, C., Boughton, E. H., Sparks, J. P., Chamberlain, S. D., & Delucia, E. H. (2018). Grazing alters net ecosystem C fluxes and the global warming potential of a subtropical pasture. Ecological Applications, 28(2), 557-572. https://doi.org/10.1002/eap.1670

Wang, Z., Sharma, V., Dien, B. S., & Singh, V. (2018). High-conversion hydrolysates and corn sweetener production in dry-grind corn process: Cereal Chemistry, 95(2), 302-311. https://doi.org/10.1002/cche.10030

Dong, G., Shen, J., Zhang, Q., Wang, J., Yu, Q., Ming, R. R., ... Zhang, J. (2018). Development and applications of chromosome-specific cytogenetic BAC-FISH probes in S. spontaneum. Frontiers in Plant Science, 9, [218]. https://doi.org/10.3389/fpls.2018.00218

Kumar, D., Long, S. P., & Singh, V. (2018). Biorefinery for combined production of jet fuel and ethanol from lipid-producing sugarcane: a techno-economic evaluation. GCB Bioenergy, 10(2), 92-107. https://doi.org/10.1111/gcbb.12478

Walker, B. J., Drewry, D. T., Slattery, R. A., VanLoocke, A., Cho, Y. B., & Ort, D. R. (2018). Chlorophyll can be reduced in crop canopies with little penalty to photosynthesis. Plant physiology, 176(2), 1215-1232. https://doi.org/10.1104/pp.17.01401

Banan, D., Paul, R. E., Feldman, M. J., Holmes, M. W., Schlake, H., Baxter, I., ... Leakey, A. (2018). High-fidelity detection of crop biomass quantitative trait loci from low-cost imaging in the field. Plant Direct, 2(2), [e00041]. https://doi.org/10.1002/pld3.41

Jin, Z., Ainsworth, E., Leakey, A., & Lobell, D. B. (2018). Increasing drought and diminishing benefits of elevated carbon dioxide for soybean yields across the US Midwest. Global change biology, 24(2), e522-e533. https://doi.org/10.1111/gcb.13946

Miao, G., Guan, K., Yang, X., Bernacchi, C., Berry, J. A., Delucia, E. H., ... Masters, M. D. (2018). Sun-Induced Chlorophyll Fluorescence, Photosynthesis, and Light Use Efficiency of a Soybean Field from Seasonally Continuous Measurements. Journal of Geophysical Research: Biogeosciences, 123(2), 610-623. https://doi.org/10.1002/2017JG004180

Slattery, R. A., Walker, B. J., Weber, A. P. M., & Ort, D. R. (2018). The impacts of fluctuating light on crop performance. Plant physiology, 176(2), 990-1003. https://doi.org/10.1104/pp.17.01234

Wolz, K. J., & Delucia, E. H. (2018). Alley cropping: Global patterns of species composition and function. Agriculture, Ecosystems and Environment, 252, 61-68. https://doi.org/10.1016/j.agee.2017.10.005

Bender, K. W., Zielinski, R. E., & Huber, S. C. (2018). Revisiting paradigms of Ca2+ signaling protein kinase regulation in plants. Biochemical Journal, 475(1), 207-223. https://doi.org/10.1042/BCJ20170022

Berenbaum, M. R. (2018). Preface: Valedictory from a Gadfly Grammarian. Annual Review of Entomology, 63, v-ix. https://doi.org/10.1146/annurev-en-63-121917-100001

Liu, J., Sharma, A., Niewiara, M. J., Singh, R., Ming, R. R., & Yu, Q. (2018). Papain-like cysteine proteases in Carica papaya: Lineage-specific gene duplication and expansion. BMC genomics, 19(1), [26]. https://doi.org/10.1186/s12864-017-4394-y

Quindlen, J. F., Topcu, U., Chowdhary, G., & How, J. P. (2018). Active sampling-based binary verification of dynamical systems. In AIAA Guidance, Navigation, and Control (210039 ed.). (AIAA Guidance, Navigation, and Control Conference, 2018; No. 210039). American Institute of Aeronautics and Astronautics Inc, AIAA. https://doi.org/10.2514/6.2018-1107

LeBauer, D. S., Kooper, R., Mulrooney, P., Rohde, S., Wang, D., Long, S. P., & Dietze, M. C. (2018). BETYdb: a yield, trait, and ecosystem service database applied to second-generation bioenergy feedstock production. GCB Bioenergy, 10(1), 61-71. https://doi.org/10.1111/gcbb.12420

Kolbe, A. R., Studer, A. J., & Cousins, A. B. (2018). Biochemical and transcriptomic analysis of maize diversity to elucidate drivers of leaf carbon isotope composition. Functional Plant Biology, 45(5), 489-500. https://doi.org/10.1071/FP17265

Kim, S. M., Lee, D., Thapa, S., Dien, B. S., Tumbleson, M. E., Rausch, K. D., & Singh, V. (2018). Cellulosic ethanol potential of feedstocks grown on marginal lands. Transactions of the ASABE, 61(6), 1775-1782. https://doi.org/10.13031/trans.12945

