2021 Publications

Adak, A., Murray, S. C., Anderson, S. L., Popescu, S. C., Malambo, L., Romay, M. C., & Leon, N. (2021). Unoccupied aerial systems discovered overlooked loci capturing the variation of entire growing period in maize. The Plant Genome, 14(2). https://doi.org/10.1002/tpg2.20102
Alamo, M. A. (2021). Impact of climate change on local tree species richness in Mexico [PhD Thesis]. Queens College.
Alex Mason, G., Cantó-Pastor, A., Brady, S. M., & Provart, N. J. (2021). Bioinformatic Tools in Arabidopsis Research. In J. J. Sanchez-Serrano & J. Salinas (Eds.), Arabidopsis Protocols (Vol. 2200, pp. 25–89). Springer US. https://doi.org/10.1007/978-1-0716-0880-7_2
Amfar, F., Fitri, L., & Suhartono, S. (2021). Molecular identification of a new isolate of actinobacteria ATIS61 and characterization of the protease activities. Biodiversitas Journal of Biological Diversity, 22(3).
Anderson, N., & Wilch, M. (2021). Online Instruction – Bioinformatics Lesson for a COVID-19 Vaccine. The American Biology Teacher, 83(7), 464–471. https://doi.org/10.1525/abt.2021.83.7.464
Anwar, Z. (2021). Investigating the Role of Onecut1 in Establishment of Cell-type-Specific Enhancers during Mouse Motor Neuron Differentiation [PhD Thesis]. University of Toronto (Canada).
Balatskyi, V. V., Vaskivskyi, V. O., Myronova, A., Avramets, D., Nahia, K. A., Macewicz, L. L., Ruban, T. P., Kucherenko, D. Yu., Soldatkin, O. O., Lushnikova, I. V., Skibo, G. G., Winata, C. L., Dobrzyn, P., & Piven, O. O. (2021). Cardiac-specific β-catenin deletion dysregulates energetic metabolism and mitochondrial function in perinatal cardiomyocytes. Mitochondrion, 60, 59–69. https://doi.org/10.1016/j.mito.2021.07.005
Barakhshan, P., & Eigenmann, R. (2021). Exchanging Best Practices and Tools for Supporting Computational and Data-Intensive Research, The Xpert Network. ArXiv:2102.09373 [Cs]. http://arxiv.org/abs/2102.09373
Barbosa, R. de S., Pereira, G. F. M., Ribeiro, S. S., Hage, A. L. F., Costa, G. F., Salomão, R. P., & Schwartz, G. (2021). Key species selection for forest restoration after bauxite mining in the Eastern Amazon. Ecological Engineering, 162, 106190. https://doi.org/10.1016/j.ecoleng.2021.106190
Barker, R., Lombardino, J., Rasmussen, K., & Gilroy, S. (2021). Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. Higher Plants, Algae and Cyanobacteria in Space Environments.
Baseggio, M., Murray, M., Wu, D., Ziegler, G., Kaczmar, N., Chamness, J., Hamilton, J. P., Buell, C. R., Vatamaniuk, O. K., Buckler, E. S., Smith, M. E., Baxter, I., Tracy, W. F., & Gore, M. A. (2021a). Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels [Preprint]. Genetics. https://doi.org/10.1101/2021.02.19.432009
Baseggio, M., Murray, M., Wu, D., Ziegler, G., Kaczmar, N., Chamness, J., Hamilton, J. P., Buell, C. R., Vatamaniuk, O. K., Buckler, E. S., Smith, M. E., Baxter, I., Tracy, W. F., & Gore, M. A. (2021b). Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels. G3 Genes|Genomes|Genetics, 11(8), jkab186. https://doi.org/10.1093/g3journal/jkab186
Bearss, J. J., Padi, S. K., Singh, N., Cardo‐Vila, M., Song, J. H., Mouneimne, G., Fernandes, N., Li, Y., Harter, M. R., Gard, J. M., Cress, A. E., Peti, W., Nelson, A. D., Buchan, J. R., Kraft, A. S., & Okumura, K. (2021). EDC3 phosphorylation regulates growth and invasion through controlling P‐body formation and dynamics. EMBO Reports, 22(4). https://doi.org/10.15252/embr.202050835
Beck, M. A., Liu, C.-Y., Bidinosti, C. P., Henry, C. J., Godee, C. M., & Ajmani, M. (2021a). An extensive lab-and field-image dataset of crops and weeds for computer vision tasks in agriculture.
Beck, M. A., Liu, C.-Y., Bidinosti, C. P., Henry, C. J., Godee, C. M., & Ajmani, M. (2021b). Presenting an extensive lab- and field-image dataset of crops and weeds for computer vision tasks in agriculture. ArXiv:2108.05789 [Cs]. http://arxiv.org/abs/2108.05789
Bedre, R., Avila, C., & Mandadi, K. (2021). HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis. Scientific Reports, 11(1), 18725. https://doi.org/10.1038/s41598-021-98124-3
Bellas, C. M., & Sommaruga, R. (2021). Polinton-like viruses are abundant in aquatic ecosystems. Microbiome, 9(1), 13. https://doi.org/10.1186/s40168-020-00956-0
Bello, A., Mukhtar, F. B., & Muellner-Riehl, A. N. (2021). Diversity and Distribution of Nigerian Legumes (Fabaceae). Phytotaxa, 480(2), 103–124.
Bendaoud, F., Kim, G., Larose, H., Westwood, J., Zermane, N., & Haak, D. (2021). GBS analysis of Orobanche crenata populations in Algeria supports local adaptation and host-specialization [Preprint]. Preprints. https://doi.org/10.22541/au.163245464.46250620/v1
Blais, B. R., Smith, B. E., Placyk, J. S., Casper, G. S., & Spellman, G. M. (2021). Phylogeography of the smooth greensnake, Opheodrys vernalis (Squamata: Colubridae): divergent lineages and variable demographics in a widely distributed yet enigmatic species. Biological Journal of the Linnean Society, blab124. https://doi.org/10.1093/biolinnean/blab124
Boopathi, N. M., & Raveendran, M. (2021). Molecular Markers and DNA Barcoding in Moringa. In N. M. Boopathi, M. Raveendran, & C. Kole (Eds.), The Moringa Genome (pp. 85–100). Springer International Publishing. https://doi.org/10.1007/978-3-030-80956-0_9
Brandies, P. A., & Hogg, C. J. (2021). Ten simple rules for getting started with command-line bioinformatics. PLOS Computational Biology, 17(2), e1008645. https://doi.org/10.1371/journal.pcbi.1008645
Brzozowski, L. J., Hu, H., Campbell, M. T., Broeckling, C. D., Caffe, M., Gutiérrez, L., Smith, K. P., Sorrells, M. E., Gore, M. A., & Jannink, J.-L. (2021). Selection for seed size has uneven effects on specialized metabolite abundance in oat ( Avena sativa L.). G3 Genes|Genomes|Genetics, jkab419. https://doi.org/10.1093/g3journal/jkab419
Butina, T. V., Bukin, Y. S., Petrushin, I. S., Tupikin, A. E., Kabilov, M. R., & Belikov, S. I. (2021). Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics. Microorganisms, 9(4), 760. https://doi.org/10.3390/microorganisms9040760
Campbell, M. T., Hu, H., Yeats, T. H., Caffe-Treml, M., Gutiérrez, L., Smith, K. P., Sorrells, M. E., Gore, M. A., & Jannink, J.-L. (2021). Translating insights from the seed metabolome into improved prediction for lipid-composition traits in oat ( Avena sativa L.). Genetics, 217(3), iyaa043. https://doi.org/10.1093/genetics/iyaa043
Chen, S., Dong, L., Quan, H., Zhou, X., Ma, J., Xia, W., Zhou, H., & Fu, X. (2021). A review of the ethnobotanical value, phytochemistry, pharmacology, toxicity and quality control of Tussilago farfara L. (coltsfoot). Journal of Ethnopharmacology, 267, 113478. https://doi.org/10.1016/j.jep.2020.113478
Chen, Y., Wang, Y., Paez-Espino, D., Polz, M. F., & Zhang, T. (2021). Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants. Nature Communications, 12(1), 5398. https://doi.org/10.1038/s41467-021-25678-1
Cheng, Z., Rowland, S. D., Czarnecki, K., Zumstein, K., Nakayama, H., & Sinha, N. R. (2021). Analysis of Classic Tomato Mutants Reveals Influence of Leaf Vein Density on Fruit BRIX [Preprint]. Plant Biology. https://doi.org/10.1101/2021.03.01.433399
Cherednichenko, O., & Gavrilova, T. (2021). Vascular plant occurrences in grasslands of Central Forest Nature Reserve (Russia): A dataset. Biodiversity Data Journal, 9, e76806. https://doi.org/10.3897/BDJ.9.e76806
Cho, K. T. (2021). Discovering relationships between genotype and phenotype: Machine learning approaches. Iowa State University.
