2012 Publications

Alakonya, N., Amos; Kumar, Ravi; Koenig, Daniel; Kimura, Seisuke; Townsley, Brad; Runo, Steven; Garces, Helena M. ;. Kang, Julie; Yanez, Andrea; David-Schwartz, Rakefet; Machuka, Jesse; 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., Jan; Ballesteros-Mejia, Liliana; Buchmann, Carsten M. ;. Dengler, Jürgen; Fritz, Susanne A. ;. Gruber, Bernd; Hof, Christian; Jansen, Florian; Knapp, Sonja; Kreft, Holger; Schneider, Anne-Kathrin; Winter, Marten; 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., Benjamin; Buzzard, Vanessa; Simova, Irena; Sloat, Lindsey; Boyle, Brad; Lipson, Rebecca; Aguilar-Beaucage, Brianna; Andrade, Angelina; Barber, Benjamin; Barnes, Chris; Bushey, Dharma; Cartagena, Paulina; Chaney, Max; Contreras, Karina; Cox, Mandarava; Cueto, Maya; Curtis, Cannon; Fisher, Mariah; Furst, Lindsey; Gallegos, Jessica; Hall, Ruby; Hauschild, Amelia; Jerez, Alex; Jones, Nadja; Klucas, Aaron; Kono, Anita; Lamb, Mary; Matthai, Jacob David Ruiz; McIntyre, Colten; McKenna, Joshua; Mosier, Nicholas; Navabi, Maya; Ochoa, Alex; Pace, Liam; Plassmann, Ryland; Richter, Rachel; Russakoff, Ben; Aubyn, Holden St. ;. Stagg, Ryan; Sterner, Marley; Stewart, Emily; Thompson, Ting Ting; Thornton, Jake; Trujillo, Parker J. ;. Volpe, Trevor 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., Manuel Gonzalo; Bautista, Rocío; Guerrero-Fernández, Darío; Benzerki, Hicham; Seoane, Pedro; 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. In J. Normanly (Ed.), High-Throughput Phenotyping in Plants (Vol. 918, pp. 1–7). Humana Press. https://doi.org/10.1007/978-1-61779-995-2_1
Council, N. R. others. (2012). Implementing the Research Strategy and Evaluating Progress.
Das, J. S., Abhiram; Bucksch, Alexander; Weitz. (2012). Infrastructure for managing and analyzing biological networks derived from collections of plant images.
D’Hont, P., Angélique; Denoeud, France; Aury, Jean-Marc; Baurens, Franc-Christophe; Carreel, Françoise; Garsmeur, Olivier; Noel, Benjamin; Bocs, Stéphanie; Droc, Gaëtan; Rouard, Mathieu; Da Silva, Corinne; Jabbari, Kamel; Cardi, Céline; Poulain, Julie; Souquet, Marlène; Labadie, Karine; Jourda, Cyril; Lengellé, Juliette; Rodier-Goud, Marguerite; Alberti, Adriana; Bernard, Maria; Correa, Margot; Ayyampalayam, Saravanaraj; Mckain, Michael R. ;. Leebens-Mack, Jim; Burgess, Diane; Freeling, Mike; Mbéguié-A.-Mbéguié, Didier; Chabannes, Matthieu; Wicker, Thomas; Panaud, Olivier; Barbosa, Jose; Hribova, Eva; Heslop-Harrison, Pat; Habas, Rémy; Rivallan, Ronan; Francois, Philippe; Poiron, Claire; Kilian, Andrzej; Burthia, Dheema; Jenny, Christophe; Bakry, Frédéric; Brown, Spencer; Guignon, Valentin; Kema, Gert; Dita, Miguel; Waalwijk, Cees; Joseph, Steeve; Dievart, Anne; Jaillon, Olivier; Leclercq, Julie; Argout, Xavier; Lyons, Eric; Almeida, Ana; Jeridi, Mouna; Dolezel, Jaroslav; Roux, Nicolas; Risterucci, Ange-Marie; Weissenbach, Jean; Ruiz, Manuel; Glaszmann, Jean-Christophe; Quétier, Francis; Yahiaoui, Nabila; Wincker. (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. 488(7410), 213–217. https://doi.org/10.1038/nature11241
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).
