2011 Publications

Banks, J. A., 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., … Grigoriev, I. V. (2011). The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants. Science, 332(6032), 960–963. https://doi.org/10.1126/science.1203810
Barthelson, R., McFarlin, A. J., Rounsley, S. D., & Young, S. (2011). Plantagora: Modeling Whole Genome Sequencing and Assembly of Plant Genomes. PLoS ONE, 6(12), e28436. https://doi.org/10.1371/journal.pone.0028436
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
Feng, X., Grossman, R., & Stein, L. (2011). PeakRanger: A cloud-enabled peak caller for ChIP-seq data. BMC Bioinformatics, 12(1), 139. https://doi.org/10.1186/1471-2105-12-139
Galbraith, D. W., Bennetzen, J. L., Kellogg, E. A., Pires, J. C., & Soltis, P. S. (2011). The Genomes of All Angiosperms: A Call for a Coordinated Global Census. Journal of Botany, 2011, 1–10. https://doi.org/10.1155/2011/646198
Goff, S. A., 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., … Stanzione, D. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Science, 2. https://doi.org/10.3389/fpls.2011.00034
Kimbrel, J. A., Di, Y., Cumbie, J. S., & Chang, J. H. (2011). RNA-Seq for Plant Pathogenic Bacteria. Genes, 2(4), 689–705. https://doi.org/10.3390/genes2040689
Liu, J. (2011). W7 model of provenance and its use in the context of wikipedia [University of Arizona]. https://repository.arizona.edu/handle/10150/145314
Liu, J., & Ram, S. (2011). Who does what: Collaboration patterns in the wikipedia and their impact on article quality. ACM Transactions on Management Information Systems, 2(2), 1–23. https://doi.org/10.1145/1985347.1985352
Macilwain, C. (2011). Systems Biology: Evolving into the Mainstream. Cell, 144(6), 839–841. https://doi.org/10.1016/j.cell.2011.02.044
McLay, R., Stanzione, D., Mckay, S. J., & Wheeler, T. (2011). A scalable parallel implementation of the neighbor joining algorithm for phylogenetic trees. ICCABS Conference.
Micklos, D., Lauter, S., & Nisselle, A. (2011). Lessons from a Science Education Portal. Science, 334(6063), 1657–1658. https://doi.org/10.1126/science.1197074
Nodine, M. D., Bryan, A. C., Racolta, A., Jerosky, K. V., & Tax, F. E. (2011). A few standing for many: Embryo receptor-like kinases. Trends in Plant Science, 16(4), 211–217. https://doi.org/10.1016/j.tplants.2011.01.005
Rogowitz, B. E., & Matasci, N. (2011). Metadata Mapper: A web service for mapping data between independent visual analysis components, guided by perceptual rules (B. E. Rogowitz & T. N. Pappas, Eds.; p. 78650I). https://doi.org/10.1117/12.881734
Schaeffer, M. L., Harper, L. C., Gardiner, J. M., Andorf, C. M., Campbell, D. A., Cannon, E. K. S., Sen, T. Z., & Lawrence, C. J. (2011). MaizeGDB: Curation and outreach go hand-in-hand. Database, 2011(0), bar022–bar022. https://doi.org/10.1093/database/bar022
Smith, S. A., Beaulieu, J. M., Stamatakis, A., & Donoghue, M. J. (2011). Understanding angiosperm diversification using small and large phylogenetic trees. American Journal of Botany, 98(3), 404–414. https://doi.org/10.3732/ajb.1000481
Stanzione, D. (2011). The iPlant Collaborative: Cyberinfrastructure to Feed the World. Computer, 44(11), 44–52. https://doi.org/10.1109/MC.2011.297
Stillman, J. H., Denny, M., Padilla, D. K., Wake, M. H., Patek, S., & Tsukimura, B. (2011). Grand Opportunities: Strategies for Addressing Grand Challenges in Organismal Animal Biology. Integrative and Comparative Biology, 51(1), 7–13. https://doi.org/10.1093/icb/icr052
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., Pedersen, B., Schnable, J. C., Paterson, A. H., & Freeling, M. (2011). Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics, 12(1), 102. https://doi.org/10.1186/1471-2105-12-102
Wang, F.-Y. (2011). From AI to SciTS: Team Science and Research Intelligence. IEEE Intelligent Systems, 26(3), 2–4. https://doi.org/10.1109/MIS.2011.49
Wang, L., Peterson, R. B., & Brutnell, T. P. (2011). Regulatory mechanisms underlying C4 photosynthesis: Tansley review. New Phytologist, 190(1), 9–20. https://doi.org/10.1111/j.1469-8137.2011.03649.x
Wang, L., Si, Y., Dedow, L. K., Shao, Y., Liu, P., & Brutnell, T. P. (2011). A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq. PLoS ONE, 6(10), e26426. https://doi.org/10.1371/journal.pone.0026426