Center for Plant Science Innovation Publications | Center for Plant Science Innovation

2024 Publications

Faculty: Edgar Cahoon, James Van Etten, Heriberto Cerutti, Yufeng Ge, Katarzyna Glowacka, David Holding, David Hyten, Saet-Byul Kim, Jeff Mower, Etsuko Moriyama, Toshihiro Obata, Clemencia Rojas, Rebecca Roston, Sabrina Russo, Daniel Schachtman, James Schnable, Harkamal Walia, Jinliang Yang, Bin Yu, LiRong Zeng, Chi Zhang.

A.K.N. Chandran, P. Paul, B.K. Dhatt, J. Sandh, L. Irvin, S. Oguro, Y. Shi§, Chi Zhang, H. Walia. (2024) Phenotypic and transcriptomics response of diverse rice accessions to transient heat stress during early grain development. Frontier Plant Science, 15:1429697. doi: 10.3389/fpls.2024.1429697.

Abshire N, Hauck AL, Walia H, Obata T*. (2024) Tissue- and time-dependent metabolite profiles during early grain development under normal and high night-time temperature conditions. BMC Plant Biol. 24(1):568.

Bai, G., Barker, B., Scoby, D., Irmak, S., Luck, J.D., Neale, C.M.U., Schnable, J.C., Awada, T., Kustas, W.P., Ge, Y.*, 2024. High-throughput physiological phenotyping of crop evapotranspiration at the plot scale. Field Crops Research 316, 109507. https://doi.org/10.1016/j.fcr.2024.109507

Bai, G., Koehler-Cole, K., Scoby, D., Thapa, V.R., Basche, A., Ge, Y., 2024. Enhancing estimation of cover crop biomass using field-based high-throughput phenotyping and machine learning models. Frontiers in Plant Science 14, 1277672. doi: 10.3389/fpls.2023.1277672

Barnes, EM, Hartman, K, Chiniquy, D, Zhao, W, Liu, P, Creech, C, Schachtman, DP, Tringe, SG. (2024) Abiotic stress reorganizes rhizosphere and endosphere network structure of Sorghum bicolor, Phytobiomes Journal, https://doi.org/10.1094/PBIOMES-02-24-0012-R

Bin, Y., S.E. Russo, J. Zhang, Y. Li, H. Cao, W. Ye, & J. Lian. 2024. Functional traits are more strongly correlated with biomass than diameter growth. Journal of Ecology 112:1225–1239, doi.org/10.1111/1365-2745.14281.

Blume RY, Hotsuliak VY, Nazarenus TJ, Cahoon EB, Blume YB (2024) Genome-wide identification and diversity of FAD2, FAD3 and FAE1 genes in terms of biotechnological importance in Camelina species. BMC Biotechnol. 2024(1):107. doi: 10.1186/s12896-024-00936-4.

Boatwright L, Thudi M, Sangiredday MKR, Coffin AW, Tadesse HK, Vutla S, Harris-Shultz K, Knoll JE, Cuevas H, Kumar N, Soman C, Schnable JC, Punnuri SM§ (2024) GWAS analysis for plant height and stem diameter in sorghum using multiple phenotyping approaches. The Plant Phenome Journal doi: 10.1002/ppj2.70008

C. He†, J. D. Washburn†, N. Schleif, Y. Hao, H. Kaeppler, S. Kaeppler, Z. Zhang, J. Yang, Sanzhen Liu§. (2024) Trait association and prediction through integrative K-mer analysis, The Plant Journal.

Cahoon EB, Kim P, Xie T, González Solis A, Han G, Gong X, Dunn TM (2024) Sphingolipid homeostasis--how do cells know when enough is enough? Implications for plant pathogen responses. Plant Physiology 197 (1), kiae460 https://doi.org/10.1093/plphys/kiae460.

Candice Hirsch, David Holding, James B Holland, Paul Scott, Ruthie Angelovici, Sarah Oliver, Sherry Flint-Garcia (2024) Reducing Corn Grain Nitrogen for on-Farm Nitrogen Recycling. Journal ASA, CSSA, SSSA International Annual Meeting Publisher ASA-CSSA-SSSA

Carvalho JVRP; Carlson RM, Ghosh J; Queiroz VF; de Oliveira EG; Botelho BB; Filho CAC; Agarkova IV; McClung OW; Van Etten JL; Dunigan DD, Rodrigues RAL. (2024) Genomics and evolutionary analysis of Chlorella variabilis-infecting viruses demarcate criteria for defining species of giant viruses. J. Virol. 98, e00361-24.

Chai, YN, Qi, Y, Goren, E, Chiniquy, D, Sheflin, AM, Tringe, SG, Prenni, JE, Liu, P, Schachtman DP (2024) Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum. mSystems 9:1 – 22.

Cruz-Powell, I., Subedi, B., Kim, Y., Morales-Sánchez, D. and Cerutti, H. 2024. Post- Translational Regulation of a Bidomain Glycerol-3-Phosphate Dehydrogenase Catalyzing Glycerol Synthesis under Salinity Stress in Chlamydomonas reinhardtii. Phycology 4:213-234.

D. Zheng, P.M. Grandgenett, Q. Zhang, M. Baine, Y. Shi, Q. Du, X. Liang, J. Wong, S. Iqbal, K. Preuss, A. Kamal, H. Yu, H. Du, M.A. Hollingsworth, Chi Zhang*. (2024) radioGWAS links radiome to genome to discover driver genes with somatic mutations for heterogeneous tumor image phenotype in pancreatic cancer. Scientific Reports; 14(1):12316.

Dahal, S., Alvarez, S., Balboa, S. J., Hicks, L. M., Rojas, C. M. (2024). Defining the secondary metabolites in the Pseudomonas protegens PBL3 secretome with antagonistic activity against Burkholderia glumae. Phytoopathology. September 2024. doi: 10.1094/PHYTO-04-24-0140-R

Daigh, A.L.M., Daroub, S.H., Kyveryga, P.M., Sorrells, M.E., Rajan, N., Ippolito, J.A., Kailer, E., Booth, C.S., Acharya, U., Ghimire, D., Das, S., Maharjan, B., Ge, Y., 2024. Communicating the use of artificial intelligence in agricultural and environmental research. Agricultural & Environmental Letters 9, e20144. https://doi.org/10.1002/ael2.20144

Delen Y, Mural RV, Xu G, Delen SP, Schnable JC, Dweikat I, Yang J§ (2024) Dissecting the genetic architecture of sunflower disc diameter using genome-wide association study. Plant Direct doi: 10.1002/pld3.70010

Dharni JS, Shi Y, Zhang C, Petersen C, Walia H, Staswick P. (2024) Growth and transcriptional response of wheat and rice to the tertiary amine BMVE. Front Plant Sci. doi: 10.3389/fpls.2023.1273620.

Fan, X., Zhang, H., Zhou, L., Bian, L., Jin, X., Tang, L., Ge, Y., 2024. Evaluating drought stress response of poplar seedlings using a proximal sensing platform via multi-parameter phenotyping and two-stage machine learning. Computers and Electronics in Agriculture 225, 109261. https://doi.org/10.1016/j.compag.2024.109261

Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fuerst-Jansen JMR, Dadras A, Zegers JMS, Rieseberg TP, Ashok AD, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Ruempler F, Archibald JM, Theissen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ben-Ari J, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J*, Yin Y*. 2024. Genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nature Genet 56, 1018–1031.

Gamba D, Lorts CM, Haile A, Sahay S, Lopez L, Xia T, Takou M, Kulesza E, Elango D, Kerby J, Yifru M, Bulafu CE, Wondimu T, Glowacka K, Lasky JR. (2024) The genomics and physiology of abiotic stressors associated with global elevation gradients in Arabidopsis thaliana. New Phytologist 244, 2062–2077. https://doi.org/10.1111/nph.20138

H. Jin, M. C. Tross, R. Tan, L. Newton, R. V. Mural, J. Yang, A. M. Thompson, J. C. Schnable§, Imitating the ‘breeder’s eye’: predicting grain yield from measurements of non-yield traits, The Plant Phenome Journal (2024).

H. Mukhtar, J. Hao, G. Xu, E. Bergmeyer, M. Ulutas, J. Yang, D. P. Schachtman§, Nitrogen input differentially shapes the rhizosphere microbiome diversity and composition across diverse maize lines, Biology and Fertility of Soils (2024).

Haupt J, Glowacka K*. (2024) Chilling- and dark-regulated photoprotection in Miscanthus, an economically important C4 grass. Communications Biology 7, 1660. DOI:10.1038/s42003-024-07320-0

Huanca-Nuñezg, N. R.L. Chazdon, S.E. Russo. 2024. Trait-mediated variation in seedling performance in Costa Rican successional forests: comparing above-ground, below-ground, and allocation-based traits. Plants 13(17): 2378, doi.org/10.3390/plants13172378 *cover article for special issue

Hubing, V., Marquis, A., Ziemann, C., Moriyama, H., Moriyama, E. N.*, Zhang, L*. 2024. Cytoplasmic shift of interferon regulatory factors co-evolved with jawed vertebrate innate immunity. Journal of Medical Virology 97: e70247.

Hussain W, Anumalla M, Ismail AM, Walia H, Singh VK, Kohli A, Bhosale S, Bhardwaj H. (2024) Revisiting FR13A for submergence tolerance: beyond the SUB1A gene. Journal of Experimental Botany. doi: 10.1093/jxb/erae299

J. Li, D. Zhang, F. Yang, Q. Zhang, S. Pan, X. Zhao, Q. Zhang, Y. Han, J. Yang, K. Wang, C. Zhao§, (2024) TrG2P: A transfer learning-based tool integrating multi-trait data for accurate prediction of crop yield, Plant Communications.

J. Vijayan, N. Wase, K. Liu$, Chi Zhang, W.R. Riekhof. (2024) ROS-mediated thylakoid membrane remodeling and triacylglycerol biosynthesis under nitrogen starvation in the alga Chlorella sorokiniana. Frontiers in Plant Science; 15:1418049. doi: 10.3389/fpls.2024.1418049.

J.S. Dharni, Y. Shi§, Chi Zhang, C. Peterson, H. Walia, P. Staswicka. (2024) Growth and transcriptional response of wheat and rice to the tertiary amine BMVE. Front. Plant Sci. - Plant Physiology; 14:1273620.

