Publications

Select peer-reviewed publications and pre-prints that leveraged The iPlant Collaborative & CyVerse for computational workflows and/or data hosting over the last 16 years:

2024

Castro, P., Carmona, A., Perez-Rial, A., Millan, T., Rubio, J., Gil, J. and Die, J.V. (2024), Finding Consensus on the Reference Genomes : A Chickpea Case Study. Legume Science, 6: e224. https://doi.org/10.1002/leg3.224

Chakraborty, T. J.T. Trujillo, T. Kendall, R.A. Mosher, (2024) Cgarophytic Green Algae Encode Ancestral Polymerase IV/Polymerase V Subunits and a CLSY/DRD1 Homolog, Genome Biology and Evolution, Volume 16, Issue 6, June 2024, evae119, https://doi.org/10.1093/gbe/evae119

Evans, M.E.K., S.M.N. Dey, K.A. Heilman, J.R. Tipton, R.J. DeRose, S. Klesse, E.L. Schultz,& J.D. Shaw (2024). Tree rings reveal the transient risk of extinction hidden inside climate envelope forecasts, Proc. Natl. Acad. Sci. U.S.A. 121 (24) e2315700121, https://doi.org/10.1073/pnas.2315700121 

Fattel, L., Yanarella, C.F., Ngara, B. et al. Gene function annotations for the maize NAM founder lines. BMC Res Notes 17, 9 (2024). https://doi.org/10.1186/s13104-023-06668-6 

Gonzalez, E., Zarei, A., Calleja, S., Christenson, C., Rozzi, B., Demieville, J., Hu, J., Eveland, A. L., Dilkes, B., Barnard, K., Lyons, E., & Pauli, D. (2024). Quantifying leaf symptoms of sorghum charcoal rot in images of field-grown plants using deep neural networks. The Plant Phenome Journal, 7, e20110. https://doi.org/10.1002/ppj2.20110

Hawkings, C. & Tamborindeguy, C. (2024) Differential expression of vitellogenin in the brain of Solenopsis invicta workers based on social and nutritional context. Physiological Entomology, 50(1), 64–76. Available from: https://doi.org/10.1111/phen.12467

Huo, X., Fox, A. M., Dashti, H., Devine, C., Gallery, W., Smith, W. K., et al. (2024). Integrating state data assimilation and innovative model parameterization reduces simulated carbon uptake in the Arctic and Boreal region. Journal of Geophysical Research: Biogeosciences, 129, e2024JG008004. https://doi.org/10.1029/2024JG008004 

León-Sobrino, C., J-B Ramond, C. Coclet, R-M Kapitango, G. Maggs-Kölling, D.A. Cowan, (2024) Temporal dynamics of microbial transcription in wetted hyperarid desert soils, FEMS Microbiology Ecology, Volume 100, Issue 3, March 2024, fiae009, https://doi.org/10.1093/femsec/fiae009

Li, D., L. Shao, J. Zhang, et al. Peculiar winter dormancy processes of perennial monocots represented by rhizomatous irises with distinct durations. Authorea. January 31, 2024. DOI: 10.22541/au.170666257.77947781/v1R

Mason-Gamer, R.J., D.M. White (2024). The phylogeny of the Triticeae: Resolution and phylogenetic conflict based on genomewide nuclear loci. American Journal of Botany, 111(10), Article e16404. https://doi.org/10.1002/ajb2.16404

Ou,S., et al. (2024). Differences in activity and stability drive transposable element variation in tropical and temperate maize. Genome Research, 34(8), 1140–1153. https://doi.org/10.1101/gr.278131.123 

Paneru, B.D., Chini, J., McCright, S.J. et al. (2024) Myeloid-derived miR-6236 potentiates adipocyte insulin signaling and prevents hyperglycemia during obesity. Nature Communications 15, 5394 (2024). https://doi.org/10.1038/s41467-024-49632-z 

Pietrzyk, P., N. Phan-Udom, C. Chutoe, L. Pingault, A. Roy, M. Libault, P. J. Saengwilai, A. Bucksch, (2024) DIRT/µ: automated extraction of root hair traits using combinatorial optimization, Journal of Experimental Botany, Volume 76, Issue 2, 10 January 2025, Pages 285–298, https://doi.org/10.1093/jxb/erae385

Priego-Cubero S., T. Toyomasu, M. Gigl, Y. Liu, Y. Hasegawa, H. Nojiri, C. Dawid, K. Okada, C. Becker (2024) bioRxiv 2024.01.11.572147; doi: https://doi.org/10.1101/2024.01.11.572147 

Richter, A., Schroeder, A.F., Marcon, C., Hochholdinger, F., Jander, G. and Negin, B. (2024), Catechol acetylglucose: a newly identified benzoxazinoid-regulated defensive metabolite in maize. New Phytol, 244: 2474-2488. https://doi.org/10.1111/nph.20209

Rodene, E., Fernando, G. D., Piyush, V., Ge, Y., Schnable, J. C., Ghosh, S., & Yang, J. (2024). Image Filtering to Improve Maize Tassel Detection Accuracy Using Machine Learning Algorithms. Sensors, 24(7), 2172. https://doi.org/10.3390/s24072172 

Roy, R., E. Ward, I. Choi, M. Cosi, T. Edgin, T. S. Hughes, Md Shafayet Islam, A. M Khan, A. Kolekar, M. Rayl, I. Robinson, P. Sarando, E. Skidmore, T.L. Swetnam, M. Wall, Z. Xu, M.L. Yung, N. Merchant, T.J. Wheeler, (2024) MDRepo—an open data warehouse for community-contributed molecular dynamics simulations of proteins, Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D477–D486, https://doi.org/10.1093/nar/gkae1109

Seipelt-Thiemann, R.L. (2024). Cryptococcus neoformans Transcriptome Analysis to Identify Differentially Expressed Genes Using the STAR Pipeline in CyVerse Discovery Environment. In: McClelland, E.E. (eds) Cryptococcus neoformans. Methods in Molecular Biology, vol 2775. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3722-7_8 

Swetnam TL, Antin PB, Bartelme R, Bucksch A, Camhy D, Chism G, et al. (2024) CyVerse: Cyberinfrastructure for open science. PLoS Comput Biol 20(2): e1011270. https://doi.org/10.1371/journal.pcbi.1011270 

Tuggle CK, Clarke JL, Murdoch BM, Lyons E, Scott NM, Beneš B, Campbell JD, Chung H, Daigle CL, Das Choudhury S, Dekkers JCM, Dórea JRR, Ertl DS, Feldman M, Fragomeni BO, Fulton JE, Guadagno CR, Hagen DE, Hess AS, Kramer LM, Lawrence-Dill CJ, Lipka AE, Lübberstedt T, McCarthy FM, McKay SD, Murray SC, Riggs PK, Rowan TN, Sheehan MJ, Steibel JP, Thompson AM, Thornton KJ, Van Tassell CP, Schnable PS. Current challenges and future of agricultural genomes to phenomes in the USA. Genome Biol. 2024 Jan 3;25(1):8. doi: 10.1186/s13059-023-03155-w. PMID: 38172911; PMCID: PMC10763150. https://doi.org/10.1186/s13059-023-03155-w 

Wu, S., Da, L., Xiao, Q. et al. (2024) ASAP: a platform for gene functional analysis in Angelica sinensis. BMC Genomics 25, 96 (2024). https://doi.org/10.1186/s12864-024-09971-z 

Yamashita, T., D.D. Rhoads, J. Pummill (2024) A robust genome assembly with transcriptomic data from the striped bark scorpion, Centruroides vittatus, G3 Genes|Genomes|Genetics, Volume 14, Issue 8, August 2024, jkae120, https://doi.org/10.1093/g3journal/jkae120

2023

Adie, Hylton, and Michael J. Lawes. “Solutions to Fire and Shade: Resprouting, Growing Tall and the Origin of Eurasian Temperate Broadleaved Forest.” Biological Reviews 98, no. 2 (April 2023): 643–61. https://doi.org/10.1111/brv.12923.

Alejandro Salado, Hanumanthrao Kannan, William Rouse Zoe Szajnfarber, and Nirav Merchant Young-Jun Son. “A Reference Architecture for a Policy Test Laboratory.” Acquisition Research Program, 2023.

Arancio, Walter, Nicolina Sciaraffa, and Claudia Coronnello. “MBS: A Genome Browser Annotation Track for High-Confident MicroRNA Binding Sites in Whole Human Transcriptome.” Database 2023 (April 22, 2023): baad015. https://doi.org/10.1093/database/baad015.

Balasubramanian, Vimal Kumar, Albert Rivas-Ubach, Tanya Winkler, Hugh Mitchell, James Moran, and Amir H. Ahkami. “Modulation of Polar Auxin Transport Identifies the Molecular Determinants of Source-Sink Carbon Relationships and Sink Strength in Poplar.” Preprint. Plant Biology, March 13, 2023. https://doi.org/10.1101/2023.03.12.532247.

Benson, Christopher W., Matthew R. Sheltra, Jeff P. Maughan, Eric N. Jellen, Matthew D. Robbins, B. Shaun Bushman, Eric L. Patterson, Nathan D. Hall, and David R. Huff. “Homoeologous Evolution of the Allotetraploid Genome of Poa Annua L.” Preprint. In Review, April 3, 2023. https://doi.org/10.21203/rs.3.rs-2729084/v1.

Bi, Li, Li-Li Han, Shuai Du, Dan-Ting Yu, Ji-Zheng He, Li-Mei Zhang, and Hang-Wei Hu. “Cross-Biome Soil Viruses as an Important Reservoir of Virulence Genes.” Journal of Hazardous Materials 442 (January 2023): 130111. https://doi.org/10.1016/j.jhazmat.2022.130111.

Buck, Ryan, Diego Ortega‐Del Vecchyo, Catherine Gehring, Rhett Michelson, Dulce Flores‐Rentería, Barbara Klein, Amy V. Whipple, and Lluvia Flores‐Rentería. “Sequential Hybridization May Have Facilitated Ecological Transitions in the Southwestern Pinyon Pine Syngameon.” New Phytologist 237, no. 6 (March 2023): 2435–49. https://doi.org/10.1111/nph.18543.

Bunting, Matt, Matthew Nice, Dan Work, Jonathan Sprinkle, and Roman Golota. “WiP Abstract: Edge-Based Privacy of Naturalistic Driving Data Collection.” In Proceedings of the ACM/IEEE 14th International Conference on Cyber-Physical Systems (with CPS-IoT Week 2023), 256–57. San Antonio TX USA: ACM, 2023. https://doi.org/10.1145/3576841.3589623.

Cai, Lirong, Holger Kreft, Amanda Taylor, Pierre Denelle, Julian Schrader, Franz Essl, Mark Van Kleunen, et al. “Global Models and Predictions of Plant Diversity Based on Advanced Machine Learning Techniques.” New Phytologist 237, no. 4 (February 2023): 1432–45. https://doi.org/10.1111/nph.18533.

