PlantGDB Publications

• Agrawal, A., Brendel, V. & Huang, X. (2008) Pairwise statistical signifiance and Empirical Determination of Eefective Ggp Opening Ppnalties for Protein Local Sequence Alignment. Int. J. of Computational Biol. and Drug Design, to appear.
• Lushbough, C.M., Duvick, J, Dong, Q., Jennewein, D., Reynoldson, J. and Brendel, V. (2008) TableleMaker: An ad hoc Query Tool for Relational Databases. In H.R. Arabnia, M.Q. Yang, and J.Y. Yang (eds.), Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP'08), Volume X, pp. xxx--xxx, July 14-17, 2008, Las Vegas, Nevada, USA. CSREA Press, ISBN x-xxxxx-xxx-x. [conference program]
• Lushbough, C.M. & Brendel, V. (2008) An overview of the BioExtract Server - a distributed, Web based application for bioinformatic analysis. In H.R. Arabnia, M.Q. Yang, and J.Y. Yang (eds.), Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP'08), Volume X, pp. xxx--xxx, July 14-17, 2008, Las Vegas, Nevada, USA. CSREA Press, ISBN x-xxxxx-xxx-x. [conference program]
• Lushbough, C., Bergman, M.K., Lawrence, C.J., Jennewein, D. & Brendel, V. (2008) BioExtract Server - an integrated workflow-enabling system to access and analyze heterogeneous, distributed biomolecular data. IEEE Transactions Comp. Biol. Bioinformatics, preprint, Sept. 11, 2008, doi:10.1109/TCBB.2008.98.
• Lu, H., Patil, P., Van Sluys, M.-A., White, F.F., Ryan, R.P., Dow, J.M., Rabinowicz, P., Salzberg, S.L., Leach, J.E., Sonti, R., Brendel, V. & Bogdanove, A.J. (2008)
• Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in Xanthomonas. PLoS ONE.
• Sparks, M.E. & Brendel, V. (2008) MetWAMer: eukaryotic translation initiation site prediction. BMC Bioinformatics, 9, 381. [abstract] [PDF]
• Tasma, I.M., Brendel, V., Whitman, S.A. & Bhattacharyya, M.K. (2008) Expression and evolution of the phosphoinositide-specific phospholipase C gene family in Arabidopsis thaliana. Plant Physiol. Biochem. 7, 627. [PubMed ID: 18534862] [online article]
• Agrawal, A., Brendel, V. & Huang, X. (2008) Pairwise statistical significance versus database statistical significance for local alignment of protein sequences. In I.I. M&#259ndoiu, R. Sunderraman & A.Z. Zelikovsky (eds.), 2008 International Symposium on Bioinformatics Research and Applications, May 6-9, 2008, Georgia State University, Atlanta GA, U.S.A.. Lecture Notes in Bioinformatics 4983, 50-61. [online abstract]
• Ru, Y., Wang, B.-B. & Brendel, V. (2008) Spliceosomal proteins in plants. In Nuclear pre-mRNA processing in plants, A.S.N. Reddy & M. Golovkin (eds.), Current Topics in Microbiology and Immunology 326, 1-15. [PDF]
• Wang, B.-B., O'Toole, M., Brendel, V. & Young, N.D. (2008) Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes. BMC Plant Biol. 8:17. [PubMed ID: 18282305] [online article]
  
• Duvick, J., Fu, A., Muppirala, U., Sabharwal, M., Wilkerson, M.D., Lawrence, C.J., Lushbough, C. & Brendel, V. (2008) PlantGDB: a resource for comparative plant genomics. Nucl. Acids Res. 36, D959-D965. [PubMed ID: 18063570] [online article]
• Lushbough, C.M., Bergman, M.K., Lawrence, C.J., Jennewein, D. & Brendel, V. (2007)
• Creating bioinformatic workflows within the BioExtract server. In H.R. Arabnia, M.Q. Yang, and J.Y. Yang (eds.), Proceedings of the 2007 International Conference on Bioinformatics & Computational Biology (BIOCOMP'07), Volume II, pp. 316-322, June 25-28, 2007, Las Vegas, Nevada, USA. CSREA Press, ISBN 1-60132-041-8. Journal version: Int. J. of Computational Biol. and Drug Design, 1(3), 302-312 (to appear).