Conti, M., Nimis, P. L., & Martellos, S. (2021). Match Algorithms for Scientific Names in FlorItaly, the Portal to the Flora of Italy. Plants, 10(5), 974. https://doi.org/10.3390/plants10050974
Cornell, C. R., Zhang, Y., Van Nostrand, J. D., Wagle, P., Xiao, X., & Zhou, J. (2021). Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils. MSphere, 6(3). https://doi.org/10.1128/mSphere.01160-20
Cosi, M., Forstedt, J. j., Gonzalez, E., Xu, Z., Peri, S., Tuteja, R., Blumberg, K., Campbell, T., Merchant, N., & Lyons, E. (2021). StarBLAST: A scalable BLAST+ solution for the classroom. Journal of Open Source Education, 4(38), 102. https://doi.org/10.21105/jose.00102
Crispatzu, G., Rehimi, R., Pachano, T., Bleckwehl, T., de la Cruz Molina, S., Xiao, C., Mahabir-Brenner, E., Bazzi, H., & Rada-Iglesias, A. (2021). The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo [Preprint]. Molecular Biology. https://doi.org/10.1101/2021.01.18.427085
Davami, F., Adabi, S., Rezaee, A., & Rahmani, A. M. (2021). Fog-based architecture for scheduling multiple workflows with high availability requirement. Computing. https://doi.org/10.1007/s00607-021-00905-1
de Deus Vidal, J., le Roux, P. C., Johnson, S. D., te Beest, M., & Clark, V. R. (2021). Beyond the Tree-Line: The C3-C4 “Grass-Line” Can Track Global Change in the World’s Grassy Mountain Systems. Frontiers in Ecology and Evolution, 9, 760118. https://doi.org/10.3389/fevo.2021.760118
Deligiannakis, A., Giatrakos, N., Kotidis, Y., Samoladas, V., & Simitsis, A. (2021). Extreme-Scale Interactive Cross-Platform Streaming Analytics–The INFORE Approach. Proceedings of the 2nd Workshop on Search, Exploration, and Analysis in Heterogeneous Datastores, SEA Data 2021, Copenhagen, DenMark, August 20, 7–13. http://pages.cs.aueb.gr/~kotidis/Publications/SEAData2021.pdf
Deshmukh, R., Rana, N., Liu, Y., Zeng, S., Agarwal, G., Sonah, H., Varshney, R., Joshi, T., Patil, G. B., & Nguyen, H. T. (2021). Soybean transporter database: A comprehensive database for identification and exploration of natural variants in soybean transporter genes. Physiologia Plantarum, 171(4), 756–770. https://doi.org/10.1111/ppl.13287
Du, J., Zayed, A. A., Kigerl, K. A., Zane, K., Sullivan, M. B., & Popovich, P. G. (2021). Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities. MSystems, 6(3). https://doi.org/10.1128/mSystems.01356-20
Du, Z., He, Y., Wang, H., Wang, C., & Duan, Y. (2021). Potential geographical distribution and habitat shift of the genus Ammopiptanthus in China under current and future climate change based on the MaxEnt model. Journal of Arid Environments, 184, 104328. https://doi.org/10.1016/j.jaridenv.2020.104328
Ehsani, M. R., Zarei, A., Gupta, H. V., Barnard, K., & Behrangi, A. (2021). Nowcasting-Nets: Deep Neural Network Structures for Precipitation Nowcasting Using IMERG. ArXiv:2108.06868 [Cs]. http://arxiv.org/abs/2108.06868
Encyclopedia of Virology. Volume 1 Volume 1. (2021). ELSEVIER ACADEMIC Press. https://search.ebscohost.com/login.aspx?direct=true&scope=site&db=nlebk&db=nlabk&AN=2431995
Eshraghi, M., Karunadharma, P. P., Blin, J., Shahani, N., Ricci, E. P., Michel, A., Urban, N. T., Galli, N., Sharma, M., Ramírez-Jarquín, U. N., Florescu, K., Hernandez, J., & Subramaniam, S. (2021). Mutant Huntingtin stalls ribosomes and represses protein synthesis in a cellular model of Huntington disease. Nature Communications, 12(1), 1461. https://doi.org/10.1038/s41467-021-21637-y
Ferdausi, A., Chang, X., & Jones, M. (2021). Transcriptomic analysis for differential expression of genes involved in secondary metabolite production in Narcissus pseudonarcissus field derived bulb and in vitro callus. Industrial Crops and Products, 168, 113615. https://doi.org/10.1016/j.indcrop.2021.113615
Fesenko, I., Shabalina, S. A., Mamaeva, A., Knyazev, A., Glushkevich, A., Lyapina, I., Ziganshin, R., Kovalchuk, S., Kharlampieva, D., Lazarev, V., Taliansky, M., & Koonin, E. V. (2021). A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants. Nucleic Acids Research, 49(18), 10328–10346. https://doi.org/10.1093/nar/gkab816
Firrao, G., Scortichini, M., & Pagliari, L. (2021). Orthology-Based Estimate of the Contribution of Horizontal Gene Transfer from Distantly Related Bacteria to the Intraspecific Diversity and Differentiation of Xylella fastidiosa. Pathogens, 10(1), 46. https://doi.org/10.3390/pathogens10010046
Freewoman, J. M., Snape, R., & Cui, F. (2021). Temporal gene regulation by p53 is associated with the rotational setting of its binding sites in nucleosomes. Cell Cycle, 20(8), 792–807. https://doi.org/10.1080/15384101.2021.1904554
Fuchsman, C. A., Carlson, M. C. G., Garcia Prieto, D., Hays, M. D., & Rocap, G. (2021). Cyanophage host‐derived genes reflect contrasting selective pressures with depth in the oxic and anoxic water column of the Eastern Tropical North Pacific. Environmental Microbiology, 23(6), 2782–2800. https://doi.org/10.1111/1462-2920.15219
Gazitúa, M. C., Vik, D. R., Roux, S., Gregory, A. C., Bolduc, B., Widner, B., Mulholland, M. R., Hallam, S. J., Ulloa, O., & Sullivan, M. B. (2021). Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. The ISME Journal, 15(4), 981–998. https://doi.org/10.1038/s41396-020-00825-6
George, S., Agathanggelou, A., Privett, G., Halpin, P., Feline, W., Ash, A., Chote, P., Scott, L., Skuljan, J., Alvino, J., & others. (2021). Phantom Echoes 2: A Five-Eyes SDA Experiment on GEO Proximity Operations. Proc 22nd AMOS Conf.
