ARID Center 

Pauli, D. Huppenthal, B., Wang, D. Schnable, J., Benes, B. Digital Twins for Plant and Crop Improvement. Accepted at Trends in Plant Science.

Yu, L., Melandri, G., Dittrich, A.C.N., Calleja, S., Ganguly, D.R., Palos, K., Brewer, E.K., Fischer, H., Rozzi, B., Srinivasan, A., Obata, T., Elgawad, H.A., Beemster, G.T.S., Henderson, R., Garcia, C.D., Zhang, X., Stern, D., Eveland, A.E., Lyons, E., Arnold, A.E., Skirycz, A., Schroeder, S.J., Gregory, B.D., Pauli, D., and Nelson, A.D.L. 2026. The mRNA Covalent Modification Dihydrouridine Regulates Transcript Turnover and Photosynthetic Capacity During Plant Abiotic Stress. Accepted at The Plant Cell.

Yu, L. A., Melandri, G., Nelson Dittrich, A. C., AbdElgawad, H., Beemster, G. T., Garcia, C., ... & Nelson, A. D. (2026). Integrated Multi‐Omic Analyses Uncover a Regulatory Link Between Photosynthesis and Drought Tolerance in Field‐Grown Sorghum. Plant, Cell & Environment. https://onlinelibrary.wiley.com/doi/10.1111/pce.70649

Legins, J., Pauli, D., and Arnold, A.E. High-Performing upland cotton shifts root-associated microbiomes under water limitation (2026). Discov. Plants 3, 121 (2026). https://doi.org/10.1007/s44372-026-00575-3

Obih, Chosen E., Jiatong Li, Giovanni Melandri, Duke Pauli, Eric Lyons, Andrew D. L. Nelson, and Brian D. Gregory (2025). “HAMRLNC: a Comprehensive and Scalable Pipeline for Integrated Epitranscriptomic Analysis.” Academia Molecular Biology and Genomics 2, no. 4. https://www.academia.edu/3064-9765/2/4/10.20935/AcadMolBioGen8059

Berlingeri, J., Fuentes, A., Ranario, Yun, H., Rim E.Y., Garrett, O., Howard, A., LaPorte, MF., Lo, S., Pauli, D., Hershberger, J., Earles, M., Deynze, A.V., Brummer, E.E., Michelmore, R., Wong, C.Y.S., Magney, T.S., Ronald, P.C., Runcie, D.E., Bailey, B.N., and Diepenbrock, C. (2025). Integration of crop modeling and sensing into molecular breeding for nutritional quality and stress tolerance. Theoretical and Applied Genetics, 138, e250. https://link.springer.com/article/10.1007/s00122-025-04984-y

Garcia, G., Pauli, D., Baltrus, D., and Arnold, A.E. (2025). Genomes of three root-associated bacteria isolated from Sorghum bicolor L. Moench under arid-land conditions. Microbiology Resource Announcements 14:e00401-2. https://doi.org/10.1128/mra.00401-25

Demieville, J., Dilkes, B., Eveland, A.L., and Pauli, D. (2025). High-resolution phenomics dataset collected on a field-grown, EMS-mutagenized sorghum population evaluated in hot, arid conditions. BMC Research Notes, 18, e332. https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-025-07407-9

Arad, N., Spraker, J., Garcia, K., Pauli, D., and Arnold, A.E. (2025). Genome sequences of five endophytic fungi isolated from Lactuca serriola, a wild relative of cultivated lettuce. Microbiology Resource Announcements, 0:e00444-25. https://doi.org/10.1128/mra.00444-25

Arad, N., Spraker, J., Garcia, K., Pauli, D., and Arnold, A.E. (2025). Biosynthetic potential of the culturable foliar mycobiome associated with field-grown lettuce. Applied Microbiology and Biotechnology, 109, e197. https://link.springer.com/article/10.1007/s00253-025-13581-4

Arnold, A.E., Arad, N., Cortez, E.J., Maro, CN., Legins, J., Porch, T. & Pauli, D. (2025). Field-grown Tepary bean (Phaseolus acutifolius) reveals symbiotic competence under arid-land agriculture conditions. In press, Bean Improvement Committee.

Yu, L., Legins, J., Nelson, A.D.L., Melandri, M., Arnold, A.E., Portch, T., & Pauli, D. (2025). Preliminary characterization and genetic mapping of nutritional compounds in Tepary bean (Phaseolus acutifolius). In press, Bean Improvement Committee.

Arad, N., Pauli, D., Truco, M., Lavelle, D., Michelmore, R., & Arnold, A. E. (2025). Diversity of leaf-and root microbiomes among genotypes and market classes of desert-grown lettuce (Lactuca sativa L.). FEMS Microbiology Letters, 372, fnaf121. https://doi.org/10.1093/femsle/fnaf121

Garcia, C., Pauli, D., Plecki, C., Alnasser, H., Rozzi, B., Calleja, S., & Arnold, A. E. (2024). The root endophytic microbiome shifts under drought in high-performing sorghum. Phytobiomes Journal, 8(3), 282-296. https://apsjournals.apsnet.org/doi/full/10.1094/PBIOMES-09-23-0095-R

Garcia, G., Pauli, D., and Arnold, A.E. (2024). Untargeted metabolomics unveils an accumulation of flavonoids associated with the microbiome of low-performing sorghum. Discover Plants 2:e197. https://link.springer.com/article/10.1007/s44372-025-00273-6

Christenson, C. G., Gohardoust, M. R., Calleja, S., Thorp, K. R., Tuller, M., & Pauli, D. (2024). Monitoring cotton water status with microtensiometers. Irrigation Science, 42(5), 995-1011. https://link.springer.com/article/10.1007/s00271-024-00930-w

Gonzalez, E. M., Zarei, A., Calleja, S., Christenson, C., Rozzi, B., Demieville, J., ... & Pauli, D. (2024). Quantifying leaf symptoms of sorghum charcoal rot in images of field‐grown plants using deep neural networks. The Plant Phenome Journal, 7(1), e20110. https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/ppj2.20110

Yu, L. A., Dittrich, A. C. N., Zhang, X., Brock, J. R., Thirumalaikumar, V. P., Melandri, G., ... & Nelson, A. D. (2024). Regulation of a single inositol 1‐phosphate synthase homeologue by HSFA6B contributes to fibre yield maintenance under drought conditions in upland cotton. Plant Biotechnology Journal, 22(10), 2756-2772. https://pmc.ncbi.nlm.nih.gov/articles/PMC11536448/