Research Topics
Species | V BrendelSummaryAffiliation: Iowa State University Country: USA Publications
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Detail Information
Publications
Community-based gene structure annotationShannon D Schlueter
Department of Genetics, Development and Cell Biology, Iowa State University, 2112 Molecular Biology Building, Ames, IA 50011, USA
Trends Plant Sci 10:9-14. 2005..We propose a dynamic, economically feasible solution to the annotation predicament: broad-based, web-technology-enabled community annotation, a prototype of which is now in use for Arabidopsis...- yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genesMatthew D Wilkerson
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011 3260, USA
Genome Biol 7:R58. 2006..yrGATE is highly portable and supports different standard input and output formats. The yrGATE software and usage cases are available at http://www.plantgdb.org/prj/yrGATE... - xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome featuresShannon D Schlueter
Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011-3260, USA
Genome Biol 7:R111. 2006..The xGDB distribution and user support utilities are available online at the xGDB project website, http://xgdb.sourceforge.net/... - The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicingBing Bing Wang
Department of Genetics, Development and Cell Biology Iowa State University, Ames, IA 50011 3260, USA
Genome Biol 5:R102. 2004.... - Genome-wide mutagenesis of Zea mays L. using RescueMu transposonsJohn Fernandes
Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
Genome Biol 5:R82. 2004..Although frequently recovered parental insertions and insertion hotspots reduce the efficiency of gene discovery per plasmid, RescueMu targets a large variety of genes and produces knockout mutants... - Cross-species EST alignments reveal novel and conserved alternative splicing events in legumesBing Bing Wang
Department of Plant Pathology, University of Minnesota, St, Paul, MN 55108, USA
BMC Plant Biol 8:17. 2008..Here we report the characteristics of AS in legumes, one of the largest and most important plant families, based on EST alignments to the genome sequences of Medicago truncatula (Mt) and Lotus japonicus (Lj)... - MetWAMer: eukaryotic translation initiation site predictionMichael E Sparks
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
BMC Bioinformatics 9:381. 2008.... - Tracembler--software for in-silico chromosome walking in unassembled genomesQunfeng Dong
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
BMC Bioinformatics 8:151. 2007.... - Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNAV Brendel
Department of Mathematics, Stanford University, Stanford, CA 94305, USA
Nucleic Acids Res 26:4748-57. 1998..A WWW version of the SplicePredictor program is available at http:/gnomic.stanford.edu/volker/SplicePredi ctor.html/.. - Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locusVolker Brendel
Department of Genetics, Development and Cell Biology, Iowa State University, 2112 Molecular Biology Building, Ames, IA 50011 3260, USA
Bioinformatics 20:1157-69. 2004..Previous spliced alignment tools were found inadequate for this task because they rely on very high sequence similarity between the ESTs and the genomic DNA... - Comparative genomics of Arabidopsis and maize: prospects and limitationsVolker Brendel
Department of Zoology and Genetics and Department of Statistics, Iowa State University, Ames, IA 50010, USA
Genome Biol 3:REVIEWS1005. 2002.... - Computational modeling of gene structure in Arabidopsis thalianaVolker Brendel
Department of Zoology and Genetics, Iowa State University, Ames 50010, USA
Plant Mol Biol 48:49-58. 2002..The purpose of this article is to discuss tools available to an individual researcher to evaluate gene structure prediction for a particular locus... - SynBrowse: a synteny browser for comparative sequence analysisXiaokang Pan
Department of Genetics, Development and Cell Biology, Iowa State University, 2112 Molecular Biology Building, Ames, IA 50011-3260, USA
Bioinformatics 21:3461-8. 2005..SynBrowse is portable with simple installation, flexible configuration, convenient data input and easy integration with other components of a model organism system. AVAILABILITY: The software is available at http://www.gmod.org CONTACT: .. - GeneSeqer@PlantGDB: Gene structure prediction in plant genomesShannon D Schlueter
Department of Zoology and Genetics, Iowa State University, Ames, IA 50011-3260, USA
Nucleic Acids Res 31:3597-600. 2003.... - Comparative EST analyses in plant systemsQunfeng Dong