Geyer, P., Singh, M. M., & Chen, X. (2021). Explainable AI for engineering design: A unified approach of systems engineering and component-based deep learning. ArXiv Preprint ArXiv:2108.13836.
Gillan, J. K., Ponce-Campos, G. E., Swetnam, T. L., Gorlier, A., Heilman, P., & McClaran, M. P. (2021). Innovations to expand drone data collection and analysis for rangeland monitoring [Preprint]. Ecology. https://doi.org/10.1101/2021.02.05.430004
Gu, C., Liang, Y., Li, J., Shao, H., Jiang, Y., Zhou, X., Gao, C., Li, X., Zhang, W., Guo, C., He, H., Wang, H., Sung, Y. Y., Mok, W. J., Wong, L. L., Suttle, C. A., McMinn, A., Tian, J., & Wang, M. (2021). Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption. IScience, 24(12), 103439. https://doi.org/10.1016/j.isci.2021.103439
Gudukbay, G., Gunasekaran, J. R., Feng, Y., Kandemir, M. T., Nekrutenko, A., Das, C. R., Medvedev, P., Gruning, B., Coraor, N., Roach, N., & Afgan, E. (2021). GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping. 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 194–203. https://doi.org/10.1109/IPDPSW52791.2021.00037
Guo, J., Bolduc, B., Zayed, A. A., Varsani, A., Dominguez-Huerta, G., Delmont, T. O., Pratama, A. A., Gazitúa, M. C., Vik, D., Sullivan, M. B., & Roux, S. (2021). VirSorter2: A multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome, 9(1), 37. https://doi.org/10.1186/s40168-020-00990-y
Gustafsson, L., Granath, G., Nohrstedt, H., Leverkus, A. B., & Johansson, V. (2021). Burn severity and soil chemistry are weak drivers of early vegetation succession following a boreal mega‐fire in a production forest landscape. Journal of Vegetation Science, 32(1). https://doi.org/10.1111/jvs.12966
Gustafsson, L., Johansson, V., Leverkus, A. B., Strengbom, J., Wikberg, S., & Granath, G. (2021). Disturbance interval modulates the starting point for vegetation succession. Wiley Online Library. https://doi.org/10.1002/ecy.3439
Hamad, Z. J., Zeebaree, S. R., & others. (2021). Recourses utilization in a distributed system: A review. International Journal of Science and Business, 5(2), 42–53.
Hancock, D. Y., Fischer, J., Lowe, J. M., Snapp-Childs, W., Pierce, M., Marru, S., Coulter, J. E., Vaughn, M., Beck, B., Merchant, N., Skidmore, E., & Jacobs, G. (2021). Jetstream2: Accelerating cloud computing via Jetstream. Practice and Experience in Advanced Research Computing, 1–8. https://doi.org/10.1145/3437359.3465565
Happel, A.-U., Balle, C., Maust, B. S., Konstantinus, I. N., Gill, K., Bekker, L.-G., Froissart, R., Passmore, J.-A., Karaoz, U., Varsani, A., & Jaspan, H. (2021). Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. Viruses, 13(12), 2341. https://doi.org/10.3390/v13122341
Harrison, K., Mendoza-Herrera, A., Levy, J. G., & Tamborindeguy, C. (2021). Lasting consequences of psyllid (Bactericera cockerelli L.) infestation on tomato defense, gene expression, and growth. BMC Plant Biology, 21(1), 114. https://doi.org/10.1186/s12870-021-02876-z
Hearnshaw, J., Brandizi, M., Singh, A., Rawlings, C., & Hassani-Pak, K. (2021). Organizing knowledge to enable faster data interpretation in COVID-19 research. F1000Research, 10, 703. https://doi.org/10.12688/f1000research.54071.1
Henningsen, E. C., Omidvar, V., Coletta, R. D., Michno, J.-M., Gilbert, E., Li, F., Miller, M. E., Myers, C. L., Gordon, S. P., Vogel, J. P., Steffenson, B. J., Kianian, S. F., Hirsch, C. D., & Figueroa, M. (2021). Identification of candidate susceptibility genes to Puccinia graminis f. Sp. Tritici in wheat [Preprint]. Plant Biology. https://doi.org/10.1101/2021.01.23.427871
Holmfeldt, K., Nilsson, E., Simone, D., Lopez-Fernandez, M., Wu, X., de Bruijn, I., Lundin, D., Andersson, A. F., Bertilsson, S., & Dopson, M. (2021). The Fennoscandian Shield deep terrestrial virosphere suggests slow motion ‘boom and burst’ cycles. Communications Biology, 4(1), 307. https://doi.org/10.1038/s42003-021-01810-1
Hu, Y., Colantonio, V., Müller, B. S. F., Leach, K. A., Nanni, A., Finegan, C., Wang, B., Baseggio, M., Newton, C. J., Juhl, E. M., Hislop, L., Gonzalez, J. M., Rios, E. F., Hannah, L. C., Swarts, K., Gore, M. A., Hennen-Bierwagen, T. A., Myers, A. M., Settles, A. M., … Resende, M. F. R. (2021). Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn. Nature Communications, 12(1), 1227. https://doi.org/10.1038/s41467-021-21380-4
Hua, X., Berkowitz, N. D., Willmann, M. R., Yu, X., Lyons, E., & Gregory, B. D. (2021). Global Analysis of RNA-Dependent RNA Polymerase-Dependent Small RNAs Reveals New Substrates and Functions for These Proteins and SGS3 in Arabidopsis. Non-Coding RNA, 7(2), 28. https://doi.org/10.3390/ncrna7020028
Janssen, M., Falcke, H., Kadler, M., Ros, E., Wielgus, M., Akiyama, K., Baloković, M., Blackburn, L., Bouman, K. L., Chael, A., Chan, C., Chatterjee, K., Davelaar, J., Edwards, P. G., Fromm, C. M., Gómez, J. L., Goddi, C., Issaoun, S., Johnson, M. D., … Zhao, S.-S. (2021). Event Horizon Telescope observations of the jet launching and collimation in Centaurus A. Nature Astronomy, 5(10), 1017–1028. https://doi.org/10.1038/s41550-021-01417-w
Jensen, S. E. (2021). Predicting Protein Temperature Adaptation from Prokaryotes to Plants [PhD Thesis]. In ProQuest Dissertations and Theses. https://ezproxy.library.arizona.edu/login?url=https://www.proquest.com/dissertations-theses/predicting-protein-temperature-adaptation/docview/2581488029/se-2?accountid=8360
Joyce, E. M. (2021). Evolution of the northern Australian flora: Role of the Sunda-Sahul Floristic Exchange [PhD Thesis]. James Cook University.