Ji Z., Davis J, Shrestha N, Ge, Y, and Schnable J. (2024) Zero-Shot CLIP-Assisted Feature Extraction and Robust Regression for Generalized Time Series Image Analysis in Predicting Flowering Time. MLCAS

Jia Y, Ullagaddi C, Allen C, Rausch K, Singh V, Schnable JC, Kamruzzaman M§ (2024) Optimizing feature selection with gradient boosting machines in PLS regression for predicting moisture and protein in multi-Country corn kernels via NIR spectroscopy. Food Chemistry doi: 10.1016/j.foodchem.2024.140062

Jin H, Tross MC, Tan R, Newton L, Mural RV, Yang J, Thompson AM, Schnable JC§ (2024) Imitating the “breeder’s eye”: predicting grain yield from measurements of non-yield traits. The Plant Phenome Journal doi: 10.1002/ppj2.20102

K.C. Zhang, N. Zhao, R. Khan, M Hung, Chi Zhang, S. Wang, T.J. Wang, C. Lin. (2024) The prognostic significance of androgen receptor expression in gliomas. Scientific Reports 14, 22122. https://doi.org/10.1038/s41598-024-72284-4

Khound R, Rajput SG, Schnable JC, Mani V, Dipak SK§ (2024) Genome-wide association study reveals marker-trait associations for major agronomic traits in proso millet (Panicum miliaceum L.). Planta 10.1007/s00425-024-04465-4

Kim P, Mahboob S, Nguyen HT, Eastman S, Fiala O, Sousek M, Gaussoin RE, Brungardt JL, Jackson-Ziems TA, Roston RL, Alfano JR, Clemente TE, Guo M. 2024. Characterization of Soybean Events with Enhanced Expression of the Microtubule-Associated Protein 65-1 (MAP65-1). Mol Plant Microbe Interact. Jan;37(1):62-71. doi: 10.1094/MPMI-09-23-0134-R.

Kim, S.B., Kim, K.T., In, S., Jaiswal, N., Lee, G. W., Jung, S., ... & Balint-Kurti, P. (2024). Use of the Puccinia sorghi haustorial transcriptome to identify and characterize AvrRp1-D recognized by the maize Rp1-D resistance protein. PLoS Pathogens, 20(11), e1012662.

Korth N, Yang Q, Van Haute MJ, Tross MC, Peng B, Shrestha N, Zwiener M,Mural RV, Schnable JC, Benson AK§ (2024) Genomic co-localization of variation affecting agronomic and human gut microbiome traits in a meta-analysis of diverse sorghum G3 doi: 10.1093/g3journal/jkae145 bioRxiv doi: 10.1101/2023.09.20.558616

Kuang WQ, Chen WJ, Lei CB, Dai YJ, Tian XD, Tang SY, Qian QY, Zhang CY, Fu LX, Zhou GQ, Wang Y, Li H*. (2024) Diversity of endophytic bacterial community in rice roots and their roles in phosphate solubilization and plant growth. Rhizosphere, 30: 100877. https://doi.org/10.1016/j.rhisph.2024.100877

Laugieri ME, Speciale I, Gimeno A, Lin S, Byers BW, Poveda A, Nunez-Franco R, Iturrioz I, Moure MJ, Jimenez-Oses G, Russo-Krauss I, Notaro A, Van Etten JL, Lowary TL, Jimenez-Barbero J, De Castro C, Tonetti M, Rojas AL. (2024) Unveiling the GT114 Family: Structural Characterization of A075L, a Glycosyltransferase from Paramecium bursaria chlorella virus-1 (PBCV-1). Protein Sci. 33, e3596.

Li D, Wang Q, Tian Y, Lyu X, Zhang H, Sun Y, Hong H, Gao H, Li Y, Zhao C, Wang J, Wang R, Yang J, Liu B, Schnable PS, Schnable JC§, Li Y§, Qiu L§ (2024) TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean. Plant Communications doi: 10.1016/j.xplc.2024.101010

Li H, Akella S, Engstler C, Omini J, Rodriguez M, Obata T, Carrie C, Cerruti H, Mower J. (2024) Parallel evolution via recurrent switches of mitochondrial cytochrome c maturation systems in Archaeplastida. Nature Communications, 15: 1548. https://doi.org/10.1038/s41467-024-45813-y

Li, J., Ge, Y., Puntel, L.A., Heeren, D.M., Bai, G., Balboa, G.R., Gamon, J.A., Arkebauer, T.J., Shi, Y., 2024. Integrating UAV hyperspectral data and radiative transfer model simulation to quantitatively estimate maize leaf and canopy nitrogen content. International Journal of Applied Earth Observation and Geoinformation 129, 103817. https://doi.org/10.1016/j.jag.2024.103817

Li, M#., Yu, H., Zhou, B., Gan, L., Li, S., Zhang, C. and Yu, B*. (2024) JANUS, a spliceosome-associated protein, promotes miRNA biogenesis in Arabidopsis. Nucleic Acids Res, 52, 420-430.

Libalah, M. G. Chuyong, S.E. Russo, D. Thomas, D. Kenfack. 2024. Tree stature structures demography and diversity in an African tropical rainforest. Ecosphere, doi.org/10.1002/ecs2.70144.

Li-Beisson Y and Roston RL, 2024. Plant and Algal Lipids: In All Their States and On All Scales, Plant and Cell Physiology, pcae061, https://doi.org/10.1093/pcp/pcae061

Linders KM, Santra D, Schnable JC, textbfSigmon B§ (2024) Variation in leaf chlorophyll concentration in response to nitrogen application across maize hybrids in contrasting environments. microPublication Biology doi: 10.17912/micropub.biology.001115

Maria Cinta Romay, Elizabeth A Ainsworth, Ruthie Angelovici, Bruno Basso, Matthew Brooks, Wolfgang Busch, Michael J Castellano, Junping Chen, Denise Costich, Natalia de Leon, Bryan Emmett, Sherry Flint-Garcia, Michael Gore, Kaiyu Guan, Candice N Hirsch, David Holding, James B Holland, Jian Hua, Matthew Hufford, Shawn M Kaeppler, Carlos Messina, Todd Michael, Seth C Murray, Sakiko Okumoto, Miguel A Pineiros, Nicholas Ace Pugh, Victor Raboy, Rubén Rellán-Álvarez, Rebecca L Roston, Ruairidh Sawers, M Paul Scott, Jacob D Washburn, Edward S Buckler 2024. Cerca-Circular Economy That Reimagines Corn Agriculture. Journal ASA, CSSA, SSSA International Annual Meeting

Marquis, A., Hubing, V., Ziemann, C., Moriyama, E. N.*, Zhang, L*. 2024. The primate-specific presence of interferon regulatory factor-5 pseudogene. Journal of Medical Virology 96: e29879.

McConaughy, S., Amundsen, K. and Hyten, D.* (2024), Effects of demographic history on recombination hotspots in soybean. The Plant Journal, 119: 1030-1038. https://doi.org/10.1111/tpj.16814

McNicholg, B., C. Helzer, S. McMahon, R. Wang, S.E. Russo. 2024. Topography-driven microclimate gradients shape forest structure, diversity, and composition in a temperate refugial forest. Plant-Environment Interactions 5(3):e10153, doi.org/10.1002/pei3.10153.

Medina-Vega JA, Zuleta D, Aguilar S, Alonso A, Bissiengou P, Brockelman WY, Bunyavejchewin S, Burslem DFRP, Castaño N, Chave J, Dalling JW, de Oliveira AA, Duque Á, Ediriweera S, Ewango CEN, Filip J, Hubbell SP, Itoh A, Kiratiprayoon S, Lum SKY, Makana JR, Memiaghe H, Mitre D, Mohamad MB, Nathalang A, Nilus R, Nkongolo NV, Novotny V, O'Brien MJ, Pérez R, Pongpattananurak N, Reynolds G, Russo SE, Tan S, Thompson J, Uriarte M, Valencia R, Vicentini A, Yao TL, Zimmerman JK, Davies SJ.. 2024. Tropical tree ectomycorrhiza are distributed independently of soil nutrients. Nature Ecology and Evolution, doi.org/10.1038/s41559-023-02298-0.

Mitu, S.M.3, Smith, C., Sanderman, J., Ferguson, R.R., Shepherd, K., Ge, Y.*, 2024. Evaluating consistency across multiple NeoSpectra (compact Fourier transform near-infrared) spectrometers for estimating common soil properties. Soil Science Society of America Journal 88(4) 1324-1339. https://doi.org/10.1002/saj2.20678

Moura Dias H, de Teledo NA, Mural RV, Schnable JC, Van Sluys MA§ (2024) THI1 gene evolutionary trends: A comprehensive plant-focused Assessment via data Mining and large-scale analysis. Genome Biology and Evolution doi: 10.1093/gbe/evae212

Mower JP*. 2024. Raison d’être of the plastid repeat. Nature Plants 10, 838–839.

Mukhtar, H, Hao, J, Xu, G, Bergmeyer, E, Ulutas, M, Yang, J, Schachtman, DP (2024) Nitrogen input differentially shapes the rhizosphere microbiome diversity and composition across diverse maize lines. Biology and Fertility of Soils, https://doi.org/10.1007/s00374-024- 01863-4

Nalini Chandran AK, Paul P, Dhatt BK, Sandhu J, Irvin L, Oguro S, Shi Y, Zhang C, Walia H*. (2024) Phenotypic and transcriptomic responses of diverse rice accessions to transient heat stress during early grain development. Front Plant Sci. doi: 10.3389/fpls.2024.1429697

Nguyen D, Groth N, Mondloch K, Cahoon EB, Jones K, Busta L (2024) Project ChemicalBlooms: Collaborating with citizen scientists to survey the chemical diversity and phylogenetic distribution of plant epicuticular wax blooms. Plant Direct 8 (5), e588 https://doi.org/10.1002/pld3.588.

Nsoh, B., Katimbo, A., Guo, H., Deeren, D.M., Nakabuye, H.N., Qiao, X., Ge, Y., Rudnick, D.R., Wanyama, J., Bwambale, E., Kiraga, S., 2024. Internet of things-based automated solutions utilizing machine learning for smart and real-time irrigation management: A review. 2024. Sensors 24(23), 7480. https://doi.org/10.3390/s24237480

Osinuga A, Solís AG, Cahoon RE, Al-Siyabi A, Cahoon EB, Saha R (2024) Deciphering Sphingolipid Biosynthesis Dynamics in Arabidopsis thaliana Cell Cultures: Quantitative Analysis Amidst Data Variability. iScience 110675 DOI: 10.1016/j.isci.2024.110675

Ostermann I, Benes B§, Gaillard M, Li B, Davis J, Grove RJ, Shrestha N, Tross MC, Schnable JC (2024) Sorghum segmentation and leaf counting using an in silico trained deep neural model. The Plant Phenome Journal doi: 10.1002/ppj2.70002

P. Li, J. Xu, Y. Guo, X. Ma, S. Zhou, Chi Zhang, H. Yu, Y. Wang, Xi. Wang, L. Yuan. (2024) Association of plasma vitamin A level with type 2 diabetes mellitus: a community aging population-based cross-sectional study. Food Science and Human Wellness; 13(4): 2079-2089 https://doi.org/10.26599/FSHW.2022.9250173.

