2011 Publications

Banks, I. V., et. al. (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., Roger; McFarlin, Adam J. ;. Rounsley, Steven 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., Roger; Wilson, Richard; 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. http://iswc2011.semanticweb.org/fileadmin/iswc/Papers/PostersDemos/iswc11pd_submission_75.pdf

Feng, L., Xin; Grossman, Robert; 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., David W. ;. Bennetzen, Jeffrey L. ;. Kellogg, Elizabeth A. ;. Pires, J. Chris; 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., Stephen A. ;. Vaughn, Matthew; McKay, Sheldon; Lyons, Eric; Stapleton, Ann E. ;. Gessler, Damian; Matasci, Naim; Wang, Liya; Hanlon, Matthew; Lenards, Andrew; Muir, Andy; Merchant, Nirav; Lowry, Sonya; Mock, Stephen; Helmke, Matthew; Kubach, Adam; Narro, Martha; Hopkins, Nicole; Micklos, David; Hilgert, Uwe; Gonzales, Michael; Jordan, Chris; Skidmore, Edwin; Dooley, Rion; Cazes, John; McLay, Robert; Lu, Zhenyuan; Pasternak, Shiran; Koesterke, Lars; Piel, William H. ;. Grene, Ruth; Noutsos, Christos; Gendler, Karla; Feng, Xin; Tang, Chunlao; Lent, Monica; Kim, Seung-Jin; Kvilekval, Kristian; Manjunath, B. S. ;. Tannen, Val; Stamatakis, Alexandros; Sanderson, Michael; Welch, Stephen M. ;. Cranston, Karen A. ;. Soltis, Pamela; Soltis, Doug; O’Meara, Brian; Ane, Cecile; Brutnell, Tom; Kleibenstein, Daniel J. ;. White, Jeffery W. ;. Leebens-Mack, James; Donoghue, Michael J. ;. Spalding, Edgar P. ;. Vision, Todd J. ;. Myers, Christopher R. ;. Lowenthal, David; Enquist, Brian J. ;. Boyle, Brad; Akoglu, Ali; Andrews, Greg; Ram, Sudha; Ware, Doreen; Stein, Lincoln; Stanzione. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. 2. https://doi.org/10.3389/fpls.2011.00034

Kimbrel, J. H., Jeffrey A. ;. Di, Yanming; Cumbie, Jason 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.-T., 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. https://repository.arizona.edu/handle/10150/145314

Liu, S., Jun; 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., Robert; Stanzione, Dan; Mckay, S. J. ;. Wheeler. (2011). A scalable parallel implementation of the neighbor joining algorithm for phylogenetic trees.

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

Nodine, F. E., Michael D. ;. Bryan, Anthony C. ;. Racolta, Adriana; Jerosky, Keith 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., Bernice E. ;. Matasci. (2011). Metadata Mapper: A web service for mapping data between independent visual analysis components, guided by perceptual rules (T. N. Rogowitz Bernice E. ;. Pappas, Ed.; p. 78650I). https://doi.org/10.1117/12.881734

Schaeffer, C. J., M. L. ;. 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., James C. ;. Lyons. (2011). Comparative genomics with maize and other grasses: From genes to genomes! Maydica, 56(2). https://journals-crea.4science.it/index.php/maydica/article/view/690

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., S. A. ;. 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., J. H. ;. 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., Haibao; Lyons, Eric; Pedersen, Brent; Schnable, James C; Paterson, Andrew 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.-Y. (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., Lin; Peterson, Richard 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., Lin; Si, Yaqing; Dedow, Lauren K. ;. Shao, Ying; Liu, Peng; 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. In T. M. Przytycka & M.-F. Sagot (Eds.), Algorithms in Bioinformatics (Vol. 6833, pp. 364–375). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-23038-7_30