iPlant Publications


Bailey, Peter E., Tapasya, Patki, Striemer, Gregory M.,et al, "Quantitative Trait Locus Analysis Using a Partitioned Linear Model on a GPU Cluster," Proceedings from HICOMB 2012.

Beaulieu, J.M., Ree, R.H., Cavender-Bares, J., Weiblen, G.D., Donoghue, M.J., "Synthesizing phylogenetic knowledge for ecological research," Ecology 93(6) Supplement, June 2012, pp. S4-S13.  

Beck, J., Ballesteros-Mejia, L., Buchmann, C.M., Dengler, J., Fritz, S.A., Gruber, B. Hof, C., Jansen, F., Knapp, S., Kreft, H., Schneider, A.-K., Winter, M., Dormann, C.F. "What's on the horizon for macroecology?" Ecography. doi: 10.1111/j. 1600-0587.22012.07364.x.

Egan, Ashley N., Schlueter, Jessica, Spooner, David M., "Applications of next-generation sequencing in plant biology," Am. J. Bot. February (2012) 99(2): 175-185. doi: 10.3732/ajb.1200020.

Goth, G., "Preserving Digital Data," Communications of the ACM, 55 (4):11-12. doi: 10.1145/2133806.2133811.

Jiao, Yuannian, Leebens-Mack, J., Ayyampalayam, S., Bowers, J.E., McKain, M.R., McNeal, J., Rolf, M., et al. 2012. "€œA genome triplication associated with early diversification of the core eudicots." Genome biology 13 (1) (January 26): R3. doi: 10.1186/gb-2012-13-1-r3

Kharitonova, Yekaterina; Q. Tung; A. Danehy, A. Efrat, and K. Barnard. 2012. "Client-side Backprojection of Presentation Slides into Educational Video."  Preprint for ACM Multimedia '12. 

Kimbrel, Jeffrey A., Di, Y., Cumbie, J.S., Chang, J.H., "RNA-Seq for Plant Pathogenic Bacteria," Genes 2012, 2(4), 689-705.  doi: 10.3390/genes2040689.

Klinov, P., Del Vescovo, C., Schneider, T., "Incrementally undateable and persistent decomposition of OWL ontologies" in: Proceedings of OWL: Experiences and Directions Workshop 2012, P. Klinov and M. Horridge (eds.), Heraklion, Crete, Greece, May 27-28, 2012.  

Miller, Robert J., Hocevar, John, Stone, Robert P., Fedorov, Dmitry V., "Structure-Forming Corals and Sponges and Their Use as Fish Habitat in Bering Sea Submarine Canyons," PloS ONE 7(3): e33885. doi: 10.1371/journal.pone.0033885.

Parr, C.S., Guralnick, R., Cellinese, N., Page, R.D.M., "Evolutionary informatics: unifying knowledge about the diversity of life," Trends in Ecology & Evolution, 27(2):94-103, February 2012. doi: 10.1016/j.tree.2011.11.001

Ram, Sudha, Liu, Jun, "A Semantic Foundation for Provenance Management," J. Data Semant (2012) 1:11-17. doi: 10.1007/s13740-012-0002-0.

Reddy, A.S.N., Rogers, M.F., Richardson, D.N., Hamilton, M., Ben-Hur, A., "Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements," Front. Plant Sci. 2012; 3:18. doi: 10.3389/fpls.2012.00018.

Reneker, J., Lyons E., Conant G. C., Pires J. C., Freeling, M., Shyu, C. R., Korkin, D. "Long identical multispecies elements in plant and animal genomes," PNAS 109 (19), E1183-E1191. doi: 10.1073/pnas.1121356109.

Schatz, M.C., Witkowski, J., McCombie, W.R., "Current challenges in de novo plant genome sequencing and assembly," Genome Biology 2012, 12:243 (27 April). doi: 10.1186/gb-2012-13-4-243.

Schnable, J.C., Freeling, M, Lyons, E., "Genome-wide analysis of syntenic gene deletion in the grasses," Genome Biology and Evolution (2012). doi :10.1093/gbe/evs009.

