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Genomic Ecology of Global Change: Publications

Bush, D. S., Demkovich, M., Aldunate, M., Siegel, J., & Berenbaum, M. R. (2023). Kaolin as a management alternative for insecticide-resistant navel orangeworm (Lepidoptera: Pyralidae). Journal of economic entomology, 116(6), 2095-2103. Article toad194.

Tran, V. G., Mishra, S., Bhagwat, S. S., Shafaei, S., Shen, Y., Allen, J. L., Crosly, B. A., Tan, S. I., Fatma, Z., Rabinowitz, J. D., Guest, J. S., Singh, V., & Zhao, H. (2023). An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis. Nature communications, 14(1), Article 6152.

Wu, J., Ackerman, A., Gaire, R., Chowdhary, G., & Rutkoski, J. (2023). A neural network for phenotyping Fusarium-damaged kernels (FDKs) in wheat and its impact on genomic selection accuracy. Plant Phenome Journal, 6(1), Article e20065.

Prochetto, S., Studer, A. J., & Reinheimer, R. (2023). De novo transcriptome assemblies of C3 and C4 non-model grass species reveal key differences in leaf development. BMC genomics, 24(1), Article 64.

Wu, W. Y., Liao, L. H., Lin, C. H., Johnson, R. M., & Berenbaum, M. R. (2023). Effects of pesticide-adjuvant combinations used in almond orchards on olfactory responses to social signals in honey bees (Apis mellifera). Scientific reports, 13(1), Article 15577.

Bao, T., Qian, Y., Xin, Y., Collins, J. J., & Lu, T. (2023). Engineering microbial division of labor for plastic upcycling. Nature communications, 14(1), Article 5712.

Guo, Y., Boughton, E. H., Bohlman, S., Bernacchi, C., Bohlen, P. J., Boughton, R., DeLucia, E., Fauth, J. E., Gomez-Casanovas, N., Jenkins, D. G., Lollis, G., Miller, R. S., Quintana-Ascencio, P. F., Sonnier, G., Sparks, J., Swain, H. M., & Qiu, J. (2023). Grassland intensification effects cascade to alter multifunctionality of wetlands within metaecosystems. Nature communications, 14(1), Article 8267.

Yun, E. J., Yu, S., Kim, D. H., Park, N. J., Liu, J. J., Jin, Y. S., & Kim, K. H. (2023). Identification of the enantiomeric nature of 2-keto-3-deoxy-galactonate in the catabolic pathway of 3,6-anhydro-l-galactose. Applied Microbiology and Biotechnology, 107(24), 7427-7438.

Singh, S., & Singh, V. (2023). Phosphorus flow in production of soy protein concentrate and isolate from defatted soybean flour. JAOCS, Journal of the American Oil Chemists' Society, 100(12), 985-991.

Lozano, A. C., Ding, H., Abe, N., & Lipka, A. E. (2023). Regularized multi-trait multi-locus linear mixed models for genome-wide association studies and genomic selection in crops. BMC bioinformatics, 24(1), Article 399.

Aziz, M. F., Mughal, F., & Caetano-Anollés, G. (2023). Tracing the birth of structural domains from loops during protein evolution. Scientific reports, 13(1), Article 14688.

Aspray, E. K., Mies, T. A., McGrath, J. A., Montes, C. M., Dalsing, B., Puthuval, K. K., Whetten, A., Herriott, J., Li, S., Bernacchi, C. J., DeLucia, E. H., Leakey, A. D. B., Long, S. P., McGrath, J. M., Miglietta, F., Ort, D. R., & Ainsworth, E. A. (2023). Two decades of fumigation data from the Soybean Free Air Concentration Enrichment facility. Scientific Data, 10(1), Article 226.

Li, S., Leakey, A. D. B., Moller, C. A., Montes, C. M., Sacks, E. J., Lee, D., & Ainsworth, E. A. (2023). Similar photosynthetic but different yield responses of C3 and C4 crops to elevated O3. Proceedings of the National Academy of Sciences, 120(46), Article e2313591120.

Nguyen, V., Xue, P., Li, Y., Zhao, H., & Lu, T. (2023). Controlling circuitry underlies the growth optimization of Saccharomyces cerevisiae. Metabolic Engineering, 80, 173-183.

Park, S., Park, B. R., Jeong, D., Park, J., Ko, J. K., Kim, S. J., Kim, J. S., Jin, Y. S., & Kim, S. R. (2023). Functional expression of RuBisCO reduces CO2 emission during fermentation by engineered Saccharomyces cerevisiae. Process Biochemistry, 134, 286-293.

Njuguna, J. N., Clark, L. V., Lipka, A. E., Anzoua, K. G., Bagmet, L., Chebukin, P., Dwiyanti, M. S., Dzyubenko, E., Dzyubenko, N., Ghimire, B. K., Jin, X., Johnson, D. A., Nagano, H., Peng, J., Petersen, K. K., Sabitov, A., Seong, E. S., Yamada, T., Yoo, J. H., ... Sacks, E. J. (2023). Genome-wide association and genomic prediction for yield and component traits of Miscanthus sacchariflorus. GCB Bioenergy, 15(11), 1355-1372.

Della Coletta, R., Fernandes, S. B., Monnahan, P. J., Mikel, M. A., Bohn, M. O., Lipka, A. E., & Hirsch, C. N. (2023). Importance of genetic architecture in marker selection decisions for genomic prediction. Theoretical and Applied Genetics, 136(11), Article 220.

You, J., Li, S., Chen, N., Yang, X., Kurambhatti, C., Cai, X., & Singh, V. (2023). Phosphorus (P) recovery from corn biorefineries is promising for mitigating environmental impacts and promoting the P circular economy. Resources, Conservation and Recycling, 198, Article 107194.

