2020 Publications

Barker, R., Lombardino, J., Rasmussen, K., & Gilroy, S. (2020). Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. Frontiers in Plant Science, 11, 147. https://doi.org/10.3389/fpls.2020.00147
Bezuidt, O. K. I., Lebre, P. H., Pierneef, R., León-Sobrino, C., Adriaenssens, E. M., Cowan, D. A., Van de Peer, Y., & Makhalanyane, T. P. (2020). Phages actively challenge niche communities in the Antarctic soils [Preprint]. Microbiology. https://doi.org/10.1101/2020.01.17.911081
Chakroborti, D., Roy, B., Mondal, A., Mostaeen, G., Roy, C. K., Schneider, K. A., & Deters, R. (2020). A Data Management Scheme for Micro-Level Modular Computation-Intensive Programs in Big Data Platforms. In R. Alhajj, M. Moshirpour, & B. Far (Eds.), Data Management and Analysis (Vol. 65, pp. 135–153). Springer International Publishing. https://doi.org/10.1007/978-3-030-32587-9_9
Chen, L.-X., Méheust, R., Crits-Christoph, A., McMahon, K. D., Nelson, T. C., Warren, L. A., & Banfield, J. F. (2020). Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation [Preprint]. Microbiology. https://doi.org/10.1101/2020.02.13.942896
Coate, Schreyer, Kum, & Doyle. (2020). Robust Cytonuclear Coordination of Transcription in Nascent Arabidopsis thaliana Autopolyploids. Genes, 11(2), 134. https://doi.org/10.3390/genes11020134
Coffman, S. M., Hufford, M. B., Andorf, C. M., & Lübberstedt, T. (2020). Haplotype structure in commercial maize breeding programs in relation to key founder lines. Theoretical and Applied Genetics, 133(2), 547–561. https://doi.org/10.1007/s00122-019-03486-y
Condon, L. E., Atchley, A. L., & Maxwell, R. M. (2020). Evapotranspiration depletes groundwater under warming over the contiguous United States. Nature Communications, 11(1), 873. https://doi.org/10.1038/s41467-020-14688-0
Danczak, R. E., Daly, R. A., Borton, M. A., Stegen, J. C., Roux, S., Wrighton, K. C., & Wilkins, M. J. (2020). Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems. MSystems, 5(2), e00098-20, /msystems/5/2/msys.00098-20.atom. https://doi.org/10.1128/mSystems.00098-20
Debauche, O., Mahmoudi, S. A., De Cock, N., Mahmoudi, S., Manneback, P., & Lebeau, F. (2020). Cloud architecture for plant phenotyping research. Concurrency and Computation: Practice and Experience. https://doi.org/10.1002/cpe.5661
Doak, T., Sanders, S., Ganote, C., Papudeshi, B., Fischer, J., & Hancock, D. Y. (2020). National Center for Genome Analysis Support (NCGAS): Genomics and other Science in the NSF-Funded Jetstream Cloud.
