Rice Genome Annotation Project Publications

  1. Childs, K.L., Davidson, R., and Buell. C. R. 2011. Gene coexpression network analysis as a source of functional annotation for rice genes. PLoS ONE 6(7):e22196..

  2. Lin, H., Moghe, G., Ouyang, S., Iezzoni, A., Shiu, S., Gu, X., and Buell, C. R. 2010. Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. BMC Evol. Biol. 10:41.

  3. Zou, C., Lehti-Shiu, M. D., Thibaud-Nissen, F., Prakash, T., Buell, C. R., and Shiu, S. -H. Evolutionary and expression signatures of pseudogenes in Arabidopsis thaliana and rice. 2009. Plant Physiology 151:3-15.

  4. McNally, K.L, Childs, K.L., Bohnert, R., Davidson, R.M., Zhao, K., Ulat, V.J., Zeller, G., Clark, R.M., Hoen, D.R., Bureau, T.E., Stokowski, R., Ballinger, D.J., Frazer, K. A., Cox, D.R., Padhukasahasram, B., Bustamante, C., Weigel, D., Mackill, D.J., Bruskiewich, R.M., Rätsch, G., Buell, C. R., Leung, H., and Leach, J. E. 2009. Genome-wide SNP variation reveals relationships among landraces and modern varieties of rice. PNAS 106: 12273-12278

  5. Thibaud-Nissen, F. Shu Ouyang, S., and Buell, C. R. 2009. Identification and characterization of pseudogenes in the rice gene complement. BMC Genomics 10:317.

  6. Buell, C. R. 2009. Poaceae Genomes: Going from unattainable to becoming a model clade for comparative plant genomics. Plant Physiology 149:111-116.

  7. Lin, H., Ouyang, S., Egan, A., Nobuta, K., Haas, B.J., Zhu, W., Gu, X., Silva, J.C., Meyers, B.C., and Buell, C. R. 2008. Characterization of paralogous protein families in rice. BMC Plant Biology 8:18.

  8. Haas, B.J., Salzberg, S., Zhu, W., Pertea, M., Allen, J., Orvis, J., White, O., Buell, C.R., and Wortman, J.R. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology 9(1):R7.

  9. Campbell, M. A., Zhu, W., Jiang, N., Lin, H., Ouyang, S., Childs, K.L., Haas, B.J., Hamilton, J. P., and Buell, C. R. 2007. Identification and characterization of lineage-specific genes within the Poaceae. Plant Physiology145:1311-1322.

  10. Thibaud-Nissen, F., Campbell, M., Hamilton, J., Zhu, W., and Buell, C. R. 2007. EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome. BMC Genomics 8:388.

  11. Zhu, W., and Buell. C. R. 2007. Improvement of whole-genome annotation of cereals through comparative analyses. Genome Research 17:299-310.

  12. Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., Thibaud-Nissen, F., Malek, R. L., Lee, Y., Zheng, L., Orvis, J., Haas, B., Wortman, J., and Buell, C. R. 2007. The TIGR Rice Genome Annotation Resource: improvements and new features. NAR 35 Database Issue: D846-851.
    (Please use this reference when citing the Rice Genome Annotation project website.)

  13. Campbell, M. A., Haas, B. J., Hamilton, J. P., Mount, S. M., and Buell C. R. 2006. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7:327

  14. Lin, H., Zhu, W., Silva, J. C., Gu, X., and Buell, C. R. 2006. Intron gain and loss in segmentally duplicated genes in rice. Genome Biology 7: R41.

  15. The Rice Chromosomes 11 and 12 Sequencing Consortia. 2005. The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and gene duplications. BMC Biology 3:20

  16. The Rice Chromosome 3 Sequencing Consortium. 2005. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res. 15(9):1284-1291

  17. International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature 436: 793-800.

  18. Yuan, Q., Ouyang, S., Wang, A., Zhu, W., Maiti, R., Lin, H., Hamilton, J., Haas, B., Sultana, R., Cheung, F., Wortman, J., and Buell, C.R. 2005. The Institute for Genomic Research Osa1 Rice Genome Annotation Database. Plant Physiology 138: 18-26.

