C Robin Buell

Summary

Affiliation: The Institute for Genomic Research
Country: USA

Publications

  1. pmc Interactions Between Xanthomonas Species and Arabidopsis thaliana
    C Robin Buell
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville MD 20850, Facsimile 301 838 0208
    Arabidopsis Book 1:e0031. 2002
  2. pmc The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000
    C Robin Buell
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 100:10181-6. 2003
  3. ncbi request reprint Obtaining the sequence of the rice genome and lessons learned along the way
    C Robin Buell
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Trends Plant Sci 7:538-42. 2002
  4. pmc Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species
    C Robin Buell
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 15:1284-91. 2005
  5. pmc Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts
    Willem Albert Rensink
    The Institute for Genomic Research, Rockville, MD 20850, USA
    BMC Genomics 6:124. 2005
  6. pmc Characterization of paralogous protein families in rice
    Haining Lin
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    BMC Plant Biol 8:18. 2008
  7. pmc The institute for genomic research Osa1 rice genome annotation database
    Qiaoping Yuan
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Plant Physiol 138:18-26. 2005
  8. pmc Identification and characterization of lineage-specific genes within the Poaceae
    Matthew A Campbell
    The Institute for Genomic Research and J Craig Venter Institute, Rockville, Maryland 20850, USA
    Plant Physiol 145:1311-22. 2007
  9. pmc Improvement of whole-genome annotation of cereals through comparative analyses
    Wei Zhu
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 17:299-310. 2007
  10. ncbi request reprint Plant database resources at The Institute for Genomic Research
    Agnes P Chan
    The Institute for Genomic Research, Rockville, MD, USA
    Methods Mol Biol 406:113-36. 2007

