2017 Publications

Adhikari, L., Razar, R. M., Paudel, D., Ding, R., & Missaoui, A. M. (2017). Insights into Seasonal Dormancy of Perennial Herbaceous Forages. American Journal of Plant Sciences, 08(11), 2650–2680. https://doi.org/10.4236/ajps.2017.811179
Agnew, E., Bray, A., Floro, E., Ellis, N., Gierer, J., Lizárraga, C., O’Brien, D., Wiechert, M., Mockler, T. C., Shakoor, N., & Topp, C. N. (2017). Whole‐Plant Manual and Image‐Based Phenotyping in Controlled Environments. Current Protocols in Plant Biology, 2(1), 1–21. https://doi.org/10.1002/cppb.20044
Aloisio, J. M. (2017). Rooftop plants: Community and nutrient dynamics of New York City green roofs [PhD Thesis]. Fordham University.
Arndt, D., Marcu, A., Liang, Y., & Wishart, D. S. (2019). PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes. Briefings in Bioinformatics, 20(4), 1560–1567. https://doi.org/10.1093/bib/bbx121
Barone, L., Williams, J., & Micklos, D. (2017). Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators. PLOS Computational Biology, 13(10), e1005755. https://doi.org/10.1371/journal.pcbi.1005755
Becker Scarpitta, A., Bardat, J., Lalanne, A., & Vellend, M. (2017). Long-term community change: Bryophytes are more responsive than vascular plants to nitrogen deposition and warming. Journal of Vegetation Science, 28(6), 1220–1229. https://doi.org/10.1111/jvs.12579
Belete, G. F. (2017). Integrating models on the web: Applications for socio-environmental studies. University of Twente Faculty of Geo-Information and Earth Observation (ITC).
Bertolini, E., Pè, M. E., & Mica, E. (2018). Transcriptional and Posttranscriptional Regulation of Drought Stress Treatments in Brachypodium Leaves. In G. Sablok, H. Budak, & P. J. Ralph (Eds.), Brachypodium Genomics (Vol. 1667, pp. 21–29). Springer New York. https://doi.org/10.1007/978-1-4939-7278-4_2
Blažun Vošner, H., Bobek, S., Sternad Zabukovšek, S., & Kokol, P. (2017). Openness and information technology: A bibliometric analysis of literature production. Kybernetes, 46(5), 750–766. https://doi.org/10.1108/K-10-2016-0292
Bolduc, B., Jang, H. B., Doulcier, G., You, Z.-Q., Roux, S., & Sullivan, M. B. (2017). vConTACT: An iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ, 5, e3243. https://doi.org/10.7717/peerj.3243
Bolger, M., Schwacke, R., Gundlach, H., Schmutzer, T., Chen, J., Arend, D., Oppermann, M., Weise, S., Lange, M., Fiorani, F., Spannagl, M., Scholz, U., Mayer, K., & Usadel, B. (2017). From plant genomes to phenotypes. Journal of Biotechnology, 261, 46–52. https://doi.org/10.1016/j.jbiotec.2017.06.003
Brasil, B. dos S. A. F., de Siqueira, F. G., Salum, T. F. C., Zanette, C. M., & Spier, M. R. (2017). Microalgae and cyanobacteria as enzyme biofactories. Algal Research, 25, 76–89. https://doi.org/10.1016/j.algal.2017.04.035
Bucksch, A., Das, A., Schneider, H., Merchant, N., & Weitz, J. S. (2017). Overcoming the Law of the Hidden in Cyberinfrastructures. Trends in Plant Science, 22(2), 117–123. https://doi.org/10.1016/j.tplants.2016.11.014
Buonaccorsi, V., Hamlin, D., Fowler, B., Sullivan, C., & Sickler, A. (2017). An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome Consortium for Active Teaching. CourseSource.
Carvajal-Endara, S., Hendry, A. P., Emery, N. C., & Davies, T. J. (2017). Habitat filtering not dispersal limitation shapes oceanic island floras: Species assembly of the Galápagos archipelago. Ecology Letters, 20(4), 495–504. https://doi.org/10.1111/ele.12753
Chao, W. S., Doğramacı, M., Horvath, D. P., Anderson, J. V., & Foley, M. E. (2017). Comparison of phytohormone levels and transcript profiles during seasonal dormancy transitions in underground adventitious buds of leafy spurge. Plant Molecular Biology, 94(3), 281–302. https://doi.org/10.1007/s11103-017-0607-7
Chard, K., Dart, E., Foster, I., Shifflett, D., Tuecke, S., & Williams, J. (2017). The Modern Research Data Portal: A design pattern for networked, data-intensive science [Preprint]. PeerJ Preprints. https://doi.org/10.7287/peerj.preprints.3194v2
Chen, Y., Zhang, Q., Hu, W., Zhang, X., Wang, L., Hua, X., Yu, Q., Ming, R., & Zhang, J. (2017). Evolution and expression of the fructokinase gene family in Saccharum. BMC Genomics, 18(1), 197. https://doi.org/10.1186/s12864-017-3535-7
Cicero, C., Spencer, C. L., Bloom, D. A., Guralnick, R. P., Koo, M. S., Otegui, J., Russell, L. A., & Wieczorek, J. R. (2017). Biodiversity Informatics and Data Quality on a Global Scale1. The Extended Specimen: Emerging Frontiers in Collections-Based Ornithological Research.