Cavanagh, A. P., & Ort, D. R. (2023). Transgenic strategies to improve the thermotolerance of photosynthesis. Photosynthesis research, 158(2), 109-120.

Fisher, A., Tadei, R., Berenbaum, M., Nieh, J., Siviter, H., Crall, J., Glass, J. R., Muth, F., Liao, L-H., Traynor, K., Desjardins, N., Nocelli, R., Simon-Delso, N., & Harrison, J. F. (2023). Breaking the cycle: Reforming pesticide regulation to protect pollinators. BioScience, Article biad088. Advance online publication.

Sun, F., & Caetano-Anollés, G. (2023). Advances in Molecular Exploration of Crop Plants under Environmental Stresses from Genetic and Genomic Perspectives. Agronomy, 13(10), Article 2653.

Holland, B. L., Matthews, M. L., Bota, P., Sweetlove, L. J., Long, S. P., & diCenzo, G. C. (2023). A genome-scale metabolic reconstruction of soybean and Bradyrhizobium diazoefficiens reveals the cost–benefit of nitrogen fixation. New Phytologist, 240(2), 744-756.

Cho, Y. B., Stutz, S. S., Jones, S. I., Wang, Y., Pelech, E. A., & Ort, D. R. (2023). Impact of pod and seed photosynthesis on seed filling and canopy carbon gain in soybean. Plant physiology, 193(2), 966-979. Article kiad324.

Nguyen, M. T., Kim, S. A., Cheng, Y. Y., Hong, S. H., Jin, Y. S., & Han, N. S. (2023). A qPCR Method to Assay Endonuclease Activity of Cas9-sgRNA Ribonucleoprotein Complexes. Journal of Microbiology and Biotechnology, 33(9), 1228-1237.

Rao, P., Yaroslavsky, M. A., Miller, J. C., & Schuler, M. A. (2023). Catalytic Site Constraints in the P450s Mediating Loganic Acid (7DLH) and Secologanic Acid Synthesis (SLAS) in Camptotheca. Biochemistry, 62(18), 2763-2774.

Wu, G., Guan, K., Ainsworth, E. A., Martin, D. G., Kimm, H., & Yang, X. (2023). Solar-induced chlorophyll fluorescence captures the effects of elevated ozone on canopy structure and acceleration of senescence in soybean. Journal of experimental botany. Advance online publication.

Murphy, M. D., & Lipka, A. E. (2023). An application of vGWAS to differences in flowering time in maize across mega-environments. Crop Science, 63(5), 2807-2817.

Kim, J., Cheong, Y. E., Yu, S., Yun, E. J., Jin, Y. S., & Kim, K. H. (2023). Biosynthesis of L-fucose and L-fuculose using engineered Saccharomyces cerevisiae. Process Biochemistry, 132, 152-156.

Singh, S., Bekal, S., Duan, J., & Singh, V. (2023). Characterization and Comparison of Wet Milling Fractions of Export Commodity Corn Originating from Different International Geographical Locations. Starch/Staerke, 75(9-10), Article 2200280.

Sullivan, M., Williams, M. M., & Studer, A. J. (2023). Genetic diversity of North American popcorn germplasm and the effect of population structure on nicosulfuron response. Crop Science, 63(5), 2894-2912.

Głowacka, K., Kromdijk, J., Salesse-Smith, C. E., Smith, C., Driever, S. M., & Long, S. P. (2023). Is chloroplast size optimal for photosynthetic efficiency? New Phytologist, 239(6), 2197-2211.

Wang, Y., Smith, J. A. C., Zhu, X. G., & Long, S. P. (2023). Rethinking the potential productivity of crassulacean acid metabolism by integrating metabolic dynamics with shoot architecture, using the example of Agave tequilana. New Phytologist, 239(6), 2180-2196.

Gomez-Casanovas, N., Mwebaze, P., Khanna, M., Branham, B., Time, A., DeLucia, E. H., Bernacchi, C. J., Knapp, A. K., Hoque, M. J., Du, X., Blanc-Betes, E., Barron-Gafford, G. A., Peng, B., Guan, K., Macknick, J., Miao, R., & Miljkovic, N. (2023). Knowns, uncertainties, and challenges in agrivoltaics to sustainably intensify energy and food production. Cell Reports Physical Science, 4(8), Article 101518.

Della Coletta, R., Liese, S. E., Fernandes, S. B., Mikel, M. A., Bohn, M. O., Lipka, A. E., & Hirsch, C. N. (2023). Linking genetic and environmental factors through marker effect networks to understand trait plasticity. Genetics, 224(4), Article iyad103.

Wu, J., Bao, W., Ainsworth, E., & He, J. (2023). Personalized Federated Learning with Parameter Propagation. In KDD 2023 - Proceedings of the 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (pp. 2594-2605). (Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining). Association for Computing Machinery.

Ort, D. R., & Lunn, J. E. (2023). Society for Experimental Biology Centenary (1923-2023). Journal of experimental botany, 74(14), 3877-3878.

Guan, K., Jin, Z., Peng, B., Tang, J., DeLucia, E. H., West, P. C., Jiang, C., Wang, S., Kim, T., Zhou, W., Griffis, T., Liu, L., Yang, W. H., Qin, Z., Yang, Q., Margenot, A., Stuchiner, E. R., Kumar, V., Bernacchi, C., ... Yang, S. J. (2023). A scalable framework for quantifying field-level agricultural carbon outcomes. Earth-Science Reviews, 243, Article 104462.

Zhang, L., Zheng, H., Li, W., Olesen, J. E., Harrison, M. T., Bai, Z., Zou, J., Zheng, A., Bernacchi, C., Xu, X., Peng, B., Liu, K., Chen, F., & Yin, X. (2023). Genetic progress battles climate variability: drivers of soybean yield gains in China from 2006 to 2020. Agronomy for Sustainable Development, 43(4), Article 50.