Cardone, Richard, Smruti Padhy, Steven Black, Sean Cleveland, and Joe Stubbs. “A Decentralized Authorization and Security Framework for Distributed Research Workflows.” arXiv, May 13, 2023. http://arxiv.org/abs/2304.08557.

Chamorro González, Rocío, Thomas Conrad, Maja C. Stöber, Robin Xu, Mădălina Giurgiu, Elias Rodriguez-Fos, Katharina Kasack, et al. “Parallel Sequencing of Extrachromosomal Circular DNAs and Transcriptomes in Single Cancer Cells.” Nature Genetics 55, no. 5 (May 2023): 880–90. https://doi.org/10.1038/s41588-023-01386-y.

Chan, Yen On, Nicholas Dietz, Shuai Zeng, Juexin Wang, Sherry Flint-Garcia, M. Nancy Salazar-Vidal, Mária Škrabišová, Kristin Bilyeu, and Trupti Joshi. “The Allele Catalog Tool: A Web-Based Interactive Tool for Allele Discovery and Analysis.” BMC Genomics 24, no. 1 (March 10, 2023): 107. https://doi.org/10.1186/s12864-023-09161-3.

Chaulagain, Diptee, Elise Schnabel, Ashley Crook, Sagar Bashyal, Lena Maria Müller, and Julia Frugoli. “A Mutation in Mediator Subunit MED16A Suppresses Nodulation and Increases Arbuscule Density in Medicago Truncatula.” Journal of Plant Growth Regulation, May 12, 2023. https://doi.org/10.1007/s00344-023-10993-2.

Chávez Montes, Ricardo A., Mauricio Ulloa, Tammy Biniashvili, Arik Zackay, Nir Kfir, Damar Lopez-Arredondo, and Luis Herrera-Estrella. “Assembly and Annotation of the Gossypium Barbadense L. ‘Pima-S6’ Genome Raise Questions about the Chromosome Structure and Gene Content of Gossypium Barbadense Genomes.” BMC Genomics 24, no. 1 (January 10, 2023): 11. https://doi.org/10.1186/s12864-022-09102-6.

Chivian, Dylan, Sean P. Jungbluth, Paramvir S. Dehal, Elisha M. Wood-Charlson, Richard S. Canon, Benjamin H. Allen, Mikayla M. Clark, et al. “Metagenome-Assembled Genome Extraction and Analysis from Microbiomes Using KBase.” Nature Protocols 18, no. 1 (January 2023): 208–38. https://doi.org/10.1038/s41596-022-00747-x.

Daradur, Jenya, Mohamad Kesserwan, Nowlan H. Freese, Ann E. Loraine, and C. Daniel Riggs. “Genomic Targets of HOP2 Are Enriched for Features Found at Recombination Hotspots.” Preprint. Plant Biology, January 25, 2023. https://doi.org/10.1101/2023.01.25.525520.

Diaz, Rudy, Zheng Wang, and Jeffrey P. Townsend. “Measurement and Meaning in Gene Expression Evolution.” In Transcriptome Profiling, 111–29. Elsevier, 2023. https://doi.org/10.1016/B978-0-323-91810-7.00008-X.

Donovan, Sam, and M. Drew LaMar. “Using Science Education Gateways to Improve Undergraduate STEM Education: The QUBES Platform as a Case Study.” arXiv, January 4, 2023. http://arxiv.org/abs/2301.01760.

Ehsani, Mohammad Reza. “Improving Global Satellite Precipiation Products Utilizing Machine Learning.” PhD Thesis, The University of Arizona, 2023.

Epstein, Ruth, Nikita Sajai, Mateusz Zelkowski, Adele Zhou, Kelly R. Robbins, and Wojciech P. Pawlowski. “Exploring Impact of Recombination Landscapes on Breeding Outcomes.” Proceedings of the National Academy of Sciences 120, no. 14 (April 4, 2023): e2205785119. https://doi.org/10.1073/pnas.2205785119.

George, Nikhil A., and Laura A. Hug. “CRISPR-Resolved Virus-Host Interactions in a Municipal Landfill Include Non-Specific Viruses, Hyper-Targeted Viral Populations, and Interviral Conflicts.” Scientific Reports 13, no. 1 (April 5, 2023): 5611. https://doi.org/10.1038/s41598-023-32078-6.

Hartwig, Thomas, Michael Banf, Gisele Passaia Prietsch, Jia-Ying Zhu, Isabel Mora-Ramírez, Jos H. M. Schippers, Samantha J. Snodgrass, et al. “Hybrid Allele-Specific ChIP-Seq Analysis Identifies Variation in Brassinosteroid-Responsive Transcription Factor Binding Linked to Traits in Maize.” Genome Biology 24, no. 1 (May 8, 2023): 108. https://doi.org/10.1186/s13059-023-02909-w.

Henning, Paige M., Eric H. Roalson, Wali Mir, Andrew G. McCubbin, and Joel S. Shore. “Annotation of the Turnera Subulata (Passifloraceae) Draft Genome Reveals the S-Locus Evolved after the Divergence of Turneroideae from Passifloroideae in a Stepwise Manner.” Plants 12, no. 2 (January 7, 2023): 286. https://doi.org/10.3390/plants12020286.

Henry, Erin, Luca Santini, Mark A. J. Huijbregts, and Ana Benítez‐López. “Unveiling the Environmental Drivers of Intraspecific Body Size Variation in Terrestrial Vertebrates.” Global Ecology and Biogeography 32, no. 2 (February 2023): 267–80. https://doi.org/10.1111/geb.13621.

Hoosain, Nisreen, Jeanne Korsman, Peter O Kimathi, Paidamoyo Kachambwa, Rembu Magoba, and Shane L Murray. “AquaSens: Exploring the Use of 16S RRNA next-Generation Sequencing to Determine Bacterial Composition of Various Water Matrices.” Water SA 49, no. 2 (2023): 117–25.

Humphrey, Jack, Sanan Venkatesh, Rahat Hasan, Jake T. Herb, Katia De Paiva Lopes, Fahri Küçükali, Marta Byrska-Bishop, et al. “Integrative Transcriptomic Analysis of the Amyotrophic Lateral Sclerosis Spinal Cord Implicates Glial Activation and Suggests New Risk Genes.” Nature Neuroscience 26, no. 1 (January 2023): 150–62. https://doi.org/10.1038/s41593-022-01205-3.

Jackson, Robert, Esha V Rajadhyaksha, Reid S Loeffler, Caitlyn E Flores, and Koenraad Van Doorslaer. “Characterization of 3D Organotypic Epithelial Tissues Reveals Tonsil-Specific Differences in Tonic Interferon Signaling.” Preprint. Cell Biology, January 21, 2023. https://doi.org/10.1101/2023.01.19.524743.

Joshi, Anand B., Abdul Gaffar, and Sonali Singh. “Security of Medical Images Based on Special Orthogonal Group and Galois Field.” Multimedia Tools and Applications, April 13, 2023. https://doi.org/10.1007/s11042-023-15033-5.

Kang, Jian, Sidharth Sen, Melvin J. Oliver, and Robert E. Sharp. “Comparative Transcriptomics Reveal Metabolic Rather than Genetic Control of Divergent Antioxidant Metabolism in the Primary Root Elongation Zone of Water-Stressed Cotton and Maize.” Antioxidants 12, no. 2 (January 27, 2023): 287. https://doi.org/10.3390/antiox12020287.

Keuler, Rachel. “Assessing the Role of Hybridization in the Evolution of Two Common Lineages of Lichen-Forming Fungi.” These and Dissertations 9888 (2023). https://scholarsarchive.byu.edu/etd/9888.

Khanam, Ruqaiya, and Gitanjali Mehta. “Application of Deep CNN for Image-Based Identification and Classification of Plant Diseases.” In 2023 10th International Conference on Signal Processing and Integrated Networks (SPIN), 224–29. Noida, India: IEEE, 2023. https://doi.org/10.1109/SPIN57001.2023.10116967.

Kruasuwan, Worarat, Karan Lohmaneeratana, John T. Munnoch, Wanwipa Vongsangnak, Chatchawan Jantrasuriyarat, Paul A. Hoskisson, and Arinthip Thamchaipenet. “Transcriptome Landscapes of Salt-Susceptible Rice Cultivar IR29 Associated with a Plant Growth Promoting Endophytic Streptomyces.” Rice 16, no. 1 (December 2023): 6. https://doi.org/10.1186/s12284-023-00622-7.

Li, Wenwen, Sizhe Wang, Xiao Chen, Yuanyuan Tian, Zhining Gu, Anna Lopez-Carr, Andrew Schroeder, Kitty Currier, Mark Schildhauer, and Rui Zhu. “GeoGraphVis: A Knowledge Graph and Geovisualization Empowered Cyberinfrastructure to Support Disaster Response and Humanitarian Aid.” ISPRS International Journal of Geo-Information 12, no. 3 (March 7, 2023): 112. https://doi.org/10.3390/ijgi12030112.

Li, Yangjie, Bin Ma, Kexin Hua, Huimin Gong, Rongrong He, Rui Luo, Dingren Bi, Rui Zhou, Paul R. Langford, and Hui Jin. “PPNet: Identifying Functional Association Networks by Phylogenetic Profiling of Prokaryotic Genomes.” Edited by Sébastien P. Faucher. Microbiology Spectrum 11, no. 1 (February 14, 2023): e03871-22. https://doi.org/10.1128/spectrum.03871-22.

Lima, Dayane Cristina, Alejandro Castro Aviles, Ryan Timothy Alpers, Alden Perkins, Dylan L. Schoemaker, Martin Costa, Shawn Kaeppler, et al. “2020-2021 Field Seasons of Maize G x E Project within Maize Genomes to Fields Initiative.” Preprint. In Review, May 11, 2023. https://doi.org/10.21203/rs.3.rs-2908766/v1.

McGarry, Róisín C, Harmanpreet Kaur, Yen-Tung Lin, Guadalupe Lopez Puc, Leor Eshed Williams, Esther Van Der Knaap, and Brian G Ayre. “Altered Expression of SELF-PRUNING Disrupts Homeostasis and Facilitates Signal Delivery to Meristems.” Plant Physiology, February 28, 2023, kiad126. https://doi.org/10.1093/plphys/kiad126.

Mitra, Saptashwa, Maxwell Roselius, Pedro Andrade‐Sanchez, John K. McKay, and Sangmi Lee Pallickara. “Radix+ : High‐throughput Georeferencing and Data Ingestion over Voluminous and Fast‐evolving Phenotyping Sensor Data.” Concurrency and Computation: Practice and Experience 35, no. 8 (April 10, 2023). https://doi.org/10.1002/cpe.7484.

Nguyen, Minh. “Cost-Effective and Performance-Preserving Secured Application Management in Cloud Environments.” PhD Thesis, City University of New York, 2023.

Prather, Ben S., Jason Dexter, Monika Moscibrodzka, Hung-Yi Pu, Thomas Bronzwaer, Jordy Davelaar, Ziri Younsi, et al. “Comparison of Polarized Radiative Transfer Codes Used by the EHT Collaboration.” arXiv, March 21, 2023. http://arxiv.org/abs/2303.12004.

