Publications

* indicates current or former lab members and visitors listed on the People page.

Feldmann, M.J., Wang, F.*, and Runcie, D.E. (2026). Philosophy of phenomic prediction and its incompatibility with causal inference. The Plant Phenome Journal 9(1), e70091. Link.

Huang, P.K.*, and Runcie, D.E. (2026). Photoperiodism‐Specific QTLs Support Switch‐Like Genetic Control of Obligate Long‐Day Photoperiodism in Mimulus guttatus. Plant Species Biology 41(6), e70074. Link.

Perez‐Limón, S., Alonso‐Nieves, A.L., Ramírez‐Flores, M.R., Cintora‐Martínez, G.C., Salazar‐Vidal, M.N., Torres-Rodriguez, J.V.*, Carcaño‐Macías, J., Perryman, M.G., Paulson, O.H.S., Sidhu, J.S., Yu, P., Llaca, V., Fengler, K.A., Li, F.*, Runcie, D.E., Ross‐Ibarra, J., Gillmor, C.S., Rellán‐Álvarez, R., and Sawers, R.J.H. (2026). The MexMAGIC population reveals the genetic architecture of traits exhibiting clinal variation in Mexican native maize. New Phytologist. Link.

LaPorte, M.F., Hu, H.*, Solomon, W., Oard, J.H., Knapp, S.J., Runcie, D.E., Edwards, J.D., McClung, A., and Diepenbrock, C.H. (2026). Multi‐environment evaluation and genomic prediction of agronomic traits in the southern US rice genepool. The Plant Genome 19(2), e70222. Link.

Wang, F.*, Feldmann, M.J., and Runcie, D.E. (2025). Do not benchmark phenomic prediction against genomic prediction accuracy. The Plant Phenome Journal 8(1), e70029. Link.

Engelhorn, J., Snodgrass, S.J., Kok, A., Seetharam, A.S., Schneider, M., Kiwit, T., Singh, A., Banf, M., Doan, D.T.H., Khaipho-Burch, M., Runcie, D.E., Sánchez-Camargo, V.A., Bader, R., Torres-Rodriguez, J.V.*, Sun, G., Stam, M., Fiorani, F., Beier, S., Schnable, J.C., Bass, H.W., Hufford, M.B., Stich, B., Frommer, W.B., Ross-Ibarra, J., and Hartwig, T. (2025). Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize. Nature Genetics 57(9), 2313–2322. Link.

Berlingeri, J., Fuentes, A., Ranario, E., Yun, H., Rim, E.Y., Garrett, O., Howard, A., LaPorte, M.F., Lo, S., Pauli, D., Hershberger, J., Earles, M., Van Deynze, A., Brummer, E.C., Michelmore, R., Wong, C.Y.S., Magney, T.S., Ronald, P.C., Runcie, D.E., Bailey, B.N., and Diepenbrock, C.H. (2025). Integration of crop modeling and sensing into molecular breeding for nutritional quality and stress tolerance. Theoretical and Applied Genetics 138(9), 205. Link.

Crossa, J., Martini, J.W.R., Vitale, P., Pérez-Rodríguez, P., Costa-Neto, G., Fritsche-Neto, R., Runcie, D.E., Cuevas, J., Toledo, F., Li, H., De Vita, P., Gerard, G., Dreisigacker, S., Crespo-Herrera, L., Saint Pierre, C., Bentley, A., Lillemo, M., Ortiz, R., Montesinos-López, O.A., and Montesinos-López, A. (2025). Expanding genomic prediction in plant breeding: harnessing big data, machine learning, and advanced software. Trends in Plant Science 30(7), 756–774. Link.

Li, F.*, Gates, D.J., Buckler, E.S., Hufford, M.B., Janzen, G.M., Rellán-Álvarez, R., Rodríguez-Zapata, F., Romero Navarro, J.A., Sawers, R.J.H., Snodgrass, S.J., Sonder, K., Willcox, M.C., Hearne, S.J., Ross-Ibarra, J., and Runcie, D.E. (2025). Environmental data provide marginal benefit for predicting climate adaptation. PLOS Genetics 21(6), e1011714. Link.