Cooper, L., Meier, A., Laporte, M.-A., Elser, J. L., Mungall, C., Sinn, B. T., Cavaliere, D., Carbon, S., Dunn, N. A., Smith, B., Qu, B., Preece, J., Zhang, E., Todorovic, S., Gkoutos, G., Doonan, J. H., Stevenson, D. W., Arnaud, E., & Jaiswal, P. (2018). The Planteome database: An integrated resource for reference ontologies, plant genomics and phenomics. Nucleic Acids Research, 46(D1), D1168–D1180. https://doi.org/10.1093/nar/gkx1152
Coppens, F., Wuyts, N., Inzé, D., & Dhondt, S. (2017). Unlocking the potential of plant phenotyping data through integration and data-driven approaches. Current Opinion in Systems Biology, 4, 58–63. https://doi.org/10.1016/j.coisb.2017.07.002
Coronel, J. B., & Mock, S. (2017). DesignSafe: Using Elasticsearch to Share and Search Data on a Science Web Portal. Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact  - PEARC17, 1–3. https://doi.org/10.1145/3093338.3093386
Craig, P. A. (2017). A survey on faculty perspectives on the transition to a biochemistry course-based undergraduate research experience laboratory: Transition to a CURE. Biochemistry and Molecular Biology Education, 45(5), 426–436. https://doi.org/10.1002/bmb.21060
Cutcher-Gershenfeld, J., Baker, K. S., Berente, N., Flint, C., Gershenfeld, G., Grant, B., Haberman, M., King, J. L., Kirkpatrick, C., Lawrence, B., Lewis, S., Lenhardt, W. C., Mayernik, M., McElroy, C., Mittleman, B., Shin, N., Stall, S., Winter, S., & Zaslavsky, I. (2017). Five ways consortia can catalyse open science. Nature, 543(7647), 615–617. https://doi.org/10.1038/543615a
D’Agostino, D., Roverelli, L., Zereik, G., De Luca, A., Salvaterra, R., Belfiore, A., Lisini, G., Novara, G., & Tiengo, A. (2017). A microservice-based portal for X-ray transient and variable sources [Preprint]. PeerJ Preprints. https://doi.org/10.7287/peerj.preprints.2519v2
DeChant, C., Wiesner-Hanks, T., Chen, S., Stewart, E. L., Yosinski, J., Gore, M. A., Nelson, R. J., & Lipson, H. (2017). Automated Identification of Northern Leaf Blight-Infected Maize Plants from Field Imagery Using Deep Learning. Phytopathology, 107(11), 1426–1432. https://doi.org/10.1094/PHYTO-11-16-0417-R
Deck, J., Stucky, B., Walls, R., Ewing, R., Genazzio, M., Loescher, H., & Guralnick, R. (2017). A High-throughput Data Ingest Pipeline for Semantic Data-stores. Proceedings of TDWG, 1, e20208. https://doi.org/10.3897/tdwgproceedings.1.20208
Deist, M. S., Gallardo, R. A., Bunn, D. A., Dekkers, J. C. M., Zhou, H., & Lamont, S. J. (2017). Resistant and susceptible chicken lines show distinctive responses to Newcastle disease virus infection in the lung transcriptome. BMC Genomics, 18(1), 989. https://doi.org/10.1186/s12864-017-4380-4
Deist, M. S., Gallardo, R. A., Bunn, D. A., Kelly, T. R., Dekkers, J. C. M., Zhou, H., & Lamont, S. J. (2017). Novel Mechanisms Revealed in the Trachea Transcriptome of Resistant and Susceptible Chicken Lines following Infection with Newcastle Disease Virus. Clinical and Vaccine Immunology, 24(5), e00027-17, /cdli/24/5/e00027-17.atom. https://doi.org/10.1128/CVI.00027-17
Dolan, R. W., Aronson, M. F. J., & Hipp, A. L. (2017). Floristic response to urbanization: Filtering of the bioregional flora in Indianapolis, Indiana, USA. American Journal of Botany, 104(8), 1179–1187. https://doi.org/10.3732/ajb.1700136
Dovrolis, N., Kolios, G., Spyrou, G. M., & Maroulakou, I. (2019). Computational profiling of the gut–brain axis: Microflora dysbiosis insights to neurological disorders. Briefings in Bioinformatics, 20(3), 825–841. https://doi.org/10.1093/bib/bbx154
Eckes, A. H., Gubała, T., Nowakowski, P., Szymczyszyn, T., Wells, R., Irwin, J. A., Horro, C., Hancock, J. M., King, G., Dyer, S. C., & Jurkowski, W. (2017). Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data. F1000Research, 6, 465. https://doi.org/10.12688/f1000research.11301.1
Eckes, A. H., Gubala, T., Nowakowski, P., Szymczyszyn, T., Wells, R., Irwin, J. A., Horro, C., Hancock, J. M., King, G., Dyer, S. C., & others. (2017). Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data. F1000Research, 6.