Priyadarshini, Parichita, Smrutirekha Sahu, Gopal Kalwan, Yashwant K. Yadava, Ramawatar Nagar, Vandna Rai, C. Bharadwaj, Kishor Gaikwad, and Pradeep K. Jain. “Unravelling the Mechanism of Fusarium Wilt Resistance in Chickpea Seedlings Using Biochemical Studies and Expression Analysis of NBS-LRR and WRKY Genes.” Physiological and Molecular Plant Pathology 124 (March 2023): 101958. https://doi.org/10.1016/j.pmpp.2023.101958.

Raevskiy, Mikhail, Vladislav Yanvarev, Sascha Jung, Antonio Del Sol, and Yulia A. Medvedeva. “Epi-Impute: Single-Cell RNA-Seq Imputation via Integration with Single-Cell ATAC-Seq.” International Journal of Molecular Sciences 24, no. 7 (March 25, 2023): 6229. https://doi.org/10.3390/ijms24076229.

———. “Epi-Impute: Single-Cell RNA-Seq Imputation via Integration with Single-Cell ATAC-Seq.” International Journal of Molecular Sciences 24, no. 7 (March 25, 2023): 6229. https://doi.org/10.3390/ijms24076229.

Rawlings, Christopher John, and Robert P. Davey. “From Farm to FAIR: The Trials of Linking and Sharing Wheat Research Data.” In Towards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development, edited by Hugh F. Williamson and Sabina Leonelli, 107–23. Cham: Springer International Publishing, 2023. https://doi.org/10.1007/978-3-031-13276-6_6.

Samuels, Mark E., Cassandra Lapointe, Sara Halwas, and Anne C. Worley. “Genomic Sequence of Canadian Chenopodium Berlandieri: A North American Wild Relative of Quinoa.” Plants 12, no. 3 (January 19, 2023): 467. https://doi.org/10.3390/plants12030467.

Sarzaeim, Parisa, Francisco Munoz-Arriola, Diego Jarquin, Hasnat Aslam, and Natalia De Leon Gatti. “CLIM4OMICS: A Geospatially Comprehensive Climate and Multi-OMICS Database for Maize Phenotype Predictability in the U.S. and Canada.” Preprint. ESSD – Land/Biogeosciences and biodiversity, February 1, 2023. https://doi.org/10.5194/essd-2023-11.

Stoy, Kayla S, Joselyne Chavez, Valeria De Las Casas, Venkat Talla, Aileen Berasategui, Levi T Morran, and Nicole M Gerardo. “Evaluating Coevolution in a Horizontally Transmitted Mutualism.” Evolution 77, no. 1 (January 23, 2023): 166–85. https://doi.org/10.1093/evolut/qpac009.

Swartz LG, Liu S, Dahlquist D, Kramer ST, Walter ES, McInturf SA, Bucksch A, Mendoza-Cózatl DG. OPEN leaf: an open-source cloud-based phenotyping system for tracking dynamic changes at leaf-specific resolution in Arabidopsis. Plant J. 2023 Dec;116(6):1600-1616. doi: 10.1111/tpj.16449. Epub 2023 Sep 21. PMID: 37733751. https://doi.org/10.1111/tpj.16449 

Tabugo, Sharon Rose M., Rose Chinly Mae H. Ortega, Chinee S. Padasas, Carl Nico P. Oñate, Grazzette Anne N. Dablo, Tricksie P. Balatero, Noel John Ian Feben S. Maguate, Joey Genevieve T. Martinez, Nancy Galvez‐Reyes, and Mylene M. Uy. “Conservation Initiatives of Syngnathiformes Species in the Southern Philippines: What Does the Mitochondrial DNA Signature Tell Us?” Aquatic Conservation: Marine and Freshwater Ecosystems 33, no. 3 (March 2023): 231–45. https://doi.org/10.1002/aqc.3924.

Thangavel, Gokilavani, Paulo G. Hofstatter, Raphaël Mercier, and André Marques. “Tracing the Evolution of the Plant Meiotic Molecular Machinery.” Plant Reproduction 36, no. 1 (March 2023): 73–95. https://doi.org/10.1007/s00497-022-00456-1.

Touchette, David, Catherine Maggiori, Ianina Altshuler, Alex Tettenborn, Louis-Jacques Bourdages, Elisse Magnuson, Olivia Blenner-Hassett, Isabelle Raymond-Bouchard, Alex Ellery, and Lyle G. Whyte. “Microbial Characterization of Arctic Glacial Ice Cores with a Semiautomated Life Detection System.” Astrobiology, April 26, 2023, ast.2022.0130. https://doi.org/10.1089/ast.2022.0130.

Tuggle, Christopher K, Jennifer Clarke, Brenda M Murdoch, Eric Lyons, Nicole M Scott, Bedrich Benes, Jacqueline Campbell, et al. “Current Challenges and Future of Agricultural Genomes to Phenomes in the US,” 2023.

Uchenna, Anukwu John, Nwamba Helen Ogochukwu, and Chiaha Ijeoma Emiliana. “DNA Barcoding of Selected Freshwater Fishes in New Calabar River, Rivers State, Nigeria.” Asian Journal of Biotechnology and Bioresource Technology, April 20, 2023, 28–38. https://doi.org/10.9734/ajb2t/2023/v9i1176.

Varma, Watan Kishor, and Vipin Kumar. “Analysis of Crop Leaf Image Classification Using Deep Learning Models over Novel Dataset.” In 2023 10th International Conference on Signal Processing and Integrated Networks (SPIN), 14–19. Noida, India: IEEE, 2023. https://doi.org/10.1109/SPIN57001.2023.10116960.

Warren, Derek, Vagner A. Benedito, R Chris Skinner, Ayad Alawadi, Eloisa Vendemiatti, David J. Laub, Casey Showman, Kristen Matak, and Janet C. Tou. “Low-Protein Diets Composed of Protein Recovered from Food Processing Supported Growth, but Induced Mild Hepatic Steatosis Compared with a No-Protein Diet in Young Female Rats.” The Journal of Nutrition, March 2023, S0022316623355019. https://doi.org/10.1016/j.tjnut.2023.03.028.

Zhang, Mujie, Yali Hao, Yi Yi, Shunzhang Liu, Qingyang Sun, Xiaoli Tan, Shan Tang, Xiang Xiao, and Huahua Jian. “Unexplored Diversity and Ecological Functions of Transposable Phages.” The ISME Journal, April 17, 2023. https://doi.org/10.1038/s41396-023-01414-z.

Zhang, Xue, Zhuo Jiang, Xilin Jiao, Yang Yu, Zhenan Wang, Yangyang Hou, Guohua Duan, et al. “Genome Assembly and Comparative Analysis of the Egg Parasitoid Wasp Trichogramma Dendrolimi Shed Light on the Composition and Evolution of Olfactory Receptors and Venoms.” Insects 14, no. 2 (January 31, 2023): 144. https://doi.org/10.3390/insects14020144.

Zhao, Zihao, Chie Amano, Thomas Reinthaler, Federico Baltar, Monica Orellana, and Gerhard Herndl. “Metaproteomic Analysis Decodes the Trophic Basis of Microbes in the Dark Ocean.” Preprint. In Review, April 7, 2023. https://doi.org/10.21203/rs.3.rs-2727130/v1.

Zheng, Kaiyang, Yue Dong, Yantao Liang, Yundan Liu, Xinran Zhang, Wenjing Zhang, Ziyue Wang, et al. “Genomic Diversity and Ecological Distribution of Marine Pseudoalteromonas Phages.” Marine Life Science & Technology, January 20, 2023. https://doi.org/10.1007/s42995-022-00160-z.

Zhou, Andy, Liam D. Kirkpatrick, Izaiah J. Ornelas, Lorenzo J. Washington, Niklas F. C. Hummel, Christopher W. Gee, Sophia N. Tang, Collin R. Barnum, Henrik V. Scheller, and Patrick M. Shih. “A Suite of Constitutive Promoters for Tuning Gene Expression in Plants.” ACS Synthetic Biology, April 21, 2023, acssynbio.3c00075. https://doi.org/10.1021/acssynbio.3c00075.

Zhou, Yifan, Liang Zhou, Shuling Yan, Lanming Chen, Mart Krupovic, and Yongjie Wang. “Diverse Viruses of Marine Archaea Discovered Using Metagenomics.” Environmental Microbiology 25, no. 2 (February 2023): 367–82. https://doi.org/10.1111/1462-2920.16287.

Zimmerman, Amy E., Justin C. Podowski, Gwendolyn E. Gallagher, Maureen L. Coleman, and Jacob R. Waldbauer. “Tracking Nitrogen Allocation to Proteome Biosynthesis in a Marine Microbial Community.” Nature Microbiology 8, no. 3 (January 12, 2023): 498–509. https://doi.org/10.1038/s41564-022-01303-9.

Zuo, Huanyan, Yao Xiao, Jiahao Han, Yuxiu Lin, Cheng Tian, Shu Zhang, Guohua Yuan, Huan Liu, and Zhi Chen. “Phosphorylation of ATF2 Promotes Odontoblastic Differentiation via Intrinsic HAT Activity.” Journal of Genetics and Genomics, February 2023, S1673852723000449. https://doi.org/10.1016/j.jgg.2023.02.005.

2022

Adams, S., Carré, I.. A. (2022). Chromatin Immunoprecipitation Protocol for Circadian Clock Proteins. Plant Circadian Networks, 2398, 135-150.

Amos, B., Aurrecoechea, C., Barba, M., Barreto, A., Basenko, E., Bażant, W., Belnap, R., Blevins, A.. S., Böhme, U., Brestelli, J., Brunk, B.. P., Caddick, M., Callan, D., Campbell, L., Christensen, M., Christophides, G., Crouch, K., Davis, K., DeBarry, J., Doherty, R., Duan, Y., Dunn, M., Falke, D., Fisher, S., Flicek, P., Fox, B., Gajria, B., Giraldo-Calderón, G.. I., Harb, O.. S., Harper, E., Hertz-Fowler, C., Hickman, M., Howington, C., Hu, S., Humphrey, J., Iodice, J., Jones, A., Judkins, J., Kelly, S.. A., Kissinger, J.. C., Kwon, D.. K., Lamoureux, K., Lawson, D., Li, W., Lies, K., Lodha, D., Long, J., MacCallum, R.. M., Maslen, G., McDowell, M.. A., Nabrzyski, J., Roos, D.. S., Rund, S.. S.. C., Schulman, S., Shanmugasundram, A., Sitnik, V., Spruill, D., Starns, D., Stoeckert, C., Tomko, S.. S., Wang, H., Warrenfeltz, S., Wieck, R., Wilkinson, P.. A., Xu, L., Zheng, J. (2022). VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Research, 50(D1), D898-D911. https://doi.org/10.1093/nar/gkab929

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. Microbiome, 10(1), 5. https://doi.org/10.1186/s40168-021-01194-8

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 Astronomy, 6(2), 259-269. https://doi.org/10.1038/s41550-021-01548-0

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. Virology, 568, 86-100. https://doi.org/10.1016/j.virol.2022.01.013

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 Biology, 102(1), 1-20. https://doi.org/10.1007/s42991-021-00186-3

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 Sciences, 119(5), e2118886119. https://doi.org/10.1073/pnas.2118886119

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 Teacher, 84(1), 40-44. https://doi.org/10.1525/abt.2022.84.1.40

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. https://doi.org/10.1093/jxb/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. Plant Gravitropism, 2368, 81-94.

