Publications 2022


Adams, S., & Carré, I. A. (2021). Chromatin Immunoprecipitation Protocol for Circadian Clock Proteins. In D. Staiger, S. Davis, & A. M. Davis (Eds.), Plant Circadian Networks (Vol. 2398, pp. 135–150). Springer US.

Aggarwal, S., Raj, A., Kumar, D., Dash, D., & Yadav, A. K. (2022). False discovery rate: The Achilles’ heel of proteogenomics. Briefings in Bioinformatics, bbac163.

Alawadi, A. A., Benedito, V. A., Skinner, R. C., Warren, D. C., Showman, C., & Tou, J. C. (2022). RNA-sequencing revealed apple pomace ameliorates expression of genes in the hypothalamus associated with neurodegeneration in female rats fed a Western diet during adolescence to adulthood. Nutritional Neuroscience, 1–13.

Amos, B., Aurrecoechea, C., Barba, M., Barreto, A., Basenko, E. Y., Bażant, W., Belnap, R., Blevins, A. S., Böhme, U., Brestelli, J., Brunk, B. P., Caddick, M., Callan, D., Campbell, L., Christensen, M. B., Christophides, G. K., Crouch, K., Davis, K., DeBarry, J., … Zheng, J. (2022). VEuPathDB: The eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Research50(D1), D898–D911.

Amundson, K. K., Borton, M. A., Daly, R. A., Hoyt, D. W., Wong, A., Eder, E., Moore, J., Wunch, K., Wrighton, K. C., & Wilkins, M. J. (2022). Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation. Microbiome10(1), 5.

Andrade-Martínez, J. S., Camelo Valera, L. C., Chica Cárdenas, L. A., Forero-Junco, L., López-Leal, G., Moreno-Gallego, J. L., Rangel-Pineros, G., & Reyes, A. (2022). Computational Tools for the Analysis of Uncultivated Phage Genomes. Microbiology and Molecular Biology Reviews86(2), e00004-21.

Arras, P., Frank, P., Haim, P., Knollmüller, J., Leike, R., Reinecke, M., & Enßlin, T. (2022). Variable structures in M87* from space, time and frequency resolved interferometry. Nature Astronomy6(2), 259–269.

Balk, M. A., Deck, J., Emery, K. F., Walls, R. L., Reuter, D., LaFrance, R., Arroyo-Cabrales, J., Barrett, P., Blois, J., Boileau, A., Brenskelle, L., Cannarozzi, N. R., Cruz, J. A., Dávalos, L. M., de la Sancha, N. U., Gyawali, P., Hantak, M. M., Hopkins, S., Kohli, B., … Guralnick, R. P. (2022). A solution to the challenges of interdisciplinary aggregation and use of specimen-level trait data. IScience, 105101.

Balushi, M. A., Kumar, R., Al-Rashdi, A., Ratna, A., Al-Jabri, A., Al-shekaili, N., Rani, R., Sumri, S. A., Al-Ghabshi, L., Al-Abri, S., & Al-Jardani, A. (2022). Genomic analysis of the emerging carbapenem-resistant Klebsiella pneumoniae sequence type 11 harbouring Klebsiella pneumoniae carbapenemase (KPC) in Oman. Journal of Infection and Public Health15(10), 1089–1096.

Barakhshan, P., & Eigenmann, R. (2022). Exchanging Best Practices for Supporting Computational and Data-Intensive Research, The Xpert Network. Practice and Experience in Advanced Research Computing, 1–7.

Beck, M. A., Liu, C.-Y., Bidinosti, C. P., Henry, C. J., Godee, C. M., & Ajmani, M. (2021). An extensive lab-and field-image dataset of crops and weeds for computer vision tasks in agriculture.

Bendaoud, F., Kim, G., Larose, H., Westwood, J. H., Zermane, N., & Haak, D. C. (2022). Genotyping‐by‐sequencing analysis of Orobanche crenata populations in Algeria reveals genetic differentiation. Ecology and Evolution12(3).

Bhinda, M. S., Sanadya, S. K., Kumari, A., Kant, L., & Debnath, A. (2022). Omics for Abiotic Stress Tolerance in Foxtail Millet. In R. N. Pudake, A. U. Solanke, A. M. Sevanthi, & P. Rajendrakumar (Eds.), Omics of Climate Resilient Small Millets (pp. 27–52). Springer Nature Singapore.

Blake Steiner. (2022). Delayed Tree Dormancy Resulted in Higher Annual Savanna Gross Primary Productivity in the Northern Sonoran Desert [The University of Arizona].

