2012 Publications

Alakonya, A., Kumar, R., Koenig, D., Kimura, S., Townsley, B., Runo, S., Garces, H. M., Kang, J., Yanez, A., David-Schwartz, R., Machuka, J., & Sinha, N. (2012). Interspecific RNA Interference of SHOOT MERISTEMLESS-Like Disrupts Cuscuta pentagona Plant Parasitism. The Plant Cell, 24(7), 3153–3166. https://doi.org/10.1105/tpc.112.099994
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. (2012). What’s on the horizon for macroecology? Ecography, 35(8), 673–683. https://doi.org/10.1111/j.1600-0587.2012.07364.x
Blonder, B., Buzzard, V., Simova, I., Sloat, L., Boyle, B., Lipson, R., Aguilar-Beaucage, B., Andrade, A., Barber, B., Barnes, C., Bushey, D., Cartagena, P., Chaney, M., Contreras, K., Cox, M., Cueto, M., Curtis, C., Fisher, M., Furst, L., … Enquist, B. J. (2012). The leaf-area shrinkage effect can bias paleoclimate and ecology research. American Journal of Botany, 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, M. G., Bautista, R., Guerrero-Fernández, D., Benzerki, H., Seoane, P., & Fernández-Pozo, N. (2012). Why Assembling Plant Genome Sequences Is So Challenging. Biology, 1(2), 439–459. https://doi.org/10.3390/biology1020439
D’Hont, A., Denoeud, F., Aury, J.-M., Baurens, F.-C., Carreel, F., Garsmeur, O., Noel, B., Bocs, S., Droc, G., Rouard, M., Da Silva, C., Jabbari, K., Cardi, C., Poulain, J., Souquet, M., Labadie, K., Jourda, C., Lengellé, J., Rodier-Goud, M., … Wincker, P. (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488(7410), 213–217. https://doi.org/10.1038/nature11241
Egan, A. N., Schlueter, J., & Spooner, D. M. (2012). Applications of next-generation sequencing in plant biology. American Journal of Botany, 99(2), 175–185. https://doi.org/10.3732/ajb.1200020
Eichten, S. R. (2012). Contribution of Epigenetic Variation to Expression Changes Among Tissues and Genotypes. Plant and Animal Genome XX, W417. https://pag.confex.com/pag/xx/webprogram/Paper2921.html
Eichten, S. R., Ellis, N. A., Makarevitch, I., Yeh, C.-T., Gent, J. I., Guo, L., McGinnis, K. M., Zhang, X., Schnable, P. S., Vaughn, M. W., Dawe, R. K., & Springer, N. M. (2012). Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons. PLoS Genetics, 8(12), e1003127. https://doi.org/10.1371/journal.pgen.1003127
Frousios, K., Iliopoulos, C. S., Tischler, G., Kossida, S., Pissis, S. P., & Arhondakis, S. (2013). Transcriptome map of mouse isochores in embryonic and neonatal cortex. Genomics, 101(2), 120–124. https://doi.org/10.1016/j.ygeno.2012.11.006
Huang, P., & Schaal, B. A. (2012). Association between the geographic distribution during the last glacial maximum of Asian wild rice, Oryza rufipogon (Poaceae), and its current genetic variation. American Journal of Botany, 99(11), 1866–1874. https://doi.org/10.3732/ajb.1200348
Jiao, Y., Leebens-Mack, J., Ayyampalayam, S., Bowers, J. E., McKain, M. R., McNeal, J., Rolf, M., Ruzicka, D. R., Wafula, E., Wickett, N. J., Wu, X., Zhang, Y., Wang, J., Zhang, Y., Carpenter, E. J., Deyholos, M. K., Kutchan, T. M., Chanderbali, A. S., Soltis, P. S., … dePamphilis, C. W. (2012). A genome triplication associated with early diversification of the core eudicots. Genome Biology, 13(1), R3. https://doi.org/10.1186/gb-2012-13-1-r3
Johnson, M. T. J., Carpenter, E. J., Tian, Z., Bruskiewich, R., Burris, J. N., Carrigan, C. T., Chase, M. W., Clarke, N. D., Covshoff, S., dePamphilis, C. W., Edger, P. P., Goh, F., Graham, S., Greiner, S., Hibberd, J. M., Jordon-Thaden, I., Kutchan, T. M., Leebens-Mack, J., Melkonian, M., … Wong, G. K.-S. (2012). Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes. PLoS ONE, 7(11), e50226. https://doi.org/10.1371/journal.pone.0050226
Kakumanu, A. (2012). Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissues as Revealed by Deep Sequencing [Virginia Tech]. http://hdl.handle.net/10919/33907
Kakumanu, A., Ambavaram, M. M. R., Klumas, C., Krishnan, A., Batlang, U., Myers, E., Grene, R., & Pereira, A. (2012). Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq. Plant Physiology, 160(2), 846–867. https://doi.org/10.1104/pp.112.200444
Klinov, P., Del Vescovo, C., & Schneider, T. (2012). Incrementally Updateable and Persistent Decomposition of OWL Ontologies. Proceedings of OWL: Experiences and Directions Workshop, CEUR Workshop Proceedings, 849, 7. http://ceur-ws.org/Vol-849/paper_7.pdf