Xavier, A., Runcie, D.E., and Habier, D. (2025). Megavariate methods capture complex genotype-by-environment interactions. Genetics 229(4), iyae179. Link.

Wang, F.*, Feldmann, M.J., and Runcie, D.E. (2025). Why usefulness is rarely useful. G3: Genes, Genomes, Genetics 15(3), jkae296. Link.

Crossa, J., Montesinos-Lopez, O.A., Costa-Neto, G., Vitale, P., Martini, J.W.R., Runcie, D.E., Fritsche-Neto, R., Montesinos-Lopez, A., Pérez-Rodríguez, P., Gerard, G., Dreisigacker, S., Crespo-Herrera, L., Saint Pierre, C., Lillemo, M., Cuevas, J., Bentley, A., and Ortiz, R. (2025). Machine learning algorithms translate big data into predictive breeding accuracy. Trends in Plant Science 30(2), 167–184. Link.

Washburn, J.D., Varela, J.I., Xavier, A., Chen, Q., Ertl, D., Gage, J.L., Holland, J.B., Lima, D.C., Romay, M.C., Lopez-Cruz, M., de los Campos, G., Barber, W., Zimmer, C., Trucillo Silva, I., Rocha, F., Rincent, R., Ali, B., Hu, H.*, Runcie, D.E., Gusev, K., Slabodkin, A., Bax, P., Aubert, J., Gangloff, H., Mary-Huard, T., Vanrenterghem, T., Quesada-Traver, C., Yates, S., Ariza-Suárez, D., Ulrich, A., Wyler, M., Kick, D.R., Bellis, E.S., Causey, J.L., Soriano Chavez, E., Wang, Y., Piyush, V., Fernando, G.D., Hu, R.K., Kumar, R., Timon, A.J., Venkatesh, R., Abá, K.S., Chen, H., Ranaweera, T., Shiu, S.H., Wang, P., Gordon, M.J., Amos, B.K., Busato, S., Perondi, D., Gogna, A., Psaroudakis, D., Chen, C.P.J., Al-Mamun, H.A., Danilevicz, M.F., Upadhyaya, S.R., Edwards, D., and de Leon, N. (2025). Global genotype by environment prediction competition reveals that diverse modeling strategies can deliver satisfactory maize yield estimates. Genetics 229(2), iyae195. Link.

Hu, H.*, Rincent, R., and Runcie, D.E. (2025). MegaLMM improves genomic predictions in new environments using environmental covariates. Genetics 229(1), iyae171. Link.

Chen, Y., Atashi, H., Qu, J., Delhez, P., Runcie, D.E., Soyeurt, H., and Gengler, N. (2024). Exploring a Bayesian sparse factor model-based strategy for the genetic analysis of thousands of mid-infrared spectra traits for animal breeding. Journal of Dairy Science 107(11), 9615–9627. Link.

Ali, B.*, Huguenin-Bizot, B., Laurent, M., Chaumont, F., Maistriaux, L.C., Nicolas, S., Duborjal, H., Welcker, C., Tardieu, F., Mary-Huard, T., Moreau, L., Charcosset, A., Runcie, D.E., and Rincent, R. (2024). High-dimensional multi-omics measured in controlled conditions are useful for maize platform and field trait predictions. Theoretical and Applied Genetics 137(7), 175. Link.

Huang, P.K.*, Schmitt, J., and Runcie, D.E. (2024). Exploring the molecular regulation of vernalization‐induced flowering synchrony in Arabidopsis. New Phytologist 242(3), 947–959. Link.

Yang, N., Wang, Y., Liu, X., Jin, M., Vallebueno-Estrada, M., Calfee, E., Chen, L., Dilkes, B.P., Gui, S., Fan, X., Harper, T.K., Kennett, D.J., Li, W., Lu, Y., Ding, J., Chen, Z., Luo, J., Mambakkam, S., Menon, M., Snodgrass, S., Veller, C., Wu, S., Wu, S., Zhuo, L., Xiao, Y., Yang, X., Stitzer, M.C., Runcie, D.E., Yan, J., and Ross-Ibarra, J. (2023). Two teosintes made modern maize. Science 382(6674), eadg8940. Link.