Boeckman, J., Korn, A., Yao, G., Ravindran, A., Gonzalez, C., & Gill, J. (2022). Sheep in wolves’ clothing: Temperate T7-like bacteriophages and the origins of the Autographiviridae. Virology568, 86–100.

Buchholz, H. H., Bolaños, L. M., Bell, A. G., Michelsen, M. L., Allen, M. J., & Temperton, B. (2022). A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria. Applied and Environmental Microbiology88(7), e00255-22.

Bunting, M., Bhadani, R., Nice, M., Elmadani, S., & Sprinkle, J. (2022). Data from the Development Evolution of a Vehicle for Custom Control. 2022 2nd Workshop on Data-Driven and Intelligent Cyber-Physical Systems for Smart Cities Workshop (DI-CPS), 40–46.

Busta, L., Dweikat, I., Sato, S. J., Qu, H., Xue, Y., Zhou, B., Gan, L., Yu, B., Clemente, T. E., Cahoon, E. B., & Zhang, C. (2022). Chemical and genetic variation in feral Cannabis sativa populations across the Nebraska climate gradient. Phytochemistry200, 113206.

Cardone, R., Stubbs, J., Black, S., Garcia, C., Jamthe, A., Packard, M., & Padhy, S. (2022). A Design Pattern for Recoverable Job Management. Practice and Experience in Advanced Research Computing, 1–4.

Chakrabarti, M., Nagabhyru, P., Schardl, C. L., & Dinkins, R. D. (2022). Differential gene expression in tall fescue tissues in response to water deficit. The Plant Genome15(2).

Chávez Montes, R. A., Haber, A., Pardo, J., Powell, R. F., Divisetty, U. K., Silva, A. T., Hernández-Hernández, T., Silveira, V., Tang, H., Lyons, E., Herrera Estrella, L. R., VanBuren, R., & Oliver, M. J. (2022). A comparative genomics examination of desiccation tolerance and sensitivity in two sister grass species. Proceedings of the National Academy of Sciences119(5), e2118886119.

Chiozzi, G., De Marchi, G., Fasola, M., Ibrahim, K. M., Bardelli, G., Hagos, F., Rocca, F., & Masseti, M. (2022). Insular gazelles of the circum-Arabian seas: Origin, distribution, dwarfism and taxonomy. Mammalian Biology102(1), 1–20.

Christine Natalie Palermo. (2022). Diversity, Relative Abundance, and Functional Potential of Viral and Bacterial Communities [University of Toronto (Canada)]

Corwin, L. A., Ramsey, M. E., Vance, E. A., Woolner, E., Maiden, S., Gustafson, N., & Harsh, J. A. (2022). Students’ Emotions, Perceived Coping, and Outcomes in Response to Research-Based Challenges and Failures in Two Sequential CUREs. CBE—Life Sciences Education21(2), ar23.

Darianne M. Alvarez-Franceschi. (2022). Macro and Microorganisms’ Behavior Based on the Janzen-Connell Hypothesis after a Hurricane in El Yunque National Rainforest [Ana G. Mendez University].

Dirk Joldersma,  Norah Sadowski,  Winston Timp &  Zhongchi Liu, ,. (2022). Assembly and annotation of Fragaria vesca “Yellow Wonder” genome, a model diploid strawberry for molecular genetic research. Fruit Research2(13).

Dominguez-Huerta, G., Zayed, A. A., Wainaina, J. M., Guo, J., Tian, F., Pratama, A. A., Bolduc, B., Mohssen, M., Zablocki, O., Pelletier, E., Delage, E., Alberti, A., Aury, J.-M., Carradec, Q., da Silva, C., Labadie, K., Poulain, J., Tara Oceans Coordinators§, Bowler, C., … Sullivan, M. B. (2022). Diversity and ecological footprint of Global Ocean RNA viruses. Science376(6598), 1202–1208.

Drummond, C. P., Cochrane, T. S., & Sytsma, K. J. (2022). Western North American Plants Disjunct in the Great Lakes Region: 40 Years after Marquis and Voss. International Journal of Plant Sciences, 000–000.

Dykes, J., Kappenman, K., & Nissen, E. D. (2022). Using DNA Barcoding Methods to Identify Wild Huckleberry, Vaccinium membranaceum , as a Classroom Project. The American Biology Teacher84(1), 40–44.

Ehsani, M. R., Zarei, A., Gupta, H. V., Barnard, K., Lyons, E., & Behrangi, A. (2022). NowCasting-Nets: Representation Learning to Mitigate Latency Gap of Satellite Precipitation Products Using Convolutional and Recurrent Neural Networks. IEEE Transactions on Geoscience and Remote Sensing60, 1–21.

