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Job Openings

There are four positions available at this time: a Postdoctoral Position in Plant Genomics, a Postdoctoral Position in Microbial Plant Pathogen Genomics, and two Bioinformatics Positions
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Links

A list of bioinformatic resources that we find useful. Read More »

MSU Links

• Michigan State University
• Department of Plant Biology
• Genetics Graduate Program
• Quantitative Biology Initiative
• Plant Breeding and Genetics Program

Publications

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

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

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.

Buell CR. Poaceae genomes: going from unattainable to becoming a model clade for comparative plant genomics. Plant Physiol. 2009 Jan;149(1):111-6. Epub 2008 Nov 12. PubMed PMID: 19005087; PubMed Central PMCID: PMC2613712.

Kuang H, Padmanabhan C, Li F, Kamei A, Bhaskar PB, Ouyang S, Jiang J, Buell CR, Baker B. Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs. Genome Res. 2009 Jan;19(1):42-56. Epub 2008 Nov 26. PubMed PMID: 19037014; PubMed Central PMCID: PMC2612961.

Childs KL. Genomic and genetic database resources for the grasses. Plant Physiol. 2009 Jan;149(1):132-6. Review. PubMed PMID: 19126704; PubMed Central PMCID: PMC2613734.

Cheung F, Win J, Lang JM, Hamilton J, Vuong H, Leach JE, Kamoun S, André Lévesque C, Tisserat N, Buell CR. Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. BMC Genomics. 2008 Nov 15;9:542. PubMed PMID: 19014603; PubMed Central PMCID: PMC2612028.

Jung KH, Dardick C, Bartley LE, Cao P, Phetsom J, Canlas P, Seo YS, Shultz M, Ouyang S, Yuan Q, Frank BC, Ly E, Zheng L, Jia Y, Hsia AP, An K, Chou HH, Rocke D, Lee GC, Schnable PS, An G, Buell CR, Ronald PC. Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS One. 2008 Oct 6;3(10):e3337. PubMed PMID: 18836531; PubMed Central PMCID: PMC2556097.

Iovene M, Wielgus SM, Simon PW, Buell CR, Jiang J. Chromatin structure and physical mapping of chromosome 6 of potato and comparative analyses with tomato. Genetics. 2008 Nov;180(3):1307-17. Epub 2008 Sep 14. PubMed PMID: 18791232; PubMed Central PMCID: PMC2581936.

Zhu, W., Ouyang, S., Iovene, M., O'Brien, K., Vuong, H., Jiang, J, and Buell, C. R. 2008. Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition. BMC Genomics 9:286.

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. http://www.biomedcentral.com/1471-2229/8/18

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. http://genomebiology.com/2008/9/1/R7

Van Deynze, A., Stoffel, K., Buell, C.R., Kozik, A., Liu, J., van der Knapp, E., and Francis, D. 2007. Diversity in conserved genes in tomato. BMC Genomics 8:465. http://www.biomedcentral.com/1471-2164/8/465

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. http://www.plantphysiol.org/cgi/content/full/145/4/1311

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. http://www.biomedcentral.com/1471-2229/8/18

Stupar, R.M., Bhaskar, P. B., Yandell, B.S., Rensink, W. A., Hart, A. L., Ouyang, S., Veilleux, R. E., Busse, J. S., Erhardt, R. J., Buell, C. R., and Jiang, J. 2007. Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics 176:2055-2067. http://www.biomedcentral.com/1471-2229/8/18

Zhu, W., and Buell. C. R. 2007. Improvement of whole-genome annotation of cereals through comparative analyses. Genome Research 17:299-310. http://www.genome.org/cgi/content/full/17/3/299

Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., Thibaud-Nissan, 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. Nucleic Acids Research 35 (Database issue):D883-D887; doi:10.1093/nar/gkl976. http://www.pubmedcentral.nih.gov/articlerender

Childs, K., Hamilton, J., Zhu, W., Ly, E., Cheung, F., Wu, H., Rabinowicz, P. B., Town, C.D., Buell, C. R., and Chan, A.P. The TIGR Plant Transcript Assemblies Database. 2007. Nucleic Acids Research 35 (Database issue):D846-D851; doi:10.1093/nar/gkl78. http://www.pubmedcentral.nih.gov/articlerender