Persa, R., Vieira, C.C., Rios, E., Hoyos-Villegas, V., Messina, C.D., Runcie, D.E., and Jarquin, D. (2023). Improving predictive ability in sparse testing designs in soybean populations. Frontiers in Genetics 14, 1269255. Link.

Martínez‐Berdeja, A., Okada, M., Cooper, M.D., Runcie, D.E., Burghardt, L.T., and Schmitt, J. (2023). Precipitation timing and soil substrate drive phenology and fitness of Arabidopsis thaliana in a Mediterranean environment. Functional Ecology 37(9), 2471–2487. Link.

Qu, J., Runcie, D.E., and Cheng, H. (2023). Mega-scale Bayesian regression methods for genome-wide prediction and association studies with thousands of traits. Genetics 223(3), iyac183. Link.

Hu, H.*, Meng, Y., Liu, W., Chen, S., and Runcie, D.E. (2022). Multi-trait genomic prediction improves accuracy of selection among doubled haploid lines in maize. International Journal of Molecular Sciences 23(23), 14558. Link.

Hu, H.*, Crow, T.*, Nojoomi, S.*, Schulz, A.J., Estévez-Palmas, J.M., Hufford, M.B., Flint-Garcia, S., Sawers, R., Rellán-Álvarez, R., Ross-Ibarra, J., and Runcie, D.E. (2022). Allele-specific expression reveals multiple paths to highland adaptation in maize. Molecular Biology and Evolution 39(11), msac239. Link.

Hine, E., Runcie, D.E., Allen, S.L., Wang, Y., Chenoweth, S.F., Blows, M.W., and McGuigan, K. (2022). Maintenance of quantitative genetic variance in complex, multitrait phenotypes: the contribution of rare, large effect variants in 2 Drosophila species. Genetics 222(2), iyac122. Link.

Barnes, A.C., Rodríguez-Zapata, F., Juárez-Núñez, K.A., Gates, D.J., Janzen, G.M., Kur, A., Wang, L., Jensen, S.E., Estévez-Palmas, J.M., Crow, T.M.*, Kavi, H.S., Pil, H.D., Stokes, R.L., Knizner, K.T., Aguilar-Rangel, M.R.*, Demesa-Arévalo, E., Skopelitis, T., Pérez-Limón, S., Stutts, W.L., Thompson, P., Chiu, Y.C., Jackson, D., Muddiman, D.C., Fiehn, O., Runcie, D.E., Buckler, E.S., Ross-Ibarra, J., Hufford, M.B., Sawers, R.J.H., and Rellán-Álvarez, R. (2022). An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time. Proceedings of the National Academy of Sciences 119(27), e2100036119. Link.

Tagkopoulos, I., Brown, S.F., Liu, X., Zhao, Q., Zohdi, T.I., Earles, J.M., Nitin, N., Runcie, D.E., Lemay, D.G., Smith, A.D., Ronald, P.C., Feng, H., and Youtsey, G.D. (2022). Special report: AI Institute for next generation food systems (AIFS). Computers and Electronics in Agriculture 196, 106819. Link.

Janzen, G.M., Aguilar‐Rangel, M.R.*, Cíntora‐Martínez, C., Blöcher‐Juárez, K.A., González‐Segovia, E., Studer, A.J., Runcie, D.E., Flint‐Garcia, S.A., Rellán‐Álvarez, R., Sawers, R.J.H., and Hufford, M.B. (2022). Demonstration of local adaptation in maize landraces by reciprocal transplantation. Evolutionary Applications 15(5), 817–837. Link.

Odell, S.G.*, Hudson, A.I., Praud, S., Dubreuil, P., Tixier, M.H., Ross-Ibarra, J., and Runcie, D.E. (2022). Modeling allelic diversity of multiparent mapping populations affects detection of quantitative trait loci. G3: Genes, Genomes, Genetics 12(3), jkac011. Link.

Hudson, A.I., Odell, S.G.*, Dubreuil, P., Tixier, M.H., Praud, S., Runcie, D.E., and Ross-Ibarra, J. (2022). Analysis of genotype-by-environment interactions in a maize mapping population. G3: Genes, Genomes, Genetics 12(3), jkac013. Link.