Stamatakis, A., Aberer, A.J., Goll, C., Smith, S.A., Berger, S.A., and Izquierdo-Carrasco, F., "RAxML-Light:  a tool for computing terabyte," Bioinformatics (2012). doi: 10.1093/bioinformatics/bts309.

Stolte, D., "Mystery Peeled Off Banana Genome", UA News, July 12, 2012. http://uanews.org/story/mystery-peeled-banana-genome.

Stolte, D., "Banana gives up its secrets", Western Farm Press, July 24, 2012, 3:16 PM, http://uanews.org/story/mystery-peeled-banana-genome Stolte, D., "Banana gives up its secrets", Western Farm Press, July 24, 2012, 3:16 PM, http://westernfarmpress.com/management/banana-gives-its-secrets">http://westernfarmpress.com/management/banana-gives-its-secrets.

Straub, S.C.K., Parks, M., Weitemier, K, Fishbein M., Cronn, R.C., Liston, A., "Navigating the tip of the genomic iceberg: Next-generation sequencing for plant semantics," Am. J. Bot., February 2012, vo. 99, no. 2, 349-364. doi: 10.3732/ajb.1100335.

Strickler, S.R., Bombarely, A., Mueller, L.A., "Designing a transcriptome next-generation sequencing project for a nonmodel plant species," Am. J. Bot., February 2012, vol 99 no. 2, 257-266. doi: 10.3732/ajb.1100292.

Tang, H., and Lyons, E., "The Evolution of Genome Structure" (Editorial), Int. J. Evol. 2012, 1:1. doi: http://dx.doi.org/10.4172/ievj.1000e105.

White, J.W., et al., "Field-based phenomics for plant genetics research," Field Crops Research, 11 July. vol. 133: 101-112. doi: 10.1016/j.fcr.2012.04.003.

Zimmer, Carl, "Tree of Life Project Aims for Every Twig and Leaf", The New York Times, Science Section, June 4, 2012. 


Ahern, Kevin, "Cyberplant Collaborative," Biotechniques 51:227. doi: 10.2144/00011374.

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. doi: 10.1371/journal.pone0028436.

Basney, Jim, Dooley, Rion, et al., "Distributed Web Security for the Science Gateways" Proceedings from Gateway Computing Environments 2001 at Supercomputing11 (2011). doi: 10.1145/2110486.2110489.

Brown, Susan A. and Thatcher, Sherry, "Factors Influencing Adoption And Non-Adoption Of Cyberinfrastructure By The Research Community," PACIS 2011 Proceedings Paper 31. (2011). http://aisel.aisnet.org/pacis2011/31.

Del Vescovo, C., Gessler, D.D.G., Klinov, P., Parsia, B., Sattler, U., Schneider, T., and Winget, A., "Decomposition and Modular Structure of BioPortal Ontologies," in: International Semantic Web Conference, Lecture Notes in Computer Science, 7031: 130-145. doi: 10.1007/978_3_642_25073-6_9.

Feng, Xin, Grossman, Robert, and Stein, Lincoln, "PeakRanger: A cloud-enabled peak caller for ChIP-seq data," BMC Bioinformatics 12:139 (2011). doi: 10.1186/1471-2105-12-13.

Goff, Stephen A. et al., "The iPlant Collaborative: Cyberinfrastructure for Plant Biology," Frontiers in Plant Science 2 (2011). doi: 10.3389/fpls.2011.00034.

Izquierdo-Carrasco, F., Smith, Stephen A., and Stamatakis, Alexandros, "Algorithms, Data Structures, and Numerics for Likelihood-based Phylogenetic Inference of Huge Trees", BMC Bioinformatics (2011). doi: 10.1186/1471-2105-12-470.