Pagliaro, Z., Burke, J., Morrissey, E., Ridgeway, J., Singh, V., Altpeter, F., & Brzostek, E. R. (2023). Lipid-enhanced Oilcane does not impact soil carbon dynamics compared with wild-type Sugarcane. GCB Bioenergy, 15(8), 969-978.

You, J. S., Kim, Y., Lee, S., Bashir, R., & Chen, J. (2023). RhoA/ROCK signalling activated by ARHGEF3 promotes muscle weakness via autophagy in dystrophic mdx mice. Journal of Cachexia, Sarcopenia and Muscle, 14(4), 1880-1893.

You, J. S., Barai, P., & Chen, J. (2023). Sex differences in skeletal muscle size, function, and myosin heavy chain isoform expression during post-injury regeneration in mice. Physiological Reports, 11(16), Article e15791.

Berenbaum, M. R. (2023). “Debugging” insect-related conspiracy theories. Annals of the Entomological Society of America, Article saad018. Advance online publication.

Wu, G., Guan, K., Jiang, C., Kimm, H., Miao, G., Yang, X., Bernacchi, C. J., Sun, X., Suyker, A. E., & Moore, C. E. (2023). Can upscaling ground nadir SIF to eddy covariance footprint improve the relationship between SIF and GPP in croplands? Agricultural and Forest Meteorology, 338, Article 109532.

Basso, T. P., Procópio, D. P., Petrin, T. H. C., Giacon, T. G., Jin, Y. S., Basso, T. O., & Basso, L. C. (2023). Engineering xylose fermentation in an industrial yeast: continuous cultivation as a tool for selecting improved strains. Letters in Applied Microbiology, 76(7).

Caetano-Anollés, G. (2023). Agency in evolution of biomolecular communication. Annals of the New York Academy of Sciences, 1525(1), 88-103.

Blanc-Betes, E., Gomez-Casanovas, N., Yang, W. H., Chandrasoma, J., Clark, T. J., De Lucia, E. H., Hyde, C. A., Kent, A. D., Pett-Ridge, J., Rabinowitz, J., Raglin, S. S., Schwender, J., Shen, Y., Van Allen, R., & von Haden, A. C. (2023). Accelerating the development of a sustainable bioenergy portfolio through stable isotopes. GCB Bioenergy, 15(7), 840-866.

Parsons, B. W., Utterback, P. L., Juneja, A., Singh, V., Parsons, C. M., & Emmert, J. L. (2023). Determination of TMEn, standardized amino acid digestibility, phosphorus digestibility, and phosphorus bioavailability in conventional and reduced phosphorus distillers dried grains with solubles. Poultry science, 102(7), Article 102743.

Lee, M. S., Boyd, R. A., Boateng, K. A., & Ort, D. R. (2023). Exploring 3D leaf anatomical traits for C4 photosynthesis: chloroplast and plasmodesmata pit field size in maize and sugarcane. New Phytologist, 239(2), 506-517.

Nguyen, P. Q., Huang, X., Collins, D. S., Collins, J. J., & Lu, T. (2023). Harnessing synthetic biology to enhance ocean health. Trends in Biotechnology, 41(7), 860-874.

Cheng, M. H., Singh, S., Carr Clennon, A. N., Dien, B. S., & Singh, V. (2023). Production of Designer Xylose-Acetic Acid Enriched Hydrolysate from Bioenergy Sorghum, Oilcane, and Energycane Bagasses. Bioresource Technology, 380, Article 129104.

Lagos-Kutz, D. M., Pawlowski, M. L., Han, J., Clough, S. J., & Hartman, G. L. (2023). Reduction in productivity of soybean plants infested with Neohyadatothrips variabilis (Thysanoptera: Thripidae) with and without soybean vein necrosis virus. Phytoparasitica, 51(3), 437-445.

Seyfried, G. S., Midgley, M. G., Phillips, R. P., & Yang, W. H. (2023). Refining the role of nitrogen mineralization in mycorrhizal nutrient syndromes. Biogeochemistry, 164(3), 473–487.

Bernacchi, C. J., Ruiz-Vera, U. M., Siebers, M. H., DeLucia, N. J., & Ort, D. R. (2023). Short- and long-term warming events on photosynthetic physiology, growth, and yields of field grown crops. Biochemical Journal, 480(13), 999-1014.

Li, S., Cai, X., Niroula, S., Wallington, K., Gramig, B. M., Cusick, R. D., Singh, V., McIsaac, G., Oh, S., Kurambhatti, C., Emaminejad, S. A., & John, S. (2023). Integrated Agricultural Practices and Engineering Technologies Enhance Synergies of Food-Energy-Water Systems in Corn Belt Watersheds. Environmental Science and Technology, 57(25), 9194-9203.

Wu, J., He, J., & Ainsworth, E. (2023). Non-IID Transfer Learning on Graphs. In B. Williams, Y. Chen, & J. Neville (Eds.), AAAI-23 Technical Tracks 9 (pp. 10342-10350). (Proceedings of the 37th AAAI Conference on Artificial Intelligence, AAAI 2023; Vol. 37). American Association for Artificial Intelligence (AAAI) Press.

Paudel, S., Gomez-Casanovas, N., Boughton, E. H., Chamberlain, S. D., Wagle, P., Peterson, B. L., Bajgain, R., Starks, P. J., Basara, J., Bernacchi, C. J., DeLucia, E. H., Goodman, L. E., Gowda, P. H., Reuter, R., Sparks, J. P., Swain, H. M., Xiao, X., & Steiner, J. L. (2023). Intensification differentially affects the delivery of multiple ecosystem services in subtropical and temperate grasslands. Agriculture, Ecosystems and Environment, 348, Article 108398.

