Research Topics
| C Robin BuellSummaryAffiliation: The Institute for Genomic Research Country: USA Publications
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Detail Information
Publications
Interactions Between Xanthomonas Species and Arabidopsis thalianaC Robin Buell
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville MD 20850, Facsimile 301 838 0208
Arabidopsis Book 1:e0031. 2002....- Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass speciesC Robin Buell
The Institute for Genomic Research, Rockville, Maryland 20850, USA
Genome Res 15:1284-91. 2005.... - The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000C 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... 
Obtaining the sequence of the rice genome and lessons learned along the wayC 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...- Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcriptsWillem 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... - Characterization of paralogous protein families in riceHaining 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... - The institute for genomic research Osa1 rice genome annotation databaseQiaoping 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... - Identification and characterization of lineage-specific genes within the PoaceaeMatthew 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... - Improvement of whole-genome annotation of cereals through comparative analysesWei 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... - Analyzing the potato abiotic stress transcriptome using expressed sequence tagsWillem 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... - Plant database resources at The Institute for Genomic ResearchAgnes 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... 
Plant genome annotation methodsShu 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...- The TIGR Rice Genome Annotation Resource: improvements and new featuresShu 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... - Identification and characterization of pseudogenes in the rice gene complementFrancoise Thibaud-Nissen
The J Craig Venter Institute, 9712 Medical Center Dr, Rockville, MD 20850, USA
BMC Genomics 10:317. 2009.... - The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologistsQiaoping 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... - The TIGR Plant Transcript Assemblies databaseKevin 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... - Microarray expression profiling resources for plant genomicsWillem 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... - EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genomeFrancoise Thibaud-Nissen
The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
BMC Genomics 8:388. 2007.... - Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced AlignmentsBrian 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... - Comprehensive analysis of alternative splicing in rice and comparative analyses with ArabidopsisMatthew 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... - The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plantsShu 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... - Intron gain and loss in segmentally duplicated genes in riceHaining 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... - A workshop on establishing a rice resource center in the United StatesC Robin Buell
The Institute for Genomic Research, Rockville, Maryland 20850, USA
Plant Physiol 132:1137. 2003 - Current status of the sequence of the rice genome and prospects for finishing the first monocot genomeC Robin Buell
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Plant Physiol 130:1585-6. 2002 - Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop speciesW 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... - Comparative analyses of potato expressed sequence tag librariesCatherine M Ronning
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Plant Physiol 131:419-29. 2003.... - Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transpositionVinita 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... - Gene expression profiling of potato responses to cold, heat, and salt stressWillem 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... - Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibersZhukuan 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... - Diversity in conserved genes in tomatoAllen 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... - Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factorDerrick 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... - Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeresKiyotaka 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... - Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence compositionWei 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... - Genomewide identification of proteins secreted by the Hrp type III protein secretion system of Pseudomonas syringae pv. tomato DC3000Tanja 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... - Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blightJunqi 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... - Phenotypic and transcriptomic changes associated with potato autopolyploidizationRobert 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... - Transcription and histone modifications in the recombination-free region spanning a rice centromereHuihuang 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... - Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesisJohn 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... - Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromereHuihuang 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... - Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypesKenneth L McNally
International Rice Research Institute, Metro Manila, The Philippines
Plant Physiol 141:26-31. 2006 - A workshop report on wheat genome sequencing: International Genome Research on Wheat ConsortiumBikram 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... - Structure, divergence, and distribution of the CRR centromeric retrotransposon family in riceKiyotaka 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... - Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposonZhukuan 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... - Mitochondrial genome sequences and molecular evolution of the Irish potato famine pathogen, Phytophthora infestansCruz 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... - Bioinformatics-enabled identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448AMonica 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... - Sequencing of a rice centromere uncovers active genesKiyotaka 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... - High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresisMing-Cheng Luo
Department of Agronomy and Range Science, University of California at Davis, Davis, CA, 95616, USA
Genomics 82:378-89. 2003....