Fernandez-Pozo, N., Haas, F. B., Gould, S. B., & Rensing, S. A. (2022). An overview of bioinformatics, genomics and transcriptomics resources for bryophytes. Journal of Experimental Botany, erac052.

Fitzgerald, C., Vens, C. S., Miller, N., Barker, R., Westphall, M., Lombardino, J., Miao, J., Swanson, S. J., & Gilroy, S. (2022). Using the Automated Botanical Contact Device (ABCD) to Deliver Reproducible, Intermittent Touch Stimulation to Plants. In E. B. Blancaflor (Ed.), Plant Gravitropism (Vol. 2368, pp. 81–94). Springer US.

Fox, A. M., Huo, X., Hoar, T. J., Dashti, H., Smith, W. K., MacBean, N., Anderson, J. L., Roby, M., & Moore, D. J. P. (2022). Assimilation of Global Satellite Leaf Area Estimates Reduces Modeled Global Carbon Uptake and Energy Loss by Terrestrial Ecosystems. Journal of Geophysical Research: Biogeosciences127(8).

Gage, J. L., Mali, S., McLoughlin, F., Khaipho-Burch, M., Monier, B., Bailey-Serres, J., Vierstra, R. D., & Buckler, E. S. (2022). Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance. Proceedings of the National Academy of Sciences119(14), e2112516119.

Guo, W.-Y., Serra-Diaz, J. M., Schrodt, F., Eiserhardt, W. L., Maitner, B. S., Merow, C., Violle, C., Anand, M., Belluau, M., Bruun, H. H., Byun, C., Catford, J. A., Cerabolini, B. E. L., Chacón-Madrigal, E., Ciccarelli, D., Cornelissen, J. H. C., Dang-Le, A. T., de Frutos, A., Dias, A. S., … Svenning, J.-C. (2022). High exposure of global tree diversity to human pressure. Proceedings of the National Academy of Sciences119(25), e2026733119.

Gupta, S., & Rather, S. A. (2022). Innovations in Crop Production: An Amalgamation of Abiotic Stress Physiology and Technology. Plant Abiotic Stress Physiology: Volume 1: Responses and Adaptations, 1.

Hackett, J., Gibson, H., Frelinger, J., & Buntzman, A. (2022). Using the Collaborative Cross and Diversity Outbred Mice in Immunology. Current Protocols2(9).

Harris, N. L., Hokamp, K., Ménager, H., Munoz-Torres, M., Unni, D., Vasilevsky, N., & Williams, J. (2022). BOSC 2022: The first hybrid and 23rd annual Bioinformatics Open Source Conference. F1000Research11, 1034.

Harrison, K., Levy, J. G., & Tamborindeguy, C. (2022). Effects of ‘Candidatus Liberibacter solanacearum’ haplotypes A and B on tomato gene expression and geotropism. BMC Plant Biology22(1), 156.

Heilman, K. A., Dietze, M. C., Arizpe, A. A., Aragon, J., Gray, A., Shaw, J. D., Finley, A. O., Klesse, S., DeRose, R. J., & Evans, M. E. K. (2022). Ecological forecasting of tree growth: Regional fusion of tree‐ring and forest inventory data to quantify drivers and characterize uncertainty. Global Change Biology, gcb.16038.

Hofstatter, P. G., Thangavel, G., Lux, T., Neumann, P., Vondrak, T., Novak, P., Zhang, M., Costa, L., Castellani, M., Scott, A., Toegelová, H., Fuchs, J., Mata-Sucre, Y., Dias, Y., Vanzela, A. L. L., Huettel, B., Almeida, C. C. S., Šimková, H., Souza, G., … Marques, A. (2022). Repeat-based holocentromeres influence genome architecture and karyotype evolution. Cell185(17), 3153-3168.e18.

Hongfei Chen1*, Zheng Xiao1,2*, Baoqing Ding1,3, Pamela K. Diggle1, Yao-Wu Yuan. (2022). Modular regulation of floral traits by a PRE1 homolog in Mimulus verbenaceus: Implications for the role of pleiotropy in floral integration.

Hossain, C., Hernandez, V., McHugh, L., Tran, P.-T., & Nash, B. (2022). Analyzing the impacts of tobacco mosaic virus on the microbial diversity of Nicotiana benthamiana. Journal of Plant Pathology104(3), 959–967.

Jhu, M.-Y., Farhi, M., Wang, L., Philbrook, R. N., Belcher, M. S., Nakayama, H., Zumstein, K. S., Rowland, S. D., Ron, M., Shih, P. M., & Sinha, N. R. (2022). Heinz-resistant tomato cultivars exhibit a lignin-based resistance to field dodder ( Cuscuta campestris ) parasitism. Plant Physiology, kiac024.