Eckes, Annemarie, Tomasz Gubala, Piotr Nowakowski, Tomasz Szymczyszyn, & Jurkowski, W. (2017). The Brassica Information Portal: Towards Integrating Phenotype and Genotype Data. Proceedings from PAG XXV, C11. http://www.intlpag.org/2017/images/pdf/PAGXXV-abstracts-computer_demos.pdf
Enke, R. A., & Rahmani-Mofrad, M. (n.d.). Genomics RNA-seq Analysis part 1-CyVerse DE, FastQC, Trimmomatic (updated 11/17).
Es, Harold van, & Woodard, J. (2017). Innovation in Agriculture and Food Systems in the Digital Age (pp. 97–104). http://www.wipo.int/edocs/pubdocs/en/wipo_pub_gii_2017-chapter4.pdf
Espiritu, Kaitlyn, Bryant Lee, & Shin, K. M. (2017). Assessment of SO2 Pollution in Central Park by DNA Barcoding of lichen specimens. Proceedings from AAAS 2017 Annual Meeting. https://aaas.confex.com/aaas/2017/webprogram/Paper19818.html
Farman, M., Peterson, G., Chen, L., Starnes, J., Valent, B., Bachi, P., Murdock, L., Hershman, D., Pedley, K., Fernandes, J. M., & Bavaresco, J. (2017). The Lolium Pathotype of Magnaporthe oryzae Recovered from a Single Blasted Wheat Plant in the United States. Plant Disease, 101(5), 684–692. https://doi.org/10.1094/PDIS-05-16-0700-RE
Fedorov, Dmitry, BS Manjunath, Christian Lang, & Kvilekval, K. G. (2017). Scalable Image Informatics. https://escholarship.org/uc/item/7nf7492x
Fischer, J., Hancock, D. Y., Lowe, J. M., Turner, G., Snapp-Childs, W., & Stewart, C. A. (2017). Jetstream: A Cloud System Enabling Learning in Higher Education Communities. Proceedings of the 2017 ACM Annual Conference on SIGUCCS - SIGUCCS ’17, 67–72. https://doi.org/10.1145/3123458.3123466
Fonner, J., & Dooley, R. (2017). Containerizing Conda. Proceedings from 9th International Workshop on Science Gateways (IWSG 2017), 19-21 June 2017.
Fonseca, L. F. S., Gimenez, D. F. J., dos Santos Silva, D. B., Barthelson, R., Baldi, F., Ferro, J. A., & Albuquerque, L. G. (2017). Differences in global gene expression in muscle tissue of Nellore cattle with divergent meat tenderness. BMC Genomics, 18(1), 945. https://doi.org/10.1186/s12864-017-4323-0
Foster, Ian, & Gannon, D. B. (2017). Cloud Computing for Science and Engineering. https://books.google.com/books?id=FYc3DwAAQBAJ&printsec=frontcover&source=gbs_ge_summary_r&cad=0#v=onepage&q&f=false
Friesner, J., Assmann, S. M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., Buell, C. R., Bucksch, A., Busch, W., Demura, T., Dinneny, J. R., Doherty, C. J., Eveland, A. L., Falter-Braun, P., Gehan, M. A., Gonzales, M., Grotewold, E., Gutierrez, R., Kramer, U., … Brady, S. M. (2017). The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiology, 175(4), 1499–1509. https://doi.org/10.1104/pp.17.01490
Geniza, M., & Jaiswal, P. (2017). Tools for building de novo transcriptome assembly. Current Plant Biology, 11–12, 41–45. https://doi.org/10.1016/j.cpb.2017.12.004
Gesing, S., Dooley, R., Pierce, M., Krüger, J., Grunzke, R., Herres-Pawlis, S., & Hoffmann, A. (2018). Gathering requirements for advancing simulations in HPC infrastructures via science gateways. Future Generation Computer Systems, 82, 544–554. https://doi.org/10.1016/j.future.2017.02.042
Gillan, J., Karl, J., Elaksher, A., & Duniway, M. (2017). Fine-Resolution Repeat Topographic Surveying of Dryland Landscapes Using UAS-Based Structure-from-Motion Photogrammetry: Assessing Accuracy and Precision against Traditional Ground-Based Erosion Measurements. Remote Sensing, 9(5), 437. https://doi.org/10.3390/rs9050437
Gilman, I. S. (2017). Systematics of Chloropyron (Orobanchaceae): Implications of missing data on quartet-based species tree methods. University of Idaho.
