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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.
- 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.
- 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.
- 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.
- Zhu, W., and Buell. C. R. 2007. Improvement of whole-genome annotation of cereals through comparative analyses. Genome Research 17:299-310.
- 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.)
- 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
- 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.
- 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
- 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
- International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature 436: 793-800.
- 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.
(Please use this reference when citing the Rice
Genome Annotation Project website.)
- 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.
- 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.
- 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.
- 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.
- 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.
- Buell, C. R. and Sundaresan, V. 2003. A workshop on establishing a rice resource center
in the United States. Plant Physiology 132: 1137.
- The Rice Chromosome 10 Sequencing Consortium. 2003. In-depth view of structure, activity,
and evolution of rice chromosome 10. Science 300: 1566-1569.
- 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.
- Buell, C. R. 2002. Current status of the rice genome sequence and prospects
for finishing the first monocot genome. Plant Physiology 130: 1585-1586.
- Buell, C. R. 2002. Obtaining the sequence of the rice genome and lessons learned
along the way. Trends in Plant Sciences 7: 538-542.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
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