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.

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. https://doi.org/10.1111/gcb.16038

Jhu, M., 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. https://doi.org/10.1093/plphys/kiac024

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 Chemistry, 41(2), 448-461. https://doi.org/10.1002/etc.5266

Martínez-Alvarez, L., Ramond, J., 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. .

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 Research, 276, 108371. https://doi.org/10.1016/j.fcr.2021.108371

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 Genetics, 135(1), 107-124. https://doi.org/10.1007/s00122-021-03954-4

Palos, K. (2022). Identifying Long Noncoding RNAs and Examining Their Functional Roles in Brassicaceae. .

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. .

Sams, E.. I., Ng, J.. K., Tate, V., Claire Hou, Y., 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 Advances, 3(1), 100081. https://doi.org/10.1016/j.xhgg.2021.100081

Satapathy, K., Psaltis, D., Özel, F., Medeiros, L., Dougall, S.. T., Chan, C., 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 Journal, 925(1), 13.

Senn, S., Pangell, K., Bowerman, A.. L. (2022). Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia. BioTech, 11(1), 1. https://doi.org/10.3390/biotech11010001

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].

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 Journal, 163(2), 62. https://doi.org/10.3847/1538-3881/ac3b5b

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 Data, 9(1), 16. https://doi.org/10.1038/s41597-022-01123-w

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 Biology, 23(1), 3, s13059-021-02570-1. https://doi.org/10.1186/s13059-021-02570-1

Wang, L., Lu, Z., Van Buren, P., Ware, D. (2022). SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data. Plant Bioinformatics, 2443, 197-209.

Williams, J. (2022). CyVerse for Reproducible Research: RNA-Seq Analysis. Plant Bioinformatics, 2443, 57-79.

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. The Medicago truncatula Genome, 1-9.

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. .

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 Genetics, 135(1), 273-290. https://doi.org/10.1007/s00122-021-03965-1

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 Research, 276, 108376. https://doi.org/10.1016/j.fcr.2021.108376

2021

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. .

Alex Mason, G., Cantó-Pastor, A., Brady, S.. M., Provart, N.. J. (2021). Bioinformatic Tools in Arabidopsis Research. Arabidopsis Protocols, 2200, 25-89.

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. .

Balatskyi, V.. V., Vaskivskyi, V.. O., Myronova, A., Avramets, D., Nahia, K.. A., Macewicz, L.. L., Ruban, T.. P., Kucherenko, D.. Y., 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].

Barbosa, R.. d.. 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. .

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. 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., Bidinosti, C.. P., Henry, C.. J., Godee, C.. M., Ajmani, M. (2021). Presenting an extensive lab- and field-image dataset of crops and weeds for computer vision tasks in agriculture. arXiv:2108.05789 [cs].

Beck, M.. A., Liu, C., 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. .

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. .

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. The Moringa Genome, 85-100.

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. (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. (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, 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., Czarnecki, K., Zumstein, K., Nakayama, H., Sinha, N.. R. (2021). Analysis of Classic Tomato Mutants Reveals Influence of Leaf Vein Density on Fruit BRIX. .

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. .

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., 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. .

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

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.

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

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].

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/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. (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.

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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. .

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. .

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., Moose, S.. P., Murray, S.. C., Nelson, R., Rocheford, T., Schnable, J.. C., Schnable, P.. S., Sekhon, R., Singh, M., Smith, M., Springer, N., Thelen, K., Thomison, P., Thompson, A., Tuinstra, M., Wallace, J., Wisser, R.. J., Xu, W., Gilmour, A.. R., Kaeppler, S.. M., De Leon, N., 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., 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

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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/10.1007/978-1-62703-580-4

Satapathy, K. (2021). The Variability of the Black-Hole Image in M87 at the Dynamical Time Scale. .

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

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

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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

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2020

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Anche, M.. T., Kaczmar, N.. S., Morales, N., Clohessy, J.. W., Ilut, D.. C., Gore, M.. A., Robbins, K.. R. (2020). Temporal covariance structure of multi-spectral phenotypes and their predictive ability for end-of-season traits in maize. Theoretical and Applied Genetics, 133(10), 2853-2868. https://doi.org/10.1007/s00122-020-03637-6

Anderson, J., Keppel, G., Thomson, S., Gibbs, J., Brunetti, G. (2020). High diversity of native plants and vegetation types in the Morialta Conservation Park and the threat of invasive species. Transactions of the Royal Society of South Australia, 144(2), 180-199. https://doi.org/10.1080/03721426.2020.1786779

Arifuzzaman, M., Horvath, D., Rahman, M. (2020). Transcriptome Analysis Suggests Cytokinin and Gibberellin Signaling May Account for Differences Between Spring and Winter Canola (Brassica napus L.) Root Development. Journal of Plant Biology. https://doi.org/10.1007/s12374-020-09270-6

Arnaud, E., Laporte, M., Kim, S., Aubert, C., Leonelli, S., Miro, B., Cooper, L., Jaiswal, P., Kruseman, G., Shrestha, R., Buttigieg, P.. L., Mungall, C.. J., Pietragalla, J., Agbona, A., Muliro, J., Detras, J., Hualla, V., Rathore, A., Das, R.. R., Dieng, I., Bauchet, G., Menda, N., Pommier, C., Shaw, F., Lyon, D., Mwanzia, L., Juarez, H., Bonaiuti, E., Chiputwa, B., Obileye, O., Auzoux, S., Yeumo, E.. D., Mueller, L.. A., Silverstein, K., Lafargue, A., Antezana, E., Devare, M., King, B. (2020). The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. Patterns, 1(7), 100105. https://doi.org/10.1016/j.patter.2020.100105

Arya, S.. S., Rookes, J.. E., Cahill, D.. M., Lenka, S.. K. (2020). Next-generation metabolic engineering approaches towards development of plant cell suspension cultures as specialized metabolite producing biofactories. Biotechnology Advances, 45, 107635. https://doi.org/10.1016/j.biotechadv.2020.107635

Bainard, J.. D., Newmaster, S.. G., Budke, J.. M. (2020). Genome size and endopolyploidy evolution across the moss phylogeny. Annals of Botany, 125(4), 543-555. https://doi.org/10.1093/aob/mcz194

Barker, R., Lombardino, J., Rasmussen, K., Gilroy, S. (2020). Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. Frontiers in Plant Science, 11, 147. https://doi.org/10.3389/fpls.2020.00147

Baránková, S., Pascual‐Díaz, J.. P., Sultana, N., Alonso‐Lifante, M.. P., Balant, M., Barros, K., D'Ambrosio, U., Malinská, H., Peska, V., Pérez Lorenzo, I., Kovařík, A., Vyskot, B., Janoušek, B., Garcia, S. (2020). Sex‐chrom, a database on plant sex chromosomes. New Phytologist, 227(6), 1594-1604. https://doi.org/10.1111/nph.16635

Beckman, N.. G. (2020). Collaborative Research: Diverse selective pressure on fruit chemical traits from mutualists and antagonists as a major driver of chemical evolution at the whole plant level. . https://doi.org/10.26078/1EDM-3130

Bekkering, C.. S., Huang, J., Tian, L. (2020). Image-Based, Organ-Level Plant Phenotyping for Wheat Improvement. Agronomy, 10(9), 1287. https://doi.org/10.3390/agronomy10091287

Bessell, T., Frith, J., Scott, L., Skuljan, J., Furfaro, R., Reddy, V. (2020). PHANTOM ECHOES: A Five-Eyes SDA Experiment to Examine GEO Rendezvous and Proximity Operations Simon George, Andrew Ash Defence Science & Technology Laboratory, UK. .

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Albert, C., Mårell, A., Picard, M., Baltzinger (2015). Using basic plant traits to predict ungulate seed dispersal potential. , 38(5), 440-449. https://doi.org/10.1111/ecog.00709

Allahverdiyeva, M., Battchikova, N., Brosché, M., Fujii, H., Kangasjärvi, S., Mulo, P., Mähönen, A.. P., Nieminen, K., Overmyer, K., Salojärvi, J., Wrzaczek (2015). Integration of photosynthesis, development and stress as an opportunity for plant biology. , 208(3), 647-655. https://doi.org/10.1111/nph.13549

Alvi, A.. V., Chu, T., Schawaroch, V., Klaus (2015). Genomic and expression analysis of transition proteins in Drosophila. , 5(3), e1178518. https://doi.org/10.1080/21565562.2016.1178518

Ananthakrishnan, S., Chard, K., Foster, I., Tuecke (2015). Globus platform-as-a-service for collaborative science applications. , 27(2), 290–305.

Antoni, A., Kutztown, P. (2015). A Bioinformatics Approach to Systemic Lupus Erythematosus and Autoimmunity. .

Antoni, P., Kutztown (2015). A Bioinformatics Approach to Systemic Lupus Erythematosus and Autoimmunity. .

Bailey, D. (2015). Using iPlant Tools and Plastome Sequencing As a Springboard into Comparative Genomics: Plastome Organization and Sequence for the Mimosoid Legume Leucaena trichandra. .

Batllori, M.. A., Ackerly, D.. D., Moritz (2015). A minimal model of fire-vegetation feedbacks and disturbance stochasticity generates alternative stable states in grassland–shrubland–woodland systems. , 10(3), 34018. https://doi.org/10.1088/1748-9326/10/3/034018

Blonder, B.. J., Nogués-Bravo, D., Borregaard, M.. K., Donoghue, J.. C., Jørgensen, P.. M., Kraft, N.. J.. B., Lessard, J., Morueta-Holme, N., Sandel, B., Svenning, J., Violle, C., Rahbek, C., Enquist (2015). Linking environmental filtering and disequilibrium to biogeography with a community climate framework. , 96(4), 972-985. https://doi.org/10.1890/14-0589.1

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Chamala, P.. S., García, N., Godden, G.. T., Krishnakumar, V., Jordon-Thaden, I.. E., Smet, R.. D., Barbazuk, W.. B., Soltis, D.. E., Soltis (2015). MarkerMiner 1.0: A New Application for Phylogenetic Marker Development Using Angiosperm Transcriptomes. , 3(4), 1400115. https://doi.org/10.3732/apps.1400115

Chard, I., Chard, K., Bubendorfer, K., Lacinski, L., Madduri, R., Foster (2015). Cost-Aware Cloud Provisioning. , 136-144. https://doi.org/10.1109/eScience.2015.67

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Cheng, C., Erik Ferlanti, VIvek Krishnakumar, Maria Kim, Svetlana Karamycheva, Benjamin D. Rosen, Matt Hanlon, Steve Mock, Joe Stubbs, Walter Moreira, Rion Dooley, Sergio Contrino, Julie Sullivan, Alex Kalderimis, Gos Micklem, Jason R. Miller, Matt Vaughn, Christopher D. Town (2015). Data Integration for the Plant Research Community: The Arabidopsis Information Portal. .