Gorgolewski, K. J., Alfaro-Almagro, F., Auer, T., Bellec, P., Capotă, M., Chakravarty, M. M., Churchill, N. W., Cohen, A. L., Craddock, R. C., Devenyi, G. A., Eklund, A., Esteban, O., Flandin, G., Ghosh, S. S., Guntupalli, J. S., Jenkinson, M., Keshavan, A., Kiar, G., Liem, F., … Poldrack, R. A. (2017). BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. PLOS Computational Biology, 13(3), e1005209. https://doi.org/10.1371/journal.pcbi.1005209
Grealy, A., Rawlence, N., & Bunce, M. (2017). Time to Spread Your Wings: A Review of the Avian Ancient DNA Field. Genes, 8(7), 184. https://doi.org/10.3390/genes8070184
Grover, J. W., Bomhoff, M., Davey, S., Gregory, B. D., Mosher, R. A., & Lyons, E. (2017). CoGe LoadExp+: A web-based suite that integrates next-generation sequencing data analysis workflows and visualization. Plant Direct, 1(2). https://doi.org/10.1002/pld3.8
Hancock, D. (2017). Jetstream: Early Operations Performance, Adoption, and Impacts. Proceedings of The10th International Conference on Utility and Cloud Computing  - UCC ’17, 7–7. https://doi.org/10.1145/3147213.3155104
Hoffman, A. M., & Smith, M. D. (2018). Gene expression differs in codominant prairie grasses under drought. Molecular Ecology Resources, 18(2), 334–346. https://doi.org/10.1111/1755-0998.12733
Holdgraf, C., Culich, A., Rokem, A., Deniz, F., Alegro, M., & Ushizima, D. (2017). Portable learning environments for hands-on computational instruction: Using container- and cloud-based technology to teach data science. ArXiv:1703.04900 [Cs]. http://arxiv.org/abs/1703.04900
Hwang, K. (2017). Cloud Computing for Machine Learning and Cognitive Applications: A Machine Learning Approach. MIT Press, Cambridge.
Hwang, Kai, & Chen, M. (2017). Big-data analytics for cloud, IoT and cognitive computing. John Wiley & Sons.
Hyman, G., Espinosa, H., Camargo, P., Abreu, D., Devare, M., Arnaud, E., Porter, C., Mwanzia, L., Sonder, K., & Traore, S. (2017). Improving agricultural knowledge management: The AgTrials experience. F1000Research, 6, 317. https://doi.org/10.12688/f1000research.11179.1
Iamartino, D., Nicolazzi, E. L., Van Tassell, C. P., Reecy, J. M., Fritz-Waters, E. R., Koltes, J. E., Biffani, S., Sonstegard, T. S., Schroeder, S. G., Ajmone-Marsan, P., Negrini, R., Pasquariello, R., Ramelli, P., Coletta, A., Garcia, J. F., Ali, A., Ramunno, L., Cosenza, G., de Oliveira, D. A. A., … Williams, J. L. (2017). Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis). PLOS ONE, 12(10), e0185220. https://doi.org/10.1371/journal.pone.0185220
Irigoyen, S., Bedre, R. H., Scholthof, K.-B. G., & Mandadi, K. K. (2018). Genomic Approaches to Analyze Alternative Splicing, A Key Regulator of Transcriptome and Proteome Diversity in Brachypodium distachyon. In G. Sablok, H. Budak, & P. J. Ralph (Eds.), Brachypodium Genomics (Vol. 1667, pp. 73–85). Springer New York. https://doi.org/10.1007/978-1-4939-7278-4_7
Jiang, Y., Li, C., Sun, S., Paterson, A. H., & Xu, R. (2017). <i>GPhenoVision: A Ground Mobile System with Multi-modal Imaging for Field-based High Throughput Phenotyping of Cotton</i> 2017 Spokane, Washington July 16 - July 19, 2017. 2017 Spokane, Washington July 16 - July 19, 2017. https://doi.org/10.13031/aim.201700438
Jin, X., Robinson, K., Lee, A., Polhill, J. G., Pritchard, C., & Parker, D. C. (2017). A prototype cloud-based reproducible data analysis and visualization platform for outputs of agent-based models. Environmental Modelling & Software, 96, 172–180. https://doi.org/10.1016/j.envsoft.2017.06.010
Joyce, B. L., Haug-Baltzell, A. K., Hulvey, J. P., McCarthy, F., Devisetty, U. K., & Lyons, E. (2017). Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms. Journal of Visualized Experiments, 123, 55009. https://doi.org/10.3791/55009
Kang, D.-W., Adams, J. B., Gregory, A. C., Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., Pollard, E. L., Roux, S., Sadowsky, M. J., Lipson, K. S., Sullivan, M. B., Caporaso, J. G., & Krajmalnik-Brown, R. (2017). Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: An open-label study. Microbiome, 5(1), 10. https://doi.org/10.1186/s40168-016-0225-7
Kissling, W. D., Ahumada, J. A., Bowser, A., Fernandez, M., Fernández, N., García, E. A., Guralnick, R. P., Isaac, N. J. B., Kelling, S., Los, W., McRae, L., Mihoub, J.-B., Obst, M., Santamaria, M., Skidmore, A. K., Williams, K. J., Agosti, D., Amariles, D., Arvanitidis, C., … Hardisty, A. R. (2018). Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale: Building global EBVs. Biological Reviews, 93(1), 600–625. https://doi.org/10.1111/brv.12359
Knepper, R. (2017). Shifting Modalities of Use in the XSEDE Project [PhD Thesis]. Indiana University.