Jiang, J.-Z., Yuan, W.-G., Shang, J., Shi, Y.-H., Yang, L.-L., Liu, M., Zhu, P., Jin, T., Sun, Y., & Yuan, L.-H. (2022). Virus classification for viral genomic fragments using PhaGCN2 [Preprint]. In Review.

Joaquim, P. I. L., Molinari, M. D. C., Marin, S. R. R., Barbosa, D. A., Viana, A. J. C., Rech, E. L., Henning, F. A., Nepomuceno, A. L., & Mertz-Henning, L. M. (2022). Nitrogen compounds transporters: Candidates to increase the protein content in soybean seeds. Journal of Plant Interactions17(1), 309–318.

Kavas, M., Mostafa, K., Seçgin, Z., Yerlikaya, B. A., Yıldırım, K., & Gökdemir, G. (2022). Genome-wide analysis of DUF221 domain-containing gene family in common bean and identification of its role on abiotic and phytohormone stress response. Genetic Resources and Crop Evolution

Keuler, R., Jensen, J., Barcena-Peña, A., Grewe, F., Thorsten Lumbsch, H., Huang, J.-P., & Leavitt, S. D. (2022). Interpreting phylogenetic conflict: Hybridization in the most speciose genus of lichen-forming fungi. Molecular Phylogenetics and Evolution174, 107543.

Kim, K. E., Jung, S. W., Park, J. S., Kim, H.-J., Lee, C., Ha, S.-Y., & Lee, T.-K. (2022). Optimized Metavirome Analysis of Marine DNA Virus Communities for Taxonomic Profiling. Ocean Science Journal57(2), 259–268.

Koontz, M. J., Scholl, V. M., Spiers, A. I., Cattau, M. E., Adler, J., McGlinchy, J., Goulden, T., Melbourne, B. A., & Balch, J. K. (2022). Democratizing macroecology: Integrating unoccupied aerial systems with the National Ecological Observatory Network. Ecosphere13(8).

Labbé, M., Thaler, M., Pitot, T. M., Rapp, J. Z., Vincent, W. F., & Culley, A. I. (2022). Climate-Endangered Arctic Epishelf Lake Harbors Viral Assemblages with Distinct Genetic Repertoires. Applied and Environmental Microbiology88(17), e00228-22.

Lamanchai, K., Salmon, D. L., Smirnoff, N., Sutthinon, P., Roytrakul, S., Leetanasaksakul, K., Kittisenachai, S., & Jantasuriyarat, C. (2022). OsVTC1-1 RNAi Mutant with Reduction of Ascorbic Acid Synthesis Alters Cell Wall Sugar Composition and Cell Wall-Associated Proteins. Agronomy12(6), 1272.

Li, F., Huang, S., Mei, Y., Wu, B., Hou, Z., Zhan, P., Hou, Z., Huang, W., Zhao, J., & Wang, J. (2022). Genome assembly provided new insights into the Cinnamomum burmannii evolution and D-borneol biosynthesis differences between chemotypes. Industrial Crops and Products186, 115181.

Liu, G., Sun, Y., Jia, L., Li, R., & Zuo, Y. (2022). Chromatin accessibility shapes meiotic recombination in mouse primordial germ cells through assisting double-strand breaks and loop formation. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms1865(5), 194844.

Lu, L., Guo, F., Zhang, Z., Zhu, X., Hao, Y., Yu, J., Ye, W., & Zhang, Z. (2022). Genome sequencing reveals the evolution and pathogenic mechanisms of the wheat sharp eyespot pathogen Rhizoctonia cerealis. The Crop Journal, S2214514122002094.

Martínez-Alvarez, L., Ramond, J.-B., Vikram, S., León-Sobrino, C., Maggs-Kölling, G., & Cowan, D. (2022). With a pinch of salt: Metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities [Preprint]. Microbiology.

Martinson, J. W., Bencic, D. C., Toth, G. P., Kostich, M. S., Flick, R. W., See, M. J., Lattier, D., Biales, A. D., & Huang, W. (2022). De Novo Assembly of the Nearly Complete Fathead Minnow Reference Genome Reveals a Repetitive but Compact Genome. Environmental Toxicology and Chemistry41(2), 448–461.

Marx, V. (2022). Why the ocean virome matters. Nature Methods19(8), 924–927.

Miyoshi, M., Kato, Y., & Makino, J. (2022). The jet and resolved features of the central supermassive black hole of M 87 observed with EHT. The Astrophysical Journal933(1), 36.

