Hu, H.*, Crow, T.M.*, Nojoomi, S., Schultz, A.J., Estévez-Palmas, J.M., Hufford, M.B., Flint-Garcia, S.A., Sawers, R.J.H, Rellán-Álvarez, R., Ross-Ibarra, J., and D.E. Runcie. Allele-specific expression reveals multiple paths to highland adaptation in maize. bioRxiv. Link.

Barnes AC, Rodríguez-Zapata F, Juárez-Núñez KA, Gates DJ, Janzen GM, Kur A, Wang L, Jensen SE, Estévez-Palmas JM, Crow TM, Kavi HS, Pil HD, Stokes RL, Knizner KT, Aguilar-Rangel MR, Demesa-Arévalo E, Skopelitis T, Pérez-Limón S, Stutts WL, Thompson P, Chiu YC, Jackson D, Muddiman DC, Fiehn O, Runcie D.E., Buckler ES, Ross-Ibarra J, Hufford MB, Sawers RJH, Rellán-Álvarez R. An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time. Proc Natl Acad Sci U S A. 2022 Jul 5;119(27):e2100036119. doi: 10.1073/pnas.2100036119. 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 Jean-Luc Jannink. Multi-omics prediction of oat agronomic and seed nutritional traits across environments and in distantly related populations. Theoretical and Applied Genetics volume 134, pages4043–4054 (2021). Link.

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

Odell, S.G., Hudson, A.I., Dubreuil, P., Tixier, M-H., Praud, S., Ross-Ibarra, J., and D.E. Runcie. Modeling Allelic Diversity of Multi-parent Mapping Populations Affects Detection of Quantitative Trait Loci. G3 Genes|Genomes|Genetics, Volume 12, Issue 3, March 2022, jkac011. 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 M. B. Hufford. Demonstration of local adaptation of maize landraces by reciprocal transplantation.  Evolutionary Applications15817– 837. Link.

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

Runcie, D.E., Qu, J., Cheng, H., and L. Crawford. (2021). MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits. Genome Biology 22(1), 1-25. Link.

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

Crow, T., Buerkle, A.C., Runcie, D.E., and K.H. Hufford. (2020) Implications of genetic heterogeneity for plant translocation during ecological restorationEcol Evol. Link.

Ta. J.K., Palmer, C., Brock, M. Rubin, M., Weinig, C., Maloof., J., and D.E. Runcie. (2020) Multiple loci control variation in plasticity to foliar shade throughout development in Arabidopsis thaliana. G3: GENES, GENOMES, GENETICS. Link.

Pincot, D., Ledda, D., Feldmann, M., Hardigan, M., Poorten, T., Runcie, D.E., Heffelfinger, C., Dellaporta, S., Cole, G., and S. Knapp. (2020) Social Network Analysis of the Genealogy of Strawberry: Retracing the Wild Roots of Heirloom and Modern Cultivars. G3: GENES, GENOMES, GENETICS. Link.

Runcie, D.E., Qu, J., Cheng, H., and L. Crawford. MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits. BioRxiv. Link. Presentation.

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

Martínez-Berdeja, A., Stitzer, M.C., Taylor, M.A., Okada, M., Ezcurra, E. Runcie, D.E., and Johanna Schmitt (2020). Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana. PNAS. Link

Gray, S., Rodriguez-Medina, J.,; Rusoff, S., Toal, T., Kajala, K., Runcie, D.E., and S. Brady (2019). Translational regulation contributes to the elevated CO2 response in two Solanum species. The Plant Journal. Link.

Gates, D.J., Runcie, D.E., Janzen, G.M., Romero Navarro, A., Willcox, M., Sonder, K., Snodgrass, S.J., Rodríguez-Zapata, F., Sawers, R.J.H., Rellán-Álvarez, R., Buckler, E.S., Hearne, S., Hufford, M.B., Ross-Ibarra, J. Single-gene resolution of locally adaptive genetic variation in Mexican maize. BioRxiv. Link.

Zu, P., Schielstl, F.P., Gervasi, D., Li, X., Runcie, D.E., and F. Guillaume. Floral signals evolve in a predictable way under artificial and pollinator selection in Brassica rapa using a G-matrix. BMC Evolutionary Biology. Link.

Taylor, M.A., Wilczek, A.M., Roe, J. L., Welch, S. M., Runcie, D.E., Cooper, M.D., and J Schmitt. (2019). Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana. PNAS. Link.

Runcie, D. E., and Cheng, H. (2019). Pitfalls and Remedies for Cross Validation with Multi-trait Genomic Prediction Methods. G3: GENES, GENOMES, GENETICS. Link.

Gaudinier, A., Rodriguez-Medina, J., Zhang, L., Olson, A., Liseron-Monfils, C., Bågman, A.-M., Foret, F. Abbitt, S., Tang, M., Li, B. Runcie, D, Shen, Bo, Frank, MJ, Ware, D,. and SM Brady (2018). Transcriptional regulation of nitrogen-associated metabolism and growth. Nature. Link.

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

Crawford, L., Flaxman, S.R., Runcie, D. E., West, M. Variable prioritization in nonlinear black box methods: A genetic association case study. AOAS: Link

Hine, E., Runcie, D. E., McGuigan, K. & M.W. Blows (2018). Uneven Distribution of Mutational Variance Across the Transcriptome of Drosophila serrata Revealed by High-Dimensional Analysis of Gene Expression. GeneticsLink

Runcie, D. E., N. Dorey, D. A. Garfield, M. Stumpp, S. Dupont & G. A. Wray. (2016) Genomic characterization of the evolutionary potential of the sea urchin Strongylocentrotus droebachiensis facing ocean acidification. Genome Biology and Evolution. Link

Hamilton, JA, Harta, AT, Runcie, D. E., El Kayala, W, Arango-Veleza, A, Cook, JEK. (2016). The joint influence of photoperiod and temperature during growth cessation and development of dormancy in white spruce (Picea glauca). Tree Physiology. Link

Burghardt, L, Runcie, D. E., Wilczek, A, Cooper, M, Roe, J, Welch, SM, Schmitt, J. (2015). Fluctuating warm temperatures decrease the effect of a key floral repressor on flowering time in Arabidopsis thaliana. New PhytologistLink

Donohue, K., Burghardt, L. T., Runcie, D. E., Bradford, K. J., & Schmitt, J. (2014). Applying developmental threshold models to evolutionary ecology. Trends in Ecology & Evolution. doi:10.1016/j.tree.2014.11.008. Link

Garfield, D. A, Runcie, D. E, Babbitt, C. C., Haygood, R., Nielsen, W. J. and G. A. Wray. (2013). Evolvability and Robustness in a Developmental Gene Regulatory Network. PloS Biology. 11(10) e1001696EP–. Link

Runcie, D. E., and Mukherjee, S. (2013). Dissecting High-Dimensional Phenotypes with Bayesian Sparse Factor Analysis of Genetic Covariance Matrices. Genetics, 194, 753-767. Link

Runcie D. E., Wiedmann, R., Archie, E. A., Altmann, J., Wray, G. A., Alberts, S. C., and J. Tung. (2013). Social environment influences the relationship between genotype and gene expression in wild baboons. Philos T Roy Soc B, 368, 20120345-20120345. Link

Runcie, D. E., Garfield, D. A. Wygoda, J. A., Mukherjee, S. and G. A. Wray. (2012). Genetics of gene expression responses to temperature stress in a sea urchin gene network. Mol Ecol, 21, 4547-4562. Link

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