Kim, J., Jin, Y. S., & Kim, K. H. (2023). L-Fucose is involved in human–gut microbiome interactions. Applied Microbiology and Biotechnology, 107(12), 3869-3875.

Lee, S. H., Yun, E. J., Han, N. R., Jung, I., Pelton, J. G., Lee, J-E., Kang, N. J., Jin, Y-S., & Kim, K. H. (2023). Production of Ethyl-agarobioside, a Novel Skin Moisturizer, by Mimicking the Alcoholysis from the Japanese Sake-Brewing Process. Marine Drugs, 21(6), Article 341.

Calera, E. S., Oliveira, G. C. D., Araujo, G. L., Filho, J. I. F., Toschi, L., Hernandes, A. C., Velasquez, A. E. B., Gasparino, M. V., Chowdhary, G., Higuti, V. A. H., & Becker, M. (2023). Under-Canopy Navigation for an Agricultural Rover Based on Image Data. Journal of Intelligent and Robotic Systems: Theory and Applications, 108(2), Article 29.

Seyfried, G. S., Corrales, A., Kent, A. D., Dalling, J. W., & Yang, W. (2023). Watershed-scale Variation in Potential Fungal Community Contributions to Ectomycorrhizal Biogeochemical Syndromes. Ecosystems, 26(4), 724-739.

Tamang, B. G., Zhang, Y., Zambrano, M. A., & Ainsworth, E. A. (2023). Anatomical determinants of gas exchange and hydraulics vary with leaf shape in soybean. Annals of botany, 131(6), 909-920.

Zegers, F. M., Sun, R., Chowdhary, G., & Dixon, W. E. (2023). Distributed State Estimation With Deep Neural Networks for Uncertain Nonlinear Systems Under Event-Triggered Communication. IEEE Transactions on Automatic Control, 68(5), 3107-3114.

Njuguna, J. N., Clark, L. V., Anzoua, K. G., Bagmet, L., Chebukin, P., Dwiyanti, M. S., Dzyubenko, E., Dzyubenko, N., Ghimire, B. K., Jin, X., Johnson, D. A., Jørgensen, U., Kjeldsen, J. B., Nagano, H., Peng, J., Petersen, K. K., Sabitov, A., Seong, E. S., Yamada, T., ... Sacks, E. J. (2023). Biomass yield in a genetically diverse Miscanthus sacchariflorus germplasm panel phenotyped at five locations in Asia, North America, and Europe. GCB Bioenergy, 15(5), 642-662.

Miller, J. C., Lee, J. H. Z., Mclean, M. A., Chao, R. R., Stone, I. S. J., Pukala, T. L., Bruning, J. B., De Voss, J. J., Schuler, M. A., Sligar, S. G., & Bell, S. G. (2023). Engineering C-C Bond Cleavage Activity into a P450 Monooxygenase Enzyme. Journal of the American Chemical Society, 145(16), 9207-9222.

Maitra, S., & Singh, V. (2023). Application of Time-Domain 1H NMR for Investigating Dynamics of Vegetative Lipids in Bioenergy Crops at Different Developmental Stages. Industrial Biotechnology, 19(2), 86-93.

Chen, J. (2023). Arginyl-tRNA synthetase in inflammation. Nature Cell Biology, 25(4), 520-521.

Kong, W., Qian, Y., Stewart, P. S., & Lu, T. (2023). De novo engineering of a bacterial lifestyle program. Nature chemical biology, 19(4), 488-497.

Lane, S., Turner, T. L., & Jin, Y. S. (2023). Glucose assimilation rate determines the partition of flux at pyruvate between lactic acid and ethanol in Saccharomyces cerevisiae. Biotechnology Journal, 18(4), Article 2200535.

Tsvetkov, N., Bahia, S., Calla, B., Berenbaum, M. R., & Zayed, A. (2023). Genetics of tolerance in honeybees to the neonicotinoid clothianidin. iScience, 26(3), Article 106084.

Burroughs, C. H., Montes, C. M., Moller, C. A., Mitchell, N. G., Michael, A. M., Peng, B., Kimm, H., Pederson, T. L., Lipka, A. E., Bernacchi, C. J., Guan, K., & Ainsworth, E. A. (2023). Reductions in Leaf Area Index, Pod Production, Seed Size and Harvest Index Drive Yield Loss to High Temperatures in Soybean. Journal of experimental botany, 74(5), 1629–1641. Article erac503.

Berenbaum, M. R. (2023). On peer review-then, now, and soon to be? Proceedings of the National Academy of Sciences of the United States of America, 120(11), Article e2302593120.

Li, Y., Kontos, G. A., Cabrera, D. V., Avila, N. M., Parkinson, T. W., Viswanathan, M. B., Singh, V., Altpeter, F., Labatut, R. A., & Guest, J. S. (2023). Design of a High-Rate Wastewater Treatment Process for Energy and Water Recovery at Biorefineries. ACS Sustainable Chemistry and Engineering, 11(9), 3861-3872.

Singh, R., Lessard, P., Michael Raab, R., & Singh, V. (2023). Effect of phytase corn addition on ethanol yield and distillers' dried grains with soluble profile in corn dry-grind process. Cereal Chemistry, 100(2), 284-288.

Wei, W., Wu, X., Garcia, A., McCoppin, N., Viana, J. P. G., Murad, P. S., Walker, D. R., Hartman, G. L., Domier, L. L., Hudson, M. E., & Clough, S. J. (2023). An NBS-LRR protein in the Rpp1 locus negates the dominance of Rpp1-mediated resistance against Phakopsora pachyrhizi in soybean. Plant Journal, 113(5), 915-933.