Park K, Quach T, Clark TJ, Kim H, Zhang T, Wang M, Sato S, Nazarenus TJ, Blume R, Blume Y, Zhang C, Moose SP, Swaminathan K, Schwender J, Clemente TE, Cahoon EB (2024) Development of vegetative oil sorghum: From lab-to-field. Plant Biotechnology Journal https://doi.org/10.1111/pbi.14527.

Powadi A, Jubery TZ, Tross M, Schnable JC, Ganapathysubramanian B§, (2024) Disentangling genotype and environment specific latent features for improved trait prediction using a compositional autoencoder. Frontiers in Plant Science doi: 10.3389/fpls.2024.1476070

Q. Zhang§, Z. Yang, J. Yang, Dissecting the colocalized GWAS and eQTLs with mediation analysis for high dimensional exposures and confounders, Biometrics (2024).

Qin P, Chen P, Zhou Y, Zhang W, Zhang Y, Xu J, Gan L, Romer J, Doermann P, Cahoon EB, Zhang C (2024) Vitamin E biofortification: enhancement of seed tocopherol concentrations by altered chlorophyll metabolism. Frontiers in Plant Biology 15, 1344095

Raju SKK, Zhang Y, Mahboub S, Ngu DW, Qiu Y, Harmon FG, Schnable JC§, Roston RL§ (2024) Rhythmic lipid and gene expression responses to chilling in panicoid grasses. Journal of Experimental Botany doi: 10.1093/jxb/erae247 bioRxiv doi: 10.1101/2023.09.29.560160

Rhee SY, Anstett DN, Cahoon EB, Covarrubias-Robles AA, Danquah E, Dudareva N, Ezura H, Gilbert KJ, Gutiérrez RA, Heck M, Lowry DB, Mittler R, Muday G, Mukankusi C, Nelson ADL, Restrepo S, Rouached H, Seki M, Walker B, Way D, Weber APM (2024) Resilient plants, sustainable future. Trends Plant Science (published online) https://doi.org/10.1016/j.tplants.2024.11.001

Rodene, E., Fernado, G.D., Piyush, V., Ge, Y., Schnable, J.C., Ghosh, S., Yang, J., 2024. Image filtering to improve maize tassel detection accuracy using machine learning algorithms. Sensors 24(7), 2172. https://doi.org/10.3390/s24072172

Sahay S, Grzybowski M, Schnable JC, Głowacka K*. (2024) Genotype-specific nonphotochemical quenching responses to nitrogen deficit are linked to chlorophyll a to b ratios. Journal of Plant Physiology 297, 154261. https://doi.org/10.1016/j.jplph.2024.154261

Sahay S, Shrestha N, Dias HM, Mural RV, Grzybowski M, Schnable JC*, Głowacka K*. (2024) Nonphotochemical quenching kinetics GWAS in sorghum identifies genes that may play conserved roles in maize and Arabidopsis thaliana photoprotection. The Plant Journal 119, 3000-3014. DOI:10.1111/tpj.16967

Sandhu J, Irvin L, Chandaran AK, Oguro S, Paul P, Dhatt B, Hussain W, Cunningham SS, Quinones CO, Lorence A, Adviento-Borbe MA, Staswick P, Morota G, Walia H*. (2024) Natural variation in LONELY GUY-Like 1 regulates rice grain weight under warmer night conditions. Plant Physiology. doi: 10.1093/plphys/kiae313

Shen, L., Ding, G., Jackson, R., Ali, M., Liu, S., Mitchell, A., Shi, Y., Lu, X., Dai, J., Deakin, G., Frels, K., Cen, H., Ge, Y., Zhou, J., 2024. GSP-AI: An AI-powered platform for identifying key growth stages and the vegetative-to-reproductive transition in wheat using trilateral drone imagery and meteorological data. Plant Phenomics 6, 0255. DOI:10.34133/plantphenomics.0255

Shomo ZD, Li F, Smith CN, Edmonds SR*, Roston RL. 2024. "From Sensing to Acclimation: The Role of Membrane Lipid Remodeling in Plant Responses to Low Temperatures" Plant Physiology, kiae382, https://doi.org/10.1093/plphys/kiae382

Shomo ZD, Mahboub S, Vanviratikul H, McCormick M*, Tulyananda T*, Roston RL1, Warakanont J1. 2024. All Members of the Arabidopsis DGAT and PDAT Acyltransferase Families Operate During High and Low Temperatures. Plant Physiol. doi: 10.1093/plphys/kiae074. 1Equal author contributions

SpecialeI, Notaro A, BruijnsS, van KooykY, Esmael A, Molinaro A, Balzarini F, Rodriguez E, Petro TM, Agarkova IV, Pattee GL, Van EttenJL, De CastroC, ChiodoF.(2024) Carbohydrate-mediated interactions between chloroviruses and the immune system. Communications Biol. 7, 1670.

Stupar, R. M., Locke, A. M., Allen, D. K., Stacey, M. G., Ma, J., Weiss, J., Nelson, R. T., Hudson, M. E., Joshi, T., Li, Z., Song, Q., Jedlicka, J. R., MacIntosh, G. C., Grant, D., Parrott, W. A., Clemente, T. E., Stacey, G., An, Y.-C., Aponte-Rivera, J., Bhattacharyya, M.K., Baxter, I., Bilyeu, K.D., Campbell, J.D., Cannon, S.B., Clough, S.J., Curtin, S.J., Diers, B.W., Dorrance, A.E., Gillman, J.D., Graef, G.L., Hancock, N., Hudson, K.A., Hyten, D.L., ….O'Rourke, J. A. (2024). Soybean genomics research community strategic plan: A vision for 2024–2028. The Plant Genome, 17, e20516. https://doi.org/10.1002/tpg2.20516

Surber SM.*, Thien Thao NP*, Smith CN, Shomo ZD, Barnes AC, & Roston RL. 2024. Exploring cotton SFR2’s conundrum in response to cold stress. Plant Signaling & Behavior, 19(1). https://doi.org/10.1080/15592324.2024.2362518

Tian, Q., Zhang, H., Bian, L., Zhou, L., Ge, Y., 2024. Three-dimensional quantification and visualization of leaf chlorophyll content in poplar saplings under drought using SFM-MVS. Forest 15(1), 20. https://doi.org/10.3390/f15010020

Torres-Rodriguez JV, Li D, Turkus J, Newton L, Davis J, Lopez-Corona L, Ali W, Sun G, Mural RV, Grzybowski M, Zamft B, Thompson AM, Schnable JC§ (2024) Population level gene expression can repeatedly link genes to functions in maize. The Plant Journal doi: 10.1111/tpj.16801 bioRxiv doi: 10.1101/2023.10.31.565032

Tross MC, Grzybowski M, Jubery TZ, Grove RJ‡, Nishimwe AV‡, Torres-Rodriguez JV, Sun G, Ganapathysubramanian B, Ge Y, Schnable JC§ (2024) Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel. The Plant Phenome Journal doi: 10.1002/ppj2.20106 bioRxiv doi: 10.1101/2023.12.15.571950

Turc B, Sahay S, Haupt J, Santos TdO, Bai G, Glowacka K*. (2024) Up-regulation of non-photochemical quenching improves water use efficiency and reduces whole-plant water consumption under drought in Nicotiana tabacum. Journal of Experimental Botany 75, 3959–3972. https://doi.org/10.1093/jxb/erae113

Villalobos JA, Cahoon RE, Cahoon EB, Wallace IS (2024) Glucosylceramides impact cellulose deposition and cellulose synthase complex motility in Arabidopsis. Glycobiology Jun;34(6):cwae035 https://doi.org/10.1093/glycob/cwae035

Wang H.‡, Zhao X., Tan L., Zhu J., Hyten D.* (2024) Crop DNA extraction with lab-made magnetic nanoparticles. PLoS ONE 19(1): e0296847. https://doi.org/10.1371/journal.pone.029

Wang J, Kan S, Kong J, Nie L, Fan W, Ren Y, Reeve W*, Mower JP*, Wu Z*. 2024. Accumulation of large lineage-specific repeats coincides with sequence acceleration and structural rearrangement in Plantago plastomes. Genome Biol Evol 16, evae177.

Wang J, Kan S, Zou Y, Mower JP, Reeve W, Wu Z*. 2024. Rethinking the mutation hypotheses of plant organellar DNA. Genomics Commun 1, e003.

Wang S, Blume RY, Zhou ZW, Nazarenus TJ, Blume YB, Cahoon EB*, Chen L*, Liang G* (2024) Chromosome-level assembly and analysis of Camelina neglecta – a novel diploid model for camelina biotechnology research. Biotechnology for Biofuels and Bioproducts 17 (1), 17 (*Co-corresponding authors)

Wang, L., Zhang, H., Bian, L., Zhou, L., Wang, S., Ge, Y., 2024. Poplar seedling varieties and drought stress classification based on multi-source, series data and deep learning. Industrial Crops and Products 218, 118905. https://doi.org/10.1016/j.indcrop.2024.118905

Wang, R., J.A. Gamon, S.E. Russo, A.V. Nishimwe, B. Wardlow. 2024. Multitemporal airborne imaging spectrometry and fluorometry reveal contrasting photoprotective responses of trees. Remote Sensing of Environment 311: 114295, doi.org/10.1016/j.rse.2024.114295.

Wei J, Guo T, Mu Q, Alladassi M, Mural RV, Boyles RE, Hoffman L, Hayes CM, Sigmon B, Thompson AM, Salas-Fernandez M, Rooney WL, Kresovich S, Schnable JC, Li X, Yu J§ (2024) Genetic and environmental patterns underlying phenotypic plasticity in flowering time and plant height in sorghum. Plant, Cell and Environment doi: 10.1111/pce.15213

Whitmang, M. and S.E. Russo. 2024. Biogeographic history and centers of richness define elevational range-size patterns for Malesian flora. Ecography e07043, doi.org/10.1111/ecog.07043.