Campbell, M.A., Haas, B.J., Hamilton, J., Mount, S.M., and Buell, C. R. 2006. Comprehensive analysis of alternative splicing in the rice genome and comparative analyses with Arabidopsis. BMC Genomics 7:327. http://www.biomedcentral.com/1471-2164/7/327

Vencato, M., Tian, F., Alfano, J. R., Buell, C. R., Cartinhour, S., DeClerck, G. A., Guttman, D. S., Stavrinides, J., Joardar, V., Lindeberg, M., Bronstein, P. A., Mansfield, J. W., Myers, C. R., Collmer, A. and Schneider, D. J. 2006. Bioinformatics-enabled identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A. Molecular Plant Microbe Interactions 19:1193-1206. http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-19-1193

Cairney, J., Zheng, L., Cowels, A., Hsiao, J., Zismann, V., Liu, J., Ouyang, S., Thibaud-Nissen, F., Hamilton, J., Childs, K., Pullman, G. S., Zhang, Y., Oh, T., and Buell, C. R. 2006. Expressed Sequence Tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis. Plant Molecular Biology 62:485-501. http://www.springerlink.com/content/w5277624v01664h6/

Yan, H., Ito, H., Nobuta, K., Ouyang, S., Jin, W., Tian, S., Lu, C., Venu, R.C., Wang, G., Green, P.J., Wing, R.A., Buell, C.R., Meyers, B.C., and Jiang, J. 2006. Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell 18:2123-33. http://www.plantcell.org/cgi/content/full/18/9/2123

Lin, H., Zhu, W., Silva, J., Gu, X., and Buell, C. R. 2006. Intron gain and loss in segmentally duplicated genes in rice. Genome Biology 7(5):R41. http://genomebiology.com/2006/7/5/R41

Avila-Adame, C., Gómez-Alpizar, L., Zismann, V., Jones, K. M., Buell, C. R., and Ristaino, J. B. 2006. Mitochondrial genome sequences and molecular evolution of the Irish potato famine pathogen, Phytophthora infestans. Current Genetics 49:39-46. http://www.springerlink.com/content/f443p6772285611n/

Yan, H., Jin, W., Nagaki, K., Tian, S., Ouyang, S., Buell, C. R., Talbert, P. B., Henikoff, S., and Jiang, J. 2005. Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell 17:3227-3238.

Rensink, W.A., Lee, Y., Liu, J., Iobst, S., Ouyang, S., and Buell, C. R. 2005. Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts. BMC Genomics 6:124. http://www.biomedcentral.com/1471-2164/6/124

The Rice Chromosomes 11 and 12 Sequencing Consortia. 2005. The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biology 3:20 doi:10.1186/1741-7007-3-20.

Kuang H., Marano, M. R., Wei, F., Wirtz, U., Wang, X., Liu, J., Shum, W. P., Zaborsky, J., Tallon, L. J., Rensink, W., Iobst S., Zhang, P., Tornqvist, C. E., Tek, A., Bamberg, J., Helegson, J., Fry, W., Luo, M.-C., Malcuit, I., Jiang, J., Buell, C. R., and Baker, B. 2005. The R1 resistance cluster contains three groups of independently evolving, Type I R1 homologues and shows substantial structural variation between haplotypes of Solanum demissum. Plant Journal 44:37-51. http://www.blackwell-synergy.com/doi/abs/

Joardar, V., Lindeberg, M., Jackson, R., Selengut, J., Dodson, R. J., Brinkac, L.M., Daugherty, S.C., Deboy, R., Durkin, A. S., Giglio, M. G., Madupu, R., Nelson, W. C., Rosovitz, M.J., Sullivan, S., Haft, D. H., Creasy, T., Davidsen, T., Zafar, N., Zhou, L., Halpin, R., Holly, T., Khouri, H., Feldblyum, T. V., White, O., Fraser, C. M., Chatterjee, A. K., Cartinhour, S., Schneider, D., Mansfield, J., Collmer, A., and Buell, C. R. 2005. Whole genome sequence analysis of Pseudomonas syringae pv phaseolicola 1448A reveals sequence divergence among pathovars in genes involved in virulence, transposition, and unknown function. Journal of Bacteriology 187:6488-6498. http://jb.asm.org/cgi/content/

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

Gardiner, J. M., Buell, C. R., Elumalai, R., Galbraith, D.W., Henderson, D.A., Iniguez, A.L., Kaeppler, S.M., Kim, J.J., Liu, J., Zheng, L., and Chandler, V.L. 2005. Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize. Maydica 50: 425-435.