Jia, Y., Maitra, S., & Singh, V. (2023). Chemical-free production of multiple high-value bioproducts from metabolically engineered transgenic sugarcane ‘oilcane’ bagasse and their recovery using nanofiltration. Bioresource Technology, 371, Article 128630.

Sinha, E., Bond‐Lamberty, B., Calvin, K. V., Drewniak, B. A., Bisht, G., Bernacchi, C., Blakely, B. J., & Moore, C. E. (2023). The Impact of Crop Rotation and Spatially Varying Crop Parameters in the E3SM Land Model (ELMv2). Journal of Geophysical Research: Biogeosciences, 128(3), Article e2022JG007187.

Zhang, Y., Blahut-Beatty, L., Zheng, S., Clough, S. J., & Simmonds, D. H. (2023). The Role of a Soybean 14-3-3 Gene (Glyma05g29080) on White Mold Resistance and Nodulation Investigations Using CRISPR-Cas9 Editing and RNA Silencing. Molecular Plant-Microbe Interactions, 36(3), 159-164.

De Souza, A. P., Burgess, S. J., Doran, L., Manukyan, L., Hansen, J., Maryn, N., Leonelli, L., Niyogi, K. K., & Long, S. P. (2023). Response to Comments on “Soybean photosynthesis and crop yield is improved by accelerating recovery from photoprotection”. Science, 379(6634), Article eadf2189.

Zhou, Y., Zhao, D., Duan, Y., Chen, L., Fan, H., Wang, Y., Liu, X., Chen, L. Q., Xuan, Y., & Zhu, X. (2023). AtSWEET1 negatively regulates plant susceptibility to root-knot nematode disease. Frontiers in Plant Science, 14, Article 1010348.

Long, S. P., Morgan, G., Kromdijk, J., Glowacka, K., Niyogi, K. K., Leonelli, L., & Gabilly, S. (2023). Transgenic Plants With Increased Photosynthesis Efficiency And Growth. (U.S. Patent No. 11572569).

Wang, S., Guan, K., Zhang, C., Jiang, C., Zhou, Q., Li, K., Qin, Z., Ainsworth, E. A., He, J., Wu, J., Schaefer, D., Gentry, L. E., Margenot, A. J., & Herzberger, L. (2023). Airborne hyperspectral imaging of cover crops through radiative transfer process-guided machine learning. Remote Sensing of Environment, 285, Article 113386.

Banerjee, S., Singh, R., & Singh, V. (2023). Bioenergy crops as alternative feedstocks for recovery of anthocyanins: A review. Environmental Technology and Innovation, 29, Article 102977.

Yukawa, T., Bamba, T., Matsuda, M., Yoshida, T., Inokuma, K., Kim, J., Won Lee, J., Jin, Y. S., Kondo, A., & Hasunuma, T. (2023). Enhanced production of 3,4-dihydroxybutyrate from xylose by engineered yeast via xylonate re-assimilation under alkaline condition. Biotechnology and bioengineering, 120(2), 511-523.

Schaerer, L. G., Wu, R., Putman, L. I., Pearce, J. M., Lu, T., Shonnard, D. R., Ong, R. G., & Techtmann, S. M. (2023). Killing two birds with one stone: chemical and biological upcycling of polyethylene terephthalate plastics into food. Trends in Biotechnology, 41(2), 184-196.

Pelech, E. A., Evers, J. B., Pederson, T. L., Drag, D. W., Fu, P., & Bernacchi, C. J. (2023). Leaf, plant, to canopy: A mechanistic study on aboveground plasticity and plant density within a maize–soybean intercrop system for the Midwest, USA. Plant Cell and Environment, 46(2), 405-421.

Keller, A. B., Walter, C. A., Blumenthal, D. M., Borer, E. T., Collins, S. L., DeLancey, L. C., Fay, P. A., Hofmockel, K. S., Knops, J. M. H., Leakey, A. D. B., Mayes, M. A., Seabloom, E. W., & Hobbie, S. E. (2023). Stronger fertilization effects on aboveground versus belowground plant properties across nine U.S. grasslands. Ecology, 104(2), Article e3891.

Nguyen, C., Sagan, V., Bhadra, S., & Moose, S. (2023). UAV Multisensory Data Fusion and Multi-Task Deep Learning for High-Throughput Maize Phenotyping. Sensors, 23(4), Article 1827.

Zhou, Y., Mirts, E. N., Yook, S., Waugh, M., Martini, R., Jin, Y. S., & Lu, Y. (2023). Reshaping the 2-Pyrone Synthase Active Site for Chemoselective Biosynthesis of Polyketides. Angewandte Chemie - International Edition, 62(5), Article e202212440.

Eckardt, N. A., Cutler, S., Juenger, T. E., Marshall-Colon, A., Udvardi, M., & Verslues, P. E. (2023). Focus on climate change and plant abiotic stress biology. The Plant cell, 35(1), 1-3. Article koac329.

Singh, R., Bhagwat, S. S., Viswanathan, M. B., Cortés‐Peña, Y. R., Eilts, K. K., Mcdonough, G., Cao, M., Guest, J. S., Zhao, H., & Singh, V. (2023). Adsorptive separation and recovery of triacetic acid lactone from fermentation broth. Biofuels, Bioproducts and Biorefining, 17(1), 109-120.

Banerjee, S., & Singh, V. (2023). Biochemical and Chemical Catalytic Routes for the Production of Biochemicals from Biomass: Current Status and Future Perspectives. In Biorefinery: A Sustainable Approach for the Production of Biomaterials, Biochemicals and Biofuels (pp. 63-86). Springer.