X. Feng, J. Zheng, I. Irisarri, ... Chi Zhang, …, Yanbin Yin. (2024) Genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nat Genet 56, 1018– 1031.

X. He, D. Wang, Y. Jiang, M. Li, M. Delgado-Baquerizo, C. McLaughlin, C. Marcon, M. Baer, L. Guo, Y. A.T. Moya, N. von Wiren, M. Deichmann, G. Schaaf, H.-P. Piepho, Z. Yang, J. Yang, B. Yim, K. Smalla, S. Goormachtig, F. T. de Vries, H. Huging, R. J. H. Sawers, J. C. Reif§, F. Hochholdinger§, X. Chen§, P. Yu§, (2024) Heritable microbiome variation is correlated with source environment in locally adapted maize varieties, Nature Plants.

X. Wei†, M. Chen†, Q. Zhang†, J. Gong†, J. Liu†, K. Yong†, Q. Wang, J. Fan, S. Chen, H. Hua, Z. Luo, X. Zhao, X. Wang, W. Li, J. Cong, X. Yu, Z. Wang, R. Huang, J. Chen, X. Zhou, J. Qiu, P. Xu, J. Murray, H. Wang, Y. Xu, C. Xu, G. Xu, J. Yang, B. Han, X. Huang§, (2024) Genomic investigation of 18,421 lines reveals the genetic architecture of rice, Science.

Xu C, Shaw T, ChoppararuYA, Lu Y, Hudson M, Weekley B, Fisher M, He F, Nascimento R, Wergeles N, Joshi T, Bates PD, Koo AJ, Allen DK, Cahoon EB, Thelen J, Xu D (2024) FatPlants: A comprehensive information system for lipid-related genes and metabolic pathways in plants. Database baae074. doi.org/10.1093/database/baae074

Y. Delen, R. V. Mural, G. Xu, S. Palali Delen, J. C. Schnable, I. Dweikat§, J. Yang§, (2024) Dissecting the genetic architecture of sunflower head diameter using genome-wide association study, Plant Direct.

Y. Delen, S. Palali-Delen, G. Xu, M. Neji, J. Yang, I. Dweikat§, (2024) Dissecting the genetic architecture of morphological traits in sunflower, Genes.

Y. Shi§, W. Yang§, H. Lin, L. Han, A.J. Cai, Y. Lei, Chi Zhang*. (2024) Identification of smRNA-based cell-type markers for the stem cell manufacture system with a statistical scoring function. Gene Reports; 34:101869.

Yangg, Y. and S.E. Russo. 2024. Trade-offs in rooting strategy dimensions along an edaphic gradient in a grassland ecosystem. Functional Ecology 38:792–807, doi.org/10.1111/1365-2435.14514.

Z. Yang, Q. Zhang§, J. Yang§, (2024) High dimensional mediation analysis for causal inference, Bio-Protocol.

Zarei A§, Li B, Schnable JC, Lyons E, Pauli D, Benes B, Barnard K (2024) PlantSegNet: 3D point cloud instance segmentation of nearby plant organs with identical semantics. Computers and Electronics in Agriculture doi: 10.1016/j.compag.2024.108922

Zhan, Y., Zhou, Y., Bai, G., Ge, Y., 2024. Bagging improves the performance of deep learning-based semantic segmentation with limited labeled images: A case study of crop segmentation for high-throughput plant phenotyping. Sensors 24(11), 3420. https://doi.org/10.3390/s24113420

Zhang, C., R. Gu, L. Lin, S.E. Russo. 2024. Functional traits and ecological niches as correlates of the interspecific growth-mortality trade-off among seedlings of 14 tropical tree species. Functional Ecology 38:1888–1901, doi.org/10.1111/1365-2435.14624

Zhong Z-P, Zablocki O, Li Y-F, Van Etten JL, Mosley-Thompson E, Rich VI, Thompson LG, Sullivan MB. (2024) Glacier-preserved Tibetan plateau viral community probably linked to warm-cold climate variations. Nature Geosci. 17, 912-919

Zhong, S., Li, X., Li, C., Bai, H., Chen, J., Gan, L., Zhu, J., Oh, T., Yan, X., Zhu, J. Yu, B., et al. (2024) SERRATE drives phase separation behaviours to regulate m6A modification and miRNA biogenesis. Nat Cell Biol, 26, 2129-2143.

Zhou S, Ma K, Mower JP*, Liu Y*, Zhou R*. 2024. Leaf variegation caused by plastome structural variation: an example from Dianella tasmanica. Hort Res 11, uhae009.

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2023 Publications

Faculty: Edgar Cahoon, James Van Etten, Heriberto Cerutti, Yufeng Ge, Katarzyna Glowacka, David Holding, David Hyten, Saet-Byul Kim, Mark Libault, Jennifer Markham, Jeff Mower, Etsuko Moriyama, Toshihiro Obata, Clemencia Rojas, Rebecca Roston, Sabrina Russo, Daniel Schachtman, James Schnable, Harkamal Walia, Jinliang Yang, Bin Yu, LiRong Zeng, Chi Zhang

Bacher, H., A. Montagu, I. Herrmann, H. Walia, N. Schwartz and Z. Peleg (2023). "Stress-induced deeper rooting introgression enhances wheat yield under terminal drought." J Exp Bot.

Bai, G., Y. Ge, B. Leavitt, J. A. Gamon and D. Scoby (2023). "Goniometer in the air: Enabling BRDF measurement of crop canopies using a cable-suspended plant phenotyping platform." Biosystems Engineering 230: 344-360.

Barnes, A. C., J. L. Myers, S. M. Surber, Z. Liang, J. P. Mower, J. C. Schnable and R. L. Roston (2023). "Oligogalactolipid production during cold challenge is conserved in early diverging lineages." Journal of Experimental Botany 74(17): 5405-5417.

Bi, Y., R. M. Yassue, P. Paul, B. K. Dhatt, J. Sandhu, P. T. Do, H. Walia, T. Obata and G. Morota (2023). "Evaluating metabolic and genomic data for predicting grain traits under high night temperature stress in rice." G3 (Bethesda) 13(5).

Blume, R. Y., R. Kalendar, L. Guo, E. B. Cahoon and Y. B. Blume "Overcoming genetic paucity of Camelina sativa: possibilities for interspecific hybridization conditioned by the genus evolution pathway." Frontiers in Plant Science 14: 1259431.

Braun, E., A. Singh, R. Tan, J. Schnable, L. Newton and A. Thompson (2023). Comparative genomics to improve genotype-phenotype associations in maize and sorghum.

Chamara, N., G. Bai and Y. Ge (2023). "AICropCAM: Deploying classification, segmentation, detection, and counting deep-learning models for crop monitoring on the edge." Computers and Electronics in Agriculture 215: 108420.

Chamara, N., G. F. Bai and Y. Ge (2023). "AICropCAM--An Edge Imaging Platform with a Stack of Deep Learning Models for Plant Phenotyping." Authorea Preprints.

Chen, J., Z. Wang, K. Tan, W. Huang, J. Shi, T. Li, J. Hu, K. Wang, C. Wang, B. Xin, H. Zhao, W. Song, M. B. Hufford, J. C. Schnable, W. Jin and J. Lai (2023). "A complete telomere-to-telomere assembly of the maize genome." Nature Genetics.

Delavaux, C. S., J. A. LaManna, J. A. Myers, R. P. Phillips, S. Aguilar, D. Allen, A. Alonso, K. J. Anderson-Teixeira, M. E. Baker, J. L. Baltzer, P. Bissiengou, M. Bonfim, N. A. Bourg, W. Y. Brockelman, D. F. R. P. Burslem, L.-W. Chang, Y. Chen, J.-M. Chiang, C. Chu, K. Clay, S. Cordell, M. Cortese, J. den Ouden, C. Dick, S. Ediriweera, E. C. Ellis, A. Feistner, A. L. Freestone, T. Giambelluca, C. P. Giardina, G. S. Gilbert, F. He, J. Holík, R. W. Howe, W. Huaraca Huasca, S. P. Hubbell, F. Inman, P. A. Jansen, D. J. Johnson, K. Kral, A. J. Larson, C. M. Litton, J. A. Lutz, Y. Malhi, K. McGuire, S. M. McMahon, W. J. McShea, H. Memiaghe, A. Nathalang, N. Norden, V. Novotny, M. J. O’Brien, D. A. Orwig, R. Ostertag, G. G. Parker, R. Pérez, G. Reynolds, S. E. Russo, L. Sack, P. Šamonil, I. F. Sun, M. E. Swanson, J. Thompson, M. Uriarte, J. Vandermeer, X. Wang, I. Ware, G. D. Weiblen, A. Wolf, S.-H. Wu, J. K. Zimmerman, T. Lauber, D. S. Maynard, T. W. Crowther and C. Averill (2023). "Mycorrhizal feedbacks influence global forest structure and diversity." Communications Biology 6(1): 1066.

DeLong, J. P., J. L. Van Etten and D. D. Dunigan (2023). "Lessons from Chloroviruses: the Complex and Diverse Roles of Viruses in Food Webs." J Virol 97(5): e0027523.

Deng, M., H. Chen, W. Zhang, E. B. Cahoon, Y. Zhou and C. Zhang (2023). "Genetic improvement of tocotrienol content enhances the oxidative stability of canola oil." Frontiers in Plant Science 14.

Diaz-Martinez, V., J. Orozco-Sandoval, V. Manian, B. K. Dhatt and H. Walia (2023). "A Deep Learning Framework for Processing and Classification of Hyperspectral Rice Seed Images Grown under High Day and Night Temperatures." Sensors (Basel) 23(9).

Drury, S., G. Claussen, A. Zetterman, H. Moriyama, E. N. Moriyama and L. Zhang (2023). "Evolution and emergence of primate-specific interferon regulatory factor 9." Journal of Medical Virology 95(2): e28521.

Esmael, A., I. V. Agarkova, D. D. Dunigan, Y. Zhou and J. L. Van Etten (2023). "Viral DNA Accumulation Regulates Replication Efficiency of Chlorovirus OSy-NE5 in Two Closely Related Chlorella variabilis Strains." Viruses 15(6).

Gaillard, M., B. Benes, M. C. Tross and J. C. Schnable (2023). "Multi-view triangulation without correspondences." Computers and Electronics in Agriculture 206: 107688.