Falcon, C. M., Kaeppler, S. M., Spalding, E. P., Miller, N. D., Haase, N., AlKhalifah, N., Bohn, M., Buckler, E. S., Campbell, D. A., Ciampitti, I., Coffey, L., Edwards, J., Ertl, D., Flint‐Garcia, S., Gore, M. A., Graham, C., Hirsch, C. N., Holland, J. B., Jarquín, D., … Leon, N. (2020). Relative utility of agronomic, phenological, and morphological traits for assessing genotype‐by‐environment interaction in maize inbreds. Crop Science, csc2.20035. https://doi.org/10.1002/csc2.20035
Francisco Ribeiro, P., & Camargo Rodriguez, A. V. (2020). Emerging Advanced Technologies to Mitigate the Impact of Climate Change in Africa. Plants, 9(3), 381. https://doi.org/10.3390/plants9030381
Gallagher, R. V., Falster, D. S., Maitner, B. S., Salguero-Gómez, R., Vandvik, V., Pearse, W. D., Schneider, F. D., Kattge, J., Poelen, J. H., Madin, J. S., Ankenbrand, M. J., Penone, C., Feng, X., Adams, V. M., Alroy, J., Andrew, S. C., Balk, M. A., Bland, L. M., Boyle, B. L., … Enquist, B. J. (2020). Open Science principles for accelerating trait-based science across the Tree of Life. Nature Ecology & Evolution, 4(3), 294–303. https://doi.org/10.1038/s41559-020-1109-6
García-Portela, Reguera, Gago, Gac, & Rodríguez. (2020). Uptake of Inorganic and Organic Nitrogen Sources by Dinophysis acuminata and D. acuta. Microorganisms, 8(2), 187. https://doi.org/10.3390/microorganisms8020187
Gemeinholzer, B., Vences, M., Beszteri, B., Bruy, T., Felden, J., Kostadinov, I., Miralles, A., Nattkemper, T. W., Printzen, C., Renz, J., Rybalka, N., Schuster, T., Weibulat, T., Wilke, T., & Renner, S. S. (2020). Data storage and data re-use in taxonomy—The need for improved storage and accessibility of heterogeneous data. Organisms Diversity & Evolution. https://doi.org/10.1007/s13127-019-00428-w
Hannah, L., Roehrdanz, P. R., Marquet, P. A., Enquist, B. J., Midgley, G., Foden, W., Lovett, J. C., Corlett, R. T., Corcoran, D., Butchart, S. H. M., Boyle, B., Feng, X., Maitner, B., Fajardo, J., McGill, B. J., Merow, C., Morueta‐Holme, N., Newman, E. A., Park, D. S., … Svenning, J. (2020). 30% land conservation and climate action reduces tropical extinction risk by more than 50%. Ecography, ecog.05166. https://doi.org/10.1111/ecog.05166
Howard-Varona, C., Lindback, M. M., Bastien, G. E., Solonenko, N., Zayed, A. A., Jang, H., Andreopoulos, B., Brewer, H. M., Glavina del Rio, T., Adkins, J. N., Paul, S., Sullivan, M. B., & Duhaime, M. B. (2020). Phage-specific metabolic reprogramming of virocells. The ISME Journal. https://doi.org/10.1038/s41396-019-0580-z
Hu, G. (2020). Evaluation of 3D Chromatin Interactions Using Hi-C. In B. L. Kidder (Ed.), Stem Cell Transcriptional Networks (Vol. 2117, pp. 65–78). Springer US. https://doi.org/10.1007/978-1-0716-0301-7_3
Jamnadass, R., Mumm, R. H., Hale, I., Hendre, P., Muchugi, A., Dawson, I. K., Powell, W., Graudal, L., Yana-Shapiro, H., Simons, A. J., & Van Deynze, A. (2020). Enhancing African orphan crops with genomics. Nature Genetics, 52(4), 356–360. https://doi.org/10.1038/s41588-020-0601-x
Joly-Lopez, Z., Platts, A. E., Gulko, B., Choi, J. Y., Groen, S. C., Zhong, X., Siepel, A., & Purugganan, M. D. (2020). An inferred fitness consequence map of the rice genome. Nature Plants, 6(2), 119–130. https://doi.org/10.1038/s41477-019-0589-3
Keuler, R., Garretson, A., Saunders, T., Erickson, R. J., St. Andre, N., Grewe, F., Smith, H., Lumbsch, H. T., Huang, J.-P., St. Clair, L. L., & Leavitt, S. D. (2020). Genome-scale data reveal the role of hybridization in lichen-forming fungi. Scientific Reports, 10(1), 1497. https://doi.org/10.1038/s41598-020-58279-x
Knight, C. A., Blois, J. L., Blonder, B., Macias-Fauria, M., Ordonez, A., & Svenning, J.-C. (2020). Community Assembly and Climate Mismatch in Late Quaternary Eastern North American Pollen Assemblages. The American Naturalist, 195(2), 000–000.