Lee, J. W., Bhagwat, S. S., Kuanyshev, N., Cho, Y. B., Sun, L., Lee, Y. G., Cortés-Peña, Y. R., Li, Y., Rao, C. V., Guest, J. S., & Jin, Y. S. (2023). Rewiring yeast metabolism for producing 2,3-butanediol and two downstream applications: Techno-economic analysis and life cycle assessment of methyl ethyl ketone (MEK) and agricultural biostimulant production. Chemical Engineering Journal, 451, Article 138886.

Jeong, Y., Kong, W., Lu, T., & Irudayaraj, J. (2023). Soft hydrogel-shell confinement systems as bacteria-based bioactuators and biosensors. Biosensors and Bioelectronics, 219, Article 114809.

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Li, S., Moller, C. A., Mitchell, N. G., Lee, D. K., Sacks, E. J., & Ainsworth, E. A. (2022). Testing unified theories for ozone response in C4 species. Global change biology, 28(10), 3379-3393.

Narazaki, Y., Hoskere, V., Chowdhary, G., & Spencer, B. F. (2022). Vision-based navigation planning for autonomous post-earthquake inspection of reinforced concrete railway viaducts using unmanned aerial vehicles. Automation in Construction, 137, [104214].

Maitra, S., Long, S. P., & Singh, V. (2022). Optimizing Chemical-Free Pretreatment for Maximizing Oil/Lipid Recovery From Transgenic Bioenergy Crops and Its Rapid Analysis Using Time Domain-NMR. Frontiers in Energy Research, 10, [840418].

Caetano-Anollés, G., Aziz, M. F., Mughal, F., Koç, I., Caetano-Anollés, K., & Caetano-Anollés, D. (2022). Recruitment: A Problem of Entangled Temporal Parts. Frontiers in Bioscience - Landmark, 27(4), 128.

Choi, J. W., Borkar, A. V., Singer, A. C., & Chowdhary, G. (2022). Broadband Acoustic Communication Aided Underwater Inertial Navigation System. IEEE Robotics and Automation Letters, 7(2), 5198-5205.

Kang, N. K., Kim, M., Baek, K., Chang, Y. K., Ort, D. R., & Jin, Y. S. (2022). Photoautotrophic organic acid production: Glycolic acid production by microalgal cultivation. Chemical Engineering Journal, 433, [133636].

Ji, T., Sivakumar, A. N., Chowdhary, G., & Driggs-Campbell, K. (2022). Proactive Anomaly Detection for Robot Navigation with Multi-Sensor Fusion. IEEE Robotics and Automation Letters, 7(2), 4975-4982.

Kamtikar, S., Marri, S., Walt, B., Uppalapati, N. K., Krishnan, G., & Chowdhary, G. (2022). Visual Servoing for Pose Control of Soft Continuum Arm in a Structured Environment. IEEE Robotics and Automation Letters, 7(2), 5504-5511.

Cavanagh, A. P., South, P. F., Bernacchi, C. J., & Ort, D. R. (2022). Alternative pathway to photorespiration protects growth and productivity at elevated temperatures in a model crop. Plant Biotechnology Journal, 20(4), 711-721.

Jia, Y., Kumar, D., Winkler-Moser, J. K., Dien, B., Rausch, K., Tumbleson, M. E., & Singh, V. (2022). Coprocessing Corn Germ Meal for Oil Recovery and Ethanol Production: A Process Model for Lipid-Producing Energy Crops. Processes, 10(4), [661].

Edwards, J. D., Yang, W. H., & Yannarell, A. C. (2022). Soil microbial communities are not altered by garlic mustard in recently invaded central Illinois forests. Ecosphere, 13(4), [e3967].

Burnham, M. B., Simon, S. J., Lee, D. K., Kent, A. D., DeLucia, E. H., & Yang, W. H. (2022). Intra- and inter-annual variability of nitrification in the rhizosphere of field-grown bioenergy sorghum. GCB Bioenergy, 14(3), 393-410.

Kang, N. K., Lee, J. W., Ort, D. R., & Jin, Y. S. (2022). L-malic Acid Production from Xylose by Engineered Saccharomyces Cerevisiae. Biotechnology Journal, 17(3), [2000431].

Mishra, P. K., Chowdhary, G., & Mehta, P. G. (2022). Minimum variance constrained estimator. Automatica, 137, [110106].

Berenbaum, M. R. (2022). Erratum: Cell engineering with microfluidic squeezing preserves functionality of primary immune cells in vivo (Proc. Natl. Acad. Sci. U.S.A. (2018) 115 (E10907-E10914) DOI: 10.1073/pnas.1809671115). Proceedings of the National Academy of Sciences of the United States of America, 119(6), [e2200126119].

Wang, X., Li, C., Lam, C. H., Subramanian, K., Qin, Z. H., Mou, J. H., Jin, M., Chopra, S. S., Singh, V., Ok, Y. S., Yan, J., Li, H. Y., & Lin, C. S. K. (2022). Emerging Waste Valorisation Techniques to Moderate the Hazardous Impacts, and Their Path Towards Sustainability. Journal of Hazardous Materials, 423, [127023].

Varela, S., Pederson, T. L., & Leakey, A. D. B. (2022). Implementing Spatio-Temporal 3D-Convolution Neural Networks and UAV Time Series Imagery to Better Predict Lodging Damage in Sorghum. Remote Sensing, 14(3), [733].

McAllister, W., Whitman, J., Varghese, J., Davis, A., & Chowdhary, G. (2022). Agbots 3.0: Adaptive Weed Growth Prediction for Mechanical Weeding Agbots. IEEE Transactions on Robotics, 38(1), 556 - 568.