Detail Information

Publications47

  1. pmc Interactions Between Xanthomonas Species and Arabidopsis thaliana
    C Robin Buell
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville MD 20850, Facsimile 301 838 0208
    Arabidopsis Book 1:e0031. 2002
    ....
  2. pmc The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000
    C Robin Buell
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 100:10181-6. 2003
    ..Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function...
  3. ncbi request reprint Obtaining the sequence of the rice genome and lessons learned along the way
    C Robin Buell
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Trends Plant Sci 7:538-42. 2002
    ..Although the multiple projects resulted in some duplicated efforts, the value of data sharing was obvious and the winner in the end will be the global public...
  4. pmc Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species
    C Robin Buell
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 15:1284-91. 2005
    ....
  5. pmc Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts
    Willem Albert Rensink
    The Institute for Genomic Research, Rockville, MD 20850, USA
    BMC Genomics 6:124. 2005
    ..The availability of large collections of Expressed Sequence Tags (ESTs) for the Solanaceae now provides the opportunity to assess sequence conservation and divergence on a genomic scale...
  6. pmc Characterization of paralogous protein families in rice
    Haining Lin
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    BMC Plant Biol 8:18. 2008
    ..This, coupled with other genetic events such as tandem duplications, has resulted in a substantial number of its genes, and resulting proteins, occurring in paralogous families...
  7. pmc The institute for genomic research Osa1 rice genome annotation database
    Qiaoping Yuan
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Plant Physiol 138:18-26. 2005
    ..To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org...
  8. pmc Identification and characterization of lineage-specific genes within the Poaceae
    Matthew A Campbell
    The Institute for Genomic Research and J Craig Venter Institute, Rockville, Maryland 20850, USA
    Plant Physiol 145:1311-22. 2007
    ..Collectively, these data confirm that we have identified a specific set of genes that are highly conserved within, as well as specific to, the Poaceae...
  9. pmc Improvement of whole-genome annotation of cereals through comparative analyses
    Wei Zhu
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 17:299-310. 2007
    ..We were able to demonstrate the utility of cross-species comparative alignments in the identification of noncoding sequences and in confirmation of gene nesting in rice...
  10. ncbi request reprint Plant database resources at The Institute for Genomic Research
    Agnes P Chan
    The Institute for Genomic Research, Rockville, MD, USA
    Methods Mol Biol 406:113-36. 2007
    ..We present here an overview of the TIGR database resources for plant genomics and describe methods to access the data...
  11. doi request reprint Plant genome annotation methods
    Shu Ouyang
    The Institute for Genomic Research, Rockville, MD, USA
    Methods Mol Biol 513:263-82. 2009
    ..With the increasing availability of plant genome sequence data, the value of comparative annotation will increase. As with any new field, methodologies are evolving for genome annotation and will improve in the future...
  12. pmc The TIGR Rice Genome Annotation Resource: improvements and new features
    Shu Ouyang
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 35:D883-7. 2007
    ..Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads...
  13. ncbi request reprint Analyzing the potato abiotic stress transcriptome using expressed sequence tags
    Willem Rensink
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Genome 48:598-605. 2005
    ..In addition, we identified a number of genes unique to the abiotic stress library with unknown function, providing new candidate genes for investigation of abiotic stress responses in potato...
  14. pmc The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists
    Qiaoping Yuan
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    Nucleic Acids Res 31:229-33. 2003
    ..All of the data is available through web-based interfaces, FTP downloads, and a Distributed Annotation System...
  15. pmc Identification and characterization of pseudogenes in the rice gene complement
    Francoise Thibaud-Nissen
    The J Craig Venter Institute, 9712 Medical Center Dr, Rockville, MD 20850, USA
    BMC Genomics 10:317. 2009
    ....
  16. pmc The TIGR Plant Transcript Assemblies database
    Kevin L Childs
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 35:D846-51. 2007
    ..Assemblies can be retrieved by a text-based keyword search or a sequence-based BLAST search. The current version of the TA database is Release 2 (July 17, 2006) and includes a total of 215 plant species...
  17. ncbi request reprint Microarray expression profiling resources for plant genomics
    Willem Albert Rensink
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    Trends Plant Sci 10:603-9. 2005
    ..Coupled to these platforms are public databases that provide access to these large-scale expression data, which can be used to aid the functional discovery of gene function...
  18. pmc EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome
    Francoise Thibaud-Nissen
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    BMC Genomics 8:388. 2007
    ....
  19. pmc Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
    Brian J Haas
    J Craig Venter Institute, The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Biol 9:R7. 2008
    ..Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation...
  20. pmc Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition
    Vinita Joardar
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    J Bacteriol 187:6488-98. 2005
    ..With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific...
  21. pmc Intron gain and loss in segmentally duplicated genes in rice
    Haining Lin
    The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 7:R41. 2006
    ..The recent completion of the rice genome in which segmental duplication has been documented has allowed us to investigate intron evolution within rice, a diploid monocotyledonous species...
  22. pmc Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
    Matthew A Campbell
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    BMC Genomics 7:327. 2006
    ..Additionally, these two plant species have extensive cDNA and expressed sequence tag (EST) libraries. We employed the Program to Assemble Spliced Alignments (PASA) to identify and analyze alternatively spliced isoforms in both species...
  23. pmc The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants
    Shu Ouyang
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:D360-3. 2004
    ..Collectively, these databases provide a resource for the identification, classification and analysis of repetitive sequences in plants...
  24. pmc A workshop on establishing a rice resource center in the United States
    C Robin Buell
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Plant Physiol 132:1137. 2003
  25. pmc Current status of the sequence of the rice genome and prospects for finishing the first monocot genome
    C Robin Buell
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Plant Physiol 130:1585-6. 2002
  26. pmc Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species
    W A Rensink
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Plant Physiol 135:622-9. 2004
    ..Genomic resource development has been essential to set the stage for hypothesis-driven research, and Arabidopsis continues to provide paradigms for testing in rice to assess function across taxonomic divisions and in a crop species...