Knepper, R., Coulter, E., Pierce, M., Marru, S., & Pamidighantam, S. (2017). Using the Jetstream Research Cloud to Provide Science Gateway Resources. 2017 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID), 753–757. https://doi.org/10.1109/CCGRID.2017.121
Krishnamurthy, A., Bradford, K., Calloway, C., Castillo, C., Conway, M., Coposky, J., Guo, Y., Idaszak, R., Lenhardt, W. C., Robasky, K., Russell, T., Scott, E., Sliwowski, M., Stealey, M., Urgo, K., Xu, H., Yi, H., & Ahalt, S. (2017). XDCI, a data science cyberinfrastructure for interdisciplinary research. 2017 IEEE High Performance Extreme Computing Conference (HPEC), 1–7. https://doi.org/10.1109/HPEC.2017.8091022
Lamsal, A., Welch, S. M., Jones, J. W., Boote, K. J., Asebedo, A., Crain, J., Wang, X., Boyer, W., Giri, A., Frink, E., Xu, X., Gundy, G., Ou, J., & Arachchige, P. G. (2017). Efficient crop model parameter estimation and site characterization using large breeding trial data sets. Agricultural Systems, 157, 170–184. https://doi.org/10.1016/j.agsy.2017.07.016
Lang, D., Ullrich, K. K., Murat, F., Fuchs, J., Jenkins, J., Haas, F. B., Piednoel, M., Gundlach, H., Van Bel, M., Meyberg, R., Vives, C., Morata, J., Symeonidi, A., Hiss, M., Muchero, W., Kamisugi, Y., Saleh, O., Blanc, G., Decker, E. L., … Rensing, S. A. (2018). The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. The Plant Journal, 93(3), 515–533. https://doi.org/10.1111/tpj.13801
Levy, J. G., Mendoza, A., Miller, J. C., Tamborindeguy, C., & Pierson, E. A. (2017). Global gene expression in two potato cultivars in response to ‘Candidatus Liberibacter solanacearum’ infection. BMC Genomics, 18(1), 960. https://doi.org/10.1186/s12864-017-4313-2
Li, Q., Hermanson, P. J., & Springer, N. M. (2018). Detection of DNA Methylation by Whole-Genome Bisulfite Sequencing. In L. M. Lagrimini (Ed.), Maize (Vol. 1676, pp. 185–196). Springer New York. https://doi.org/10.1007/978-1-4939-7315-6_11
Liang, Z., Pandey, P., Stoerger, V., Xu, Y., Qiu, Y., Ge, Y., & Schnable, J. C. (2018). Conventional and hyperspectral time-series imaging of maize lines widely used in field trials. GigaScience, 7(2). https://doi.org/10.1093/gigascience/gix117
List, M. (2017). Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform. Journal of Integrative Bioinformatics, 14(2). https://doi.org/10.1515/jib-2017-0016
Liu, H., Zhang, L., Wang, J., Li, C., Zeng, X., Xie, S., Zhang, Y., Liu, S., Hu, S., Wang, J., Lee, M., Lübberstedt, T., & Zhao, G. (2017). Quantitative Trait Locus Analysis for Deep-Sowing Germination Ability in the Maize IBM Syn10 DH Population. Frontiers in Plant Science, 8, 813. https://doi.org/10.3389/fpls.2017.00813
Lobet, G. (2017). Image Analysis in Plant Sciences: Publish Then Perish. Trends in Plant Science, 22(7), 559–566. https://doi.org/10.1016/j.tplants.2017.05.002
Lopes dos Santos, A., Pollina, T., Gourvil, P., Corre, E., Marie, D., Garrido, J. L., Rodríguez, F., Noël, M.-H., Vaulot, D., & Eikrem, W. (2017). Chloropicophyceae, a new class of picophytoplanktonic prasinophytes. Scientific Reports, 7(1), 14019. https://doi.org/10.1038/s41598-017-12412-5
Luo, M.-C., Gu, Y. Q., Puiu, D., Wang, H., Twardziok, S. O., Deal, K. R., Huo, N., Zhu, T., Wang, L., Wang, Y., McGuire, P. E., Liu, S., Long, H., Ramasamy, R. K., Rodriguez, J. C., Van, S. L., Yuan, L., Wang, Z., Xia, Z., … Dvořák, J. (2017). Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature, 551(7681), 498–502. https://doi.org/10.1038/nature24486
Maitner, B. S., Boyle, B., Casler, N., Condit, R., Donoghue, J., Durán, S. M., Guaderrama, D., Hinchliff, C. E., Jørgensen, P. M., Kraft, N. J. B., McGill, B., Merow, C., Morueta-Holme, N., Peet, R. K., Sandel, B., Schildhauer, M., Smith, S. A., Svenning, J.-C., Thiers, B., … Enquist, B. J. (2018). The bien r package: A tool to access the Botanical Information and Ecology Network (BIEN) database. Methods in Ecology and Evolution, 9(2), 373–379. https://doi.org/10.1111/2041-210X.12861
Manching, H. C., Carlson, K., Kosowsky, S., Smitherman, C. T., & Stapleton, A. E. (2017). Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth. F1000Research, 6, 1698. https://doi.org/10.12688/f1000research.12490.2
Michener, W. K. (2018). Creating and Managing Metadata. In F. Recknagel & W. K. Michener (Eds.), Ecological Informatics (pp. 71–88). Springer International Publishing. https://doi.org/10.1007/978-3-319-59928-1_5
Minervini, M., Giuffrida, M. V., Perata, P., & Tsaftaris, S. A. (2017). Phenotiki: An open software and hardware platform for affordable and easy image-based phenotyping of rosette-shaped plants. The Plant Journal, 90(1), 204–216. https://doi.org/10.1111/tpj.13472
Molin, W. T., Wright, A. A., Lawton-Rauh, A., & Saski, C. A. (2017). The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: A repetitive path to resistance. BMC Genomics, 18(1), 91. https://doi.org/10.1186/s12864-016-3336-4
Mondal, T. K., Rawal, H. C., Gaikwad, K., Sharma, T. R., & Singh, N. K. (2017). First de novo draft genome sequence of Oryza coarctata, the only halophytic species in the genus Oryza. F1000Research, 6, 1750. https://doi.org/10.12688/f1000research.12414.1