Chougule, K. (2015). Flash Demo: Atmosphere Cloud Computing - Applied to Visualizing RNA-Seq Data. .

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Council, N.. R., others (2015). Enhancing the effectiveness of team science. .

Crivelli, S., The WeFold Community, S., Dooley, R., Holmes, R., Mock (2015). Creating a gateway that enables large-scale science coopetition: LARGE-SCALE SCIENCE COOPETITION. , 27(2), 446-457. https://doi.org/10.1002/cpe.3270

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Das, A., Schneider, H., Burridge, J., Ascanio, A.. K.. M., Wojciechowski, T., Topp, C.. N., Lynch, J.. P., Weitz, J.. S., Bucksch (2015). Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics. , 11(1), 51. https://doi.org/10.1186/s13007-015-0093-3

DeBarry, J. (2015). Flash Demo: Secure, Collaborative, Management of Your Life Sciences Data with the Data Store. .

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Deck, J., Guralnick, R., Walls, R., Blum, S., Haendel, M., Matsunaga, A., Wieczorek (2015). Meeting report: Identifying practical applications of ontologies for biodiversity informatics. , 10(1), 25. https://doi.org/10.1186/s40793-015-0014-0

Deng, D.. E., Drew, B.. T., Mavrodiev, E.. V., Gitzendanner, M.. A., Soltis, P.. S., Soltis (2015). Phylogeny, divergence times, and historical biogeography of the angiosperm family Saxifragaceae. , 83, 86-98. https://doi.org/10.1016/j.ympev.2014.11.011

Devisetty, U.. K. (2015). A Hybrid Approach to Assemble and Annotate the Brassica rapa Transcriptome in the Cloud through the iPlant Collaborative and XSEDE. .

Dhanapal, M., Govindaraj (2015). Unlimited thirst for genome sequencing, data interpretation, and database usage in genomic era: the road towards fast-track crop plant improvement. , 2015.

Docherty, R.. E., Borton, H.. M., Espinosa, N., Gebhardt, M., Gil-Loaiza, J., Gutknecht, J.. L.. M., Maes, P.. W., Mott, B.. M., Parnell, J.. J., Purdy, G., Rodrigues, P.. A.. P., Stanish, L.. F., Walser, O.. N., Gallery (2015). Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes. , 10(11), e0135352. https://doi.org/10.1371/journal.pone.0135352

Dooley, M.. R., Hanlon (2015). Recipes 2.0: building for today and tomorrow: RECIPES 2.0: BUILDING FOR TODAY AND TOMORROW. , 27(2), 258-270. https://doi.org/10.1002/cpe.3285

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Dvorak, J.. e.. a. (2015). BAC-Based Sequencing of the Aegilops tauschii Genome. .

Eastmond, J.. M., Astley, H.. M., Parsley, K., Aubry, S., Williams, B.. P., Menard, G.. N., Craddock, C.. P., Nunes-Nesi, A., Fernie, A.. R., Hibberd (2015). Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment. , 6(1), 6659. https://doi.org/10.1038/ncomms7659

Engemann, J., Enquist, B.. J., Sandel, B., Boyle, B., Jørgensen, P.. M., Morueta-Holme, N., Peet, R.. K., Violle, C., Svenning (2015). Limited sampling hampers “big data” estimation of species richness in a tropical biodiversity hotspot. , 5(3), 807-820. https://doi.org/10.1002/ece3.1405

Etemadpour, A., Bomhoff, M., Lyons, E., Murray, P., Forbes (2015). Designing and evaluating scientific workflows for big data interactions. , 1–8.

Fahlgren, I., Gehan, M.. A., Baxter (2015). Lights, camera, action: high-throughput plant phenotyping is ready for a close-up. , 24, 93-99. https://doi.org/10.1016/j.pbi.2015.02.006

Fischer, C.. A., Tuecke, S., Foster, I., Stewart (2015). Jetstream: A distributed cloud infrastructure for underresourced higher education communities. , 53–61.

Flis, A.. J., Fernández, A.. P., Zielinski, T., Mengin, V., Sulpice, R., Stratford, K., Hume, A., Pokhilko, A., Southern, M.. M., Seaton, D.. D., McWatters, H.. G., Stitt, M., Halliday, K.. J., Millar (2015). Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure. , 5(10), 150042. https://doi.org/10.1098/rsob.150042

Fox, A., Qiu, J., Kamburugamuve, S., Jha, S., Luckow (2015). HPC-ABDS High Performance Computing Enhanced Apache Big Data Stack. , 1057-1066. https://doi.org/10.1109/CCGrid.2015.122

Gardiner, A., Quinton-Tulloch, M., Olohan, L., Price, J., Hall, N., Hall (2015). A genome-wide survey of DNA methylation in hexaploid wheat. , 16(1), 273. https://doi.org/10.1186/s13059-015-0838-3

Gardiner, J., Darwin Campbell, Carolyn J. Lawrence-Dill (2015). Identification and Development of Data Standards for Maize Field Phenotypic Measurements: Working with the GxE Subgroup of ht eGenomes2Fields Initiative. .

Gesing, A., Dooley, R., Pierce, M., Kruger, J., Grunzke, R., Herres-Pawlis, S., Hoffmann (2015). Science gateways - leveraging modeling and simulations in HPC infrastructures via increased usability. , 19-26. https://doi.org/10.1109/HPCSim.2015.7237017

Gesing, I., Connor, T.. R., Taylor (2015). Genomics and Biological Big Data: Facing Current and Future Challenges around Data and Software Sharing and Reproducibility. .

Goggin, C.. N., Lorence, A., Topp (2015). Applying high-throughput phenotyping to plant–insect interactions: picturing more resistant crops. , 9, 69-76. https://doi.org/10.1016/j.cois.2015.03.002

González, C., Larrainzar, E., Marino, D., Wienkoop, S., Gil-Quintana, E., Arrese-Igor (2015). Physiological Responses of N2-Fixing Legumes to Water Limitation. , May-33.

Goring, J.. W., Dawson, A., Simpson, G.. L., Ram, K., Graham, R.. W., Grimm, E.. C., Williams (2015). neotoma: A Programmatic Interface to the Neotoma Paleoecological Database. , 1. https://doi.org/10.5334/oq.ab

Goscinski, P., Church (2015). Clouds for Masses - Toward Ubiquitous and Transparent Clouds. , 1141-1148. https://doi.org/10.1109/CLOUD.2015.168

Gray, K., others, J., Burdo, B., Goetting-Minesky, M., Wittler, B., Hunt, M., Li, T., Velliquette, D., Thomas, J., Agarwal, T., Key (2015). Protocol for the generation of a transcription factor open reading frame collection (TFome). , 5(15), e15.

Guralnick, R., Cellinese, N., Deck, J., Pyle, R.. L., Kunze, J., Penev, L., Walls, R., Hagedorn, G., Agosti, D., Wieczorek, J., Catapano, T., Page (2015). Community Next Steps for Making Globally Unique Identifiers Work for Biocollections Data. , 494, 133-154. https://doi.org/10.3897/zookeys.494.9352

Hanlon, E., Vaughn, M., Mock, S., Dooley, R., Moreira, W., Stubbs, J., Town, C., Miller, J., Krishnakumar, V., Ferlanti, E., Pence (2015). Araport: an application platform for data discovery: Araport: an application platform for data discovery. , 27(16), 4412-4422. https://doi.org/10.1002/cpe.3542

Harper, L.. e.. a. (2015). An Ontology Approach to Comparative Phenomics in the Plants: Arabidopsis, Tomato, Maize, Rice, Soybean and Medicago. .

Hart, D., Rast, R., Jefferies, S., Hope (2015). Resolved observations of geostationary satellites from the 6.5 m MMT. .

Haug-Baltzell, E., Jarvis, E.. D., McCarthy, F.. M., Lyons (2015). Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates. , 9. https://doi.org/10.3389/fnins.2015.00361

Haug-Baltzell, E.. J.. A., Dopamine (2015). Receptors DRD1a and DRD1b Arise from an Ancient Vertebrate Whole Genome Duplication. .

Heiland, V., Koranda, S., Marru, S., Pierce, M., Welch (2015). Authentication and Authorization Considerations for a Multi-tenant Service. , 29-35. https://doi.org/10.1145/2753524.2753534

Horvath, M., Anderson, J.. V., Chao, W.. S., Foley, M.. E., Doğramaci (2015). Leafy Spurge Genomics: A Model Perennial Weed to Investigate Development, Stress Responses, and Invasiveness. , 63–78.

Horvath, S.. A., Hansen, S.. A., Moriles-Miller, J.. P., Pierik, R., Yan, C., Clay, D.. E., Scheffler, B., Clay (2015). RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean. , 207(1), 196-210. https://doi.org/10.1111/nph.13351

Huala, E.. e.. a. (2015). Flash Talk: An Ontology Approach to Comparative Phenomics in Plants. .

Huang, J.. H., Jennings, S.. F., Bruce, B., Buchan, A., Cai, L., Chen, P., Cramer, C.. L., Guan, W., Hilgert, U.. K., Jiang, H., Li, Z., McClure, G., McMullen, D.. F., Nanduri, B., Perkins, A., Rekepalli, B., Salem, S., Specker, J., Walker, K., Wunsch, D., Xiong, D., Zhang, S., Zhang, Y., Zhao, Z., Moore (2015). Big data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm. , 8(1), 7. https://doi.org/10.1186/s13040-015-0037-5

Huck, K., Jain, A., Gunter, D., Winston, D., Persson (2015). A Community Contribution Framework for Sharing Materials Data with Materials Project. , 535-541. https://doi.org/10.1109/eScience.2015.75

Hurwitz, M.. B., Brum, J.. R., Sullivan (2015). Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome. , 9(2), 472-484. https://doi.org/10.1038/ismej.2014.143

James, M., McLay, R., Liu, S., Evans, R.. T., Barth, W.. L., Lamas-Linares, A., Budiardja, R., Fahey (2015). Tales from the trenches: can user support tools make a difference?. , 11-Jan. https://doi.org/10.1145/2834996.2834998

Jonquet, P., Dzalé-Yeumo, E., Arnaud, E., Larmande (2015). AgroPortal: a proposition for ontology-based services in the agronomic domain. .

Jordan, D., Walling, D., Xu, W., Mock, S.. A., Gaffney, N., Stanzione (2015). Wrangler's user environment: A software framework for management of data-intensive computing system. , 2479-2486. https://doi.org/10.1109/BigData.2015.7364043

Kociumaka, T., Pissis, S.. P., Radoszewski, J., Rytter, W., Waleń (2015). Fast algorithm for partial covers in words. , 73(1), 217–233.