Morey, J. S., Balmer, B. C., Zolman, E. S., Takeshita, R., De Guise, S., Rowles, T. K., Smith, C. R., Wells, R. S., & Schwacke, L. H. (2022). Transcriptome profiling of blood from common bottlenose dolphins (Tursiops truncatus) in the northern Gulf of Mexico to enhance health assessment capabilities. PLOS ONE17(8), e0272345.

Morisse, M., Wells, D. M., Millet, E. J., Lillemo, M., Fahrner, S., Cellini, F., Lootens, P., Muller, O., Herrera, J. M., Bentley, A. R., & Janni, M. (2022). A European perspective on opportunities and demands for field-based crop phenotyping. Field Crops Research276, 108371.

Naithani, K., Jones, M., & Grayson, K. L. (2022). Building communities of teaching practice and data‐driven open education resources with NEON faculty mentoring networks. Ecosphere13(8).

Nandety, R. S., Wen, J., & Mysore, K. S. (2022). Medicago truncatula resources to study legume biology and symbiotic nitrogen fixation. Fundamental Research, S2667325822002904.

Nazranov, H., Orzalieva, M., Shalov, T., Tamakhina, A., & Knyazev, B. (2022). The effectiveness of the use of mineral fertilizers in the technology of potato seed production in the conditions of the mountainous zone of Kabardino-Balkaria. BIO Web of Conferences51, 04014.

Nelson, A. R., Narrowe, A. B., Rhoades, C. C., Fegel, T. S., Daly, R. A., Roth, H. K., Chu, R. K., Amundson, K. K., Young, R. B., Steindorff, A. S., Mondo, S. J., Grigoriev, I. V., Salamov, A., Borch, T., & Wilkins, M. J. (2022). Wildfire-dependent changes in soil microbiome diversity and function. Nature Microbiology7(9), 1419–1430.

Nelson Dittrich, A. C., & Nelson, A. D. L. (2022). High-Throughput Evolutionary Comparative Analysis of Long Intergenic Noncoding RNAs in Multiple Organisms. In A. Pereira-Santana, S. D. Gamboa-Tuz, & L. C. Rodríguez-Zapata (Eds.), Plant Comparative Genomics (Vol. 2512, pp. 45–60). Springer US.

Nguyen, D. T., Hayes, J. E., Atieno, J., Li, Y., Baumann, U., Pattison, A., Bramley, H., Hobson, K., Roorkiwal, M., Varshney, R. K., Colmer, T. D., & Sutton, T. (2022). The genetics of vigour-related traits in chickpea (Cicer arietinum L.): Insights from genomic data. Theoretical and Applied Genetics135(1), 107–124.

Nguyen, N. T., Khan, M. A., Castro–Guerrero, N. A., Chia, J.-C., Vatamaniuk, O. K., Mari, S., Jurisson, S. S., & Mendoza-Cozatl, D. G. (2022). Iron Availability within the Leaf Vasculature Determines the Magnitude of Iron Deficiency Responses in Source and Sink Tissues in ArabidopsisPlant and Cell Physiology63(6), 829–841.

Nicola Kuhn. (2022). Vegetation response to climate change: A functional traits-based approach [University of Oxford, St Edmund Hall College].

Oruche, R., Milman, E., Lemus Alarcon, M., Cheng, X., Pandey, A., Wang, S., Calyam, P., & Kee, K. (2022). Science gateway adoption using plug‐in middleware for evidence‐based healthcare data management. Concurrency and Computation: Practice and Experience

Palacio, S., Cera, A., Escudero, A., Luzuriaga, A. L., Sánchez, A. M., Mota, J. F., Pérez‐Serrano Serrano, M., Merlo, M. E., Martínez‐Hernández, F., Salmerón‐Sánchez, E., Mendoza‐Fernández, A. J., Pérez‐García, F. J., Montserrat‐Martí, G., & Tejero, P. (2022). Recent and ancient evolutionary events shaped plant elemental composition of edaphic endemics: A phylogeny‐wide analysis of Iberian gypsum plants. New Phytologist235(6), 2406–2423.

Palos, K. (2022). Identifying Long Noncoding RNAs and Examining Their Functional Roles in Brassicaceae [PhD Thesis]. In ProQuest Dissertations and Theses

Palos, K., Nelson Dittrich, A. C., Yu, L., Brock, J. R., Railey, C. E., Wu, H.-Y. L., Sokolowska, E., Skirycz, A., Hsu, P. Y., Gregory, B. D., Lyons, E., Beilstein, M. A., & Nelson, A. D. L. (2022). Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae. The Plant Cell34(9), 3233–3260.