Gamon, J. A., R. Wang and S. E. Russo (2023). "Contrasting photoprotective responses of forest trees revealed using PRI light responses sampled with airborne imaging spectrometry." New Phytologist 238(3): 1318-1332.

Głowacka, K., J. Kromdijk, C. E. Salesse-Smith, C. Smith, S. M. Driever and S. P. Long "Is chloroplast size optimal for photosynthetic efficiency?" New Phytologist.

Grzybowski, M. W., R. V. Mural, G. Xu, J. Turkus, J. Yang and J. C. Schnable (2023). "A common resequencing-based genetic marker data set for global maize diversity." The Plant Journal 113(6): 1109-1121.

Hao, J., Y. Yang, S. Futrell, E. A. Kelly, C. M. Lorts, B. Nebie, S. Runo, J. Yang, S. Alvarez, J. R. Lasky and D. P. Schachtman "CRISPR/Cas9-Mediated Mutagenesis of Carotenoid Cleavage Dioxygenase (CCD) Genes in Sorghum Alters Strigolactone Biosynthesis and Plant Biotic Interactions." Phytobiomes Journal 0(0): PBIOMES-08-22-0053-R.

Hao, J., Y. Yang, S. Futrell, E. A. Kelly, C. M. Lorts, B. Nebie, S. Runo, J. Yang, S. Alvarez, J. R. Lasky and D. P. Schachtman (2023). "CRISPR/Cas9-Mediated Mutagenesis of Carotenoid Cleavage Dioxygenase (CCD) Genes in Sorghum Alters Strigolactone Biosynthesis and Plant Biotic Interactions." Phytobiomes Journal 7(3): 339-351.

Hartwig, T., M. Banf, G. P. Prietsch, J.-Y. Zhu, I. Mora-Ramírez, J. H. M. Schippers, S. J. Snodgrass, A. S. Seetharam, B. Huettel, J. M. Kolkman, J. Yang, J. Engelhorn and Z.-Y. Wang (2023). "Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize." Genome Biology 24(1): 108.

Huerter, B. G., K. C. Johnson, B. G. Coutu, B. Thedinger, N. R. Bennion, C. Zheng and C. Zhang (2023). "COX inhibitor use during definitive radiotherapy is associated with worse hearing preservation in patients with vestibular schwannoma." Journal of Neuro-Oncology.

Hurst, J. P., A. Yobi, A. Li, S. Sato, T. E. Clemente, R. Angelovici and D. R. Holding (2023). "Large and stable genome edits at the sorghum alpha kafirin locus result in changes in chromatin accessibility and globally increased expression of genes encoding lysine enrichment." Front Plant Sci 14: 1116886.

Jin, X., H. Du, C. Zhu, H. Wan, F. Liu, J. Ruan, J. P. Mower and A. Zhu (2023). "Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry." Nature Plants 9(8): 1252-1266.

Katimbo, A., D. R. Rudnick, J. Zhang, Y. Ge, K. C. DeJonge, T. E. Franz, Y. Shi, W.-z. Liang, X. Qiao, D. M. Heeren, I. Kabenge, H. N. Nakabuye and J. Duan (2023). "Evaluation of artificial intelligence algorithms with sensor data assimilation in estimating crop evapotranspiration and crop water stress index for irrigation water management." Smart Agricultural Technology 4: 100176.

Kick, D. R., J. G. Wallace, J. C. Schnable, J. M. Kolkman, B. Alaca, T. M. Beissinger, J. Edwards, D. Ertl, S. Flint-Garcia, J. L. Gage, C. N. Hirsch, J. E. Knoll, N. de Leon, D. C. Lima, D. E. Moreta, M. P. Singh, A. Thompson, T. Weldekidan and J. D. Washburn (2023). "Yield prediction through integration of genetic, environment, and management data through deep learning." G3 Genes|Genomes|Genetics 13(4).

Konda, A. R., M. Gelli, C. Pedersen, R. E. Cahoon, C. Zhang, T. Obata and E. B. Cahoon (2023). "Vitamin E biofortification: Maximizing oilseed tocotrienol and total vitamin E tocochromanol production by use of metabolic bypass combinations." Metabolic Engineering 79: 66-77.

Kudo, Y., K. Umemoto, T. Obata, A. Kaneda, S.-r. Ni, M. Mikage, Y. Sasaki and H. Ando (2023). "Seasonal variation of alkaloids and polyphenol in Ephedra sinica cultivated in Japan and controlling factors." Journal of Natural Medicines 77(1): 137-151.

Lewis, G. L., R. J. Fenton, E. N. Moriyama, J. D. Loy and R. A. Moxley (2023). "Association of ISVsa3 with Multidrug Resistance in Salmonella enterica Isolates from Cattle (Bos taurus)." Microorganisms 11(3): 631.

Li, J., N. K. Wijewardane, Y. Ge and Y. Shi (2023). "Improved chlorophyll and water content estimations at leaf level with a hybrid radiative transfer and machine learning model." Computers and Electronics in Agriculture 206: 107669.

Li, J., Y. Ge, L. Puntel, D. Heeren, G. Balboa and Y. Shi (2023). Combining machine learning with a mechanistic model to estimate maize nitrogen content from UAV-acquired hyperspectral imagery. Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping VIII, SPIE.

Li, J., Y. Su, C. A. Shapiro, D. P. Schachtman and X. Wang (2023). "Phosphate deficiency modifies lipid composition and seed oil production in camelina." Plant Science 330: 111636.

Li, Y., E.-j. Kim, A. Voshall, E. Moriyama and H. Cerutti (2023). "Small RNAs >26 nt in length associate with AGO1 and are upregulated by nutrient deprivation in the alga Chlamydomonas." The Plant cell.

Li, Y., X. Zhan, S. Liu, H. Lu, R. Jiang, W. Guo, S. Chapman, Y. Ge, B. Solan, Y. Ding and F. Baret (2023). "Self-Supervised Plant Phenotyping by Combining Domain Adaptation with 3D Plant Model Simulations: Application to Wheat Leaf Counting at Seedling Stage." Plant Phenomics 5: 0041.

Liang, S., C. Zhang and M. Zhu (2023). "Ab Initio Prediction of 3-D Conformations for Protein Long Loops with High Accuracy and Applications to Antibody CDRH3 Modeling." Journal of Chemical Information and Modeling.

Liang, W.-z., J. Oboamah, X. Qiao, Y. Ge, B. Harveson, D. R. Rudnick, J. Wang, H. Yang and A. Gradiz (2023). "CanopyCAM – an edge-computing sensing unit for continuous measurement of canopy cover percentage of dry edible beans." Computers and Electronics in Agriculture 204: 107498.

Liang, Z., X. Meng and J. C. Schnable (2023). A Transferable Machine Learning Framework for Predicting Transcriptional Responses of Genes Across Species. Plant Gene Regulatory Networks: Methods and Protocols. K. Kaufmann and K. Vandepoele. New York, NY, Springer US: 361-379.

Lima, D. C., A. C. Aviles, R. T. Alpers, B. A. McFarland, S. Kaeppler, D. Ertl, M. C. Romay, J. L. Gage, J. Holland, T. Beissinger, M. Bohn, E. Buckler, J. Edwards, S. Flint-Garcia, C. N. Hirsch, E. Hood, D. C. Hooker, J. E. Knoll, J. M. Kolkman, S. Liu, J. McKay, R. Minyo, D. E. Moreta, S. C. Murray, R. Nelson, J. C. Schnable, R. S. Sekhon, M. P. Singh, P. Thomison, A. Thompson, M. Tuinstra, J. Wallace, J. D. Washburn, T. Weldekidan, R. J. Wisser, W. Xu and N. de Leon (2023). "2018–2019 field seasons of the Maize Genomes to Fields (G2F) G x E project." BMC Genomic Data 24(1): 29.

Liu, P., T. Xie, X. Wu, G. Han, S. D. Gupta, Z. Zhang, J. Yue, F. Dong, K. Gable, S. Niranjanakumari, W. Li, L. Wang, W. Liu, R. Yao, E. B. Cahoon, T. M. Dunn and X. Gong (2023). "Mechanism of sphingolipid homeostasis revealed by structural analysis of <i>Arabidopsis</i> SPT-ORM1 complex." Science Advances 9(13): eadg0728.

Lopes, L. D. and D. P. Schachtman (2023). "Rhizosphere and bulk soil bacterial community succession is influenced more by changes in soil properties than in rhizosphere metabolites across a maize growing season." Applied Soil Ecology 189: 104960.

Lopes, L. D., S. L. Futrell, E. Bergmeyer, J. Hao and D. P. Schachtman (2023). "Root exudate concentrations of indole-3-acetic acid (IAA) and abscisic acid (ABA) affect maize rhizobacterial communities at specific developmental stages." FEMS Microbiology Ecology 99(3).

Luo, M., T. J. Sarnowski, M. Libault, G. Rios, J. B. Charron, N. Mantri and S. D. Zhang (2023). "Editorial: New insights into mechanisms of epigenetic modifiers in plant growth and development, volume II." Frontiers in Plant Science 14.

McNichol, B. H. and S. E. Russo (2023). "Plant Species’ Capacity for Range Shifts at the Habitat and Geographic Scales: A Trade-Off-Based Framework." Plants 12(6): 1248.

Murad, M. O. F., J. Ackerson, C. Tolles, K. Meissner, C. L. S. Morgan and Y. Ge (2023). "Estimating soil organic carbon content at variable moisture contents using a low-cost spectrometer." Geoderma 440: 116723.

Nan, Y., H. Zhang, Y. Zeng, J. Zheng and Y. Ge (2023). "Faster and accurate green pepper detection using NSGA-II-based pruned YOLOv5l in the field environment." Computers and Electronics in Agriculture 205: 107563.

Nan, Y., H. Zhang, Y. Zeng, J. Zheng and Y. Ge (2023). "Intelligent detection of Multi-Class pitaya fruits in target picking row based on WGB-YOLO network." Computers and Electronics in Agriculture 208: 107780.

Nie, S., Y. Ge and M. C. Vuran (2023). On Crop Canopy Scattering for Integrated mmWave Sensing and Communication in Agricultural Fields. 2023 IEEE 20th International Conference on Mobile Ad Hoc and Smart Systems (MASS), IEEE.

Nolasco, E., I. Krassovskaya, K. Hong, K. Hansen, S. Alvarez, T. Obata and K. Majumder (2023). "Sprouting alters metabolite and peptide contents in the gastrointestinal digest of soybean and enhances in-vitro anti-inflammatory activity." Journal of Functional Foods 109: 105780.