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011-3260, USA
Methods Enzymol 395:400-18. 2005.... - Comparative plant genomics resources at PlantGDBQunfeng Dong
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, 50011-3260, USA
Plant Physiol 139:610-8. 2005..plantgdb.org/OsGDB/). In addition, a number of bioinformatic tools have been integrated at PlantGDB that enable researchers to carry out sequence analyses on-site using both their own data and data residing within the database... - PlantGDB: a resource for comparative plant genomicsJon Duvick
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
Nucleic Acids Res 36:D959-65. 2008..PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training... - Efficient clustering of large EST data sets on parallel computersAnantharaman Kalyanaraman
Department of Computer Science, Iowa State University, Ames, IA 50011, USA
Nucleic Acids Res 31:2963-74. 2003..Using PaCE, we clustered EST data from 23 plant species and the results are available at the PlantGDB website... - Refined annotation of the Arabidopsis genome by complete expressed sequence tag mappingWei Zhu
Department of Zoology and Genetics, Iowa State University, Ames 50011-3260, USA
Plant Physiol 132:469-84. 2003..All results of this study were parsed into a database and are accessible via a flexible Web interface at http://www.plantgdb.org/AtGDB/... - Expression and evolution of the phosphoinositide-specific phospholipase C gene family in Arabidopsis thalianaI Made Tasma
Department of Agronomy, Iowa State University, G303 Agronomy Hall, Ames, IA 50011, USA
Plant Physiol Biochem 46:627-37. 2008.... - MaizeGDB, the community database for maize genetics and genomicsCarolyn J Lawrence
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA
Nucleic Acids Res 32:D393-7. 2004..Web-based curation tools for both designated experts and general researchers are currently under development. MaizeGDB can be accessed at http://www.maizegdb.org/... - PlantGDB, plant genome database and analysis toolsQunfeng Dong
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA
Nucleic Acids Res 32:D354-9. 2004..plantgdb.org/AtGDB/)... - Multi-query sequence BLAST output examination with MuSeqBoxL Xing
Department of Zoology and Genetics, Iowa State University, Ames, IA 50011, USA
Bioinformatics 17:744-5. 2001..The program is also available over the web at http://bioinformatics.iastate.edu/bioinformatics2go/mb/MuSeqBox.html... - Genomewide comparative analysis of alternative splicing in plantsBing-Bing Wang
Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA
Proc Natl Acad Sci U S A 103:7175-80. 2006..We created a comprehensive web-interfaced database to compile and visualize the evidence for alternative splicing in plants (Alternative Splicing in Plants, available at www.plantgdb.org/ASIP)... - Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plantsMichael E Sparks
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA
Bioinformatics 21:iii20-30. 2005..iastate.edu/cgi-bin/sp.cgi. Software to generate training data and parameterizations for Bayesian splice site models is available at http://gremlin1.gdcb.iastate.edu/~volker/SB05B/BSSM4GSQ/.. - Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridizationJohn Fernandes
Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA
Plant Physiol 128:896-910. 2002..Reassembly of ESTs at the criterion of 90% identity suggests how cross hybridization among gene family members can overestimate the overlap in genes expressed in micro-array hybridization experiments... - Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genomeWei Zhu
Department of Zoology and Genetics, Iowa State University, Ames, IA 50011 3260, USA
Nucleic Acids Res 31:4561-72. 2003..Furthermore, phylogenetic analysis suggests that both U12-type AT-AC and U12-type GT-AG introns occurred in Na+/H+ antiporters in a progenitor of animals and plants... - A compilation of soybean ESTs: generation and analysisRandy Shoemaker
USDA ARS, Corn Insect and Crop Genetics Research Unit, and Department of Agronomy, Iowa State University, Ames 50011, USA
Genome 45:329-38. 2002..These studies provide a rich source of publicly available gene sequences as well as valuable insight into the structure, function, and evolution of a model crop legume genome... - Gene Structure Annotation at PlantGDBVolker Brendel
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