Park, C. H., Bi, Y., Youn, J.-H., Kim, S.-H., Kim, J.-G., Xu, N. Y., Shrestha, R., Burlingame, A. L., Xu, S.-L., Mudgett, M. B., Kim, S.-K., Kim, T.-W., & Wang, Z.-Y. (2022). Deconvoluting signals downstream of growth and immune receptor kinases by phosphocodes of the BSU1 family phosphatases. Nature Plants8(6), 646–655.

Patel, R., Roachell, B., Caino-Lores, S., Ketron, R., Leonard, J., Tan, N., Brown, D., Deelman, E., & Taufer, M. (2022). Reproducibility of the First Image of a Black Hole in the Galaxy M87 from the Event Horizon Telescope (EHT) Collaboration (arXiv:2205.10267). arXiv.

Patel, S. R. (2022). VERITAS highlights of observations and results (arXiv:2208.11597). arXiv.

Petersen, T. K., Vuorinen, K. E. M., Bendiksby, M., & Speed, J. D. M. (2022). Climate and land‐use drive the functional composition of vascular plant assemblages across Norway. Nordic Journal of Botany2022(7).

Procko, C., Lee, T., Borsuk, A., Bargmann, B. O. R., Dabi, T., Nery, J. R., Estelle, M., Baird, L., O’Connor, C., Brodersen, C., Ecker, J. R., & Chory, J. (2022). Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection. The Plant Cell, koac167.

Pucker, B., Irisarri, I., de Vries, J., & Xu, B. (2022). Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions. Quantitative Plant Biology3, e5.

Rahman, M. A., Tutul, A. A., Abdullah, S. M., & Bayzid, Md. S. (2022). CHAPAO: Likelihood and hierarchical reference-based representation of biomolecular sequences and applications to compressing multiple sequence alignments. PLOS ONE17(4), e0265360.

Ramstein, G. P., & Buckler, E. S. (2022). Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize. Genome Biology23(1), 183.

Ratnaparkhe, M. B., Nataraj, V., Shivakumar, M., Chandra, S., Ramesh, S. V., Kumawat, G., Kamble, V., Rajput, L. S., Kumar, S., Rajesh, V., Satpute, G. K., Ramteke, R., Kavishwar, R., Dubey, A., Marmat, N., Shroti, R., Shrivastava, M., Gupta, S., Sharma, M. P., … Nguyen, H. (2022). Genomic Design for Biotic Stresses in Soybean. In C. Kole (Ed.), Genomic Designing for Biotic Stress Resistant Oilseed Crops (pp. 1–54). Springer International Publishing.

Ratnaparkhe, M. B., Satpute, G. K., Kumawat, G., Chandra, S., Kamble, V. G., Kavishwar, R., Singh, V., Singh, J., Singh, A. K., Ramesh, S. V., Kumar, V., Sudhakaran, S., Srivastava, M. K., Shesh, N., Jajoo, A., Gupta, S., Singh, M., Xu, D., Bhattacharya, M., & Nguyen, H. T. (2022). Genomic Designing for Abiotic Stress Tolerant Soybean. In C. Kole (Ed.), Genomic Designing for Abiotic Stress Resistant Oilseed Crops (pp. 1–73). Springer International Publishing.

Rhoades, N. S., Davies, M., Lewis, S. A., Cinco, I. R., Kohama, S. G., Bermudez, L. E., Winthrop, K. L., Fuss, C., Mattison, J. A., Spindel, E. R., & Messaoudi, I. (2022). Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging: Insights from rhesus macaques [Preprint]. Immunology.

Rosario, K., Van Bogaert, N., López-Figueroa, N. B., Paliogiannis, H., Kerr, M., & Breitbart, M. (2022). Freshwater macrophytes harbor viruses representing all five major phyla of the RNA viral kingdom OrthornaviraePeerJ10, e13875.

Salgado-Salazar, C., Romberg, M. K., Blomquist, C., Nunziata, S., Cai, W., & Rivera, Y. (2022). Lifestyle, mating type and mitochondrial genome features of the plant pathogen Calonectria hawksworthii (Hypocreales, Nectriaceae) as revealed by genome analyses. Canadian Journal of Plant Pathology, 1–14.

Sams, E. I., Ng, J. K., Tate, V., Claire Hou, Y.-C., Cao, Y., Antonacci-Fulton, L., Belhassan, K., Neidich, J., Mitra, R. D., Cole, F. S., Dickson, P., Milbrandt, J., & Turner, T. N. (2022). From karyotypes to precision genomics in 9p deletion and duplication syndromes. Human Genetics and Genomics Advances3(1), 100081.

