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