  27. pmc Comparative analyses of potato expressed sequence tag libraries
    Catherine M Ronning
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Plant Physiol 131:419-29. 2003
    ....
  28. ncbi request reprint Gene expression profiling of potato responses to cold, heat, and salt stress
    Willem Albert Rensink
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Funct Integr Genomics 5:201-7. 2005
    ..In addition, we identified expression profiles which are indicative for the type of stress applied to the plants...
  29. ncbi request reprint Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers
    Zhukuan Cheng
    Department of Horticulture, University of Wisconsin Madison, 53706, USA
    Chromosome Res 10:379-87. 2002
    ..21 kb/microm among the seven BAC clones. Fiber-FISH results derived from a BAC contig that spanned 1 Mb DNA matched remarkably to the sequencing data, demonstrating the high resolution of this technique in cytological mapping...
  30. pmc Diversity in conserved genes in tomato
    Allen Van Deynze
    Seed Biotechnology Center, University of California, 1 Shields Ave, Davis, CA, USA
    BMC Genomics 8:465. 2007
    ..We describe the results of a study to identify nucleotide variation within tomato breeding germplasm and mapping parents for a set of conserved single-copy ESTs that are orthologous between tomato and Arabidopsis...
  31. pmc Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor
    Derrick E Fouts
    Department of Plant Pathology, Cornell University, Ithaca, NY 14853 4203, USA
    Proc Natl Acad Sci U S A 99:2275-80. 2002
    ..Additional candidate effector genes, hopPtoA2, hopPtoB2, and an avrRps4 homolog, were preceded by Hrp promoter-like sequences, but these had HMM expectation values of relatively low significance and were not detectably activated by HrpL...
  32. pmc Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres
    Kiyotaka Nagaki
    Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 163:759-70. 2003
    ..Highly conserved sequence motifs were found in the LTRs of the centromere-specific retrotransposons in the grass species, suggesting that the LTRs may be important for the centromere specificity of this retrotransposon family...
  33. pmc Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition
    Wei Zhu
    Department of Plant Biology, Michigan State University, 166 Plant Biology Building, East Lansing, MI 48824, USA
    BMC Genomics 9:286. 2008
    ..While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses...
  34. pmc Genomewide identification of proteins secreted by the Hrp type III protein secretion system of Pseudomonas syringae pv. tomato DC3000
    Tanja Petnicki-Ocwieja
    Plant Science Initiative and Department of Plant Pathology, University of Nebraska, Lincoln, NE 68588 0660, USA
    Proc Natl Acad Sci U S A 99:7652-7. 2002
    ..One ADP-ribosyltransferase and the SrfC homolog were tested and shown to be secreted in a Hrp-dependent manner. These proteins, designated HopPtoS2 and HopPtoL, respectively, bring the DC3000 Hrp-secreted protein inventory to 22...
  35. pmc Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight
    Junqi Song
    Department of Horticulture, Biotechnology Center, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 100:9128-33. 2003
    ..Our results also demonstrate that LR-PCR is a valuable approach to isolate genes that cannot be maintained in the bacterial artificial chromosome system...
  36. pmc Phenotypic and transcriptomic changes associated with potato autopolyploidization
    Robert M Stupar
    Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
    Genetics 176:2055-67. 2007
    ..We demonstrated that there are few genes, if any, whose expression is linearly correlated with the ploidy and can be dramatically changed because of ploidy alteration...
  37. pmc A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium
    Bikram S Gill
    Plant Pathology Department, Kansas State University, Manhattan, Kansas 66506 5502, USA
    Genetics 168:1087-96. 2004
    ..The purpose of this report is to convey the information discussed at the workshop and provide the basis for an ongoing dialogue, bringing forth comments and suggestions from the genetics community...
  38. pmc Transcription and histone modifications in the recombination-free region spanning a rice centromere
    Huihuang Yan
    Department of Horticulture, University of Wisconsin, Madison, 53706, USA
    Plant Cell 17:3227-38. 2005
    ..Rather, the varied distribution of histone modifications might reflect the composition and abundance of sequence elements that inhabit centromeric DNA...
  39. ncbi request reprint Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis
    John Cairney
    School of Biology and Institute of Paper Science and Technology, Georgia Institute of Technology, 500, 10th Street, NW, Atlanta, GA 30332 0620, USA
    Plant Mol Biol 62:485-501. 2006
    ..We also identified sequences from the pine embryo transcriptome that have no known function and may contribute to the programming of gene expression and embryo development...
  40. pmc Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere
    Huihuang Yan
    Department of Horticulture, University of Wisconsin, Madison, 53706, USA
    Plant Cell 18:2123-33. 2006
    ..These results support the hypothesis that centromeres can evolve from gene-containing genomic regions...
  41. pmc Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes
    Kenneth L McNally
    International Rice Research Institute, Metro Manila, The Philippines
    Plant Physiol 141:26-31. 2006
  42. ncbi request reprint Sequencing of a rice centromere uncovers active genes
    Kiyotaka Nagaki
    Department of Horticulture, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Nat Genet 36:138-45. 2004
    ..These results suggest that Cen8 may represent an intermediate stage in the evolution of centromeres from genic regions, as in human neocentromeres, to fully mature centromeres that accumulate megabases of homogeneous satellite arrays...
  43. pmc Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon
    Zhukuan Cheng
    Department of Horticulture, University of Wisconsin Madison, Madison, WI 53706, USA
    Plant Cell 14:1691-704. 2002
    ..Our results demonstrate that the CentO satellite may be a key DNA element for rice centromere function...
  44. ncbi request reprint Mitochondrial genome sequences and molecular evolution of the Irish potato famine pathogen, Phytophthora infestans
    Cruz Avila-Adame
    Department of Plant Pathology, North Carolina State University, Box 7616, Raleigh, 27695, USA
    Curr Genet 49:39-46. 2006
    ..The type I haplotypes diverged more recently and the mutations associated with the evolution of the Ia and Ib types were identified...
  45. ncbi request reprint Bioinformatics-enabled identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A
    Monica Vencato
    Department of Plant Pathology, Cornell University, Ithaca, NY 14853, USA
    Mol Plant Microbe Interact 19:1193-206. 2006
    ..These results establish the utility of the bioinformatic or candidate gene approach to identifying effectors and other genes relevant to pathogenesis in P. syringae genomes...
  46. ncbi request reprint High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis
    Ming Cheng Luo
    Department of Agronomy and Range Science, University of California at Davis, Davis, CA, 95616, USA
    Genomics 82:378-89. 2003
    ....
  47. ncbi request reprint Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice
    Kiyotaka Nagaki
    Department of Horticulture, University of Wisconsin Madison, USA
    Mol Biol Evol 22:845-55. 2005
    ..Mechanisms of the targeting specificity of the CRR elements, as well as their role in centromere function, are discussed...