Lamb, A., Weers, B., McKinley, B., Rooney, W., Morgan, C., Marshall-Colon, A., & Mullet, J. (2022). Bioenergy sorghum’s deep roots: A key to sustainable biomass production on annual cropland. GCB Bioenergy, 14(2), 132-156.

Fu, P., Jaiswal, D., McGrath, J. M., Wang, S., Long, S. P., & Bernacchi, C. J. (2022). Drought imprints on crops can reduce yield loss: Nature's insights for food security. Food and Energy Security, 11(1), [e332].

Taylor, S. H., Gonzalez-Escobar, E., Page, R., Parry, M. A. J., Long, S. P., & Carmo-Silva, E. (2022). Faster than expected Rubisco deactivation in shade reduces cowpea photosynthetic potential in variable light conditions. Nature plants, 8(2), 118-124.

Chen, L. Q. (2022). Low sugar, under pressure? Nature plants, 8(2), 102-103.

Kang, N. K., Baek, K., Koh, H. G., Atkinson, C. A., Ort, D. R., & Jin, Y. S. (2022). Microalgal metabolic engineering strategies for the production of fuels and chemicals. Bioresource Technology, 345, [126529].

Keller, A. B., Borer, E. T., Collins, S. L., DeLancey, L. C., Fay, P. A., Hofmockel, K. S., Leakey, A. D. B., Mayes, M. A., Seabloom, E. W., Walter, C. A., Wang, Y., Zhao, Q., & Hobbie, S. E. (2022). Soil carbon stocks in temperate grasslands differ strongly across sites but are insensitive to decade-long fertilization. Global change biology, 28(4), 1659-1677.

Carlone, L., Axelrod, A., Karaman, S., & Chowdhary, G. (2022). Aided Optimal Search: Data-Driven Target Pursuit from On-Demand Delayed Binary Observations. In Handbook of Dynamic Data Driven Applications Systems: Volume 1: Second Edition (Vol. 1, pp. 303-343). Springer.

Axelrod, A., Carlone, L., Chowdhary, G., & Karaman, S. (2022). Data-Driven Prediction of Confidence for EVAR in Time-Varying Datasets. In Handbook of Dynamic Data Driven Applications Systems: Volume 1: Second Edition (Vol. 1, pp. 389-412). Springer.

Shameer, S., Wang, Y., Bota, P., Ratcliffe, R. G., Long, S. P., & Sweetlove, L. J. (2022). A hybrid kinetic and constraint-based model of leaf metabolism allows predictions of metabolic fluxes in different environments. Plant Journal, 109(1), 295-313.

Montes, C. M., Demler, H. J., Li, S., Martin, D. G., & Ainsworth, E. A. (2022). Approaches to investigate crop responses to ozone pollution: from O3-FACE to satellite-enabled modeling. Plant Journal, 109(2), 432-446.

Smith, P., Beaumont, L., Bernacchi, C. J., Byrne, M., Cheung, W., Conant, R. T., Cotrufo, F., Feng, X., Janssens, I., Jones, H., Kirschbaum, M. U. F., Kobayashi, K., LaRoche, J., Luo, Y., McKechnie, A., Penuelas, J., Piao, S., Robinson, S., Sage, R. F., ... Long, S. P. (2022). Essential outcomes for COP26. Global change biology, 28(1), 1-3.

Chen, Q., Hu, T., Li, X., Song, C. P., Zhu, J. K., Chen, L., & Zhao, Y. (2022). Phosphorylation of SWEET sucrose transporters regulates plant root:shoot ratio under drought. Nature plants, 8(1), 68-77.

Kumagai, E., Burroughs, C. H., Pederson, T. L., Montes, C. M., Peng, B., Kimm, H., Guan, K., Ainsworth, E. A., & Bernacchi, C. J. (2022). Predicting biochemical acclimation of leaf photosynthesis in soybean under in-field canopy warming using hyperspectral reflectance. Plant Cell and Environment, 45(1), 80-94.

Tomaszewski, T., Gurtler, V., Caetano-Anollés, K., & Caetano-Anollés, G. (2022). The emergence of SARS-CoV-2 variants of concern in Australia by haplotype coalescence reveals a continental link to COVID-19 seasonality. In C. S. Pavia, C. S. Pavia, & V. Gurtler (Eds.), Covid-19: Biomedical Perspectives (pp. 233-268). (Methods in Microbiology; Vol. 50). Academic Press Inc..

Lee, M. S., Boyd, R. A., & Ort, D. R. (2022). The photosynthetic response of C3 and C4 bioenergy grass species to fluctuating light. GCB Bioenergy, 14(1), 37-53.

Wu, J., Tong, H., Ainsworth, E., & He, J. R. (2022). Adaptive Knowledge Transfer on Evolving Domains. In S. Tsumoto, Y. Ohsawa, L. Chen, D. Van den Poel, X. Hu, Y. Motomura, T. Takagi, L. Wu, Y. Xie, A. Abe, & V. Raghavan (Eds.), Proceedings - 2022 IEEE International Conference on Big Data, Big Data 2022 (pp. 1389-1394). (Proceedings - 2022 IEEE International Conference on Big Data, Big Data 2022). Institute of Electrical and Electronics Engineers Inc..

Berenbaum, M. R. (2022). A Hard Pill to Swallow. American Entomologist, 68(4), 14-17.

Taylor, S. H., Gonzalez-Escobar, E., Page, R., Parry, M. A. J., Long, S. P., & Carmo-Silva, E. (Accepted/In press). Author Correction: Faster than expected Rubisco deactivation in shade reduces cowpea photosynthetic potential in variable light conditions (Nature Plants, (2022), 8, 2, (118-124), 10.1038/s41477-021-01068-9). Nature plants.