Krampis, C., Wultsch (2015). A Review of Cloud Computing Bioinformatics Solutions for Next-Gen Sequencing Data Analysis and Research. , 2(1). https://doi.org/10.1515/mngs-2015-0003

Krishnakumar, C.. D., Hanlon, M.. R., Contrino, S., Ferlanti, E.. S., Karamycheva, S., Kim, M., Rosen, B.. D., Cheng, C., Moreira, W., Mock, S.. A., Stubbs, J., Sullivan, J.. M., Krampis, K., Miller, J.. R., Micklem, G., Vaughn, M., Town (2015). Araport: the Arabidopsis Information Portal. , 43(D1), D1003-D1009. https://doi.org/10.1093/nar/gku1200

Köhl, J., Gremmels (2015). A software tool for the input and management of phenotypic data using personal digital assistants and other mobile devices. , 11(1), 25. https://doi.org/10.1186/s13007-015-0069-3

Lapatas, M.. V., Stefanidakis, M., Jimenez, R.. C., Via, A., Schneider (2015). Data integration in biological research: an overview. , 22(1), 9. https://doi.org/10.1186/s40709-015-0032-5

Law, M., Childs, K.. L., Campbell, M.. S., Stein, J.. C., Olson, A.. J., Holt, C., Panchy, N., Lei, J., Jiao, D., Andorf, C.. M., Lawrence, C.. J., Ware, D., Shiu, S., Sun, Y., Jiang, N., Yandell (2015). Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes. , 167(1), 25-39. https://doi.org/10.1104/pp.114.245027

Lewis, J.. H., Hartman (2015). Accordion: multi-scale recipes for adaptive detection of duplication. .

Li, J., Hou, J., Sun, L., Wilkins, J.. M., Lu, Y., Niederhuth, C.. E., Merideth, B.. R., Mawhinney, T.. P., Mossine, V.. V., Greenlief, C.. M., Walker, J.. C., Folk, W.. R., Hannink, M., Lubahn, D.. B., Birchler, J.. A., Cheng (2015). From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data. , 10(4), e0125000. https://doi.org/10.1371/journal.pone.0125000

Li, N.. M., Song, J., West, P.. T., Zynda, G., Eichten, S.. R., Vaughn, M.. W., Springer (2015). Examining the Causes and Consequences of Context-Specific Differential DNA Methylation in Maize. , 168(4), 1262-1274. https://doi.org/10.1104/pp.15.00052

Lin, D.. J., Lashbrook, C.. C., Cho, S.. K., Butler, N.. M., Sharma, P., Muppirala, U., Severin, A.. J., Hannapel (2015). Transcriptional analysis of phloem-associated cells of potato. , 16(1), 665. https://doi.org/10.1186/s12864-015-1844-2

Liu, A., Ramsay, T., Zinkgraf, M., Sundell, D., Street, N.. R., Filkov, V., Groover (2015). A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus. , 82(5), 887-898. https://doi.org/10.1111/tpj.12850

Liu, G., Niu, Y., Gonzalez-Portilla, P.. J., Zhou, H., Wang, L., Zuo, T., Qin, C., Tai, S., Jansen, C., Shen, Y., Lin, H., Lee, M., Ware, D., Zhang, Z., Lübberstedt, T., Pan (2015). An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize. , 16(1), 1078. https://doi.org/10.1186/s12864-015-2242-5

Liu, Y.. e.. a. (2015). Large-Scale Next-Generation Resequencing of Soybean Germplasm for Trait Discovery. .

Lushbough, R., Gnimpieba, E.. Z., Dooley (2015). Life science data analysis workflow development using the bioextract server leveraging the iPlant collaborative cyberinfrastructure: BIOEXTRACT SERVER WORKFLOWS LEVERAGING IPLANT COLLABORATIVE. , 27(2), 408-419. https://doi.org/10.1002/cpe.3237

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Ma, A.. G., Hunt (2015). A 3′ RACE Protocol to Confirm Polyadenylation Sites. , 1255, 135-144.

Macías-Duarte, C.. J., Conway (2015). Spatial patterns in hydrogen isotope ratios in feathers of Burrowing Owls from western North America. , 132(1), 25-36. https://doi.org/10.1642/AUK-13-061.1

Macías-Duarte, C.. J., Conway (2015). Distributional Changes in the Western Burrowing Owl ( Athene cunicularia hypugaea ) in North America from 1967 to 2008. , 49(1), 75-83. https://doi.org/10.3356/JRR-14-00004.1

Madduri, I., Chard, K., Chard, R., Lacinski, L., Rodriguez, A., Sulakhe, D., Kelly, D., Dave, U., Foster (2015). The Globus Galaxies platform: delivering science gateways as a service. , 27(16), 4344–4360.

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Marru, C., Pierce, M., Pamidighantam, S., Wimalasena (2015). Apache Airavata as a Laboratory: Architecture and Case Study for Component-Based Gateway Middleware. , 19-26. https://doi.org/10.1145/2753524.2753529

Martin, R., Cook, C., Matasci, N., Williams, J., Bastow (2015). Data mining with iPlant: A meeting report from the 2013 GARNet workshop, Data mining with iPlant. , 66(1), 6-Jan. https://doi.org/10.1093/jxb/eru402

McCarthy, F. (2015). Functional Analysis of Your RNAseq Data. .

McGregor, J., Bennett, D., Majumdar, S., Nandy, B., Melendez, J., St-Hilaire, M., Lau, D., Liu (2015). A Cloud-Based Platform for Supporting Research Collaboration. , 1107-1110. https://doi.org/10.1109/CLOUD.2015.162

Michaletz, B.. J., Weiser, M.. D., Zhou, J., Kaspari, M., Helliker, B.. R., Enquist (2015). Plant Thermoregulation: Energetics, Trait–Environment Interactions, and Carbon Economics. , 30(12), 714-724. https://doi.org/10.1016/j.tree.2015.09.006

Micklos, D. (2015). Simplifying Genome Annotation and Examples of Large-Scale Projects in DNA Barcoding (Red and Blue Lines). .

Micklos, D. (2015). Using Students' Own DNA Sequences to Explore Human Evolution. .

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Hurwitz, M.. B., Westveld, A.. H., Brum, J.. R., Sullivan (2014). Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. , 111(29), 10714-10719. https://doi.org/10.1073/pnas.1319778111

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Izquierdo-Carrasco, A., Cazes, J., Smith, S.. A., Stamatakis (2014). PUmPER: phylogenies updated perpetually. , 30(10), 1476–1477.

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2013

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Bayzid, T., Warnow (2013). Naive binning improves phylogenomic analyses. , 29(18), 2277-2284. https://doi.org/10.1093/bioinformatics/btt394

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2012

Alakonya, N., Kumar, R., Koenig, D., Kimura, S., Townsley, B., Runo, S., Garces, H.. M., Kang, J., Yanez, A., David-Schwartz, R., Machuka, J., Sinha (2012). Interspecific RNA Interference of SHOOT MERISTEMLESS-Like Disrupts Cuscuta pentagona Plant Parasitism. , 24(7), 3153-3166. https://doi.org/10.1105/tpc.112.099994

Beaulieu, J.. M., Ree, R.. H., Cavender-Bares, J., Weiblen, G.. D., Donoghue, M.. J. (2012). Synthesizing phylogenetic knowledge for ecological research. Ecology, 93(sp8), S4-S13. https://doi.org/10.1890/11-0638.1

Beck, C.. F., Ballesteros-Mejia, L., Buchmann, C.. M., Dengler, J., Fritz, S.. A., Gruber, B., Hof, C., Jansen, F., Knapp, S., Kreft, H., Schneider, A., Winter, M., Dormann (2012). What's on the horizon for macroecology?. , 35(8), 673-683. https://doi.org/10.1111/j.1600-0587.2012.07364.x

Blonder, B.. J., Buzzard, V., Simova, I., Sloat, L., Boyle, B., Lipson, R., Aguilar-Beaucage, B., Andrade, A., Barber, B., Barnes, C., Bushey, D., Cartagena, P., Chaney, M., Contreras, K., Cox, M., Cueto, M., Curtis, C., Fisher, M., Furst, L., Gallegos, J., Hall, R., Hauschild, A., Jerez, A., Jones, N., Klucas, A., Kono, A., Lamb, M., Matthai, J.. D.. R., McIntyre, C., McKenna, J., Mosier, N., Navabi, M., Ochoa, A., Pace, L., Plassmann, R., Richter, R., Russakoff, B., Aubyn, H.. S., Stagg, R., Sterner, M., Stewart, E., Thompson, T.. T., Thornton, J., Trujillo, P.. J., Volpe, T.. J., Enquist (2012). The leaf-area shrinkage effect can bias paleoclimate and ecology research. , 99(11), 1756-1763. https://doi.org/10.3732/ajb.1200062

Christou, M., Crochemore, M., Flouri, T., Iliopoulos, C.. S., Janoušek, J., Melichar, B., Pissis, S.. P. (2012). Computing all subtree repeats in ordered trees. Information Processing Letters, 112(24), 958-962. https://doi.org/10.1016/j.ipl.2012.09.001

Claros, N., Bautista, R., Guerrero-Fernández, D., Benzerki, H., Seoane, P., Fernández-Pozo (2012). Why Assembling Plant Genome Sequences Is So Challenging. , 1(2), 439-459. https://doi.org/10.3390/biology1020439

Cole, B.. J., Chory, J. (2012). Image-Based Analysis of Light-Grown Seedling Hypocotyls in Arabidopsis. High-Throughput Phenotyping in Plants, 918, 1-7.

Council, N.. R., others (2012). Implementing the Research Strategy and Evaluating Progress. .

Das, J.. S., Bucksch, A., Weitz (2012). Infrastructure for managing and analyzing biological networks derived from collections of plant images. .

Dooley, R., Vaughn, M., Terry, S., Stanzione, D., Skidmore, E., Merchant, N. (2012). Your data, your way the iPlant Foundation API Data Services. Proceedings of The Third International Workshop on Data Intensive Computing in the Clouds.

Dooley, R., Vaughn, M., Stanzione, D., Terry, S., Skidmore, E. (2012). Software-as-a-service: the iPlant foundation API. 5th IEEE Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS).