Li, J., Demesyeux, L., Brym, M., & Chambers, A. H. (2020). Development of species-specific molecular markers in Vanilla for seedling selection of hybrids. Molecular Biology Reports. https://doi.org/10.1007/s11033-020-05287-9
Liu, J., Seetharam, A. S., Chougule, K., Ou, S., Swentowsky, K. W., Gent, J. I., Llaca, V., Woodhouse, M. R., Manchanda, N., Presting, G. G., Kudrna, D. A., Alabady, M., Hirsch, C. N., Fengler, K. A., Ware, D., Michael, T. P., Hufford, M. B., & Dawe, R. K. (2020). Gapless assembly of maize chromosomes using long read technologies [Preprint]. Bioinformatics. https://doi.org/10.1101/2020.01.14.906230
Mcardle, D., Powers, J., & Joyce, R. A. (2020). Self-healing architecture for resilient computing services (Patent No. 01554685).
McFarland, B. A., AlKhalifah, N., Bohn, M., Bubert, J., Buckler, E. S., Ciampitti, I., Edwards, J., Ertl, D., Gage, J. L., Falcon, C. M., Flint-Garcia, S., Gore, M. A., Graham, C., Hirsch, C. N., Holland, J. B., Hood, E., Hooker, D., Jarquin, D., Kaeppler, S. M., … 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), 71. https://doi.org/10.1186/s13104-020-4922-8
Miao, C., Xu, Y., Liu, S., Schnable, P. S., & Schnable, J. C. (2020). Functional principal component based time-series genome-wide association in sorghum [Preprint]. Plant Biology. https://doi.org/10.1101/2020.02.16.951467
Nguyen, M., Debroy, S., Calyam, P., Lyu, Z., & Joshi, T. (2020). Security-aware Resource Brokering for Bioinformatics Workflows across Federated Multi-cloud Infrastructures. Proceedings of the 21st International Conference on Distributed Computing and Networking, 1–10. https://doi.org/10.1145/3369740.3369791
Shenton, M., Kobayashi, M., Terashima, S., Ohyanagi, H., Copetti, D., Hernández-Hernández, T., Zhang, J., Ohmido, N., Fujita, M., Toyoda, A., Ikawa, H., Fujiyama, A., Furuumi, H., Miyabayashi, T., Kubo, T., Kudrna, D., Wing, R., Yano, K., Nonomura, K., … Kurata, N. (2020). Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels. Genome Biology and Evolution, evaa037. https://doi.org/10.1093/gbe/evaa037
Staude, I. R., Navarro, L. M., & Pereira, H. M. (2020). Range size predicts the risk of local extinction from habitat loss. Global Ecology and Biogeography, 29(1), 16–25. https://doi.org/10.1111/geb.13003
Taylor, L. J., Abbas, A., & Bushman, F. D. (2020). grabseqs: Simple downloading of reads and metadata from multiple next-generation sequencing data repositories. Bioinformatics, btaa167. https://doi.org/10.1093/bioinformatics/btaa167
Tirado, S. B., St Dennis, S., Enders, T. A., & Springer, N. M. (2020). Utilizing top-down hyperspectral imaging for monitoring genotype and growth conditions in maize [Preprint]. Plant Biology. https://doi.org/10.1101/2020.01.21.914069
Wegrzyn, J. L., Falk, T., Grau, E., Buehler, S., Ramnath, R., & Herndon, N. (2020). Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. Evolutionary Applications, 13(1), 228–241. https://doi.org/10.1111/eva.12860
Yasuhara-Bell, J., Arif, M., Busot, G. Y., Mann, R., Rodoni, B., & Stack, J. P. (2020). Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. Microorganisms, 8(3), 366. https://doi.org/10.3390/microorganisms8030366
Zhong, Z.-P., Solonenko, N. E., Li, Y.-F., Gazitúa, M. C., Roux, S., Davis, M. E., Van Etten, J. L., Mosley-Thompson, E., Rich, V. I., Sullivan, M. B., & Thompson, L. G. (2020). Glacier ice archives fifteen-thousand-year-old viruses [Preprint]. Ecology. https://doi.org/10.1101/2020.01.03.894675