Juneau, S., Olsen, K., Nikutta, R., Jacques, A., & Bailey, S. (2021). Jupyter-Enabled Astrophysical Analysis Using Data-Proximate Computing Platforms. Computing in Science & Engineering, 23(2), 15–25. https://doi.org/10.1109/MCSE.2021.3057097
Kadow, C., Illing, S., Lucio-Eceiza, E. E., Bergemann, M., Ramadoss, M., Sommer, P. S., Kunst, O., Schartner, T., Pankatz, K., Grieger, J., Schuster, M., Richling, A., Thiemann, H., Kirchner, I., Rust, H. W., Ludwig, T., Cubasch, U., & Ulbrich, U. (2021). Introduction to Freva – A Free Evaluation System Framework for Earth System Modeling. Journal of Open Research Software, 9, 13. https://doi.org/10.5334/jors.253
Katiyar, N., Ramadoss, N., Gupta, D., Pakala, S. B., Cooper, K., & Basu, C. (2021). Transcriptomic profiling of Paulownia elongata in response to heat stress. Plant Gene, 28, 100330. https://doi.org/10.1016/j.plgene.2021.100330
Kavas, M., Yıldırım, K., Seçgin, Z., Abdulla, M. F., & Gökdemir, G. (2021). Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris. Physiology and Molecular Biology of Plants, 27(9), 1885–1902. https://doi.org/10.1007/s12298-021-01052-9
Ketron, R., Leonard, J., Roachell, B., Patel, R., White, R., Caino-Lores, S., Tan, N., Miles, P., Vahi, K., Deelman, E., Brown, D., & Taufer, M. (2021). A Case Study in Scientific Reproducibility from the Event Horizon Telescope (EHT). 2021 IEEE 17th International Conference on EScience (EScience), 249–250. https://doi.org/10.1109/eScience51609.2021.00045
Kim, Y. (2021). Imagery Acquisition Methods for Root Analysis in Crops under Field Conditions. The Korean Journal of Crop Science, 452–458.
Kocherlakota, P., Rezzolla, L., Falcke, H., Fromm, C. M., Kramer, M., Mizuno, Y., Nathanail, A., Olivares, H., Younsi, Z., Akiyama, K., Alberdi, A., Alef, W., Algaba, J. C., Anantua, R., Asada, K., Azulay, R., Baczko, A.-K., Ball, D., Baloković, M., … EHT Collaboration. (2021). Constraints on black-hole charges with the 2017 EHT observations of M87*. Physical Review D, 103(10), 104047. https://doi.org/10.1103/PhysRevD.103.104047
Komissarov, S., & Porth, O. (2021). Numerical simulations of jets. New Astronomy Reviews, 92, 101610. https://doi.org/10.1016/j.newar.2021.101610
Kranawetter, C., Zeng, S., Joshi, T., & Sumner, L. W. (2021). A Medicago truncatula Metabolite Atlas Enables the Visualization of Differential Accumulation of Metabolites in Root Tissues. Metabolites, 11(4), 238. https://doi.org/10.3390/metabo11040238
Kumar, A., Kumar, R., Shukla, P., & Patel, H. K. (2021). Omics Technologies for Sustainable Agriculture and Global Food Security (Vol II). Springer. https://link.springer.com/content/pdf/10.1007/978-981-16-2956-3.pdf
Kusmec, A. M. (2021). Phenotypic Plasticity and Breeding for Future Climates: Case Studies in Zea mays [PhD Thesis]. In ProQuest Dissertations and Theses. http://ezproxy.library.arizona.edu/login?url=https://www.proquest.com/dissertations-theses/phenotypic-plasticity-breeding-future-climates/docview/2576925279/se-2?accountid=8360
Lama, T., Minyety, R., Navarro, M., & Ward, N. (2021). Biodiversity of Plants in Highly Polluted Areas [Poster]. https://dnabarcoding101.org/files/uploads/0000/ubp/joralemon-2997-poster-NCJNT.pdf
Lee, J.-Y., Song, J., LeBlanc, L., Davis, I., Kim, J., & Beck, S. (2021). Conserved dual-mode gene regulation programs in higher eukaryotes. Nucleic Acids Research, 49(5), 2583–2597. https://doi.org/10.1093/nar/gkab108
Lee, Y.-J., Dai, N., Müller, S. I., Guan, C., Parker, M. J., Fraser, M. E., Walsh, S. E., Sridar, J., Mulholland, A., Nayak, K., Sun, Z., Lin, Y.-C., Comb, D. G., Marks, K., Gonzalez, R., Dowling, D. P., Bandarian, V., Saleh, L., Corrêa, I. R., & Weigele, P. R. (2021). Pathways of thymidine hypermodification. Nucleic Acids Research, gkab781. https://doi.org/10.1093/nar/gkab781
Li, Y., Li, T., Wang, Z., Wang, S., Qin, X., & Liao, Y. (2021). Plastic film mulch changes the microbial community in maize root-associated compartments. Plant and Soil. https://doi.org/10.1007/s11104-021-05060-2
Lichwa, E. M. (2021). Ecological and social drivers of Mexican gray wolf (Canis lupus baileyi) home range patterns across spatiotemporal scales [Masters Thesis]. Humboldt State University.