Obata, T., J. Omini, T. Dele-Osibanjo and I. Krassovskaya (2023). "Malate dehydrogenase-citrate synthase multienzyme complex formation is associated with the pH changes in the mitochondrial matrix in living yeast cells." Journal of Biological Chemistry 299(3): S340-S341.

Orozco, J., V. Manian, E. Alfaro, H. Walia and B. K. Dhatt (2023). "Graph Convolutional Network Using Adaptive Neighborhood Laplacian Matrix for Hyperspectral Images with Application to Rice Seed Image Classification." Sensors 23(7): 3515.

Ozturk, O. K., A. M. Salgado, D. R. Holding, O. H. Campanella and B. R. Hamaker (2023). "Dispersion of zein into pea protein with alkaline agents imparts cohesive and viscoelastic properties for plant-based food analogues." Food Hydrocolloids 134: 108044.

Palali Delen, S., G. Xu, J. Velazquez-Perfecto and J. Yang (2023). "Estimating the genetic parameters of yield-related traits under different nitrogen conditions in maize." Genetics 223(4).

Palali Delen, S., J. Lee and J. Yang (2023). "Improving the metal composition of plants for reduced Cd and increased Zn content: molecular mechanisms and genetic regulations." Cereal Research Communications.

Quattrone, A., M. Lopez-Guerrero, P. Yadav, M. A. Meier, S. E. Russo and K. A. Weber "Interactions between root hairs and the soil microbial community affect the growth of maize seedlings." Plant, Cell & Environment n/a(n/a).

Quiñones, C., M. A. Adviento-Borbe, W. Larazo, R. S. Harris, K. Mendez, S. S. Cunningham, Z. C. Campbell, K. Medina-Jimenez, N. T. Hein, D. Wagner, B. Ottis, H. Walia and A. Lorence (2023). "Field-based infrastructure and cyber–physical system for the study of high night air temperature stress in irrigated rice." The Plant Phenome Journal 6(1): e20085.

Rodrigues de Queiroz, A., C. Hines, J. Brown, S. Sahay, J. Vijayan, J. M. Stone, N. Bickford, M. Wuellner, K. Glowacka, N. R. Buan and R. L. Roston (2023). "The effects of exogenously applied antioxidants on plant growth and resilience." Phytochemistry Reviews.

Sahay, S., M. Grzybowski, J. C. Schnable and K. Głowacka (2023). "Genetic control of photoprotection and photosystem II operating efficiency in plants." New Phytologist 239(3): 1068-1082.

Saucedo-García, M., A. González-Solís, P. Rodríguez-Mejía, G. Lozano-Rosas, T. d. J. Olivera-Flores, L. Carmona-Salazar, A. A. Guevara-García, E. B. Cahoon and M. Gavilanes-Ruíz (2023). "Sphingolipid Long-Chain Base Signaling in Compatible and Non-Compatible Plant–Pathogen Interactions in Arabidopsis." International Journal of Molecular Sciences 24(5): 4384.

Sun, G., H. Yu, P. Wang, M. Lopez-Guerrero, R. V. Mural, O. N. Mizero, M. Grzybowski, B. Song, K. van Dijk, D. P. Schachtman, C. Zhang and J. C. Schnable (2023). "A role for heritable transcriptomic variation in maize adaptation to temperate environments." Genome Biology 24(1): 55.

Sun, S., B. Wang, C. Li, G. Xu, J. Yang, M. B. Hufford, J. Ross-Ibarra, H. Wang and L. Wang (2023). "Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding." Molecular Biology and Evolution 40(8).

Walia, H. (2023). "Capturing the Spatiotemporal Dynamics of Heat Stress Response Using a 3D-Reconstrution Approach." Authorea Preprints.

Wang, H., B. Campbell, M. Happ, S. McConaughy, A. Lorenz, K. Amundsen, Q. Song, V. Pantalone and D. Hyten (2023). "Development of molecular inversion probes for soybean progeny genomic selection genotyping." The Plant Genome 16(1): e20270.

Wijewardane, N. K., H. Zhang, J. Yang, J. C. Schnable, D. P. Schachtman and Y. Ge (2023). "A leaf-level spectral library to support high throughput plant phenotyping: Predictive accuracy and model transfer." Journal of Experimental Botany.

Xie, X., Y. Ge, H. Walia, J. Yang and H. Yu (2023). "Leaf-Counting in Monocot Plants Using Deep Regression Models." Sensors 23(4): 1890.

Zhan, Y., R. Zhang, Y. Zhou, V. Stoerger, J. Hiller, T. Awada and Y. Ge (2023). "Rapid online plant leaf area change detection with high-throughput plant image data." Journal of Applied Statistics 50(14): 2984-2998.

Zhang, J., K. Thapa, N. Chamara, G. Bai and Y. Ge (2023). Estimating crop stomatal conductance from RGB, NIR, and thermal infrared images. Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping VIII, SPIE.

2022 Publications

Faculty: Edgar Cahoon, James Van Etten, Heriberto Cerutti, Yufeng Ge, Katarzyna Glowacka, David Holding, David Hyten, Saet-Byul Kim, Marc Libault, Jennifer Markham, Jeff Mower, Etsuko Moriyama, Toshihiro Obata, Clemencia Rojas, Rebecca Roston, Sabrina Russo, Daniel Schachtman, James Schnable, Harkamal Walia, Jinliang Yang, Bin Yu, LiRong Zeng, Chi Zhang