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. DataCloud 2012. http://www.cse.buffalo.edu/faculty/tkosar/DataCloud2012/papers/datacloud2012_paper_3.pdf
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
Egan, D. M., Ashley N. ;. Schlueter, Jessica; Spooner. (2012). Applications of next-generation sequencing in plant biology. 99(2), 175–185. https://doi.org/10.3732/ajb.1200020
Eichten, N. M., Steven R. ;. Ellis, Nathanael A. ;. Makarevitch, Irina; Yeh, Cheng-Ting; Gent, Jonathan I. ;. Guo, Lin; McGinnis, Karen M. ;. Zhang, Xiaoyu; Schnable, Patrick S. ;. Vaughn, Matthew W. ;. Dawe, R. Kelly; 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. https://pag.confex.com/pag/xx/webprogram/Paper2921.html
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. http://www.stringology.org/papers/PSC2012.pdf#page=83
Flouri, T., Iliopoulos, C. S., Park, K., & Pissis, S. P. (2012). GapMis-OMP: Pairwise Short-Read Alignment on Multi-core Architectures. In L. Iliadis, I. Maglogiannis, H. Papadopoulos, K. Karatzas, & S. Sioutas (Eds.), Artificial Intelligence Applications and Innovations (Vol. 382, pp. 593–601). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-33412-2_61
Fox, D., Geoffrey C; 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., Pu; 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., Yuannian; Leebens-Mack, Jim; Ayyampalayam, Saravanaraj; Bowers, John E; McKain, Michael R; McNeal, Joel; Rolf, Megan; Ruzicka, Daniel R; Wafula, Eric; Wickett, Norman J; Wu, Xiaolei; Zhang, Yong; Wang, Jun; Zhang, Yeting; Carpenter, Eric J; Deyholos, Michael K; Kutchan, Toni M; Chanderbali, Andre S; Soltis, Pamela S; Stevenson, Dennis W; McCombie, Richard; Pires, J; Wong, Gane; Soltis, Douglas 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.-S., Marc T. J. ;. Carpenter, Eric J. ;. Tian, Zhijian; Bruskiewich, Richard; Burris, Jason N. ;. Carrigan, Charlotte T. ;. Chase, Mark W. ;. Clarke, Neil D. ;. Covshoff, Sarah; dePamphilis, Claude W. ;. Edger, Patrick P. ;. Goh, Falicia; Graham, Sean; Greiner, Stephan; Hibberd, Julian M. ;. Jordon-Thaden, Ingrid; Kutchan, Toni M. ;. Leebens-Mack, James; Melkonian, Michael; Miles, Nicholas; Myburg, Henrietta; Patterson, Jordan; Pires, J. Chris; Ralph, Paula; Rolf, Megan; Sage, Rowan F. ;. Soltis, Douglas; Soltis, Pamela; Stevenson, Dennis; Stewart, C. Neal; Surek, Barbara; Thomsen, Christina J. M. ;. Villarreal, Juan Carlos; Wu, Xiaolei; Zhang, Yong; Deyholos, Michael 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. (2012a). Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissues as Revealed by Deep Sequencing. http://hdl.handle.net/10919/33907
Kakumanu, A., Akshay; Ambavaram, Madana M. R. ;. Klumas, Curtis; Krishnan, Arjun; Batlang, Utlwang; Myers, Elijah; Grene, Ruth; Pereira. (2012b). 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., Pavel; Del Vescovo, Chiara; Schneider. (2012). Incrementally Updateable and Persistent Decomposition of OWL Ontologies. 849, 7. http://ceur-ws.org/Vol-849/paper_7.pdf
Kolker, V., Eugene; Stewart, Elizabeth; 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., Eric; Tang, Haibao; Schnable. (2012). Whole Genome Comparisons with Oryza and Brachypodium using CoGe and SynMap. W267. https://pag.confex.com/pag/xx/webprogram/Paper2041.html
McDonald, S., John; Hart. (2012). Latest Technology in Irrigation Management in Nursery Production\copyright. 89–93.
McKay, M., Sheldon; Lyons, Eric; Tang, Haibao; Miller, Nathan; Eichten, Steven R. ;. Goff, Stephen A. ;. Stanzione, Dan; Vaughn. (2012). The iPlant Collaborative. W416. https://pag.confex.com/pag/xx/webprogram/Paper2918.html
McKay, S. (2012). How to Use the iPlant’s Discovery Environment for Your Research. W420. https://pag.confex.com/pag/xx/webprogram/Paper2931.html
Miller, D. V., Robert J. ;. Hocevar, John; Stone, Robert 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. https://pag.confex.com/pag/xx/webprogram/Paper2923.html
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. M., Cynthia S. ;. Guralnick, Robert; Cellinese, Nico; 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., Sudha; Liu. (2012). A Semantic Foundation for Provenance Management. 1(1), 17-Nov. https://doi.org/10.1007/s13740-012-0002-0
Reddy, A., Anireddy S. N. ;. Rogers, Mark F. ;. Richardson, Dale N. ;. Hamilton, Michael; 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., Michael C; Witkowski, Jan; 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., James C. ;. Freeling, Michael; 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 Communiqué 3, 357–371. https://doi.org/10.3233/AO-2012-0111
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., Stephen A. ;. 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., A. ;. 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. (2012a). The Evolution of Genome Structure. Int J Evol 1, 1, 2.
Tang, H., & Lyons, E. (2012b). Unleashing the Genome of Brassica Rapa. 3. https://doi.org/10.3389/fpls.2012.00172
Tang, K., Haibao; Krampis. (2012). Leverage iPlant Computing Resources for Collaborative Genomic Research. W419. https://pag.confex.com/pag/xx/webprogram/Paper2920.html
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., Lecong; Franck, Christopher; Yang, Kuan; Pilot, Guillaume; Heath, Lenwood 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