Lin, J. Y.-Y., Pesce, D. W., Wong, G. N., Arasanipalai, A. U., Prather, B. S., & Gammie, C. F. (2021). VLBInet: Radio Interferometry Data Classification for EHT with Neural Networks. ArXiv:2110.07185 [Astro-Ph]. http://arxiv.org/abs/2110.07185
Liu, Z.-F., Ma, H., Ci, X.-Q., Li, L., Song, Y., Liu, B., Li, H.-W., Wang, S.-L., Qu, X.-J., Hu, J.-L., Zhang, X.-Y., Conran, J. G., Twyford, A. D., Yang, J.-B., Hollingsworth, P. M., & Li, J. (2021). Can plastid genome sequencing be used for species identification in Lauraceae? Botanical Journal of the Linnean Society, 197(1), 1–14. https://doi.org/10.1093/botlinnean/boab018
Lo, C.-C., Shakya, M., Davenport, K., Flynn, M., Gutiérrez, A. M. y, Hu, B., Li, P.-E., Jackson, E. P., Xu, Y., & Chain, P. S. G. (2021). EDGE COVID-19: A Web Platform to generate submission-ready genomes for SARS-CoV-2 sequencing efforts. ArXiv:2006.08058 [q-Bio]. http://arxiv.org/abs/2006.08058
Lozano, R., Gazave, E., dos Santos, J. P. R., Stetter, M. G., Valluru, R., Bandillo, N., Fernandes, S. B., Brown, P. J., Shakoor, N., Mockler, T. C., Cooper, E. A., Taylor Perkins, M., Buckler, E. S., Ross-Ibarra, J., & Gore, M. A. (2021). Comparative evolutionary genetics of deleterious load in sorghum and maize. Nature Plants, 7(1), 17–24. https://doi.org/10.1038/s41477-020-00834-5
Macías-Duarte, A., & Conway, C. J. (2021). Geographic variation in dispersal of western burrowing owl ( Athene cunicularia hypugaea ) populations across North America. Behavioral Ecology, arab100. https://doi.org/10.1093/beheco/arab100
Malhotra, S., Kaur, R., Jossan, A., Bhullar, K., & Handa, A. (2021). Adhesion to Enamel and Dentin: A Review. Science Progress and Research, 1(4), 368–376. https://doi.org/10.52152/spr/2021.156
Martínez‐Meyer, E., González‐Bernal, A., Velasco, J. A., Swetnam, T. L., González‐Saucedo, Z. Y., Servín, J., López‐González, C. A., Oakleaf, J. K., Liley, S., & Heffelfinger, J. R. (2021). Rangewide habitat suitability analysis for the Mexican wolf ( Canis lupus baileyi ) to identify recovery areas in its historical distribution. Diversity and Distributions, 27(4), 642–654. https://doi.org/10.1111/ddi.13222
Martinson, J., Bencic, D. C., Toth, G. P., Kostich, M. S., Flick, R. W., See, M. J., Lattier, D., Biales, A. D., & Huang, W. (2021). De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure [Preprint]. Genomics. https://doi.org/10.1101/2021.02.24.432777
Maximova, I., Vasiliev, E., Getmanskaya, A., Kior, D., Sukhov, V., Vodeneev, V., & Turlapov, V. (2021). Study of XAI-capabilities for early diagnosis of plant drought. 2021 International Joint Conference on Neural Networks (IJCNN), 1–8. https://doi.org/10.1109/IJCNN52387.2021.9534105
McLean, J., Cleveland, S. B., Dodge, M., Lucas, M. P., Longman, R. J., Giambelluca, T. W., & Jacobs, G. A. (2021). Building a portal for climate data—Mapping automation, visualization, and dissemination. Concurrency and Computation: Practice and Experience. https://doi.org/10.1002/cpe.6727
Melendrez, M. C., Goodner, B. W., Kvaal, C., Brown, C. T., & Shaw, S. (2021). Curriculum Applications In Microbiology: Bioinformatics In The Classroom. Frontiers Media SA. https://books.google.com/books?id=orFBEAAAQBAJ
Metzger, S., Durden, D., Paleri, S., Sühring, M., Butterworth, B. J., Florian, C., Mauder, M., Plummer, D. M., Wanner, L., Xu, K., & Desai, A. R. (2021). Novel approach to observing system simulation experiments improves information gain of surface–atmosphere field measurements. Atmospheric Measurement Techniques, 14(11), 6929–6954. https://doi.org/10.5194/amt-14-6929-2021
Mickelson-Young, L., Wear, E. E., Song, J., Zynda, G. J., & Thompson, W. F. (2021). A protocol for genome-wide analysis of DNA replication timing in intact root tips.
Moeinizade, S., Pham, H., Han, Y., Dobbels, A., & Hu, G. (2021). An Applied Deep Learning Approach for Estimating Soybean Relative Maturity from UAV Imagery to Aid Plant Breeding Decisions. ArXiv:2108.00952 [Cs, Eess]. http://arxiv.org/abs/2108.00952
Moore, R. M., Harrison, A. O., Nasko, D. J., Chopyk, J., Cebeci, M., Ferrell, B. D., Polson, S. W., & Wommack, K. E. (2021). PASV: Automatic protein partitioning and validation using conserved residues [Preprint]. Bioinformatics. https://doi.org/10.1101/2021.01.20.427478
Morales, N., Gore, M. A., Mueller, L. A., & Robbins, K. R. (2021). Spatio-temporal modeling of high-throughput multi-spectral images improves agronomic trait genomic prediction in hybrid maize.
Moyer, T. B., Allen, J. L., Shaw, L. N., & Hicks, L. M. (2021). Multiple Classes of Antimicrobial Peptides in Amaranthus tricolor Revealed by Prediction, Proteomics, and Mass Spectrometric Characterization. Journal of Natural Products, 84(2), 444–452. https://doi.org/10.1021/acs.jnatprod.0c01203
Nagy, R. C., Balch, J. K., Bissell, E. K., Cattau, M. E., Glenn, N. F., Halpern, B. S., Ilangakoon, N., Johnson, B., Joseph, M. B., Marconi, S., & others. (2021). Harnessing the NEON data revolution to advance open environmental science with a diverse and data-capable community. Ecosphere, 12(12), e03833.
Nakayama, H., Rowland, S. D., Cheng, Z., Zumstein, K., Kang, J., Kondo, Y., & Sinha, N. R. (2021). Leaf form diversification in an ornamental heirloom tomato results from alterations in two different HOMEOBOX genes. Current Biology, S0960982221011271. https://doi.org/10.1016/j.cub.2021.08.023
Natarajan, P., Tang, K. S., Khochfar, S., Nord, B., Sigurdsson, S., Tricot, J., Cappelluti, N., George, D., & Hidary, J. (2021). QuasarNet: A new research platform for the data-driven investigation of black holes. ArXiv:2103.13932 [Astro-Ph]. http://arxiv.org/abs/2103.13932
Neves, D. M., Kerkhoff, A. J., Echeverría-Londoño, S., Merow, C., Morueta-Holme, N., Peet, R. K., Sandel, B., Svenning, J.-C., Wiser, S. K., & Enquist, B. J. (2021). The adaptive challenge of extreme conditions shapes evolutionary diversity of plant assemblages at continental scales. Proceedings of the National Academy of Sciences, 118(37), e2021132118. https://doi.org/10.1073/pnas.2021132118
Ostezan, A., McDonald, S. C., Tran, D. T., Souza, R. S. E., & Li, Z. (2021). Target region sequencing and applications in plants. Journal of Crop Science and Biotechnology, 24(1), 13–26. https://doi.org/10.1007/s12892-020-00056-3
Pandey, A., Calyam, P., Debroy, S., Wang, S., & Alarcon, M. L. (2021). VECTrust: Trusted resource allocation in volunteer edge-cloud computing workflows. Proceedings of the 14th IEEE/ACM International Conference on Utility and Cloud Computing, 1–10. https://doi.org/10.1145/3468737.3494099
Pappas, N., Roux, S., Hölzer, M., Lamkiewicz, K., Mock, F., Marz, M., & Dutilh, B. E. (2021). Virus Bioinformatics. In Encyclopedia of Virology (pp. 124–132). Elsevier. https://doi.org/10.1016/B978-0-12-814515-9.00034-5
Park, I. W., Ramirez‐Parada, T., & Mazer, S. J. (2021). Advancing frost dates have reduced frost risk among most North American angiosperms since 1980. Global Change Biology, 27(1), 165–176. https://doi.org/10.1111/gcb.15380
Patel, N. P., Jain, A., & Haldar, S. (2021). Advancement in tools and techniques to divulge vital biological molecules from microbes associated with corals. In Microbial and Natural Macromolecules (pp. 455–493). Elsevier. https://doi.org/10.1016/B978-0-12-820084-1.00019-3
Peterson, A. L. (2021). Evolution and Sexual Dimorphism in Meiotic Recombination Rates in Murids. The University of Wisconsin-Madison.