Methods Mol Biol 406:521-33. 2007..The implementation of the tool at the PlantGDB resource also allows immediate communication of the novel annotations to the community through Web display... - The maize genetics and genomics database. The community resource for access to diverse maize dataCarolyn J Lawrence
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011-3260, USA
Plant Physiol 138:55-8. 2005.... - Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictionsWei Zhu
Department of Zoology and Genetics, Iowa State University, Ames, IA 50011, USA
Bioinformatics 18:761-2. 2002..AVAILABILITY: The program was written in Java and is freely available to non-commercial users by electronic download from http://bioinformatics.iastate.edu/bioinformatics2go/MyGV... - A combinatorial role for exon, intron and splice site sequences in splicing in maizeJ C Carle-Urioste
Department of Biological Sciences, Stanford University, CA 94305 5020, USA
Plant J 11:1253-63. 1997..It is also shown that GC-rich intron constructs that are poorly spliced can be partially rescued by an improved 3' splice site... - Molecular characterization and phylogeny of U2AF35 homologs in plantsBing Bing Wang
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50010, USA
Plant Physiol 140:624-36. 2006..A C-terminal motif (named SERE) is highly conserved in all seed plant protein homologs, suggesting it may have an important function specific to higher plants... - ZmDB, an integrated database for maize genome researchQunfeng Dong
Department of Zoology and Genetics, Iowa State University, Ames, IA 50011-3260, USA
Nucleic Acids Res 31:244-7. 2003..ZmDB can be accessed at http://zmdb.iastate.edu/... - Spliceosomal proteins in plantsY Ru
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011 3260, USA
Curr Top Microbiol Immunol 326:1-15. 2008..Large-scale proteomics and gene expression studies may be required to unravel the many intricate mechanisms involved in splice site recognition and selection... - Quantitative model of ColE1 plasmid copy number controlV Brendel
Department of Mathematics, Stanford University, CA 94305
J Mol Biol 229:860-72. 1993..Our model predicts the quantitative increase of plasmid copy number in rom- mutants. Several experiments are suggested to investigate the predictions of the model... - Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organismsV Brendel
Department of Mathematics, Stanford University, Stanford, CA 94305 2125, USA
J Mol Evol 44:528-41. 1997..We propose that RecA-like proteins derive evolutionarily from an assortment of independent domains and that the functional homologs of RecA in noneubacteria comprise an array of RecA-like proteins acting in series or cooperatively... - Charge configurations in viral proteinsS Karlin
Department of Mathematics, Stanford University, CA 94305
Proc Natl Acad Sci U S A 85:9396-400. 1988..This contrast might reflect the role of protein charge structures in facilitating competitive virus-host interactions involving the cellular transcription, translation, protein sorting, and transport apparatus... - Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonasHong Lu
Department of Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
PLoS ONE 3:e3828. 2008..Collectively, members cause diseases on over 392 plant species. Individually, they exhibit marked host- and tissue-specificity. The determinants of this specificity are unknown... - Plant genome research outreach portal. A gateway to plant genome research "outreach" programs and activitiesSanford B Baran
Department of Genetics, Development and Cell Biology, Iowa State University, 2112 Molecular Biology Building, Ames, Iowa 50011, USA
Plant Physiol 134:889. 2004 - Methods and algorithms for statistical analysis of protein sequencesV Brendel
Department of Mathematics, Stanford University, CA 94305 2125
Proc Natl Acad Sci U S A 89:2002-6. 1992..B. (volker/genomic@stanford.edu)... - Visualization of syntenic relationships with SynBrowseVolker Brendel
Methods Mol Biol 396:153-63. 2007..The complete set of programs making up these pipelines as well as the data sets used are available on the SynBrowse homepage... - The Maize Genome Sequencing ProjectVicki L Chandler
Plant Sciences Department, University of Arizona, Tuscon 85721, USA
Plant Physiol 130:1594-7. 2002 - The maize genome contains a helitron insertionShailesh K Lal
Program in Plant Molecular and Cellular Biology and Horticultural Sciences, University of Florida, Gainesville, Florida 32611-0690, USA
Plant Cell 15:381-91. 2003..A second Helitron insertion was found in the maize genomic database. These data strongly suggest an active Helitron in the present-day maize genome...