2021 Publications

Alamo, M. A. (n.d.). Impact of climate change on local tree species richness in Mexico [PhD Thesis]. Queens College.
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).
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. (2021). 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
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
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.
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
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
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
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
Das, S., & RanjanDash, H. (Eds.). (2020). Microbial and natural macromolecules: Synthesis and applications (1st ed.). Elsevier.
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
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
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
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
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
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
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.
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
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
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
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
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
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
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
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
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.
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
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
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
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
Peterson, A. L. (2021). Evolution and Sexual Dimorphism in Meiotic Recombination Rates in Murids. The University of Wisconsin-Madison.
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
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
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
Samal, A., & Choudhury, S. D. (2020). Intelligent Image Analysis for Plant Phenotyping. CRC Press.
Sanchez-Serrano, J. J., & Salinas, J. (Eds.). (2021). Arabidopsis protocols (Fourth Edition). Humana Press. https://doi.org/10.1007/978-1-07-160880-7
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
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
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
Stahlman, G. R. (2020). Exploring the long tail of astronomy: A mixed-methods approach to searching for dark data [PhD Thesis, The University of Arizona]. https://repository.arizona.edu/bitstream/handle/10150/642070/azu_etd_18157_sip1_m.pdf?sequence=1
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
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
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
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
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
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
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
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
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