Lochocki, E. B., Rohde, S., Jaiswal, D., Matthews, M. L., Miguez, F., Long, S. P., & McGrath, J. M. (2022). BioCro II: A software package for modular crop growth simulations. In Silico Plants, 4(1), [diac003].

York, L. M., Cumming, J. R., Trusiak, A., Bonito, G., von Haden, A. C., Kalluri, U. C., Tiemann, L. K., Andeer, P. F., Blanc-Betes, E., Diab, J. H., Favela, A., Germon, A., Gomez-Casanovas, N., Hyde, C. A., Kent, A. D., Ko, D. K., Lamb, A., Missaoui, A. M., Northen, T. R., ... Yang, W. H. (2022). Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production. Plant Phenome Journal, 5(1), [e20028].

Berenbaum, M. R. (2022). Bowl Games. American Entomologist, 68(1), 12-15.

Kim, S. H., Van Stralen, N., Chowdhary, G., & Tran, H. T. (2022). Disentangling Successor Features for Coordination in Multi-agent Reinforcement Learning. In International Conference on Autonomous Agents and Multiagent Systems, AAMAS 2022 (pp. 751-760). (Proceedings of the International Joint Conference on Autonomous Agents and Multiagent Systems, AAMAS; Vol. 2). International Foundation for Autonomous Agents and Multiagent Systems (IFAAMAS).

Sun, J., Gu, M., Yeh, C. C. M., Fan, Y., Chowdhary, G., & Zhang, W. (2022). Dynamic Graph Node Classification via Time Augmentation. In S. Tsumoto, Y. Ohsawa, L. Chen, D. Van den Poel, X. Hu, Y. Motomura, T. Takagi, L. Wu, Y. Xie, A. Abe, & V. Raghavan (Eds.), Proceedings - 2022 IEEE International Conference on Big Data, Big Data 2022 (pp. 800-805). (Proceedings - 2022 IEEE International Conference on Big Data, Big Data 2022). Institute of Electrical and Electronics Engineers Inc..

Long, S. P., Taylor, S. H., Burgess, S. J., Carmo-Silva, E., Lawson, T., De Souza, A. P., Leonelli, L., & Wang, Y. (2022). Into the Shadows and Back into Sunlight: Photosynthesis in Fluctuating Light. Annual Review of Plant Biology, 73, 617-648.

Sun, R., Greene, M. L., Le, D. M., Bell, Z. I., Chowdhary, G., & Dixon, W. E. (2022). Lyapunov-Based Real-Time and Iterative Adjustment of Deep Neural Networks. IEEE Control Systems Letters, 6, 193-198. [9337905].

Mercado, M. A., & Studer, A. J. (2022). Meeting in the Middle: Lessons and Opportunities from Studying C3-C4Intermediates. Annual Review of Plant Biology, 73, 43-65.

Choi, J. W., Chowdhary, G., Singer, A. C., Vishnu, H., Weiss, A., Wornell, G. W., & Deane, G. (2022). Online Segmented Recursive Least-Squares for Multipath Doppler Tracking. In 2022 6th Underwater Communications and Networking Conference, UComms 2022 (2022 6th Underwater Communications and Networking Conference, UComms 2022). Institute of Electrical and Electronics Engineers Inc..

Hetti-Arachchilage, M., Challa, G. S., & Marshall-Colón, A. (2022). Rewiring Network Plasticity to Improve Crops. In Plant Breeding Reviews (pp. 143-183). (Plant Breeding Reviews; Vol. 45). John Wiley & Sons, Ltd..

Berenbaum, M. R. (2022). Sew-Sew Jokes. American Entomologist, 68(2), 12-15.

Montag, W., Liao, L. H., & Berenbaum, M. R. (Accepted/In press). Sexually dimorphic responses to monofloral honeys in the small hive beetle, Aethina tumida Murray (Coleoptera: Nitidulidae). Journal of Apicultural Research.

Matthews, M. L., Marshall-Colón, A., McGrath, J. M., Lochocki, E. B., & Long, S. P. (2022). Soybean-BioCro: A semi-mechanistic model of soybean growth. In Silico Plants, 4(1), [diab032].

Moore, C. E., Gibson, C. D., Miao, G., Dracup, E. C., Gomez-Casanovas, N., Masters, M. D., Miller, J., C Von Haden, A., Meyers, T., Delucia, E. H., & Bernacchi, C. J. (2022). Substantial carbon loss respired from a corn-soybean agroecosystem highlights the importance of careful management as we adapt to changing climate. Environmental Research Letters, 17(5), [054029].

Berenbaum, M. R. (2022). Terms of Art and Terms of Arthropods. American Entomologist, 68(3), 12-15.

Cheng, M. H., Maitra, S., Clennon, A. N. C., Appell, M., Dien, B. S., & Singh, V. (Accepted/In press). The effects of sequential hydrothermal-mechanical refining pretreatment on cellulose structure changes and sugar recoveries. Biomass Conversion and Biorefinery.

Caetano-Anollés, K., Hernandez, N., Mughal, F., Tomaszewski, T., & Caetano-Anollés, G. (2022). The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike. In C. S. Pavia, & V. Gurtler (Eds.), Covid-19: Biomedical Perspectives: Biomedical Perspectives (pp. 27-81). (Methods in Microbiology; Vol. 50). Academic Press Inc..

Seyfried, G. S., Corrales, A., Kent, A. D., Dalling, J. W., & Yang, W. (Accepted/In press). Watershed-scale Variation in Potential Fungal Community Contributions to Ectomycorrhizal Biogeochemical Syndromes. Ecosystems.

Xue, X., Wang, J., Shukla, D., Cheung, L. S., & Chen, L. Q. (2022). When SWEETs Turn Tweens: Updates and Perspectives. Annual Review of Plant Biology, 73, 379-403.