2023
Farmer, E., Michael, P., Yan, R., Lepak, N., Romay, C., Buckler, E. S., … & Gore, M. A. (2023). Synergizing Proximal Remote Sensing Modalities for Enhanced Prediction of Key Agronomic Crop Traits. Authorea Preprints.
Kick, D. R., Wallace, J. G., Schnable, J. C., Kolkman, J. M., Alaca, B., Beissinger, T. M., … & Washburn, J. D. (2023). Yield prediction through integration of genetic, environment, and management data through deep learning. G3: Genes, Genomes, Genetics, 13(4), jkad006.
Lima, D. C., Washburn, J. D., Varela, J. I., Chen, Q., Gage, J. L., Romay, M. C., … & de Leon, N. (2023). Genomes to Fields 2022 Maize genotype by Environment Prediction Competition. BMC Research Notes, 16(1), 148.
Lima, D. C., Aviles, A. C., Alpers, R. T., McFarland, B. A., Kaeppler, S., Ertl, D., … & de Leon, N. (2023). 2018–2019 field seasons of the Maize Genomes to Fields (G2F) G x E project. BMC Genomic Data, 24(1), 29.
Lima, D. C., Aviles, A. C., Alpers, R. T., Perkins, A., Schoemaker, D. L., Costa, M., … & de Leon, N. (2023). 2020-2021 Field Seasons of Maize G x E Project within Maize Genomes to Fields Initiative.
2022
Gage, J. L., Mali, S., McLoughlin, F., Khaipho-Burch, M., Monier, B., Bailey-Serres, J., … & Buckler, E. S. (2022). Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance. Proceedings of the National Academy of Sciences, 119(14), e2112516119.
Kick, D. R., Wallace, J. G., Schnable, J. C., Kolkman, J. M., Alaca, B., Beissinger, T. M., … & Washburn, J. D. (2022). Yield Prediction Through Integration of Genetic, Environment, and Management Data Through Deep Learning. bioRxiv.
2021
Feldmann, M. J., Gage, J. L., Turner‐Hissong, S. D., & Ubbens, J. R. (2021). Images carried before the fire: The power, promise, and responsibility of latent phenotyping in plants. The Plant Phenome Journal, 4(1), e20023.
2020
McFarland, B. A., AlKhalifah, N., Bohn, M., Bubert, J., Buckler, E. S., Ciampitti, I., … & De Leon, N. (2020). Maize genomes to fields (G2F): 2014–2017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets. BMC research notes, 13(1), 1-6.
Gage, J. L., Monier, B., Giri, A., & Buckler, E. S. (2020). Ten years of the maize nested association mapping population: impact, limitations, and future directions. The Plant Cell, 32(7), 2083-2093.
Franco, J. A. V., Gage, J. L., Bradbury, P. J., Johnson, L. C., Miller, Z. R., Buckler, E. S., & Romay, M. C. (2020). A maize practical haplotype graph leverages diverse NAM assemblies. bioRxiv.
2019
Mazaheri, M., Heckwolf, M., Vaillancourt, B., Gage, J. L., Burdo, B., Heckwolf, S., … & Kaeppler, S. M. (2019). Genome-wide association analysis of stalk biomass and anatomical traits in maize. BMC plant biology, 19(1), 1-17.
Gage, J. L., Richards, E., Lepak, N., Kaczmar, N., Soman, C., Chowdhary, G., … & Buckler, E. S. (2019). In‐field whole‐plant maize architecture characterized by subcanopy rovers and latent space phenotyping. The Plant Phenome Journal, 2(1), 1-11.
Gage, J. L., Vaillancourt, B., Hamilton, J. P., Manrique‐Carpintero, N. C., Gustafson, T. J., Barry, K., … & de Leon, N. (2019). Multiple maize reference genomes impact the identification of variants by genome‐wide association study in a diverse inbred panel. The plant genome, 12(2), 180069.
Marand, A. P., Jansky, S. H., Gage, J. L., Hamernik, A. J., de Leon, N., & Jiang, J. (2019). Residual heterozygosity and epistatic interactions underlie the complex genetic architecture of yield in diploid potato. Genetics, 212(1), 317-332.
Gage, J. L., Vaillancourt, B., Hamilton, J. P., Manrique-Carpintero, N. C., Gustafson, T. J., Barry, K., … & de Leon, N. (2019). Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel. Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States); Univ. of Wisconsin, Madison, WI (United States).
2018
Gage, J. L., de Leon, N., & Clayton, M. K. (2018). Comparing genome-wide association study results from different measurements of an underlying phenotype. G3: Genes, Genomes, Genetics, 8(11), 3715-3722.
Gage, J. L., White, M. R., Edwards, J. W., Kaeppler, S., & de Leon, N. (2018). Selection signatures underlying dramatic male inflorescence transformation during modern hybrid maize breeding. Genetics, 210(3), 1125-1138.
Gage, J. L. (2018). Tassel Morphology in Zea Mays: Novel Phenotyping Tools and Signatures of Selection (Doctoral dissertation, University of Wisconsin–Madison).
2017
Gage, J. L., Miller, N. D., Spalding, E. P., Kaeppler, S. M., & de Leon, N. (2017). TIPS: a system for automated image-based phenotyping of maize tassels. Plant Methods, 13(1), 1-12.
Gage, J. L., Jarquin, D., Romay, C., Lorenz, A., Buckler, E. S., Kaeppler, S., … & De Leon, N. (2017). The effect of artificial selection on phenotypic plasticity in maize. Nature communications, 8(1), 1-11.
Gage, D. J., Shor, L. M., Gage, J. L., Micciulla, J. L., & Rubinstein, R. L. (2017). U.S. Patent No. 9,603,368. Washington, DC: U.S. Patent and Trademark Office.
2013
Spindel, J., Wright, M., Chen, C., Cobb, J., Gage, J., Harrington, S., … & McCouch, S. (2013). Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theoretical and applied genetics, 126(11), 2699-2716.