Satapathy, K., Psaltis, D., Özel, F., Medeiros, L., Dougall, S. T., Chan, C.-K., Wielgus, M., Prather, B. S., Wong, G. N., Gammie, C. F., & others. (2022). The Variability of the Black Hole Image in M87 at the Dynamical Timescale. The Astrophysical Journal925(1), 13.

Senn, S., Bhattacharyya, S., Presley, G., Taylor, A. E., Ford, J., Jasinski, B., & Badalova, Y. (2022). The Functional Biogeography of eDNA Metacommunities in the Post-fire Landscape of the Angeles National Forest [Preprint]. EARTH SCIENCES.

Senn, S., Pangell, K., & Bowerman, A. L. (2022). Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia. BioTech11(1), 1.

Shang, J., & Sun, Y. (2022). CHERRY: A Computational metHod for accuratE pRediction of virus-pRokarYotic interactions using a graph encoder-decoder model. ArXiv:2201.01018 [Cs, q-Bio]


Soneral, P. (2022). RNA‐Seq and Recurrence Risk Testing for Breast Cancer: Implications for Patient Education. The FASEB Journal36(S1), fasebj.2022.36.S1.R1989.

Soneral, P., Khomcyk, A., Enke, R., Nash, B., & Seto, J. (2022). EDNA Analysis of Goat‐Grazed Rhamnus cathartica Soil Microbial Communities. The FASEB Journal36(S1), fasebj.2022.36.S1.R5509.

Song, X., Li, Y., Stirling, E., Zhao, K., Wang, B., Zhu, Y., Luo, Y., Xu, J., & Ma, B. (2022). AsgeneDB: A curated orthology arsenic metabolism gene database and computational tool for metagenome annotation [Preprint]. Preprints.

Spalding, E., Morzinski, K. M., Hinz, P., Males, J., Meyer, M., Quanz, S. P., Leisenring, J., & Power, J. (2022). High-contrast Imaging with Fizeau Interferometry: The Case of Altair*. The Astronomical Journal163(2), 62.

Stillson, P. T., Baltrus, D. A., & Ravenscraft, A. (2022). Prevalence of an Insect-Associated Genomic Region in Environmentally Acquired Burkholderiaceae Symbionts. Applied and Environmental Microbiology88(9), e02502-21.

Suárez, C. A., Carrasco, S. T., Brandolisio, F. N. A., Abatangelo, V., Boncompain, C. A., Peresutti-Bacci, N., & Morbidoni, H. R. (2022). Bioinformatic Analysis of a Set of 14 Temperate Bacteriophages Isolated from Staphylococcus aureus Strains Highlights Their Massive Genetic Diversity. Microbiology Spectrum10(4), e00334-22.

Sundaray, J. K., Dixit, S., Rather, A., Rasal, K. D., & Sahoo, L. (2022). Aquaculture omics: An update on the current status of research and data analysis. Marine Genomics64, 100967.

Toby, I., Williams, J., Lu, G., Cai, C., Crandall, K. A., Dinsdale, E. A., Drew, J., Edgington, N. P., Goller, C. C., Grandgenett, N. F., Grant, B. J., Hauser, C., Johnson, K. A., Jones, C. J., Jue, N. K., Jungck, J. R., Kerby, J., Kleinschmit, A. J., Miller, K. G., … Robic, S. (2022). Making Change Sustainable: Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) Meeting Review. CourseSource9

Tran, H., Zhang, J., O’Neill, M. M., Ryken, A., Condon, L. E., & Maxwell, R. M. (2022). A hydrological simulation dataset of the Upper Colorado River Basin from 1983 to 2019. Scientific Data9(1), 16.

Tuggle, C. K., Clarke, J., Dekkers, J. C. M., Ertl, D., Lawrence-Dill, C. J., Lyons, E., Murdoch, B. M., Scott, N. M., & Schnable, P. S. (2022). The Agricultural Genome to Phenome Initiative (AG2PI): Creating a shared vision across crop and livestock research communities. Genome Biology23(1), 3, s13059-021-02570–02571.

Vogeley, C., Nguyen, T., Woeste, S., Krutmann, J., Haarmann-Stemmann, T., & Rossi, A. (2022). Rapid and simple analysis of short and long sequencing reads using DuesselporeTM. Frontiers in Genetics13, 931996.

Wang, L., Lu, Z., Van Buren, P., & Ware, D. (2022). SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data. In D. Edwards (Ed.), Plant Bioinformatics (Vol. 2443, pp. 197–209). Springer US.