The Rice Chromosome 3 Sequencing Consortium (C. R. Buell is corresponding contributor). 2005. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Research 15:1284-1291. http://www.genome.org/cgi/content/full/15/9/1284

Restrepo, S., Meyers, K.L., del Poz, O., Martin, G.B., Hart, A., Buell, C.R., Fry, W.E., and Smart, C. D. 2005. Gene profiling of a compatible interaction between Phytophthora infestans and Solanum tuberosum suggests a role for carbonic anhydrase. Molecular Plant Microbe Interactions 18:913-922. http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-18-0913

Rensink, W. A., Hart, A., Liu, J., Ouyang, S., Zismann, V., and Buell, C. R. 2005. Analyzing the potato abiotic stress transcriptome using Expressed Sequence Tags. Genome 48:598-605. http://article.pubs.nrc-cnrc.gc.ca

Rensink, W. A., Iobst, S., Hart, A., Stegalkina, S., Liu, J., and Buell, C. R. 2005. Gene expression profiling of potato responses to cold, heat, and salt stress. Integrative and Functional Genomics 5: 201-207. http://www.springerlink.com/content/l0266j81k4753w14/

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 TIGR Osa1 rice genome annotation database. Plant Physiology 138:18-26. http://www.plantphysiol.org/cgi/content/full/138/1/18

Joardar, V., Lindeberg, M., Collmer, A. and Buell, C. R. 2005. Lineage specific regions in Pseudomonas syringae pv tomato DC3000 are associated with features of lateral gene transfer. Molecular Plant Pathology 6: 53-64.

Nagaki, K., Neumann, P., Zhang, D., Ouyang, S., Buell, C. R., Cheng, Z., and Jiang, J. 2005. Structure, divergence, and distribution of the CRR centromeric retrotransposon family in the rice genome. Molecular Biology and Evolution 22:845-855. http://mbe.oxfordjournals.org/cgi/content/full/22/4/845

Sorghum Genomics Planning Workshop Participants. 2005. c. Plant Physiology 138:1898-1902.

Rensink, W.A. and Buell, C. R. 2005. Microarray expression profiling resources for plant genomics. Trends in Plant Science 10:603-609.

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.

Gill, B. S., Appels, R., Botha-Oberholster, A. M., Buell, C. R., Bennetzen, J. L., Chalhoub, B., Chumley, F., Dvorak, J., Iwanaga, M., Keller, B., Li, W., McCombie, W. R., Ogihara, Y., Quetier, F., and Sasaki, T. 2004. A Workshop Report on Wheat Genome Sequencing: International Genome Research on Wheat (IGROW) Consortium. Genetics168:1087-1096.

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. http://www.nature.com/ng/journal

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. http://nar.oxfordjournals.org/cgi/content/full/32/suppl_1/D360

Buell, C. R., Joardar, V., Lindeberg, M., Selengut, J., Paulsen, I. T., Gwinn, M. L., Dodson, R. J., Deboy, R. T., Durkin, A. S., Kolonay, J. F., Madupu, R., Daugherty, S. Brinkac, L., Beanan, M. J., Haft, D. H., Nelson, W. C., Davidsen, T., Zafar, N., Zhou, L., Liu, J., Yuan, Q., Khouri, H., Fedorova, N., Tran, B., Russell, D., Berry, K., Utterback, T., Vanaken, S. E., Feldblyum, T. V., D'Ascenzo, M., Deng, W. L., Ramos, A. R., Alfano, J. R., Cartinhour, S., Chatterjee, A. K., Delaney, T. P., Lazarowitz, S. G., Martin, G. B., Schneider, D. J., Tang, X., Bender, C. L., White , O., Fraser, C. M., and Collmer, A. 2003. The complete sequence of the tomato and Arabidopsis pathogen, Pseudomonas syringae pv tomato DC3000. Proc. Natl. Acad. Sci. USA 100:10181-10186. http://www.pnas.org/cgi/content/full/100/18/10181