Hu, H.*, Campbell, M.T., Yeats, T.H., Zheng, X., Runcie, D.E., Covarrubias-Pazaran, G., Broeckling, C., Yao, L., Caffe-Treml, M., Gutiérrez, L., Smith, K.P., Tanaka, J., Hoekenga, O.A., Sorrells, M.E., Gore, M.A., and Jannink, J.L. (2021). Multi-omics prediction of oat agronomic and seed nutritional traits across environments and in distantly related populations. Theoretical and Applied Genetics 134(12), 4043–4054. Link.

Montesinos-López, A., Runcie, D.E., Ibba, M.I., Pérez-Rodríguez, P., Montesinos-López, O.A., Crespo, L.A., Bentley, A.R., and Crossa, J. (2021). Multi-trait genomic-enabled prediction enhances accuracy in multi-year wheat breeding trials. G3: Genes, Genomes, Genetics 11(10), jkab270. Link.

Runcie, D.E., Qu, J., Cheng, H., and Crawford, L. (2021). MegaLMM: mega-scale linear mixed models for genomic predictions with thousands of traits. Genome Biology 22(1), 213. Link.

Kajala, K., Gouran, M., Shaar-Moshe, L., Mason, G.A., Rodriguez-Medina, J., Kawa, D., Pauluzzi, G., Reynoso, M., Canto-Pastor, A., Manzano, C., Lau, V., Artur, M.A.S., West, D.A., Gray, S.B., Borowsky, A.T., Moore, B.P., Yao, A.I., Morimoto, K.W., Bajic, M., Formentin, E., Nirmal, N.A., Rodriguez, A., Pasha, A., Deal, R.B., Kliebenstein, D.J., Hvidsten, T.R., Provart, N.J., Sinha, N.R., Runcie, D.E., Bailey-Serres, J., and Brady, S.M. (2021). Innovation, conservation, and repurposing of gene function in root cell type development. Cell 184(12), 3333–3348.e19. Link.

Pincot, D.D.A., Ledda, M., Feldmann, M.J., Hardigan, M.A., Poorten, T.J., Runcie, D.E., Heffelfinger, C., Dellaporta, S.L., Cole, G.S., and Knapp, S.J. (2021). Social network analysis of the genealogy of strawberry: retracing the wild roots of heirloom and modern cultivars. G3: Genes, Genomes, Genetics 11(3), jkab015. Link.

Crow, T.M.*, Buerkle, C.A., Runcie, D.E., and Hufford, K.M. (2021). Implications of genetic heterogeneity for plant translocation during ecological restoration. Ecology and Evolution 11(3), 1100–1110. Link.

Crow, T.*, Ta, J.*, Nojoomi, S.*, Aguilar-Rangel, M.R.*, Torres-Rodriguez, J.V.*, Gates, D., Rellan-Alvarez, R., Sawers, R., and Runcie, D.E. (2020). Gene regulatory effects of a large chromosomal inversion in highland maize. PLOS Genetics 16(12), e1009213. Link.

Ta, J.*, Palmer, C., Brock, M., Rubin, M., Weinig, C., Maloof, J., and Runcie, D.E. (2020). Multiple Loci Control Variation in Plasticity to Foliar Shade Throughout Development in Arabidopsis thaliana. G3: Genes, Genomes, Genetics 10(11), 4103–4114. Link.

Zu, P., Schiestl, F.P., Gervasi, D., Li, X., Runcie, D.E., and Guillaume, F. (2020). Floral signals evolve in a predictable way under artificial and pollinator selection in Brassica rapa. BMC evolutionary biology 20(1), 127. Link.

Gray, S.B., Rodriguez‐Medina, J., Rusoff, S., Toal, T.W., Kajala, K., Runcie, D.E., and Brady, S.M. (2020). Translational regulation contributes to the elevated CO2 response in two Solanum species. The Plant Journal 102(2), 383–397. Link.

Martínez-Berdeja, A., Stitzer, M.C., Taylor, M.A., Okada, M., Ezcurra, E., Runcie, D.E., and Schmitt, J. (2020). Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana. Proceedings of the National Academy of Sciences 117(5), 2526–2534. Link.