Peterson, A. L., & Payseur, B. A. (2021a). Sex-specific variation in the genome-wide recombination rate. Genetics, 217(1), iyaa019. https://doi.org/10.1093/genetics/iyaa019
Peterson, A. L., & Payseur, B. A. (2021b). Higher Intercellular Variation in Genome-Wide Recombination Rate in Female Mice. Cytogenetic and Genome Research, 1–7. https://doi.org/10.1159/000516998
Pinto, R. T., Cardoso, T. B., Paiva, L. V., & Benedito, V. A. (2021). Genomic and transcriptomic inventory of membrane transporters in coffee: Exploring molecular mechanisms of metabolite accumulation. Plant Science, 312, 111018. https://doi.org/10.1016/j.plantsci.2021.111018
Piombo, E., Rosati, M., Sanna, M., Mezzalama, M., Gullino, M. L., & Spadaro, D. (2021). Sequencing of non-virulent strains of Fusarium fujikuroi reveals genes putatively involved in bakanae disease of rice. Fungal Genetics and Biology, 156, 103622. https://doi.org/10.1016/j.fgb.2021.103622
Ponsero, A. J., Bomhoff, M., Blumberg, K., Youens-Clark, K., Herz, N. M., Wood-Charlson, E. M., Delong, E. F., & Hurwitz, B. L. (2021). Planet Microbe: A platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data. Nucleic Acids Research, 49(D1), D792–D802. https://doi.org/10.1093/nar/gkaa637
Qin, C., Bartelme, R., Chung, Y. A., Fairbanks, D., Lin, Y., Liptzin, D., Muscarella, C., Naithani, K., Peay, K., Pellitier, P., St. Rose, A., Stanish, L., Werbin, Z., & Zhu, K. (2021). From DNA sequences to microbial ecology: Wrangling NEON soil microbe data with the neonMicrobe R package. Ecosphere, 12(11). https://doi.org/10.1002/ecs2.3842
Ramos‐Barbero, M. D., Viver, T., Zabaleta, A., Senel, E., Gomariz, M., Antigüedad, I., Santos, F., Martínez‐García, M., Rosselló‐Móra, R., & Antón, J. (2021). Ancient saltern metagenomics: Tracking changes in microbes and their viruses from the underground to the surface. Environmental Microbiology, 23(7), 3477–3498. https://doi.org/10.1111/1462-2920.15630
Reiter, T., Brooks†, P. T., Irber†, L., Joslin†, S. E. K., Reid†, C. M., Scott†, C., Brown, C. T., & Pierce-Ward, N. T. (2021). Streamlining data-intensive biology with workflow systems. GigaScience, 10(1), giaa140. https://doi.org/10.1093/gigascience/giaa140
Rengifo Faiffer, M. C. (2021). From Community to Transcriptome: Responses of 0RW1S34RfeSDcfkexd09rT2Syntrichia caninervis1RW1S34RfeSDcfkexd09rT2 and Biocrusts to Climate Change [PhD Thesis]. In ProQuest Dissertations and Theses. http://ezproxy.library.arizona.edu/login?url=https://www.proquest.com/dissertations-theses/community-transcriptome-responses-em-syntrichia/docview/2572554339/se-2?accountid=8360
Rodríguez-Ramos, J. A., Borton, M. A., McGivern, B. B., Smith, G. J., Solden, L. M., Shaffer, M., Daly, R. A., Purvine, S. O., Nicora, C. D., Eder, E. K., Lipton, M., Hoyt, D. W., Stegen, J. C., & Wrighton, K. C. (2021). Microbial Genome-Resolved Metaproteomic Analyses Frame Intertwined Carbon and Nitrogen Cycles in River Hyporheic Sediments [Preprint]. In Review. https://doi.org/10.21203/rs.3.rs-746574/v1
Rogers, A. R., Dunne, J. C., Romay, C., Bohn, M., Buckler, E. S., Ciampitti, I. A., Edwards, J., Ertl, D., Flint-Garcia, S., Gore, M. A., Graham, C., Hirsch, C. N., Hood, E., Hooker, D. C., Knoll, J., Lee, E. C., Lorenz, A., Lynch, J. P., McKay, J., … Holland, J. B. (2021). The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment. G3 Genes|Genomes|Genetics, 11(2), jkaa050. https://doi.org/10.1093/g3journal/jkaa050
Rubio-Portillo, E., Martin-Cuadrado, A.-B., Ramos-Esplá, A. Á., & Antón, J. (2021). Metagenomics Unveils Posidonia oceanica “Banquettes” as a Potential Source of Novel Bioactive Compounds and Carbohydrate Active Enzymes (CAZymes). MSystems. https://doi.org/10.1128/mSystems.00866-21
Runck, B. C., Joglekar, A., Silverstein, K., Chan‐Kang, C., Pardey, P., & Wilgenbusch, J. C. (2021). Digital agriculture platforms: Driving data‐enabled agricultural innovation in a world fraught with privacy and security concerns. Agronomy Journal, agj2.20873. https://doi.org/10.1002/agj2.20873
Sahneh, F., Balk, M. A., Kisley, M., Chan, C., Fox, M., Nord, B., Lyons, E., Swetnam, T., Huppenkothen, D., Sutherland, W., Walls, R. L., Quinn, D. P., Tarin, T., LeBauer, D., Ribes, D., Birnie, D. P., Lushbough, C., Carr, E., Nearing, G., … Merchant, N. (2021). Ten simple rules to cultivate transdisciplinary collaboration in data science. PLOS Computational Biology, 17(5), e1008879. https://doi.org/10.1371/journal.pcbi.1008879
Salgado-Salazar, C., Skaltsas, D. N., Phipps, T., & Castlebury, L. A. (2021). Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea. G3 Genes|Genomes|Genetics, 11(4), jkab071. https://doi.org/10.1093/g3journal/jkab071
Sanchez-Serrano, J. J., & Salinas, J. (Eds.). (2021). Arabidopsis protocols (Fourth Edition). Humana Press. https://doi.org/10.1007/978-1-62703-580-4
Satapathy, K. (2021). The Variability of the Black-Hole Image in M87 at the Dynamical Time Scale (2111.01317v1). arXiv.