Kolker, E., Stewart, E., & Ozdemir, V. (2012). Opportunities and Challenges for the Life Sciences Community. OMICS: A Journal of Integrative Biology, 16(3), 138–147. https://doi.org/10.1089/omi.2011.0152
Lisch, D. (2013). How important are transposons for plant evolution? Nature Reviews Genetics, 14(1), 49–61. https://doi.org/10.1038/nrg3374
Lyons, E., Tang, H., & Schnable, J. C. (2012). Whole Genome Comparisons with Oryza and Brachypodium using CoGe and SynMap. Plant and Animal Genome XX, W267. https://pag.confex.com/pag/xx/webprogram/Paper2041.html
McKay, S. (2012). How to Use the iPlant’s Discovery Environment for Your Research. Plant and Animal Genome XX, W420. https://pag.confex.com/pag/xx/webprogram/Paper2931.html
McKay, S., Lyons, E., Tang, H., Miller, N., Eichten, S. R., Goff, S. A., Stanzione, D., & Vaughn, M. (2012). The iPlant Collaborative. Plant and Animal Genome XX, W416. https://pag.confex.com/pag/xx/webprogram/Paper2918.html
Miller, N. (2012). Enabling Phenotypic Image Analysis Using Shared Cyberinfrastructure. Plant and Animal Genome XX, W418. https://pag.confex.com/pag/xx/webprogram/Paper2923.html
Miller, R. J., Hocevar, J., Stone, R. P., & Fedorov, D. V. (2012). Structure-Forming Corals and Sponges and Their Use as Fish Habitat in Bering Sea Submarine Canyons. PLoS ONE, 7(3), e33885. https://doi.org/10.1371/journal.pone.0033885
O’Meara, B. C. (2012). Evolutionary Inferences from Phylogenies: A Review of Methods. Annual Review of Ecology, Evolution, and Systematics, 43(1), 267–285. https://doi.org/10.1146/annurev-ecolsys-110411-160331
Parr, C. S., Guralnick, R., Cellinese, N., & Page, R. D. M. (2012). Evolutionary informatics: Unifying knowledge about the diversity of life. Trends in Ecology & Evolution, 27(2), 94–103. https://doi.org/10.1016/j.tree.2011.11.001
Ram, S., & Liu, J. (2012). A Semantic Foundation for Provenance Management. Journal on Data Semantics, 1(1), 11–17. https://doi.org/10.1007/s13740-012-0002-0
Reddy, A. S. N., Rogers, M. F., Richardson, D. N., Hamilton, M., & Ben-Hur, A. (2012). Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements. Frontiers in Plant Science, 3. https://doi.org/10.3389/fpls.2012.00018
Reinders, A. (2012). Evolution of plant sucrose uptake transporters. Frontiers in Plant Science, 3. https://doi.org/10.3389/fpls.2012.00022
Schatz, M. C., Witkowski, J., & McCombie, W. R. (2012). Current challenges in de novo plant genome sequencing and assembly. Genome Biology, 13(4), 243. https://doi.org/10.1186/gb-2012-13-4-243
Schnable, J. C., Freeling, M., & Lyons, E. (2012). Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses. Genome Biology and Evolution, 4(3), 265–277. https://doi.org/10.1093/gbe/evs009
Schnable, J. C., & Lyons, E. (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
Smith, S. A., & O’Meara, B. C. (2012). treePL: Divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics, 28(20), 2689–2690. https://doi.org/10.1093/bioinformatics/bts492
Stamatakis, A., Aberer, A. J., Goll, C., Smith, S. A., Berger, S. A., & Izquierdo-Carrasco, F. (2012). RAxML-Light: A tool for computing terabyte phylogenies. Bioinformatics, 28(15), 2064–2066. https://doi.org/10.1093/bioinformatics/bts309
Tang, H., & Krampis, K. (2012). Leverage iPlant Computing Resources for Collaborative Genomic Research. Plant and Animal Genome XX, W419. https://pag.confex.com/pag/xx/webprogram/Paper2920.html
Tang, H., & Lyons, E. (2012). Unleashing the Genome of Brassica Rapa. Frontiers in Plant Science, 3. https://doi.org/10.3389/fpls.2012.00172
Todd, S., Ali, H., Mike, B., Mary, B., Cory, C., Henson, G., Michael, G., Nicola, G., Anatoly, L., Ernie, L., Leo, O., Steve, R., D, S. R., Amanda, V., Matthew, W., Trish, W., & Peter, Y. (2012). Ontology for Big Systems: The Ontology Summit 2012 Communiqué Applied Ontology, 3, 357–371. https://doi.org/10.3233/AO-2012-0111
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
Zhou, L., Franck, C., Yang, K., Pilot, G., Heath, L. S., & Grene, R. (2012). Mining for Meaning: Visualization Approaches to Deciphering Arabidopsis Stress Responses in Roots and Shoots. OMICS: A Journal of Integrative Biology, 16(4), 208–228. https://doi.org/10.1089/omi.2011.0111