Monier, A., Chambouvet, A., Milner, D. S., Attah, V., Terrado, R., Lovejoy, C., Moreau, H., Santoro, A. E., Derelle, É., & Richards, T. A. (2017). Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton. Proceedings of the National Academy of Sciences, 114(36), E7489–E7498. https://doi.org/10.1073/pnas.1708097114
Morey, J. S., Burek Huntington, K. A., Campbell, M., Clauss, T. M., Goertz, C. E., Hobbs, R. C., Lunardi, D., Moors, A. J., Neely, M. G., Schwacke, L. H., & Van Dolah, F. M. (2017). De novo transcriptome assembly and RNA-Seq expression analysis in blood from beluga whales of Bristol Bay, AK. Marine Genomics, 35, 77–92. https://doi.org/10.1016/j.margen.2017.08.001
Mozzherin, D. Y., Myltsev, A. A., & Patterson, D. J. (2017). “gnparser”: A powerful parser for scientific names based on Parsing Expression Grammar. BMC Bioinformatics, 18(1), 279. https://doi.org/10.1186/s12859-017-1663-3
Nasko, D. J. (2017). Uncovering the Biological Features of Unknown Viruses Using Shotgun Metagenomic Sequence Data [PhD Thesis]. University of Delaware.
Nelson, A. D. L., Devisetty, U. K., Palos, K., Haug-Baltzell, A. K., Lyons, E., & Beilstein, M. A. (2017a). Evolinc: A comparative transcriptomics and genomics pipeline for quickly identifying sequence conserved lincRNAs for functional analysis [Preprint]. Bioinformatics. https://doi.org/10.1101/110148
Nelson, A. D. L., Devisetty, U. K., Palos, K., Haug-Baltzell, A. K., Lyons, E., & Beilstein, M. A. (2017b). Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs. Frontiers in Genetics, 8, 52. https://doi.org/10.3389/fgene.2017.00052
Nigro, O. D., Jungbluth, S. P., Lin, H.-T., Hsieh, C.-C., Miranda, J. A., Schvarcz, C. R., Rappé, M. S., & Steward, G. F. (2017). Viruses in the Oceanic Basement. MBio, 8(2), e02129-16, /mbio/8/2/e02129-16.atom. https://doi.org/10.1128/mBio.02129-16
Nualart, N., Ibáñez, N., Soriano, I., & López-Pujol, J. (2017). Assessing the Relevance of Herbarium Collections as Tools for Conservation Biology. The Botanical Review, 83(3), 303–325. https://doi.org/10.1007/s12229-017-9188-z
Oliveira Alvarenga, D., Moreira, L. M., Chandler, M., & Varani, A. M. (2018). A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes. In J. C. Setubal, J. Stoye, & P. F. Stadler (Eds.), Comparative Genomics (Vol. 1704, pp. 213–242). Springer New York. https://doi.org/10.1007/978-1-4939-7463-4_7
Orcutt, J., Rajasekar, A., Moore, R., & Vernon, F. (2015). Workflow-Oriented Cyberinfrastructure for Sensor Data Analytics. AGU Fall Meeting Abstracts.
Paez-Espino, D., Pavlopoulos, G. A., Ivanova, N. N., & Kyrpides, N. C. (2017). Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data. Nature Protocols, 12(8), 1673–1682. https://doi.org/10.1038/nprot.2017.063
Pelletier, J. D., Barron-Gafford, G. A., Gutiérrez-Jurado, H., Hinckley, E.-L. S., Istanbulluoglu, E., McGuire, L. A., Niu, G.-Y., Poulos, M. J., Rasmussen, C., Richardson, P., Swetnam, T. L., & Tucker, G. E. (2018). Which way do you lean? Using slope aspect variations to understand Critical Zone processes and feedbacks: Which way do you lean? Earth Surface Processes and Landforms, 43(5), 1133–1154. https://doi.org/10.1002/esp.4306
Perrin, H., Denorme, M., Grosjean, J., community, Omic., Dynomant, E., Henry, V. J., Pichon, F., Darmoni, S., Desfeux, A., & Gonzalez, B. J. (2017). OMICtools: A community-driven search engine for biological data analysis. ArXiv:1707.03659 [Cs, q-Bio]. http://arxiv.org/abs/1707.03659
Polański, K., Gao, B., Mason, S. A., Brown, P., Ott, S., Denby, K. J., & Wild, D. L. (2018). Bringing numerous methods for expression and promoter analysis to a public cloud computing service. Bioinformatics, 34(5), 884–886. https://doi.org/10.1093/bioinformatics/btx692
Rai, A., Saito, K., & Yamazaki, M. (2017). Integrated omics analysis of specialized metabolism in medicinal plants. The Plant Journal, 90(4), 764–787. https://doi.org/10.1111/tpj.13485
Reyer, H., Shirali, M., Ponsuksili, S., Murani, E., Varley, P. F., Jensen, J., & Wimmers, K. (2017). Exploring the genetics of feed efficiency and feeding behaviour traits in a pig line highly selected for performance characteristics. Molecular Genetics and Genomics, 292(5), 1001–1011. https://doi.org/10.1007/s00438-017-1325-1
Riemer, K., Guralnick, R. P., & White, E. (2017). No general relationship between mass and temperature in endothermic species [Preprint]. Ecology. https://doi.org/10.1101/113753
Robbins, N. E., & Dinneny, J. R. (2017). Growth is required for perception of water availability to pattern plant root branches [Preprint]. Plant Biology. https://doi.org/10.1101/097758
Roux, S., Chan, L.-K., Egan, R., Malmstrom, R. R., McMahon, K. D., & Sullivan, M. B. (2017). Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nature Communications, 8(1), 858. https://doi.org/10.1038/s41467-017-01086-2
Roux, S., Emerson, J. B., Eloe-Fadrosh, E. A., & Sullivan, M. B. (2017). Benchmarking viromics: An in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ, 5, e3817.