Acevedo-Siaca, L. G., K. Glowacka, S. M. Driever, C. E. Salesse-Smith, N. Lugassi, D. Granot, S. P. Long and J. Kromdijk (2022). "Guard-cell-targeted overexpression of Arabidopsis Hexokinase 1 can improve water use efficiency in field-grown tobacco plants." J Exp Bot 73(16): 5745-5757.
Anderson-Teixeira, K. J., V. Herrmann, C. R. Rollinson, B. Gonzalez, E. B. Gonzalez-Akre, N. Pederson, M. R. Alexander, C. D. Allen, R. Alfaro-Sánchez, T. Awada, J. L. Baltzer, P. J. Baker, J. D. Birch, S. Bunyavejchewin, P. Cherubini, S. J. Davies, C. Dow, R. Helcoski, J. Kašpar, J. A. Lutz, E. Q. Margolis, J. T. Maxwell, S. M. McMahon, C. Piponiot, S. E. Russo, P. Šamonil, A. E. Sniderhan, A. J. Tepley, I. Vašíčková, M. Vlam and P. A. Zuidema (2022). "Joint effects of climate, tree size, and year on annual tree growth derived from tree-ring records of ten globally distributed forests." Global Change Biology 28(1): 245-266.
Arias, C. L., T. Quach, T. Huynh, H. Nguyen, A. Moretti, Y. Shi, M. Guo, A. Rasoul, K. Van, L. McHale, T. E. Clemente, A. P. Alonso and C. Zhang (2022). "Expression of AtWRI1 and AtDGAT1 during soybean embryo development influences oil and carbohydrate metabolism." Plant Biotechnology Journal 20(7): 1327-1345.
Bacher, H., Y. Sharaby, H. Walia and Z. Peleg (2021). "Modifying root-to-shoot ratio improves root water influxes in wheat under drought stress." Journal of Experimental Botany 73(5): 1643-1654.
Berry, J. C., M. Qi, B. V. Sonawane, A. Sheflin, A. Cousins, J. Prenni, D. P. Schachtman, P. Liu and R. S. Bart (2022). "Increased signal-to-noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components." Elife 11.
Bhatti, S., D. M. Heeren, S. R. Evett, S. A. O’Shaughnessy, D. R. Rudnick, T. E. Franz, Y. Ge and C. M. Neale (2022). "Crop response to thermal stress without yield loss in irrigated maize and soybean in Nebraska." Agricultural Water Management 274: 107946.
Bian, L., H. Zhang, Y. Ge, J. Čepl, J. Stejskal and Y. A. EL-Kassaby (2022). "Closing the gap between phenotyping and genotyping: review of advanced, image-based phenotyping technologies in forestry." Annals of Forest Science 79(1): 1-21.
Boatwright, J. L., S. Sapkota, H. Jin, J. C. Schnable, Z. Brenton, R. Boyles and S. Kresovich (2022). "Sorghum Association Panel whole-genome sequencing establishes cornerstone resource for dissecting genomic diversity." Plant J 111(3): 888-904.
Busta, L., K. D. Chapman and E. B. Cahoon (2022). "Better together: Protein partnerships for lineage-specific oil accumulation." Curr Opin Plant Biol 66: 102191.
Cao, M., R. Ma, H. Li, J. Cui, C. Zhang and J. Zhao (2022). "Therapy-resistant and -sensitive lncRNAs, SNHG1 and UBL7-AS1 promote glioblastoma cell proliferation." Oxidative Medicine and Cellular Longevity 2022: 2623599.
Cervantes-Perez, S. A. and M. Libault (2022). "Cell-Type-Specific Profiling of the Arabidopsis thaliana Membrane Protein-Encoding Genes." Membranes (Basel) 12(9).
Cervantes-Perez, S. A., S. Thibivilliers, C. Laffont, A. D. Farmer, F. Frugier and M. Libault (2022). "Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume." Mol Plant 15(12): 1868-1888.
Cervantes-Perez, S. A., S. Thibivillliers, S. Tennant and M. Libault (2022). "Review: Challenges and perspectives in applying single nuclei RNA-seq technology in plant biology." Plant Sci 325: 111486.
Chai, Y. N. and D. P. Schachtman (2022). "Root exudates impact plant performance under abiotic stress." Trends Plant Sci 27(1): 80-91.
Chai, Y. N., S. Futrell and D. P. Schachtman (2022). "Assessment of Bacterial Inoculant Delivery Methods for Cereal Crops." Front Microbiol 13: 791110.
Chamara, N., M. D. Islam, G. F. Bai, Y. Shi and Y. Ge (2022). "Ag-IoT for crop and environment monitoring: Past, present, and future." Agricultural Systems 203: 103497.
Chandran, A. K. N., J. Sandhu, L. Irvin, P. Paul, B. K. Dhatt, W. Hussain, T. Gao, P. Staswick, H. Yu and G. Morota (2022). "Rice Chalky Grain 5 regulates natural variation for grain quality under heat stress." Frontiers in Plant Science 13: 1026472.
Clarke, J. L., Y. Qiu and J. C. Schnable (2022). "Experimental Design for Controlled Environment High-Throughput Plant Phenotyping." Methods Mol Biol 2539: 57-68.
DeLong, J. P., M. A. Al-Sammak, Z. T. Al-Ameeli, D. D. Dunigan, K. F. Edwards, J. J. Fuhrmann, J. P. Gleghorn, H. Li, K. Haramoto, A. O. Harrison, M. F. Marston, R. M. Moore, S. W. Polson, B. D. Ferrell, M. E. Salsbery, C. R. Schvarcz, J. Shirazi, G. F. Steward, J. L. Van Etten and K. E. Wommack (2022). "Towards an integrative view of virus phenotypes." Nat Rev Microbiol 20(2): 83-94.
Demattê, J. A., A. F. d. S. Paiva, R. R. Poppiel, N. A. Rosin, L. F. C. Ruiz, F. A. d. O. Mello, B. Minasny, S. Grunwald, Y. Ge and E. Ben Dor (2022). "The Brazilian S oil S pectral S ervice (BraSpecS): A User-Friendly System for Global Soil Spectra Communication." Remote Sensing 14(3): 740.
Deng, S., M. A. Meier, D. Caddell, J. Yang and D. Coleman-Derr (2022). Plant Microbiome-Based Genome-Wide Association Studies. Genome-Wide Association Studies. D. Torkamaneh and F. Belzile. New York, NY, Springer US: 353-367.
Dharni, J. S., B. K. Dhatt, P. Paul, T. Gao, T. Awada, H. Bacher, Z. Peleg, P. Staswick, J. Hupp, H. Yu and H. Walia (2022). "A non-destructive approach for measuring rice panicle-level photosynthetic responses using 3D-image reconstruction." Plant Methods 18(1): 126.
Dietz, N., Y. O. Chan, A. Scaboo, G. Graef, D. Hyten, M. Happ, B. Diers, A. Lorenz, D. Wang, T. Joshi and K. Bilyeu (2022). "Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines Identified in Soybean Alleles of Arabidopsis Flowering Orthologs With Divergent Latitude Distribution." Front Plant Sci 13: 889066.
Du, Q., M. T. Campbell, H. Yu, K. Liu, H. Walia, Q. Zhang and C. Zhang (2022). Gene Co-expression Network Analysis and Linking Modules to Phenotyping Response in Plants. High-Throughput Plant Phenotyping: Methods and Protocols. A. Lorence and K. Medina Jimenez. New York, NY, Springer US: 261-268.
Fan, W., F. Liu, Q. Jia, H. Du, W. Chen, J. Ruan, J. Lei, D. Z. Li, J. P. Mower and A. Zhu (2022). "Fragaria mitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions." New Phytol 236(2): 745-759.
Folkerts, C., J. D. Luck, S. K. Pitla and Y. Ge (2022). "Optical Sensor System for Chemical Flow Rate Monitoring with Direct Nozzle Injection." Journal of the ASABE 65(1): 87-95.
Gan, L., K. Park, J. Chai, E. M. Updike, H. Kim, A. Voshall, S. Behera, X. H. Yu, Y. Cai, C. Zhang, M. A. Wilson, J. P. Mower, E. N. Moriyama, C. Zhang, S. Kaewsuwan, Q. Liu, J. Shanklin and E. B. Cahoon (2022). "Divergent evolution of extreme production of variant plant monounsaturated fatty acids." Proc Natl Acad Sci U S A 119(30): e2201160119.
Gonzalez-Akre, E., C. Piponiot, M. Lepore, V. Herrmann, J. A. Lutz, J. L. Baltzer, C. W. Dick, G. S. Gilbert, F. He, M. Heym, A. I. Huerta, P. A. Jansen, D. J. Johnson, N. Knapp, K. Král, D. Lin, Y. Malhi, S. M. McMahon, J. A. Myers, D. Orwig, D. I. Rodríguez-Hernández, S. E. Russo, J. Shue, X. Wang, A. Wolf, T. Yang, S. J. Davies and K. J. Anderson-Teixeira (2022). "allodb: An R package for biomass estimation at globally distributed extratropical forest plots." Methods in Ecology and Evolution 13(2): 330-338.
Han, L., C. P. Jara, O. Wang, Y. Shi, X. Wu, S. Thibivilliers, R. K. Woycicki, M. A. Carlson, W. H. Velander, E. P. Araujo, M. Libault, C. Zhang and Y. Lei (2022). "Isolating and cryopreserving pig skin cells for single-cell RNA sequencing study." PLoS One 17(2): e0263869.
Huang, F., P. Chen, X. Tang, T. Zhong, T. Yang, C. C. Nwafor, C. Yang, X. Ge, H. An, Z. Li, E. B. Cahoon and C. Zhang (2022). "Genome assembly of the Brassicaceae diploid Orychophragmus violaceus reveals complex whole-genome duplication and evolution of dihydroxy fatty acid metabolism." Plant Commun: 100432.
Hyten, D. L. (2022). "Genotyping Platforms for Genome-Wide Association Studies: Options and Practical Considerations." Methods Mol Biol 2481: 29-42.
Katimbo, A., D. R. Rudnick, W.-z. Liang, K. C. DeJonge, T. H. Lo, T. E. Franz, Y. Ge, X. Qiao, I. Kabenge and H. N. Nakabuye (2022). "Two source energy balance maize evapotranspiration estimates using close-canopy mobile infrared sensors and upscaling methods under variable water stress conditions." Agricultural Water Management 274: 107972.
Khan, A. L., A. Al-Harrasi, J. P. Wang, S. Asaf, J. M. Riethoven, T. Shehzad, C. S. Liew, X. M. Song, D. P. Schachtman, C. Liu, J. G. Yu, Z. K. Zhang, F. B. Meng, J. Q. Yuan, C. D. Wei, H. Guo, X. Wang, A. Al-Rawahi, I. J. Lee, J. L. Bennetzen and X. Y. Wang (2022). "Genome structure and evolutionary history of frankincense producing Boswellia sacra." iScience 25(7): 104574.
Khan, A. L., L. D. Lopes, S. Bilal, S. Asaf, K. M. Crawford, V. Balan, A. Al-Rawahi, A. Al-Harrasi and D. P. Schachtman (2022). "Microbiome Variation Across Populations of Desert Halophyte Zygophyllum qatarensis." Front Plant Sci 13: 841217.
Khound, R., G. Sun, R. V. Mural, J. C. Schnable and D. K. Santra (2022). "SNP discovery in proso millet (Panicum miliaceum L.) using low-pass genome sequencing." Plant Direct 6(9): e447.
Kong, Y., M. Kuss, Y. Shi, F. Fang, W. Xue, W. Shi, Y. Liu, C. Zhang, P. Zhong and B. Duan (2022). "Exercise facilitates regeneration after severe nerve transection and further modulates neural plasticity." Brain Behav Immun Health 26: 100556.
Korth, N., L. Parsons, M. J. Van Haute, Q. Yang, P. Hurst, J. C. Schnable, D. R. Holding and A. K. Benson (2022). "The Unique Seed Protein Composition of Quality Protein Popcorn Promotes Growth of Beneficial Bacteria From the Human Gut Microbiome." Front Microbiol 13: 921456.
Li, D., D. Bai, Y. Tian, Y. H. Li, C. Zhao, Q. Wang, S. Guo, Y. Gu, X. Luan, R. Wang, J. Yang, M. J. Hawkesford, J. C. Schnable, X. Jin and L. J. Qiu (2022). "Time series canopy phenotyping enables the identification of genetic variants controlling dynamic phenotypes in soybean." J Integr Plant Biol.
Li, J., D. P. Schachtman, C. F. Creech, L. Wang, Y. Ge and Y. Shi (2022). "Evaluation of UAV-derived multimodal remote sensing data for biomass prediction and drought tolerance assessment in bioenergy sorghum." The Crop Journal 10(5): 1363-1375.
Liao, X., Y. Ye, X. Zhang, D. Peng, M. Hou, G. Fu, J. Tan, J. Zhao, R. Jiang, Y. Xu, J. Liu, J. Yang, W. Liu, L. R. Tembrock, G. Zhu and Z. Wu (2022). "The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation." aBIOTECH 3(3): 178-196.