*This paper was a Fast Breaking Paper in the Field of Microbiology for December, 2004; ISI Essential Science Indicators Special Topics
*This paper was a New Hot Paper in Microbiology for January 2005; ISI Essential Science Indicators Special Topics

Bradeen, J.M., Naess, S.K., Song, J., Haberlach, G.T., Wielgus, S.M., Buell, C.R., Jiang, J., and Helgeson, J.P. 2003. Concomitant reiterative BAC walking and fine genetic mapping enable physical map development for the broad-spectrum late blight resistance region, RB. Molecular Genetics and Genomics 269:603-611. http://www.springerlink.com/content/

Song, J., Bradeen, J. M., Naess, S. K., Raasch, J. A., Wielgus, S. M., Haberlach, G. T., Liu, J., Kuang, H., Austin-Phillips, S., Buell, C. R., Helgeson, J. P., and Jiang, J. 2003. Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight pathogen. Proc. Natl. Acad. Sci. USA 100:9128-9133. http://www.pnas.org/cgi/content/full/100/16/9128

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. http://www.sciencedirect.com/science?_ob=ArticleURL

The Rice Chromosome 10 Sequencing Consortium (Buell, C.R. is a corresponding author). 2003. In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300: 1566-1569. http://www.ncbi.nlm.nih.gov/sites/entrez

Nagaki, K., Song J., Stupar, R.M., Parokonny, A. S., Yuan, Q., Ouyang, S., Liu, J., Hsiao, J., Jones, K. M., Dawe, R. K., Buell, C. R., and Jiang, J. 2003. Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 163: 739-770.

Ronning, C. M., Stegalkina, S., Ascenzi, R., Bougri, O., Hart, A., Utterback, T., Vanaken, S., Reidmuller, S., White, J., Cho, J., Karamycheva, S., Pertea, G. M., Lee, Y., Karamycheva, S., Sultana, R., Tsai, J., Quackenbush, J., Griffiths, H. M., Restrepo, S., Smart, C. D., Fry, W. E., van der Hoeven, R., Tanksley, S., Zhang, P., Jin, H., Yamamoto, M., Baker, B. J., and Buell, C. R. 2003. Comparative analyses of potato Expressed Sequence Tag libraries. Plant Physiology 131: 419-429. http://www.ncbi.nlm.nih.gov/pubmed/12586867

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. http://nar.oxfordjournals.org/cgi/content/full/31/1/229

Buell, C. R. 2002. Current status of the rice genome sequence and prospects for finishing the first monocot genome. Plant Physiology 130: 1585-1586. http://www.plantphysiol.org/cgi/content/full/130/4/1585

Buell, C. R. 2002. Obtaining the sequence of the rice genome and lessons learned along the way. Trends in Plant Sciences 7: 538-542. http://www.sciencedirect.com/science?_ob=ArticleURL

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. http://www.springerlink.com/content/7v4hwt4dk9dlvvkq/

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. http://www.springerlink.com/content/89acbvf08q494f4c/

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.

Petnicki-Ocwieja, T., Schneider, D. J., Tam, V. C., Chancey, S. T., Shan, L., Jamir, Y., Schechter, L. M., Janes, M. D., Buell, C. R., Tang, X., Collmer, A., and Alfano, J. R. 2002. Genomewide identification of proteins secreted by the Hrp type III protein secretion system of Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 99: 7652-7657. http://www.pnas.org/cgi/content/full/99/11/7652

Fouts, D. E., Abramovitch, R. B., Alfano, J. R., Baldo, A. M., Buell, C. R., Cartinhour, S., Chatterjee, A. K., D'Ascenzo, M., Gwinn, M. L., Lazarowitz, S. G., Lin, N. C., Martin, G. B., Rehm, A. H., Schneider, D. J., van Dijk, K., Tang, X. and Collmer, A. 2002. Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor. Proc. Natl. Acad. Sci. USA 99: 2275-2280. http://www.pnas.org/cgi/content/full/99/4/2275

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. http://www.genome.org/cgi/content/full/11/12/2133

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. http://www.plantphysiol.org/cgi/content/full/125/3/1166

Stupar, R. M., Lilly, J. W., Town, C. D., Cheng, Z., Kaul, S., Buell, C. R., and Jiang, J. 2001. Complex mt-DNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: Implication of potential sequencing errors caused by large unit repeats. Proc. Natl. Acad. Sci. USA 98:5099-5103.