Roy, B., Mondal, A. K., Roy, C. K., Schneider, K. A., & Wazed, K. (2017). Towards a Reference Architecture for Cloud-Based Plant Genotyping and Phenotyping Analysis Frameworks. 2017 IEEE International Conference on Software Architecture (ICSA), 41–50. https://doi.org/10.1109/ICSA.2017.42
Satjarak, A., Burns, J. A., Kim, E., & Graham, L. E. (2017). Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis. Journal of Phycology, 53(3), 601–615. https://doi.org/10.1111/jpy.12521
Satjarak, A., & Graham, L. E. (2017). Comparative DNA sequence analyses of Pyramimonas parkeae (Prasinophyceae) chloroplast genomes. Journal of Phycology, 53(2), 415–424. https://doi.org/10.1111/jpy.12515
Schneider, M. V., Griffin, P. C., Tyagi, S., Flannery, M., Dayalan, S., Gladman, S., Watson-Haigh, N., Bayer, P. E., Charleston, M., Cooke, I., Cook, R., Edwards, R. J., Edwards, D., Gorse, D., McConville, M., Powell, D., Wilkins, M. R., & Lonie, A. (2019). Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. Briefings in Bioinformatics, 20(2), 384–389. https://doi.org/10.1093/bib/bbx071
Shi, S., Zhang, X., Mandel, M. A., Zhang, P., Zhang, Y., Ferguson, M., Amuge, T., Rounsley, S., Liu, Z., & Xiong, Z. (2017). Variations of five eIF4E genes across cassava accessions exhibiting tolerant and susceptible responses to cassava brown streak disease. PLOS ONE, 12(8), e0181998. https://doi.org/10.1371/journal.pone.0181998
Singh, A. K. (2017). Discovery and Role of Molecular Markers Involved in Gene Mapping, Molecular Breeding, and Genetic Diversity. In K. R. Hakeem, A. Malik, F. Vardar-Sukan, & M. Ozturk (Eds.), Plant Bioinformatics (pp. 303–328). Springer International Publishing. https://doi.org/10.1007/978-3-319-67156-7_12
Sparks, E. E., & Benfey, P. N. (2017). Tissue-Specific Transcriptome Profiling in Arabidopsis Roots. In W. Busch (Ed.), Plant Genomics (Vol. 1610, pp. 107–122). Springer New York. https://doi.org/10.1007/978-1-4939-7003-2_8
Stanzione, Dan, & Vaughn, M. (2017). The New Advanced Computing Landscape: Opportunities for Molecular Biology. Proceedings of the Society of Molecular Biology and Evolution 2017 Meeting, 55. http://www.smbe2017.org/wp-content/uploads/2016/02/SMBE-Abstract-Book-22-June.pdf
Stoltzfus, A., Rosenberg, M., Lapp, H., Budd, A., Cranston, K., Pontelli, E., Oliver, S., & Vos, R. A. (2017). Community and Code: Nine Lessons from Nine NESCent Hackathons. F1000Research, 6, 786. https://doi.org/10.12688/f1000research.11429.1
Stucky, B., Walls, R., Deck, J., Denny, E., Bolmgren, K., & Guralnick, R. (2017). An Update on the Plant Phenology Ontology and Plant Phenology Data Integration. Proceedings of TDWG, 1, e20487. https://doi.org/10.3897/tdwgproceedings.1.20487
Swetnam, T. L., Brooks, P. D., Barnard, H. R., Harpold, A. A., & Gallo, E. L. (2017). Topographically driven differences in energy and water constrain climatic control on forest carbon sequestration. Ecosphere, 8(4), e01797. https://doi.org/10.1002/ecs2.1797
Taber, K. S., Sumida, M., & McClure, L. (2017). Teaching Gifted Learners in STEM Subjects: Developing talent in science, technology, engineering and mathematics. Taylor & Francis.