Runcie, D.E., and Cheng, H. (2019). Pitfalls and remedies for cross validation with multi-trait genomic prediction methods. G3: Genes, Genomes, Genetics 9(11), 3727–3741. Link.

Taylor, M.A., Wilczek, A.M., Roe, J.L., Welch, S.M., Runcie, D.E., Cooper, M.D., and Schmitt, J. (2019). Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana. Proceedings of the National Academy of Sciences 116(36), 17890–17899. Link.

Crawford, L., Flaxman, S.R., Runcie, D.E., and West, M. (2019). Variable prioritization in nonlinear black box methods: A genetic association case study. The Annals of Applied Statistics 13(2), 958. Link.

Runcie, D.E., and Crawford, L. (2019). Fast and flexible linear mixed models for genome-wide genetics. PLOS Genetics 15(2), e1007978. Link.

Gaudinier, A., Rodriguez-Medina, J., Zhang, L., Olson, A., Liseron-Monfils, C., Bågman, A.M., Foret, J., Abbitt, S., Tang, M., Li, B., Runcie, D.E., Kliebenstein, D.J., Shen, B., Frank, M.J., Ware, D., and Brady, S.M. (2018). Transcriptional regulation of nitrogen-associated metabolism and growth. Nature 563(7730), 259–264. Link.

Hine, E., Runcie, D.E., McGuigan, K., and Blows, M.W. (2018). Uneven Distribution of Mutational Variance Across the Transcriptome of Drosophila serrata Revealed by High-Dimensional Analysis of Gene Expression. Genetics 209(4), 1319–1328. Link.

Runcie, D.E., Dorey, N., Garfield, D.A., Stumpp, M., Dupont, S., and Wray, G.A. (2016). Genomic Characterization of the Evolutionary Potential of the Sea Urchin Strongylocentrotus droebachiensis Facing Ocean Acidification. Genome Biology and Evolution 8(12), 3672–3684. Link.

Hamilton, J.A., El Kayal, W., Hart, A.T., Runcie, D.E., Arango-Velez, A., and Cooke, J.E.K. (2016). The joint influence of photoperiod and temperature during growth cessation and development of dormancy in white spruce (Picea glauca). Tree Physiology 36(11), 1432–1448. Link.

Burghardt, L.T., Runcie, D.E., Wilczek, A.M., Cooper, M.D., Roe, J.L., Welch, S.M., and Schmitt, J. (2016). Fluctuating, warm temperatures decrease the effect of a key floral repressor on flowering time in Arabidopsis thaliana. New Phytologist 210(2), 564–576. Link.

Donohue, K., Burghardt, L.T., Runcie, D.E., Bradford, K.J., and Schmitt, J. (2015). Applying developmental threshold models to evolutionary ecology. Trends in Ecology & Evolution 30(2), 66–77. Link.

Garfield, D.A., Runcie, D.E., Babbitt, C.C., Haygood, R., Nielsen, W.J., and Wray, G.A. (2013). The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network. PLOS Biology 11(10), e1001696. Link.

Runcie, D.E., and Mukherjee, S. (2013). Dissecting high-dimensional phenotypes with Bayesian sparse factor analysis of genetic covariance matrices. Genetics 194(3), 753–767. Link.

Runcie, D.E., Wiedmann, R.T., Archie, E.A., Altmann, J., Wray, G.A., Alberts, S.C., and Tung, J. (2013). Social environment influences the relationship between genotype and gene expression in wild baboons. Philosophical Transactions of the Royal Society B: Biological Sciences 368(1618), 20120345. Link.

Runcie, D.E., Garfield, D.A., Babbitt, C.C., Wygoda, J.A., Mukherjee, S., and Wray, G.A. (2012). Genetics of gene expression responses to temperature stress in a sea urchin gene network. Molecular Ecology 21(18), 4547–4562. Link.

Runcie, D.E., and Noor, M.A.F. (2009). Sequence signatures of a recent chromosomal rearrangement in Drosophila mojavensis. Genetica 136(1), 5–11. Link.