Dragut, E.. C., Ouzzani, M., Madkour, A., Mohamed, N., Baker, P., Salt, D.. E. (2012). Lonomics Atlas: a tool to explore interconnected ionomic, genomic and environmental data. Proceedings of the 21st ACM international conference on Information and knowledge management - CIKM '12, 2680. https://doi.org/10.1145/2396761.2398724

D’Hont, P., Denoeud, F., Aury, J., Baurens, F., Carreel, F., Garsmeur, O., Noel, B., Bocs, S., Droc, G., Rouard, M., Da Silva, C., Jabbari, K., Cardi, C., Poulain, J., Souquet, M., Labadie, K., Jourda, C., Lengellé, J., Rodier-Goud, M., Alberti, A., Bernard, M., Correa, M., Ayyampalayam, S., Mckain, M.. R., Leebens-Mack, J., Burgess, D., Freeling, M., Mbéguié-A-Mbéguié, D., Chabannes, M., Wicker, T., Panaud, O., Barbosa, J., Hribova, E., Heslop-Harrison, P., Habas, R., Rivallan, R., Francois, P., Poiron, C., Kilian, A., Burthia, D., Jenny, C., Bakry, F., Brown, S., Guignon, V., Kema, G., Dita, M., Waalwijk, C., Joseph, S., Dievart, A., Jaillon, O., Leclercq, J., Argout, X., Lyons, E., Almeida, A., Jeridi, M., Dolezel, J., Roux, N., Risterucci, A., Weissenbach, J., Ruiz, M., Glaszmann, J., Quétier, F., Yahiaoui, N., Wincker (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. , 488(7410), 213-217. https://doi.org/10.1038/nature11241

Egan, D.. M., Schlueter, J., Spooner (2012). Applications of next-generation sequencing in plant biology. , 99(2), 175-185. https://doi.org/10.3732/ajb.1200020

Eichten, N.. M., Ellis, N.. A., Makarevitch, I., Yeh, C., Gent, J.. I., Guo, L., McGinnis, K.. M., Zhang, X., Schnable, P.. S., Vaughn, M.. W., Dawe, R.. K., Springer (2012). Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons. , 8(12), e1003127. https://doi.org/10.1371/journal.pgen.1003127

Eichten, S.. R. (2012). Contribution of Epigenetic Variation to Expression Changes Among Tissues and Genotypes. , W417.

Flouri, T., Iliopoulos, C.. S., Kociumaka, T., Pissis, S.. P., Puglisi, S.. J., Smyth, W.. F., Tyczynski, W. (2012). New and Efficient Approaches to the Quasiperiodic Characterisation of a String.. Stringology, 75–88.

Flouri, T., Iliopoulos, C.. S., Park, K., Pissis, S.. P. (2012). GapMis-OMP: Pairwise Short-Read Alignment on Multi-core Architectures. Artificial Intelligence Applications and Innovations, 382, 593-601.

Fox, D., Gannon (2012). Using Clouds for Technical Computing.. , 81–102.

Geser, G., Jaques, Y., Manouselis, N., Protonotarios, V., Keizer, J., Sicilia, M. (2012). Building blocks for a data infrastructure and services to empower agricultural research communities. AGRIS on-line Papers in Economics and Informatics, 4(665-2016-44926), 11–18.

Gessler, D.. D., Bulka, B., Sirin, E., Kang, Y., Klinov, P., Vasquez-Gross, H., Yu, J., Wegrzyn, J. (2012). iPlant Semantic Web Platform uses SSWAP (Simple Semantic Web Architecture and Protocol) to enable Semantic Pipelines across Distributed Web and High Performance Computing Resources. .

Huang, B.. A., Schaal (2012). Association between the geographic distribution during the last glacial maximum of Asian wild rice, Oryza rufipogon (Poaceae), and its current genetic variation. , 99(11), 1866-1874. https://doi.org/10.3732/ajb.1200348

Jiao, C.. W., Leebens-Mack, J., Ayyampalayam, S., Bowers, J.. E., McKain, M.. R., McNeal, J., Rolf, M., Ruzicka, D.. R., Wafula, E., Wickett, N.. J., Wu, X., Zhang, Y., Wang, J., Zhang, Y., Carpenter, E.. J., Deyholos, M.. K., Kutchan, T.. M., Chanderbali, A.. S., Soltis, P.. S., Stevenson, D.. W., McCombie, R., Pires, J., Wong, G., Soltis, D.. E., dePamphilis (2012). A genome triplication associated with early diversification of the core eudicots. , 13(1), R3. https://doi.org/10.1186/gb-2012-13-1-r3

Johnson, G.. K., Carpenter, E.. J., Tian, Z., Bruskiewich, R., Burris, J.. N., Carrigan, C.. T., Chase, M.. W., Clarke, N.. D., Covshoff, S., dePamphilis, C.. W., Edger, P.. P., Goh, F., Graham, S., Greiner, S., Hibberd, J.. M., Jordon-Thaden, I., Kutchan, T.. M., Leebens-Mack, J., Melkonian, M., Miles, N., Myburg, H., Patterson, J., Pires, J.. C., Ralph, P., Rolf, M., Sage, R.. F., Soltis, D., Soltis, P., Stevenson, D., Stewart, C.. N., Surek, B., Thomsen, C.. J.. M., Villarreal, J.. C., Wu, X., Zhang, Y., Deyholos, M.. K., Wong (2012). Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes. , 7(11), e50226. https://doi.org/10.1371/journal.pone.0050226

Kakumanu, A. (2012). Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissues as Revealed by Deep Sequencing. .

Kakumanu, A., Ambavaram, M.. M., Klumas, C., Krishnan, A., Batlang, U., Myers, E., Grene, R., Pereira (2012). Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq. , 160(2), 846-867. https://doi.org/10.1104/pp.112.200444

Kharitonova, Y., Tung, Q., Danehy, A., Efrat, A., Barnard, K. (2012). Client-side backprojection of presentation slides into educational video. Proceedings of the 20th ACM international conference on Multimedia - MM '12, 1005. https://doi.org/10.1145/2393347.2396368

Klinov, T., Del Vescovo, C., Schneider (2012). Incrementally Updateable and Persistent Decomposition of OWL Ontologies. , 849, 7.

Kolker, V., Stewart, E., Ozdemir (2012). Opportunities and Challenges for the Life Sciences Community. , 16(3), 138-147. https://doi.org/10.1089/omi.2011.0152

Kvilekval, K., Fedorov, D., Gaur, U., Goff, S., Merchant, N., Manjunath, B., Singh, A.. K. (2012). Bisque: Advances in Bioimage Databases.. IEEE Data Eng. Bull., 35(3), 56–64.

Lyons, J.. C., Tang, H., Schnable (2012). Whole Genome Comparisons with Oryza and Brachypodium using CoGe and SynMap. , W267.

McDonald, S., Hart (2012). Latest Technology in Irrigation Management in Nursery Production\copyright. , 89–93.

McKay, M., Lyons, E., Tang, H., Miller, N., Eichten, S.. R., Goff, S.. A., Stanzione, D., Vaughn (2012). The iPlant Collaborative. , W416.

McKay, S. (2012). How to Use the iPlant's Discovery Environment for Your Research. , W420.

Miller, D.. V., Hocevar, J., Stone, R.. P., Fedorov (2012). Structure-Forming Corals and Sponges and Their Use as Fish Habitat in Bering Sea Submarine Canyons. , 7(3), e33885. https://doi.org/10.1371/journal.pone.0033885

Miller, M.. A., Pfeiffer, W., Schwartz, T. (2012). The CIPRES science gateway: enabling high-impact science for phylogenetics researchers with limited resources. Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment on Bridging from the eXtreme to the campus and beyond - XSEDE '12, 1. https://doi.org/10.1145/2335755.2335836

Miller, N. (2012). Enabling Phenotypic Image Analysis Using Shared Cyberinfrastructure. , W418.

O'Meara, B.. C. (2012). Evolutionary Inferences from Phylogenies: A Review of Methods. , 43(1), 267-285. https://doi.org/10.1146/annurev-ecolsys-110411-160331

Parr, R.. D., Guralnick, R., Cellinese, N., Page (2012). Evolutionary informatics: unifying knowledge about the diversity of life. , 27(2), 94-103. https://doi.org/10.1016/j.tree.2011.11.001

Ram, J., Liu (2012). A Semantic Foundation for Provenance Management. , 1(1), 17-Nov. https://doi.org/10.1007/s13740-012-0002-0

Reddy, A., Rogers, M.. F., Richardson, D.. N., Hamilton, M., Ben-Hur (2012). Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements. , 3. https://doi.org/10.3389/fpls.2012.00018

Reinders, A. (2012). Evolution of plant sucrose uptake transporters. , 3. https://doi.org/10.3389/fpls.2012.00022

Schatz, W.. R., Witkowski, J., McCombie (2012). Current challenges in de novo plant genome sequencing and assembly. , 13(4), 243. https://doi.org/10.1186/gb-2012-13-4-243

Schnable, E., Freeling, M., Lyons (2012). Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses. , 4(3), 265-277. https://doi.org/10.1093/gbe/evs009

Schneider, T. (2012). Ontology for Big Systems: The Ontology Summit 2012 Communiqu&eacute. , 3. https://doi.org/1570-5838

Simmerman, S., Wang, J., Osborne, J., Shook, K., Huang, J., Godsoe, W., Simons, T. (2012). Exploring similarities among many species distributions. Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment on Bridging from the eXtreme to the campus and beyond - XSEDE '12, 1. https://doi.org/10.1145/2335755.2335835

Smith, B.. C., O’Meara (2012). treePL: divergence time estimation using penalized likelihood for large phylogenies. , 28(20), 2689-2690. https://doi.org/10.1093/bioinformatics/bts492

Stamatakis, F., Aberer, A.. J., Goll, C., Smith, S.. A., Berger, S.. A., Izquierdo-Carrasco (2012). RAxML-Light: a tool for computing terabyte phylogenies. , 28(15), 2064-2066. https://doi.org/10.1093/bioinformatics/bts309

Straub, S.. C.. K., Parks, M., Weitemier, K., Fishbein, M., Cronn, R.. C., Liston, A. (2012). Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. American Journal of Botany, 99(2), 349-364. https://doi.org/10.3732/ajb.1100335

Strickler, S.. R., Bombarely, A., Mueller, L.. A. (2012). Designing a transcriptome next-generation sequencing project for a nonmodel plant species ¹. American Journal of Botany, 99(2), 257-266. https://doi.org/10.3732/ajb.1100292

Tang, H., Lyons, E. (2012). The Evolution of Genome Structure. Int J Evol 1, 1, 2.

Tang, H., Lyons, E. (2012). Unleashing the Genome of Brassica Rapa. , 3. https://doi.org/10.3389/fpls.2012.00172

Tang, K., Krampis (2012). Leverage iPlant Computing Resources for Collaborative Genomic Research. , W419.