Satjarak, A., Graham, L. E., Piotrowski, M. J., Trest, M. T., Wilcox, L. W., Cook, M. E., Knack, J. J., & Arancibia‐Avila, P. (2021). Shotgun metagenomics and microscopy indicate diverse cyanophytes, other bacteria, and microeukaryotes in the epimicrobiota of a northern Chilean wetland Nostoc (Cyanobacteria). Journal of Phycology, 57(1), 39–50. https://doi.org/10.1111/jpy.13084
Satjarak, A., Piotrowski, M. J., Graham, L. E., Trest, M. T., Wilcox, L. W., Knack, J. J., Cook, M. E., & Arancibia-Avila, P. (2021). Microscopic and Metagenomic Evidence for Eukaryotic Microorganisms Associated with Atacama Desert Populations of Giant Equisetum. American Fern Journal, 111(2). https://doi.org/10.1640/0002-8444-111.2.86
Sawyer, S., Snyder, J., Willis, M., Sharma, S., Østerlund, C., & Allen, E. (Eds.). (2021). 2. Stabilizing Digital Infrastructures in Distributed Social Science Collaboration. In Fields of practice and applied solutions within distributed team cognition (First edition). CRC Press, Taylor & Francis Group. https://books.google.com/books?hl=en&lr=&id=5EX1DwAAQBAJ&oi=fnd&pg=PA21&ots=_iTask9Ypv&sig=dQTJ52SrYErrlf5yDOvEACjyYU0#v=onepage&q&f=false
Schmitz, A. M., Pian, B., Medin, S., Reid, M. C., Wu, M., Gazel, E., & Barstow, B. (2021). Generation of a Gluconobacter oxydans knockout collection for improved extraction of rare earth elements. Nature Communications, 12(1), 6693. https://doi.org/10.1038/s41467-021-27047-4
Senn, S., Pangell, K., & Bowerman, A. L. (2021). Microbes in the Datura Rootzone Contribute to an Antioxidant Support System of Flavonoids and Other Aromatic Compounds [Preprint]. BIOLOGY. https://doi.org/10.20944/preprints202111.0076.v1
Shan, Q., Tian, G., Wang, J., Hui, H., Shou, Q., Fu, H., Hao, M., Wang, K., Wu, X., Cao, G., Chen, G., & Qin, L. (2021). Change in the active component of processed Tetradium ruticarpum extracts leads to improvement in efficacy and toxicity attenuation. Journal of Ethnopharmacology, 264, 113292. https://doi.org/10.1016/j.jep.2020.113292
Shimizu, K. K., Copetti, D., Okada, M., Wicker, T., Tameshige, T., Hatakeyama, M., Shimizu-Inatsugi, R., Aquino, C., Nishimura, K., Kobayashi, F., Murata, K., Kuo, T., Delorean, E., Poland, J., Haberer, G., Spannagl, M., Mayer, K. F. X., Gutierrez-Gonzalez, J., Muehlbauer, G. J., … Handa, H. (2021). De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium -Resistant Genes in East Asian Genotypes. Plant and Cell Physiology, 62(1), 8–27. https://doi.org/10.1093/pcp/pcaa152
Sorgini, C. A., Roberts, L. M., Sullivan, M., Cousins, A. B., Baxter, I., & Studer, A. J. (2021). The genetic architecture of leaf stable carbon isotope composition in Zea mays and the effect of transpiration efficiency on leaf elemental accumulation. G3 Genes|Genomes|Genetics, 11(9), jkab222. https://doi.org/10.1093/g3journal/jkab222
Stanschewski, C. S., Rey, E., Fiene, G., Craine, E. B., Wellman, G., Melino, V. J., S. R. Patiranage, D., Johansen, K., Schmöckel, S. M., Bertero, D., Oakey, H., Colque-Little, C., Afzal, I., Raubach, S., Miller, N., Streich, J., Amby, D. B., Emrani, N., Warmington, M., … on behalf of the Quinoa Phenotyping Consortium. (2021). Quinoa Phenotyping Methodologies: An International Consensus. Plants, 10(9), 1759. https://doi.org/10.3390/plants10091759
Stubbs, J., Cardone, R., Cleveland, S., Jacobs, G., Packard, M., Jamthe, A., Padhy, S., Black, S., Terry, S., Looney, J., Meiring, J., & Dahan, M. (2021). Sustainability in the Tapis Framework. Hawaii International Conference on System Sciences. https://doi.org/10.24251/HICSS.2021.874
Stubbs, J., Cardone, R., Packard, M., Jamthe, A., Padhy, S., Terry, S., Looney, J., Meiring, J., Black, S., Dahan, M., Cleveland, S., & Jacobs, G. (2021). Tapis: An API Platform for Reproducible, Distributed Computational Research. In K. Arai (Ed.), Advances in Information and Communication (Vol. 1363, pp. 878–900). Springer International Publishing. https://doi.org/10.1007/978-3-030-73100-7_61
Subramaniam, S., & Shahani, N. (2021). Ribosome Profiling Reveals a Dichotomy Between Ribosome Occupancy of Nuclear-Encoded and Mitochondrial-Encoded OXPHOS mRNA Transcripts in a Striatal Cell Model of Huntington Disease [Preprint]. Neuroscience. https://doi.org/10.1101/2021.01.30.428960
Swartz, L. G., Liu, S., Dahlquist, D., Walter, E. S., Mcinturf, S., Bucksch, A., & Mendoza-Cozatl, D. G. (2021). Tracking dynamic changes of leaves in response to nutrient availability using an open-source cloud-based phenotyping system (OPEN Leaf) [Preprint]. Agricultural, Veterinary and Food Sciences. https://doi.org/10.1002/essoar.10508290.1
Swetnam, T. L., Yool, S. R., Roy, S., & Falk, D. A. (2021). On the Use of Standardized Multi-Temporal Indices for Monitoring Disturbance and Ecosystem Moisture Stress across Multiple Earth Observation Systems in the Google Earth Engine. Remote Sensing, 13(8), 1448. https://doi.org/10.3390/rs13081448
Tan, P., Du, X., Shang, Y., Zhu, K., Joshi, S., Kaur, K., Khare, T., & Kumar, V. (2021). Ion transporters and their exploration for conferring abiotic stress tolerance in plants. Plant Growth Regulation, 96(1), 1–23. https://doi.org/10.1007/s10725-021-00762-0
Taş, N., de Jong, A. E., Li, Y., Trubl, G., Xue, Y., & Dove, N. C. (2021). Metagenomic tools in microbial ecology research. Current Opinion in Biotechnology, 67, 184–191. https://doi.org/10.1016/j.copbio.2021.01.019
Tello-Ruiz, M. K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B., Chougule, K., Garg, P., Elser, J., Kumari, S., Kumar, V., Contreras-Moreira, B., Naamati, G., George, N., Cook, J., Bolser, D., D’Eustachio, P., … Ware, D. (2021). Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research, 49(D1), D1452–D1463. https://doi.org/10.1093/nar/gkaa979
Thessen, A. E., Bogdan, P., Patterson, D. J., Casey, T. M., Hinojo-Hinojo, C., de Lange, O., & Haendel, M. A. (2021). From Reductionism to Reintegration: Solving society’s most pressing problems requires building bridges between data types across the life sciences. PLOS Biology, 19(3), e3001129. https://doi.org/10.1371/journal.pbio.3001129
Tisza, M. J., & Buck, C. B. (2021). A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. Proceedings of the National Academy of Sciences, 118(23), e2023202118. https://doi.org/10.1073/pnas.2023202118