Wei, W., Zhao, Q., Wang, Z., Liau, W.-S., Basic, D., Ren, H., Marshall, P. R., Zajaczkowski, E. L., Leighton, L. J., Madugalle, S. U., Musgrove, M., Periyakaruppiah, A., Shi, J., Zhang, J., Mattick, J. S., Mercer, T. R., Spitale, R. C., Li, X., & Bredy, T. W. (2022). ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3. Cell Reports38(12), 110546.

Wiesner, S., Desai, A. R., Duff, A. J., Metzger, S., & Stoy, P. C. (2022). Quantifying the Natural Climate Solution Potential of Agricultural Systems by Combining Eddy Covariance and Remote Sensing. Journal of Geophysical Research: Biogeosciences127(9).

Williams, J. (2022). CyVerse for Reproducible Research: RNA-Seq Analysis. In D. Edwards (Ed.), Plant Bioinformatics (Vol. 2443, pp. 57–79). Springer US.

Wu, D., Li, X., Tanaka, R., Wood, J. C., Tibbs-Cortes, L. E., Magallanes-Lundback, M., Bornowski, N., Hamilton, J. P., Vaillancourt, B., Diepenbrock, C. H., Li, X., Deason, N. T., Schoenbaum, G. R., Yu, J., Buell, C. R., DellaPenna, D., & Gore, M. A. (2022). Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain. Genetics221(4), iyac091.

Wyman, C. L., Gontijo Silva Maia, L., Yang, L., & Benedito, V. A. (2022). The Model Legume, Medicago truncatula in the Genomic Era: Speeding Up Discoveries in Legume Biology. In S. Sinharoy, Y. Kang, & V. Benedito (Eds.), The Medicago truncatula Genome (pp. 1–9). Springer International Publishing.

Xiao, Y., Jiao, S., He, M., Lin, D., Zuo, H., Han, J., Sun, Y., Cao, G., Chen, Z., & Liu, H. (2022). Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants. International Journal of Oral Science14(1), 43.

Xu, G., Lyu, J., Obata, T., Liu, S., Ge, Y., Schnable, J. C., & Yang, J. (2022). A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding [Preprint]. Genomics.

Xu, Q., Wang, X., Wang, Y., Zhang, H., Zhang, H., Di, H., Zhang, L., Dong, L., Zeng, X., Liu, X., Lee, M., Wang, Z., & Zhou, Y. (2022). Combined QTL mapping and RNA-Seq pro-filing reveal candidate genes related to low-temperature tolerance in maize. Molecular Breeding42(6), 33.

Yang, D., Morrison, B. D., Davidson, K. J., Lamour, J., Li, Q., Nelson, P. R., Hantson, W., Hayes, D. J., Swetnam, T. L., McMahon, A., Anderson, J., Ely, K. S., Rogers, A., & Serbin, S. P. (2022). Remote sensing from unoccupied aerial systems: Opportunities to enhance Arctic plant ecology in a changing climate. Journal of Ecology, 1365-2745.13976.

Zhang, J., Sun, H., Guo, S., Ren, Y., Li, M., Wang, J., Yu, Y., Zhang, H., Gong, G., He, H., Zhang, C., & Xu, Y. (2022). ClZISO mutation leads to photosensitive flesh in watermelon. Theoretical and Applied Genetics

Zhang, X., Zhu, Y., Kremling, K. A. G., Romay, M. C., Bukowski, R., Sun, Q., Gao, S., Buckler, E. S., & Lu, F. (2022). Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. Theoretical and Applied Genetics135(1), 273–290.

Zhang, Y., Clancy, J., Jensen, J., McMullin, R. T., Wang, L., & Leavitt, S. D. (2022). Providing Scale to a Known Taxonomic Unknown—At Least a 70-Fold Increase in Species Diversity in a Cosmopolitan Nominal Taxon of Lichen-Forming Fungi. Journal of Fungi8(5), 490.

Zhao, Y., Zhang, S., Lv, Y., Ning, F., Cao, Y., Liao, S., Wang, P., & Huang, S. (2022). Optimizing ear-plant height ratio to improve kernel number and lodging resistance in maize (Zea mays L.). Field Crops Research276, 108376.

Zhou, Y., Zhang, C., Zhang, L., Ye, Q., Liu, N., Wang, M., Long, G., Fan, W., Long, M., & Wing, R. A. (2022). Gene fusion as an important mechanism to generate new genes in the genus Oryza. Genome Biology23(1), 130.


Create Account

An Open Science Workspace for Collaborative Data-driven Discovery