Ramchandran, D., Hojilla-Evangelista, M. P., Moose, S. P., Rausch, K. D., Tumbleson, M. E., & Singh, V. (Accepted/In press). Changes in Corn Protein Content During Storage and Their Relationship with Dry Grind Ethanol Production. JAOCS, Journal of the American Oil Chemists' Society. https://doi.org/10.1002/aocs.12070

Gomez-Casanovas, N., DeLucia, N. J., Hudiburg, T. W., Bernacchi, C., & Delucia, E. H. (2018). Conversion of grazed pastures to energy cane as a biofuel feedstock alters the emission of GHGs from soils in Southeastern United States. Biomass and Bioenergy, 108, 312-322. https://doi.org/10.1016/j.biombioe.2017.11.020

Bai, J., Sun, F., Wang, M., Su, L., Li, R., & Caetano-Anolles, G. (Accepted/In press). Correction to: Genome-wide analysis of the MYB-CC gene family of maize (Genetica, (2018), 10.1007/s10709-018-0042-y). Genetica. https://doi.org/10.1007/s10709-018-0045-8

Caddell, D. F., Wei, T., Sharma, S., Oh, M. H., Park, C. J., Canlas, P., ... Ronald, P. C. (2018). Four tyrosine residues of the rice immune receptor XA21 are not required for interaction with the co-receptor OsSERK2 or resistance to Xanthomonas oryzae pv. oryzae. PeerJ, 2018(12), [e6074]. https://doi.org/10.7717/peerj.6074

Orozco-Arias, S., Liu, J., Tabares-Soto, R., Ceballos, D., Domingues, D. S., Garavito, A., ... Guyot, R. (2018). Inpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamics. Biology, 7(2), [32]. https://doi.org/10.3390/biology7020032

Larson, T. H., Balikian, R. J., Ruiz-Vera, U., & Ort, D. R. (2018). In-situ cassava root size measurement using ground penetrating radar (GPR). Proceedings of the Symposium on the Application of Geophyics to Engineering and Environmental Problems, SAGEEP, 2018-March.

Twohey, R. J., Roberts, L. M., & Studer, A. J. (Accepted/In press). Leaf stable carbon isotope composition reflects transpiration efficiency in Zea mays. Plant Journal. https://doi.org/10.1111/tpj.14135

Gog, L., Berenbaum, M. R., & Delucia, E. H. (Accepted/In press). Mediation of Impacts of Elevated CO2 and Light Environment on Arabidopsis thaliana (L.) Chemical Defense against Insect Herbivory Via Photosynthesis. Journal of Chemical Ecology. https://doi.org/10.1007/s10886-018-1035-0

Berenbaum, M. R. (2018). Reality bites. American Entomologist, 64(3), 134-137. https://doi.org/10.1093/ae/tmy044

Zhang, J., Zhang, Q., Li, L., Tang, H., Zhang, Q., Chen, Y., ... Ming, R. R. (Accepted/In press). Recent polyploidization events in three Saccharum founding species. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.12962

Shamshiri, R. R., Weltzien, C., Hameed, I. A., Yule, I. J., Grift, T. E., Balasundram, S. K., ... Chowdhary, G. (2018). Research and development in agricultural robotics: A perspective of digital farming. International Journal of Agricultural and Biological Engineering, 11(4), 1-14. https://doi.org/10.25165/ijabe.v11i4.4278

Pattanaik, A., Tang, Z., Liu, S., Bommannan, G., & Chowdhary, G. (2018). Robust Deep Reinforcement Learning with adversarial attacks. In 17th International Conference on Autonomous Agents and Multiagent Systems, AAMAS 2018 (Vol. 3, pp. 2040-2042). International Foundation for Autonomous Agents and Multiagent Systems (IFAAMAS).

Shamshiri, R. R., Hameed, I. A., Pitonakova, L., Weltzien, C., Balasundram, S. K., Yule, I. J., ... Chowdhary, G. (2018). Simulation software and virtual environments for acceleration of agricultural robotics: Features highlights and performance comparison. International Journal of Agricultural and Biological Engineering, 11(4), 15-31. https://doi.org/10.25165/ijabe.v11i4.4032

Zhu, P., Jin, Z., Zhuang, Q., Ciais, P., Bernacchi, C., Wang, X., ... Lobell, D. (Accepted/In press). The important but weakening maize yield benefit of grain filling prolongation in the US Midwest. Global Change Biology. https://doi.org/10.1111/gcb.14356

Berenbaum, M. R. (2018). The superposition principle. American Entomologist, 64(4), 204-206. https://doi.org/10.1093/ae/tmy058

Kayacan, E., & Chowdhary, G. (Accepted/In press). Tracking Error Learning Control for Precise Mobile Robot Path Tracking in Outdoor Environment. Journal of Intelligent and Robotic Systems: Theory and Applications. https://doi.org/10.1007/s10846-018-0916-3