  19. Rensink, W. A. and Buell, C. R. 2004. Arabidopsis to Rice. Applying knowledge from a weed to enhance our understanding of a crop species. Plant Physiology 135: 622-629.

  20. Nagaki, K., Cheng, Z., Ouyang, S., Talbert, P. B., Kim, M, Jones, K. M., Henikoff, S., Buell, C. R., and Jiang, J. 2004. Sequencing of a rice centromere uncovers active genes. Nature Genetics 36:138-145.

  21. Ouyang, S. and Buell, C. R. 2004. The TIGR Plant Repeat Databases: A Collective Resource for Identification of Repetitive Sequences in Plants. NAR 32 Database Issue: D360-363.

  22. Buell, C. R. 2004. Annotation of the rice genome: Producing relevant information for plant biologists. In Rice science:innovations and impact for livelihood. Proceedings of the International Rice Research Conference, 16-19 September 2002, Beijing, China. International Rice Research Institute, Chinese Academy of Engineering, and Chinese Academy of Agricultural Sciences. Eds Mew, T.W., Peng S., Dawe, D., and Hardy, B. pp. 183-193.

  23. Luo, M., Thomas, C., You, F. M., Hsiao, J., Ouyang, S., Buell, C. R., Malandro, M., McGuire, P. E., Anderson, O. D., and Dvorak, J. 2003. High-throughput fingerprinting of bacterial artificial chromosomes using the SNaPshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82:378-389.

  24. Buell, C. R. and Sundaresan, V. 2003. A workshop on establishing a rice resource center in the United States. Plant Physiology 132: 1137.

  25. The Rice Chromosome 10 Sequencing Consortium. 2003. In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300: 1566-1569.

  26. Yuan, Q., Ouyang, S., Liu, J., Suh, B., Cheung, F., Sultana, R., Lee, D., Quackenbush, J, and Buell, C. R. 2003. The TIGR Rice Genome Annotation Resource: Annotating the rice genome and creating resources for plant biologists. Nucleic Acids Research 31: 229-233.

  27. Buell, C. R. 2002. Current status of the rice genome sequence and prospects for finishing the first monocot genome. Plant Physiology 130: 1585-1586.

  28. Buell, C. R. 2002. Obtaining the sequence of the rice genome and lessons learned along the way. Trends in Plant Sciences 7: 538-542.

  29. Cheng, Z., Buell, C.R., Wing, R.A. and Jiang, J. 2002. Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosome Research 10: 379-387.

  30. Yuan, Q, Hill, J., Hsiao, J., Moffat, K., Ouyang, S., Cheng, Z., Jiang, J., and Buell, C. R. 2002. Genome sequencing of a 239 Kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast insertion. Molecular Genetics and Genomics 267:713-720.

  31. Cheng, Z., Dong, F., Langdon, T., Ouyang, S., Buell, C. R., Gu, M., Blattner, F. R., and Jiang J. 2002. Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14:1691-1704.

  32. Cheng, Z., Buell, C. R., Wing, R. A., Gu, M., and Jiang, J. 2001. Toward a cytological characterization of the rice genome. Genome Research 11: 2133-2141.

  33. Yuan, Q., Quackenbush, J., Sultana, R., Pertea, M., Salzberg, S. L., and Buell, C. R. 2001. Rice Bioinformatics. Analysis of rice sequence data and leveraging the data to other plant species. Plant Physiology 125:1166-1174.

  34. Cheng, Z., Presting, G. G., Buell, C. R., Wing, R. A., and Jiang, J. 2001. High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 157: 1749-1757.

  35. Yuan, Q., Liang, F., Hsiao, J., Zismann, V., Benito, M. -I., Quackenbush, J., Wing, R., and Buell, C. R. 2000. Anchoring of rice BAC clones to the rice genetic map in silico. Nucleic Acids Research 28:3636-3641.

NSF Logo This work is supported by grants (DBI-0321538/DBI-0834043) from the National Science Foundation.