Tserej, O., & Feeley, K. J. (2021). Variation in leaf temperatures of tropical and subtropical trees are related to leaf thermoregulatory traits and not geographic distributions. Biotropica, 53(3), 868–878. https://doi.org/10.1111/btp.12919
Valliyodan, B., Brown, A. V., Wang, J., Patil, G., Liu, Y., Otyama, P. I., Nelson, R. T., Vuong, T., Song, Q., Musket, T. A., Wagner, R., Marri, P., Reddy, S., Sessions, A., Wu, X., Grant, D., Bayer, P. E., Roorkiwal, M., Varshney, R. K., … Nguyen, H. T. (2021). Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data, 8(1), 50. https://doi.org/10.1038/s41597-021-00834-w
Varshney, R. K., Roorkiwal, M., Sun, S., Bajaj, P., Chitikineni, A., Thudi, M., Singh, N. P., Du, X., Upadhyaya, H. D., Khan, A. W., Wang, Y., Garg, V., Fan, G., Cowling, W. A., Crossa, J., Gentzbittel, L., Voss-Fels, K. P., Valluri, V. K., Sinha, P., … Liu, X. (2021). A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature, 599(7886), 622–627. https://doi.org/10.1038/s41586-021-04066-1
Vuorinen, K. E. M., Austrheim, G., Mysterud, A., Gya, R., Vandvik, V., Grytnes, J., & Speed, J. D. M. (2021). Functional traits of alpine plant communities show long‐term resistance to changing herbivore densities. Ecosphere, 12(12). https://doi.org/10.1002/ecs2.3887
Wang, B., Jiao, Y., Chougule, K., Olson, A., Huang, J., Llaca, V., Fengler, K., Wei, X., Wang, L., Wang, X., Regulski, M., Drenkow, J., Gingeras, T., Hayes, C., Armstrong, J. S., Huang, Y., Xin, Z., & Ware, D. (2021). Pan-genome Analysis in Sorghum Highlights the Extent of Genomic Variation and Sugarcane Aphid Resistance Genes [Preprint]. Genomics. https://doi.org/10.1101/2021.01.03.424980
Wang, X., Liu, J., Liang, C., Zhao, Z., Feng, G., & Zhang, J. (2021). Biodiversity dataset of vascular plants and birds in Chinese urban greenspace. Ecological Research, 36(4), 755–761. https://doi.org/10.1111/1440-1703.12240
Werbin, Z. R., Hackos, B., Dietze, M. C., & Bhatnagar, J. M. (2021). The National Ecological Observatory Network’s soil metagenomes: Assembly and basic analysis. F1000Research, 10, 299. https://doi.org/10.12688/f1000research.51494.1
Wieser, F., Stryeck, S., Lang, K., Hahn, C., Thallinger, G. G., Feichtinger, J., Hack, P., Stepponat, M., Merchant, N., Lindstaedt, S., & Oberdorfer, G. (2021). A local platform for user-friendly FAIR data management and reproducible analytics. Journal of Biotechnology, 341, 43–50. https://doi.org/10.1016/j.jbiotec.2021.08.004
Woltz, M. (2021). Barcoding US Ants: Ozarks Region-Research Highlight. The Confluence, 1(1), 3.
Wu, D., Tanaka, R., Li, X., Ramstein, G. P., Cu, S., Hamilton, J. P., Buell, C. R., Stangoulis, J., Rocheford, T., & Gore, M. A. (2021). High-resolution genome-wide association study pinpoints metal transporter and chelator genes involved in the genetic control of element levels in maize grain. G3 Genes|Genomes|Genetics, 11(4), jkab059. https://doi.org/10.1093/g3journal/jkab059
Wulff, J. A., Kjeldgaard, M. K., Eubanks, M. D., & Sword, G. A. (2021). From the bellies of babes: A larval-based approach to ant molecular gut content analysis. Insectes Sociaux, 68(2–3), 245–253. https://doi.org/10.1007/s00040-021-00822-8
Xin, Z., Wang, M., Cuevas, H. E., Chen, J., Harrison, M., Pugh, N. A., & Morris, G. (2021). Sorghum genetic, genomic, and breeding resources. Planta, 254(6), 114. https://doi.org/10.1007/s00425-021-03742-w
Yan, H., Haak, D. C., Li, S., Huang, L., & Bombarely, A. (2021). Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice. Plant Communications, 100270. https://doi.org/10.1016/j.xplc.2021.100270
Yue, L., Wang, Y., Wang, L., Yao, S., Cong, C., Ren, L., & Zhang, B. (2021). Impacts of soil compaction and historical soybean variety growth on soil macropore structure. Soil and Tillage Research, 214, 105166. https://doi.org/10.1016/j.still.2021.105166
Zayed, A. A., Lücking, D., Mohssen, M., Cronin, D., Bolduc, B., Gregory, A. C., Hargreaves, K. R., Piehowski, P. D., White III, R. A., Huang, E. L., Adkins, J. N., Roux, S., Moraru, C., & Sullivan, M. B. (2021). efam: An e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies. Bioinformatics, btab451. https://doi.org/10.1093/bioinformatics/btab451
Zeng, S., Mao, Z., Ren, Y., Wang, D., Xu, D., & Joshi, T. (2021). G2PDeep: A web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers. Nucleic Acids Research, 49(W1), W228–W236. https://doi.org/10.1093/nar/gkab407
Zeng, S., Škrabišová, M., Lyu, Z., Chan, Y. O., Dietz, N., Bilyeu, K., & Joshi, T. (2021). Application of SNPViz v2.0 using next-generation sequencing data sets in the discovery of potential causative mutations in candidate genes associated with phenotypes. International Journal of Data Mining and Bioinformatics, 25(1/2), 65. https://doi.org/10.1504/IJDMB.2021.116886
Zhang, J., Cavallaro, M., & Hebenstreit, D. (2021). Timing RNA polymerase pausing with TV-PRO-seq. Cell Reports Methods, 100083. https://doi.org/10.1016/j.crmeth.2021.100083
Zhang, J., Condon, L. E., Tran, H., & Maxwell, R. M. (2021). A national topographic dataset for hydrological modeling over the contiguous United States. Earth System Science Data, 13(7), 3263–3279.
Zhang, T., Mudgett, M., Rambabu, R., Abramson, B., Dai, X., Michael, T. P., & Zhao, Y. (2021). Selective inheritance of target genes from only one parent of sexually reproduced F1 progeny in Arabidopsis. Nature Communications, 12(1), 3854. https://doi.org/10.1038/s41467-021-24195-5
Zhao, L., Liu, L., Liu, Y., Dou, X., Cai, H., Aslam, M., Hou, Z., Jin, X., Li, Y., Wang, L., Zhao, H., Wang, X., Sicard, A., & Qin, Y. (2021). Characterization of germline development and identification of genes associated with germline specification in pineapple. Horticulture Research, 8(1), 239. https://doi.org/10.1038/s41438-021-00669-x
Zhong, Z.-P., Tian, F., Roux, S., Gazitúa, M. C., Solonenko, N. E., Li, Y.-F., Davis, M. E., Van Etten, J. L., Mosley-Thompson, E., Rich, V. I., Sullivan, M. B., & Thompson, L. G. (2021). Glacier ice archives nearly 15,000-year-old microbes and phages. Microbiome, 9(1), 160. https://doi.org/10.1186/s40168-021-01106-w
Zhuang, H., Wang, C., Wang, Y., Jin, T., Huang, R., Lin, Z., & Wang, Y. (2021). Native useful vascular plants of China: A checklist and use patterns. Plant Diversity, 43(2), 134–141. https://doi.org/10.1016/j.pld.2020.09.003