Tardieu, F., Cabrera-Bosquet, L., Pridmore, T., & Bennett, M. (2017). Plant Phenomics, From Sensors to Knowledge. Current Biology, 27(15), R770–R783. https://doi.org/10.1016/j.cub.2017.05.055
Tello-Ruiz, M. K., Naithani, S., Stein, J. C., Gupta, P., Campbell, M., Olson, A., Wei, S., Preece, J., Geniza, M. J., Jiao, Y., Lee, Y. K., Wang, B., Mulvaney, J., Chougule, K., Elser, J., Al-Bader, N., Kumari, S., Thomason, J., Kumar, V., … Ware, D. (2018). Gramene 2018: Unifying comparative genomics and pathway resources for plant research. Nucleic Acids Research, 46(D1), D1181–D1189. https://doi.org/10.1093/nar/gkx1111
Trail, F., Wang, Z., Stefanko, K., Cubba, C., & Townsend, J. P. (2017). The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. PLOS Genetics, 13(7), e1006867. https://doi.org/10.1371/journal.pgen.1006867
Vaidya, G. G. (2017). Taxonomic Checklists as Biodiversity Data: How Series of Checklists can Provide Information on Synonymy, Circumscription Change and Taxonomic Discovery.
Van Es, H., & Woodard, J. (2017). Innovation in agriculture and food systems in the digital age. The Global Innovation Index, 97–104.
Via, A., Attwood, T. K., Fernandes, P. L., Morgan, S. L., Schneider, M. V., Palagi, P. M., Rustici, G., & Tractenberg, R. E. (2019). A new pan-European Train-the-Trainer programme for bioinformatics: Pilot results on feasibility, utility and sustainability of learning. Briefings in Bioinformatics, 20(2), 405–415. https://doi.org/10.1093/bib/bbx112
Walls, R., & Buttigieg, P. L. (2017). Semantically Defining Populations for ’Omics Research. Proceedings of TDWG, 1, e20435. https://doi.org/10.3897/tdwgproceedings.1.20435
Wang, C.-K., & Xu, H. (2017). Formalizing Data Management Systems: A Case Study of Syndicate Protocol. 2017 International Conference on Computational Science and Computational Intelligence (CSCI), 1031–1034.
Wang, H., Tian, L., Goldstein, A., Liu, J., Lo, H.-C., Sheng, K., Welte, T., Wong, S. T. C., Gugala, Z., Stossi, F., Zong, C., Li, Z., Mancini, M. A., & Zhang, X. H.-F. (2017). Bone-in-culture array as a platform to model early-stage bone metastases and discover anti-metastasis therapies. Nature Communications, 8(1), 15045. https://doi.org/10.1038/ncomms15045
Willis, C., Lambert, M., McHenry, K., & Kirkpatrick, C. (2017). Container-based Analysis Environments for Low-Barrier Access to Research Data. Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact - PEARC17, 1–4. https://doi.org/10.1145/3093338.3104164
Xu, S., Brockmöller, T., Navarro-Quezada, A., Kuhl, H., Gase, K., Ling, Z., Zhou, W., Kreitzer, C., Stanke, M., Tang, H., Lyons, E., Pandey, P., Pandey, S. P., Timmermann, B., Gaquerel, E., & Baldwin, I. T. (2017). Wild tobacco genomes reveal the evolution of nicotine biosynthesis. Proceedings of the National Academy of Sciences, 114(23), 6133–6138. https://doi.org/10.1073/pnas.1700073114
Xu, W., Huang, R., Esteva, M., Song, J., & Walls, R. (2016). Content-based comparison for collections identification. 2016 IEEE International Conference on Big Data (Big Data), 3283–3289.
Yang, A., Troup, M., & Ho, J. W. K. (2017). Scalability and Validation of Big Data Bioinformatics Software. Computational and Structural Biotechnology Journal, 15, 379–386. https://doi.org/10.1016/j.csbj.2017.07.002
Yang, J., Mezmouk, S., Baumgarten, A., Buckler, E. S., Guill, K. E., McMullen, M. D., Mumm, R. H., & Ross-Ibarra, J. (2017). Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLOS Genetics, 13(9), e1007019. https://doi.org/10.1371/journal.pgen.1007019
Zajitschek, F., Zajitschek, S., & Manier, M. (2017). High-protein paternal diet confers an advantage to sons in sperm competition. Biology Letters, 13(2), 20160914. https://doi.org/10.1098/rsbl.2016.0914
Zhang, H., Chu, S., & Zhang, D. (2017). Transcriptome Dataset of Soybean (Glycine max) Grown under Phosphorus-Deficient and -Sufficient Conditions. Data, 2(2), 17. https://doi.org/10.3390/data2020017
Zhang, J., Schmidt, C. J., & Lamont, S. J. (2017). Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress. BMC Genomics, 18(1), 295. https://doi.org/10.1186/s12864-017-3675-9
Zhang, Y., Calyam, P., Debroy, S., & Nuguri, S. S. (2018). Social Plane for Recommenders in Network Performance Expectation Management. IEEE Transactions on Network and Service Management, 15(1), 97–111. https://doi.org/10.1109/TNSM.2017.2772905
Zhao, L., Song, C. X., Kalyanam, R., Biehl, L., Campbell, R., Delgass, L., Kearney, D., Wan, W., Shin, J., Kim, I. L., & others. (2017). GABBs-Reusable Geospatial Data Analysis Building Blocks for Science Gateways. IWSG.
Zou, B., Li, J., Zhou, Q., & Quan, Z.-X. (2017). MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool. PLOS ONE, 12(3), e0174609. https://doi.org/10.1371/journal.pone.0174609