Lopes, L. D., P. Wang, S. L. Futrell and D. P. Schachtman (2022). "Sugars and Jasmonic Acid Concentration in Root Exudates Affect Maize Rhizosphere Bacterial Communities." Appl Environ Microbiol 88(18): e0097122.
Lopez-Guerrero, M. G., P. Wang, F. Phares, D. P. Schachtman, S. Alvarez and K. van Dijk (2022). "A glass bead semi-hydroponic system for intact maize root exudate analysis and phenotyping." Plant Methods 18(1): 25.
Maitra, S., M. B. Viswanathan, K. Park, B. Kannan, S. C. Alfanar, S. M. McCoy, E. B. Cahoon, F. Altpeter, A. D. Leakey and V. Singh "Bioprocessing, Recovery, and Mass Balance of Vegetative Lipids from Metabolically Engineered “Oilcane” Demonstrates Its Potential as an Alternative Feedstock for Drop-In Fuel Production." ACS Sustainable Chemistry & Engineering.
Malakar, A., D. D. Snow, M. Kaiser, J. Shields, B. Maharjan, H. Walia, D. Rudnick and C. Ray (2022). "Ferrihydrite enrichment in the rhizosphere of unsaturated soil improves nutrient retention while limiting arsenic and uranium plant uptake." Science of The Total Environment 806: 150967.
Murad, M. O. F., E. J. Jones, B. Minasny, A. B. McBratney, N. Wijewardane and Y. Ge (2022). "Assessing a VisNIR penetrometer system for in-situ estimation of soil organic carbon under variable soil moisture conditions." Biosystems Engineering 224: 197-212.
Mural, R. V. and J. C. Schnable (2022). "Can the grains offer each other helping hands? Convergent molecular mechanisms associated with domestication and crop improvement in rice and maize." Mol Plant 15(5): 793-795.
Mural, R. V., G. Sun, M. Grzybowski, M. C. Tross, H. Jin, C. Smith, L. Newton, C. M. Andorf, M. R. Woodhouse, A. M. Thompson, B. Sigmon and J. C. Schnable (2022). "Association mapping across a multitude of traits collected in diverse environments in maize." Gigascience 11.
Nwafor, C. C., D. Li, P. Qin, L. Li, W. Zhang, Y. Zhou, J. Xu, Y. Yin, J. Cao, L. He, F. Xiang, C. Liu, L. Guo, Y. Zhou, E. B. Cahoon and C. Zhang (2022). "Genetic and Biochemical Investigation of Seed Fatty Acid Accumulation in Arabidopsis." Front Plant Sci 13: 942054.
Omini, J. J., I. Krassovskaya and T. Obata (2022). "Malate Dehydrogenase-Citrate Synthase Multienzyme Complex Dynamics Is Affected By TCA Cycle Flux In Living Yeast Cells." The FASEB Journal 36(S1).
Petro, T.M., Agarkova, I.V., Esmael, A., Dunigan, D.D., Van Etten, J.L., Pattee, G.L. (2022). The chlorovirus types detected in ALS patients through serum antibodies also accelerate motor deterioration in SODG93A transgenic mice. Frontiers in Neurology. 13, 821166.
Qi, M., J. C. Berry, K. W. Veley, L. O'Connor, O. M. Finkel, I. Salas-Gonzalez, M. Kuhs, J. Jupe, E. Holcomb, T. Glavina Del Rio, C. Creech, P. Liu, S. G. Tringe, J. L. Dangl, D. P. Schachtman and R. S. Bart (2022). "Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons." ISME J 16(8): 1957-1969.
Qu, X. J., X. J. Zhang, D. L. Cao, X. X. Guo, J. P. Mower and S. J. Fan (2022). "Plastid and mitochondrial phylogenomics reveal correlated substitution rate variation in Koenigia (Polygonoideae, Polygonaceae) and a reduced plastome for Koenigia delicatula including loss of all ndh genes." Mol Phylogenet Evol 174: 107544.
Rice, S. L., E. Lazarus, C. Anderton, K. Birnbaum, J. Brophy, B. Cole, D. Dickel, D. Ehrhardt, N. Fahlgren, M. Frank, E. Haswell, S. C. Huang, S. Leiboff, M. Libault, M. S. Otegui, N. Provart, R. G. Uhrig, S. Y. Rhee and C. Plant Cell Atlas (2022). "First Plant Cell Atlas symposium report." Plant Direct 6(6): e406.
Rodene, E., G. Xu, S. Palali Delen, X. Zhao, C. Smith, Y. Ge, J. Schnable and J. Yang (2022). "A UAV-based high-throughput phenotyping approach to assess time-series nitrogen responses and identify trait-associated genetic components in maize." The Plant Phenome Journal 5(1): e20030.
Rodrigues, R. A. L., V. F. Queiroz, J. Ghosh, D. D. Dunigan and J. L. Van Etten (2022). "Functional Genomic Analyses Reveal an Open Pan-genome for the Chloroviruses and a Potential for Genetic Innovation in New Isolates." J Virol 96(2): e0136721.
Russell, A. E., T. M. Aide, E. Braker, C. N. Ganong, R. D. Hardin, K. D. Holl, S. C. Hotchkiss, J. A. Klemens, E. K. Kuprewicz, D. McClearn, G. Middendorf, R. Ostertag, J. S. Powers, S. E. Russo, J. L. Stynoski, U. Valdez and C. G. Willis (2022). "Integrating tropical research into biology education is urgently needed." PLOS Biology 20(6): e3001674.
Russo, S. E., G. Ledder, E. B. Muller and R. M. Nisbet (2022). "Dynamic Energy Budget models: fertile ground for understanding resource allocation in plants in a changing world." Conservation Physiology 10(1).
Santos, P., L. Busta, W. C. Yim, E. B. Cahoon and D. K. Kosma (2022). "Structural diversity, biosynthesis, and function of plant falcarin-type polyacetylenic lipids." J Exp Bot 73(9): 2889-2904.
Scott, S., E. B. Cahoon and L. Busta (2022). "Variation on a theme: the structures and biosynthesis of specialized fatty acid natural products in plants." Plant J 111(4): 954-965.
Segnitz, R. M., S. E. Russo and K. G. Peay (2022). "Interactions with soil fungi alter density dependence and neighborhood effects in a locally abundant dipterocarp species." Ecology and Evolution 12(1): e8478.
Shao Q, Agarkova IV, Noel E, Dunigan DD, Liu Y, Wang A, Guo M, Xie L, Zhao X, Rossmann MG, Van Etten JL, Klose T, Fang Q.. (2022) First near-atomic, non icosahedrally averaged, structure of giant viruses and implications for viral assembly. Nature Commun. 13, 6476.
Shepherd, K. D., R. Ferguson, D. Hoover, F. van Egmond, J. Sanderman and Y. Ge (2022). "A global soil spectral calibration library and estimation service." Soil Security 7: 100061.
Singh, J., Y. Ge, D. M. Heeren, E. Walter-Shea, C. M. Neale, S. Irmak and M. S. Maguire (2022). "Unmanned Aerial System-Based Data Ferrying over a Sensor Node Station Network in Maize." Sensors 22(5): 1863.
Speciale, I., A. Notaro, C. Abergel, R. Lanzetta, T. L. Lowary, A. Molinaro, M. Tonetti, J. L. Van Etten and C. De Castro (2022). "The Astounding World of Glycans from Giant Viruses." Chem Rev 122(20): 15717-15766.
Speciale, I., Di Lorenzo, F., Notaro, A., Noel, E., Agarkova, I., Molinaro, A., Van Etten, J.L., De Castro, C. (2022). N-glycan from Paramecium bursaria chlorella virus MA-1D: re-evaluation of the oligosaccharide common core structure. Glycobiology 32, 260 - 273.
Sun, G., N. Wase, S. Shu, J. Jenkins, B. Zhou, J. V. Torres-Rodriguez, C. Chen, L. Sandor, C. Plott, Y. Yoshinga, C. Daum, P. Qi, K. Barry, A. Lipzen, L. Berry, C. Pedersen, T. Gottilla, A. Foltz, H. Yu, R. O'Malley, C. Zhang, K. M. Devos, B. Sigmon, B. Yu, T. Obata, J. Schmutz and J. C. Schnable (2022). "Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass." Nat Commun 13(1): 7731.
Sun, G., R. V. Mural, J. D. Turkus and J. C. Schnable (2022). "Quantitative Resistance Loci to Southern Rust Mapped in a Temperate Maize Diversity Panel." Phytopathology 112(3): 579-587.
Thibivilliers, S., A. Farmer, S. Schroeder and M. Libault (2022). Plant Single-Cell/Nucleus RNA-seq Workflow. Single Cell Transcriptomics: Methods and Protocols, Springer: 165-181.
Viscarra Rossel, R. A., T. Behrens, E. Ben‐Dor, S. Chabrillat, J. A. M. Demattê, Y. Ge, C. Gomez, C. Guerrero, Y. Peng and L. Ramirez‐Lopez (2022). "Diffuse reflectance spectroscopy for estimating soil properties: A technology for the 21st century." European Journal of Soil Science 73(4): e13271.
Wang, C. and L. Zeng (2022). "The Exploitation of Host 26S Proteasome as a New Stratedy for Bacterial Pathogenicity." Frontiers in Plant Science 13.
Wang, H.-L., B.-J. Ding, J.-Q. Dai, T. J. Nazarenus, R. Borges, A. Mafra-Neto, E. B. Cahoon, P. Hofvander, S. Stymne and C. Löfstedt (2022). "Insect pest management with sex pheromone precursors from engineered oilseed plants." Nature Sustainability 5(11): 981-990.
Wang, P., L. D. Lopes, M. G. Lopez-Guerrero, K. van Dijk, S. Alvarez, J.-J. Riethoven and D. P. Schachtman (2022). "Natural variation in root exudation of GABA and DIMBOA impacts the maize root endosphere and rhizosphere microbiomes." Journal of Experimental Botany 73(14): 5052-5066.
Wang, S., K. Guan, C. Zhang, D. Lee, A. J. Margenot, Y. Ge, J. Peng, W. Zhou, Q. Zhou and Y. Huang (2022). "Using soil library hyperspectral reflectance and machine learning to predict soil organic carbon: Assessing potential of airborne and spaceborne optical soil sensing." Remote Sensing of Environment 271: 112914.
Wang, X., J. Wang, H. Cui, W. Yang, B. Yu, C. Zhang, J. Wen, J. Kang, Z. Wang and Q. Yang (2022). "The UDP-glycosyltransferase MtUGT84A1 regulates anthocyanin accumulation and plant growth via JA signaling in Medicago truncatula." Environmental and Experimental Botany 201: 104972.
Wase, N., N. Abshire and T. Obata (2022). High-Throughput Profiling of Metabolic Phenotypes Using High-Resolution GC-MS. High-Throughput Plant Phenotyping: Methods and Protocols. A. Lorence and K. Medina Jimenez. New York, NY, Springer US: 235-260.
Wu, J., S. Wen, Y. Lan, X. Yin, J. Zhang and Y. Ge (2022). "Estimation of cotton canopy parameters based on unmanned aerial vehicle (UAV) oblique photography." Plant Methods 18(1): 129.
Yang, Q., M. Van Haute, N. Korth, S. E. Sattler, J. Toy, D. J. Rose, J. C. Schnable and A. K. Benson (2022). "Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome." Nat Commun 13(1): 5641.
Yang, Z., G. Xu, Q. Zhang, T. Obata and J. Yang (2022). "Genome-wide mediation analysis: an empirical study to connect phenotype with genotype via intermediate transcriptomic data in maize." Genetics 221(2).
Yin, L., G. Xu, J. Yang and M. Zhao (2022). "The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments." Molecular Biology and Evolution 39(10).
Yu, R., C. Sun, Y. Zhong, Y. Liu, M. V. Sanchez-Puerta, J. P. Mower and R. Zhou (2022). "The minicircular and extremely heteroplasmic mitogenome of the holoparasitic plant Rhopalocnemis phalloides." Curr Biol 32(2): 470-479 e475.
Zhan, Y., R. Zhang, Y. Zhou, V. Stoerger, J. Hiller, T. Awada and Y. Ge (2022). "Rapid online plant leaf area change detection with high-throughput plant image data." Journal of Applied Statistics: 1-15.
Zhang, H., Y. Ge, X. Xie, A. Atefi, N. K. Wijewardane and S. Thapa (2022). "High throughput analysis of leaf chlorophyll content in sorghum using RGB, hyperspectral, and fluorescence imaging and sensor fusion." Plant Methods 18(1): 1-17.
Zhang, K., Y. Yang, X. Zhang, L. Zhang, Y. Fu, Z. Guo, S. Chen, J. Wu, J. C. Schnable, K. Yi, X. Wang and F. Cheng (2022). "The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceae polyploidization and its distinct traits." Plant Commun: 100431.