Koesterke, Lars, Stanzione, Dan, Vaughn, Matt, Welch, Stephen M., et al., "An Efficient and Scalable Implementation of SNP-Pair Interaction Testing for Genetic Association Studies," Proceedings from IEEE International Symposium on Parallel and Distributed Processing Workshops and PhD Forum (2011). doi: 10.1109/IPDPS.2011.190.

Lenards, Andrew; Merchant, Nirav; and Stanzione, Dan, "Building an Environment to Facilitate Discoveries for Plant Sciences," GCE'11: Proceedings of the 2011 ACM workshop on Gateway computing environments, pp. 51-58. doi: 10.1145/2110486.2110494.

Liu, Jun, "W7 Model of Provenance and its use in the context of Wikipedia," The University of Arizona Campus Repository (2011). doi: 10150/145314.

Liu, Jun, and Ram, Suhda, "Who does what: Collaboration patterns in the wikipedia and their impact on article quality," ACM Transactions on Management Information Systems (TMIS) (2011). doi: 10.1145/1985347.1985352.

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

Makumburage, G. Buddhika and Stapleton, Ann E., "Phenotype uniformity in combined-stress environments has a different genetic architecture than in single-stress treatments," Frontiers in Plant Science 2 (2011). doi: 10.3389/fpls.2011.00012.

Matasci, Naim, et al., "Correcting and Standardizing Taxonomic Names with the Taxonomic Name Resolution Service," Proceedings from Biodiversity Information Standards-TDWG (2011).

Micklos, David, Lauter, Susan, and Nisselle, Amy, "Lessons from a Science Education Portal," Science 334 (2011): 1657-1658. doi: http://www.sciencemag.org/content/334/6063/1657.full.

Perianayagam, S., Andrews, G.R., Hartman, J.H., "Rex: A toolset for reproducing software experiments," Bioinformatics and Biomedicine (BIBM), 2010 IEEE International Conference on, pp.613-617, (2010). doi: 10.1109/BIBM.2010.5706639.

Rogowitz, Bernice E. and Matasci, Naim, "Metadata mapper: A user interface web service for mapping data between independent visual analysis components, guided by perceptual rules," Proceedings of the SPIE Conference on Human Vision and Electronic Imaging (2011). doi: 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., "MaizeGDB: curation and outreach go hand-in-hand," Database (Oxford), 2011. doi: 10.1093/database/bar022.

Schnable, James C., and Lyons, Eric, "Comparative genomics with maize and other grasses: from genes to genomes!," Maydica 56-1763 (2011).

Skidmore, Edwin, Kim, Seung-jin, Kuchimanchi, Sangeeta, Singaram, Sriramu, Merchant, Nirav, and Stanzione, Daniel, "iPlant Atmosphere: A Gateway to Cloud Infrastructure for the Plant Sciences," Proceedings from Gateway Computing Environments 2011 at Supercomputing11 (2011).

Smith, Stephen A. et al., "Understanding angiosperm diversification using small and large phylogenetic trees," American Journal of Botany 98:404-414 (2011), doi: 10.3732/ajb.1000481.

Stamatakis, A., Aberer, A.J., Goll, C., Smith, S.A., Berger, S.A., Izquierdo-Carrasco, F., "Supplementary Material: RAxML-Light: A Tool for computing TeraByte Phylogenies," Bioinformatics 2011: 1-6.

Stanzione, Dan, "The iPlant Collaborative: Cyberinfrastructure to Feed the World," IEEE Computer, November 2011. doi: 10.1109/MC.2011.297.

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

Wang, L., Peterson, R.B., Brutnell, T., "Regulatory mechanisms underlying C4 photosynthesis," New Phytologist, vol 190 1:9-20, April 2011. doi: 10.1111/j.1469-8137.2011.03649.x.

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

Whitfield, J., "Species spellchecker fixes plant glitches", Nature 474, 263 (2011). doi: 10.1038/474263a.

Zheng, C., Swensen, K., Lyons, E., Sankoff, D., "OMG! Orthologs in Multiple Genomes-Competing Graph-Theoretical Formulations," Algorithms in Bioinformatics: Lecture Notes in Computer Science, 2011, Vol. 6833/2011, 364-375. doi: 10.1007/978-3-642-23038-7_30.