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. http://www.genetics.org/cgi/content/full/157/4/1749

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. http://nar.oxfordjournals.org/cgi/content/full/28/18/3636

Lin, X., Kaul, S., Rounsley, S., Shea, T., Benito, M. –I, Town, C. D. Fujii, C. Y., Mason, T., Bowman, C. L., Barnstead, M., Feldblyum, T., Buell, C. R., Ketchum, K. A., Ronning, C. M., Koo, H. L., Moffat, K. M., Cronin, L. A., Shen, M., Pai, G., Van Aken, S., Umayam, L., Tallon, L. J., Gill, J. E., Lee, J., Adams, M. D., Carrera, A., Creasy, T. H., Goodman, H., Somerville, C., Copenhaver, G. P., Preuss, D., Nierman, W. C., White, O., Eisen, J., Salzberg, S., Fraser, C. M., and Venter, J. C. 1999. Sequence and analysis of chromosome 2 of Arabidopsis thaliana. Nature 402: 761-768. http://www.nature.com/nature/journal/v402/n6763/abs/402761a0.html

Alfenito, M. R., Souer, E., Goodman, C. D., Buell, R., Mol, J., Koes, R., and Walbot, V. 1998. Functional complementation of anthocyanin sequestration in the vacuole by widely divergent glutathione S-transferases. The Plant Cell 10: 1135-1149. http://www.plantcell.org/cgi/content/full/10/7/1135

Buell, C. R. 1998. Arabidopsis: a weed leading the field of plant-pathogen interactions. Plant Physiology and Biochemistry 36: 177-186.

Buell, C. R., and Somerville, S. C. 1997. Use of Arabidopsis recombinant inbred lines reveals a monogenic and a novel digenic resistance mechanism to Xanthomonas campestris pv campestris. The Plant Journal 12: 21-29. http://www.blackwell-synergy.com/doi/abs/10.1046/

Buell, C. R., and Somerville, S. C. 1995. Expression of defense-related and putative signaling genes during the tolerant and susceptible interactions of Arabidopsis with Xanthomonas campestris pv campestris. Molecular Plant-Microbe Interactions 8: 435-443.

Buell, C. R., and Anderson, A. J. 1993. Expression of the aggA locus of Pseudomonas putida in vitro and in planta as detected by the reporter gene, xylE. Molecular Plant-Microbe Interactions 6: 331-340.

Buell, C. R., Whetton, R., Tari, P., and Anderson, A. J. 1993. Characterization of cell surface properties in agglutinable and nonagglutinable mutants of Pseudomonas putida. Canadian Journal of Microbiology 39: 787-794.

Buell, C. R., and Anderson, A. J. 1992. Genetic analysis of the aggA locus involved in agglutination and adherence in Pseudomonas putida, a beneficial fluorescent pseudomonad. Molecular Plant-Microbe Interactions 5: 154-162.

Book Chapters/Magazine Articles/Letters to the Editor/Commentaries

Kellogg EA, Buell CR. Splendor in the grasses. Plant Physiol. 2009 Jan;149(1):1-3. PubMed PMID: 19126688; PubMed Central PMCID: PMC2613704.

Gray J, Bevan M, Brutnell T, Buell CR, Cone K, Hake S, Jackson D, Kellogg E, Lawrence C, McCouch S, Mockler T, Moose S, Paterson A, Peterson T, Rokshar D, Souza GM, Springer N, Stein N, Timmermans M, Wang GL, Grotewold E. A recommendation for naming transcription factor proteins in the grasses. Plant Physiol. 2009 Jan;149(1):4-6. PubMed PMID: 19126689; PubMed Central PMCID: PMC2613739.

Wicker, T., and Buell, C. R. 2009. Gene and Repetitive Sequence Annotation in the Triticeae. In: Genetics and Genomics of the Triticeae. C. Fueillet and G. Muehlbaher, eds. In Press.

Ouyang S, Thibaud-Nissen F, Childs KL, Zhu W, Buell CR. Plant genome annotation methods. Methods Mol Biol. 2009;513:263-82. PubMed PMID: 19347655.