White, J.. W., Andrade-Sanchez, P., Gore, M.. A., Bronson, K.. F., Coffelt, T.. A., Conley, M.. M., Feldmann, K.. A., French, A.. N., Heun, J.. T., Hunsaker, D.. J., Jenks, M.. A., Kimball, B.. A., Roth, R.. L., Strand, R.. J., Thorp, K.. R., Wall, G.. W., Wang, G. (2012). Field-based phenomics for plant genetics research. Field Crops Research, 133, 101-112. https://doi.org/10.1016/j.fcr.2012.04.003

Woodward, N.. J., Xu, W., Norsworthy, K. (2012). On automatically tagging web documents from examples. Proceedings of the 35th international ACM SIGIR conference on Research and development in information retrieval - SIGIR '12, 1111. https://doi.org/10.1145/2348283.2348494

Zhou, R., Franck, C., Yang, K., Pilot, G., Heath, L.. S., Grene (2012). Mining for Meaning: Visualization Approaches to Deciphering Arabidopsis Stress Responses in Roots and Shoots. , 16(4), 208-228. https://doi.org/10.1089/omi.2011.0111

2011

Banks, I.. V., Nishiyama, T., Hasebe, M., Bowman, J.. L., Gribskov, M., dePamphilis, C., Albert, V.. A., Aono, N., Aoyama, T., Ambrose, B.. A., Ashton, N.. W., Axtell, M.. J., Barker, E., Barker, M.. S., Bennetzen, J.. L., Bonawitz, N.. D., Chapple, C., Cheng, C., Correa, L.. G.. G., Dacre, M., DeBarry, J., Dreyer, I., Elias, M., Engstrom, E.. M., Estelle, M., Feng, L., Finet, C., Floyd, S.. K., Frommer, W.. B., Fujita, T., Gramzow, L., Gutensohn, M., Harholt, J., Hattori, M., Heyl, A., Hirai, T., Hiwatashi, Y., Ishikawa, M., Iwata, M., Karol, K.. G., Koehler, B., Kolukisaoglu, U., Kubo, M., Kurata, T., Lalonde, S., Li, K., Li, Y., Litt, A., Lyons, E., Manning, G., Maruyama, T., Michael, T.. P., Mikami, K., Miyazaki, S., Morinaga, S., Murata, T., Mueller-Roeber, B., Nelson, D.. R., Obara, M., Oguri, Y., Olmstead, R.. G., Onodera, N., Petersen, B.. L., Pils, B., Prigge, M., Rensing, S.. A., Riano-Pachon, D.. M., Roberts, A.. W., Sato, Y., Scheller, H.. V., Schulz, B., Schulz, C., Shakirov, E.. V., Shibagaki, N., Shinohara, N., Shippen, D.. E., Sorensen, I., Sotooka, R., Sugimoto, N., Sugita, M., Sumikawa, N., Tanurdzic, M., Theissen, G., Ulvskov, P., Wakazuki, S., Weng, J., Willats, W.. W.. G.. T., Wipf, D., Wolf, P.. G., Yang, L., Zimmer, A.. D., Zhu, Q., Mitros, T., Hellsten, U., Loque, D., Otillar, R., Salamov, A., Schmutz, J., Shapiro, H., Lindquist, E., Lucas, S., Rokhsar, D., Grigoriev (2011). The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants. , 332(6032), 960-963. https://doi.org/10.1126/science.1203810

Barthelson, S., McFarlin, A.. J., Rounsley, S.. D., Young (2011). Plantagora: Modeling Whole Genome Sequencing and Assembly of Plant Genomes. , 6(12), e28436. https://doi.org/10.1371/journal.pone.0028436

Basney, J., Dooley, R., Gaynor, J., Marru, S., Pierce, M. (2011). Distributed web security for science gateways. Proceedings of the 2011 ACM workshop on Gateway computing environments, 13–20.

Boerma, E., Wilson, R., Ready (2011). Soybean genomics research program strategic plan. , 4(1), 1–11.

Brown, S.. A., Thatcher, S.. M. (2011). Factors Influencing Adoption And Non-Adoption Of Cyberinfrastructure By The Research Community.. PACIS, 31.

Carey, H.. V. (2011). Grand challenges in organismal physiology. The Physiologist, 54(5), 169, 171-172.

Del Vescovo, C., Klinov, P., Parsia, B., Sattler, U., Schneider, T. (2011). DeMoSt: a tool for exploring the decomposition and the modular structure of OWL ontologies. Proceedings of the 10th International Semantic Web Conference (ISWC-11), 191. https://doi.org/10.1007/978-3-642- 25073-6_9

Feng, L., Grossman, R., Stein (2011). PeakRanger: A cloud-enabled peak caller for ChIP-seq data. , 12(1), 139. https://doi.org/10.1186/1471-2105-12-139

Galbraith, P.. S., Bennetzen, J.. L., Kellogg, E.. A., Pires, J.. C., Soltis (2011). The Genomes of All Angiosperms: A Call for a Coordinated Global Census. , 2011, 10-Jan. https://doi.org/10.1155/2011/646198

Goff, D., Vaughn, M., McKay, S., Lyons, E., Stapleton, A.. E., Gessler, D., Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M., Jordan, C., Skidmore, E., Dooley, R., Cazes, J., McLay, R., Lu, Z., Pasternak, S., Koesterke, L., Piel, W.. H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S., Kvilekval, K., Manjunath, B.. S., Tannen, V., Stamatakis, A., Sanderson, M., Welch, S.. M., Cranston, K.. A., Soltis, P., Soltis, D., O'Meara, B., Ane, C., Brutnell, T., Kleibenstein, D.. J., White, J.. W., Leebens-Mack, J., Donoghue, M.. J., Spalding, E.. P., Vision, T.. J., Myers, C.. R., Lowenthal, D., Enquist, B.. J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L., Stanzione (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. , 2. https://doi.org/10.3389/fpls.2011.00034

Kimbrel, J.. H., Di, Y., Cumbie, J.. S., Chang (2011). RNA-Seq for Plant Pathogenic Bacteria. , 2(4), 689-705. https://doi.org/10.3390/genes2040689

Koesterke, L., Stanzione, D., Vaughn, M., Welch, S.. M., Kusnierczyk, W., Yang, J., Yeh, C., Nettleton, D., Schnable, P.. S. (2011). An efficient and scalable implementation of SNP-pair interaction testing for genetic association studies. 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum, 523–530.

Lenards, A., Merchant, N., Stanzione, D. (2011). Building an environment to facilitate discoveries for plant sciences. Proceedings of the 2011 ACM workshop on Gateway computing environments, 51–58.

Liu, J. (2011). W7 model of provenance and its use in the context of wikipedia. .

Liu, S., Ram (2011). Who does what: Collaboration patterns in the wikipedia and their impact on article quality. , 2(2), 23-Jan. https://doi.org/10.1145/1985347.1985352

Macilwain, C. (2011). Systems Biology: Evolving into the Mainstream. , 144(6), 839-841. https://doi.org/10.1016/j.cell.2011.02.044

Makumburage, G.. B., Stapleton, A.. E. (2011). Phenotype Uniformity in Combined-Stress Environments has a Different Genetic Architecture than in Single-Stress Treatments. Frontiers in Plant Science, 2. https://doi.org/10.3389/fpls.2011.00012

Matasci, N., Boyd, B., Lu, Z., Hopkins, N., Piel, W.. H., Garay, J.. A.. R., Gregory, S., Lowry, S., McKay, S.. J., Narro, M.. L., others (2011). Correcting and Standardizing Taxonomic Names with the Taxonomic Name Resolution Service. TDWG 2011 Annual Conference.

McLay, T., Stanzione, D., Mckay, S., Wheeler (2011). A scalable parallel implementation of the neighbor joining algorithm for phylogenetic trees. .

Micklos, A., Lauter, S., Nisselle (2011). Lessons from a Science Education Portal. , 334(6063), 1657-1658. https://doi.org/10.1126/science.1197074

Nodine, F.. E., Bryan, A.. C., Racolta, A., Jerosky, K.. V., Tax (2011). A few standing for many: embryo receptor-like kinases. , 16(4), 211-217. https://doi.org/10.1016/j.tplants.2011.01.005

Rogowitz, N., Matasci (2011). Metadata Mapper: a web service for mapping data between independent visual analysis components, guided by perceptual rules. , 78650I. https://doi.org/10.1117/12.881734

Schaeffer, C.. J., Harper, L.. C., Gardiner, J.. M., Andorf, C.. M., Campbell, D.. A., Cannon, E.. K.. S., Sen, T.. Z., Lawrence (2011). MaizeGDB: curation and outreach go hand-in-hand. , 2011(0), bar022-bar022. https://doi.org/10.1093/database/bar022

Schnable, E., Lyons (2011). Comparative genomics with maize and other grasses: from genes to genomes!. Maydica, 56(2).

Skidmore, E., Kim, S., Kuchimanchi, S., Singaram, S., Merchant, N., Stanzione, D. (2011). iPlant atmosphere: a gateway to cloud infrastructure for the plant sciences. Proceedings of the 2011 ACM workshop on Gateway computing environments, 59–64.

Smith, M.. J., Beaulieu, J.. M., Stamatakis, A., Donoghue (2011). Understanding angiosperm diversification using small and large phylogenetic trees. , 98(3), 404-414. https://doi.org/10.3732/ajb.1000481

Stanzione, D. (2011). The iPlant Collaborative: Cyberinfrastructure to Feed the World. , 44(11), 44-52. https://doi.org/10.1109/MC.2011.297

Stillman, B., Denny, M., Padilla, D.. K., Wake, M.. H., Patek, S., Tsukimura (2011). Grand Opportunities: Strategies for Addressing Grand Challenges in Organismal Animal Biology. , 51(1), 13-Jul. https://doi.org/10.1093/icb/icr052

Tang, M., Lyons, E., Pedersen, B., Schnable, J.. C., Paterson, A.. H., Freeling (2011). Screening synteny blocks in pairwise genome comparisons through integer programming. , 12(1), 102. https://doi.org/10.1186/1471-2105-12-102

Wang, F. (2011). From AI to SciTS: Team Science and Research Intelligence. , 26(3), 4-Feb. https://doi.org/10.1109/MIS.2011.49

Wang, T.. P., Peterson, R.. B., Brutnell (2011). Regulatory mechanisms underlying C4 photosynthesis: Tansley review. , 190(1), 20-Sep. https://doi.org/10.1111/j.1469-8137.2011.03649.x

Wang, T.. P., Si, Y., Dedow, L.. K., Shao, Y., Liu, P., Brutnell (2011). A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq. , 6(10), e26426. https://doi.org/10.1371/journal.pone.0026426

Zamer, W.. E. (2011). A Cohesive Biology of Organisms Is on the Horizon. BioScience, 61(11), 848-849. https://doi.org/10.1525/bio.2011.61.11.3

Zheng, C., Swenson, K., Lyons, E., Sankoff, D. (2011). OMG! Orthologs in Multiple Genomes – Competing Graph-Theoretical Formulations. Algorithms in Bioinformatics, 6833, 364-375.

2010

Brown, S.. A., Thatcher, S., Dang, Y. (2010). Managing knowledge in a changing scientific landscape: The impact of cyberinfrastructure. 2010 43rd Hawaii International Conference on System Sciences, 1–10.

Hanlon, M.. R., Mock, S., Nuthulapati, P., Gonzales, M.. B., Soltis, P., Soltis, D., Majure, L.. C., Payton, A., Mishler, B., Tremblay, S., Madsen, T., Olmstead, R., McCourt, R., Wojciechowski, M., Merchant, N. (2010). My-Plant.org: A phylogenetically structured social network. 2010 Gateway Computing Environments Workshop (GCE), 1-8. https://doi.org/10.1109/GCE.2010.5676118

Macías-Duarte, A., Conway, C.. J., Munguia-Vega, A., Culver, M. (2010). Novel microsatellite loci for the burrowing owl Athene cunicularia. Conservation Genetics Resources, 2(1), 67–69.

McKay, J.. E., Vergara, I.. A., Stajich (2010). Using the Generic Synteny Browser (GBrowse_syn). , bi0912s31.

Moore, W.. L., Anderson (2010). ASIS&T research data access and preservation summit: Conference summary. , 36(6), 42-45. https://doi.org/10.1002/bult.2010.1720360611

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