Goff, Stephen A., "A unifying theory for general multigenic heterosis: energy efficiency, protein metabolism, and implications for molecular breeding," New Phytologist 189 (2010): 923-937. doi: 10.1111/j.1469-8137.2010.03574.x.

Hanlon, Matthew et al., "My-Plant.org: A phylogenetically structured social network", Paper presented at Gateway Computing Environments Workshop (GCE), New Orleans, LA, November 14, 2010. doi: 10.1109/GCE.2010.5676118.

Jordan, Chris et al., "Comprehensive data infrastructure for plant bioinformatics," Paper presented at IEEE International Conference on Cluster Computing, 20-24 Sept. 2010. doi: 10.1109/CLUSTERWKSP.2010.5613093.

Nelson, Rex T., et al., “Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery ad disparate data and service integration”. BioData Mining 3 (2010). doi: 10.1186/1756-0381-3-3.

Ram, Sudha and Liu, Jun, “Provenance Management in BioSciences” in Advances in Conceptual Modeling – Applications and Challenges ER 2010 Workshops ACM-L, CMLSA, CMS, DE@ER, FP-UML, SeCoGIS, WISM. Proceedings, Vancouver, British Columbia, Canada, November 1-4, 2010. 54-64. doi: 10.1007/978-3-642-16385-2.

Wang, Liya and Stein, Lincoln, “Localizing triplet periodicity in DNA and cDNA sequences,” BMC Bioinformatics 11:550 (2010). doi: 10.1186/1471-2105-11-550.

Wolf, Frederic, Hobby, R., Lowry, S., Bauman, A., Franza, B.R., Lin, B., Rapson, S., Stewart, E., Kolker, E., "OMICS: A Journal of Integrative Biology" April 2011, 15(4): 217-219. doi: 10.1089/omi.2011.0009.


Brown, Susan A., Thatcher, S., and Dang, Y., "Managing Knowledge in a Changing Scientific Landscape: The Impact of Cyberinfrastructure," System Sciences (HICSS), 2010 43rd Hawaii International Conference on, 1-10, 5-8 Jan. 2010. doi: 10.1109/HICSS.2010.263.

Gessler, Damian D.G. et al., "SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services," BMC Bioinformatics (2009). doi: 10.1186/1471-2105-10-309.

Han, Y.,  Burnette, J.M., and Wessler, S.R., "TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences," Nucleic Acids Research, (2009). doi: 10.1093/nar/gkp295.

Liu, Jun and Sudha Ram, "Who Does What: Collaboration Patterns in the Wikipedia and Their Impact on Data Quality," 19th Workshop on Information Technologies and Systems, 175-180, December 8, 2009, http://ssrn.com/abstract=1565682.

Macías-Duarte, Alberto et al., "Novel microsatellite loci for the burrowing owl Athene cunicularia," Conservation Genetics Resources 2 (2009): 67-69, doi: 10.1007/s12686-009-9150-4.


Holuigue, Loreto, Vilelle-Calzada, Jean Philippe, and Guiterrez, Rodrigo A., "Crops in all shapes and sizes," Genome Biology 9 (2008): 319, doi: 10.1186/gb-2008-9-9-319.


Piel, William H., "Obstacles and Avenues Facing Phyloinformatic Research," Proceedings of TDWG 2008 (2008): 28-29, url: http://www.tdwg.org/fileadmin/2008conference/documents/Proceedings2008.pdf#page=28.


Ram, Sudha, Zhang, K., and Wei, W., "Linking Biological Databases for Knowledge Discovery," Advances in Conceptual Modeling - Challenges and Opportunities Lecture Notes in Computer Science 5232 (2008): 22-32. doi: 10.1007/978-3-540-87991-6_4.


Stein, Lincoln, "Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges," Nature Reviews Genetics 9 (2008): 678-688 doi: 10.1038/nrg2414.