Thibaud-Nissen, F., J. Wortman, C. R. Buell, and Zhu, W. 2007. Structural, functional, and comparative annotation of plant genomes. The Handbook of Plant Functional Genomics, G. Kahl, K. Meksem, eds., in press.

Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Lee, Y., Malek, R.L., Wang, A., Yuan, Q., Haas, B.J., Wortman, J., and Buell, C. R. 2007. Annotation of the rice genome. In Rice Genetics V: Proceedings of the Fifth International Rice Genetics Symposium, eds. D. S. Brar, D. J. MacKill and B. Hardy, pp. 29-48, World Scientific Publishing Co.

Chan, A.P. Rabinowicz, P.D., Quackenbush, J. Buell, C.R., and Town, C.D. 2007. Plant Database Resources at the Institute for Genomic Research. Methods Mol. Biol. 406:113-136. http://biomed.humanapress.com/index.php

Antonio, B.A., Buell, R. C., Yamazaki, K., Yap, I., Perin C. and Bruskiewich. R. 2006. Informatics resources for rice functional genomics. In: NM Upadhyaya (ed) Rice Functional Genomics- Challenges, Progress and Prospects. Springer, NY.

McNally, K.L, Bruskiewich, R., Mackill, D., Buell, C. R., Leach, J.E., and Leung, H. 2006. Sequencing multiple and diverse rice varieties: Connecting whole-genome variation with phenotypes. Plant Physiology 141:26-31. http://www.plantphysiol.org/cgi/content/full/141/1/26*

Buell, C. R. 2005. The International Rice Genome Sequencing Project: A case study. In Economic Perspectives:The Promise of Biotechnology, U.S. Department of State/Bureau of International Information Programs, pp. 29-31.

Buell, C. R. 2004. A survey of plant pathogen genomes.pp. 213-223. In Microbial Genomes, C. Fraser, T. Read, and K. Nelson, eds, Humana Press Inc, Totowa NJ.

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.

Alfano, J. R., Buell, C. R., Chancey, S. T., Collmer, A., Espinosa, A, Guo, M., Hanks, M., Jamir, Y, Janes, M. D., Schneider, D. J., Shan, L., Petnicki-Ocwieja, T., Schechter, L. M., Tam, V. C. and Tang, X. 2003. Genomic mining for substrates of the type III secretion system of Pseudomonas syringae pv. tomato DC3000: New insights into mechanisms of pathogenesis. pp. 363-372. In Pseudomonas syringae and related pathogens. N. S. Iacobellis, ed., Kluwer Academic Publishers, Dordrecht, The Netherlands.

Buell, C. R. and Sundaresan, V. 2003. A workshop on establishing a rice resource center in the United States. Plant Physiology 132: 1137. http://www.plantphysiol.org/cgi/content/full/132/3/1137

Buell, C. R. 2002. Interactions between Xanthomonas species and Arabidopsis thaliana. In: The Arabidopsis Book, eds. C. R. Somerville and E. M. Meyerowitz, American Society of Plant Biologists, Rockville MD, DOI 10.119/tab.0031 http://www.aspb.org/publications/arabidopsis/

C. R. Buell. 1999. Genes involved in plant-pathogen interactions. In: Induced Plant Defenses Against Pathogens and Herbivores: Biochemistry, ecology, and agriculture. Pages 73-93. Agrawal, A. A., Tuzun, S., and Bent, E., eds. APS press, St. Paul, MN.

Anderson, A. J., Buell, R., Katsuwon, J., Heck, C., and Zdor, R. 1992. Genetic and molecular analysis of survival mechanisms of pseudomonads. Pages 81-86 in: Proceedings of the 4th Investigators Meeting for EPA's Biotechnology-Biological Control Agent Risk Assessment Research Program.

Buell, C. R. and Anderson, A. J. 1991. Genetic analysis of agglutination in Pseudomonas putida. Pages 318-322 in: Plant Growth-Promoting Rhizobacteria-Progress and Prospects. C. Keel, B. Koller, and G. Défago, eds.

Anderson, A. J., Buell, R., Lovic, B., and Katsuwon, J. 1990. Bacterial traits involved in root surface colonization. Pages 97-99 in: Review of Progress in the Biotechnology-Microbial Pest Control Agent Risk Assessment Program.