• Brendel, V., Kurtz, S. & Pan, X. (2007) Visualization of syntenic relationships with SynBrowse. In N.H Bergman (ed.), Comparative Genomics, Volume II. Methods in Molecular Biology 396, 153-163. Humana Press, Totowa, NJ. [PubMed ID: 18025692 ] [Publisher's Web site]
• Brendel, V. (2007) Gene structure annotation at PlantGDB. In D. Edwards (ed.), Plant Bioinformatics: Methods and Protocols. Methods in Molecular Biology 406, 519-531. Humana Press, Totowa, NJ. [PubMed ID: 18287710 ] [Publisher's Web site]
• Sparks, M.E., Brendel, V. & Dorman, K.S. (2007) Markov model variants for appraisal of coding potential in plant DNA. In I. Mandoiu & A. Zelikovsky (eds.), 2007 International Symposium on Bioinformatics Research and Applications, May 7-10, 2007, Georgia State University, Atlanta GA, U.S.A.. Lecture Notes in Bioinformatics 4463, 394-405. [online article] [conference proceedings]
• Dong, Q., Wilkerson, M.D. & Brendel, V. (2007) Tracembler - software for in silico chromosome walking in unassembled genomes. BMC Bioinformatics 8, 151. [PubMed ID: 17490482] [online abstract]
• Schlueter S.D., Wilkerson M.D., Dong Q., & Brendel V. (2006) xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features. Genome Biol. 7(11): R111. [PubMed ID: 17116260] [online article]
• Wilkerson, M.D., Schlueter, S.D. & Brendel, V. (2006) yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. Genome Biol. 7, R58. [PubMed ID: 16859520]
• Wang, B.-B. & Brendel, V. (2006) Genome-wide comparative analysis of alternative splicing in plants. Proc. Natl. Acad. Sci. USA 103, 7175-7180. [PubMed ID: 16632598]
• Wang, B.-B. & Brendel, V. (2006) Molecular characterization and phylogeny of U2AF1 homologs in plants. Plant Physiol. 140, 624-636. [PubMed ID: 16407443]
• Gremme, G., Brendel, V., Sparks, M.E. & Kurtz, S. (2005) Engineering a software tool for gene structure prediction in higher organisms. Information Software Technol. 47, 965-978. [online abstract]
• Brendel, V. (2005) Novel tools for plant genome annotation and applications to Arabidopsis and rice. In J.P. Gustafson, R. Shoemaker & J.W. Snape (eds.), Genome Exploitation: Data Mining the Genome, Stadler Genetics Symposia Series, 23rd Symposium, Springer, NY, U.S.A. [Publisher's Web site]
• Sparks, M.E. & Brendel, V. (2005) Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants. Bioinformatics 21, iii20-iii30. [PubMed ID: 16306388]
• Dong, Q., Lawrence, C.J., Schlueter, S.D., Wilkerson, M.D., Kurtz, S., Lushbough, C. & Brendel, V. (2005) Comparative plant genomics resources at PlantGDB. Plant Physiol. 139, 610-618. [PubMed ID: 16219921]
• Pan, X., Stein, L. & Brendel, V. (2005) SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics 21, 3461-3468. [PubMed ID: 15994196]
• Lawrence, C.J., Seigfried, T.E. & Brendel, V. (2005) MaizeGDB - the community resource for access to diverse maize data. Plant Physiol. 138, 55-58. [PubMed ID: 15888678]
• Dong, Q., Kroiss, L., Oakley, F.D., Wang, B.-B. & Brendel, V. (2005) Comparative EST analyses in plant systems. In Molecular Evolution: Producing the Biochemical Data, E.A. Zimmer and E.H. Roalson (eds.), Methods Enzymol. 395, 400-418. [PubMed ID: 15984049] [online abstract]
• Brendel, V. (2005) Gene structure prediction in plant genomes. In M.J. Dunn, L.B. Jorde, P.F.R. Little and S. Subramaniam (eds.), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Wiley & Sons, Chichester, UK. DOI: 10.1002/047001153X.g402303.
• Dong, Q. & Brendel, V. (2005) Computational identification of related proteins: BLAST, PSI-BLAST, and other tools. In J.M. Walker (ed.), The Proteomics Protocols Handbook, Humana Press, U.S.A., pp. 555-570. [Publisher's Web site]
• Schlueter, S.D., Wilkerson, M.D., Huala, E., Rhee, S.Y. & Brendel, V. (2005) Community-based gene structure annotation for the Arabidopsis thaliana genome. Trends Plant Sci. 10, 9-14. [PubMed ID: 15642518]
• Wang, B.-B. & Brendel, V. (2004) The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing. Genome Biol. 5, R102. [PubMed ID: 15575968] [ online article]
• Fernandes, J.F., Dong, Q., Schneider, B., Morrow, D.J., Nan, G.-L., Brendel, V. & Walbot, V. (2004) Genome-wide mutagenesis of Zea mays L. using RescueMu transposons. Genome Biol. 5, R82. [PubMed ID: 15461800]
• Brendel, V., Pan, X. & Sparks, M.E. (2004) Bioinformatics: The interpretation of genomic information. In R.F. Wilson, H.T. Stalker and C. Brummer (eds.), Legume Crop Genomics, pp. 255-266. Am. Oil Chem. Soc. Press, Champaign, IL, U.S.A.
• Baran, S., Lawrence, C.J. & Brendel, V. (2004) PGROP - A gateway to plant genome research 'outreach' programs and activities. Plant Physiol. 134, 889. [PubMed ID: 15020751]
• Brendel, V., Xing, L. & Zhu, W. (2004) Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 20, 1157-1169. [PubMed ID: 14764557]
• Lawrence, C.J., Dong, Q., Polacco, M.L., Seigfried, T.E. & Brendel, V. (2004) MaizeGDB, the community database for maize genetics and genomics. Nucl. Acids Res. 32, D393-D397. [PubMed ID: 14681441]
• Dong, Q., Schlueter, S.D. & Brendel, V. (2004) PlantGDB, plant genome database and analysis tools. Nucl. Acids Res. 32, D354-D359. [PubMed ID: 14681433]
• Kalyanaraman, A., Aluru, S., Brendel, V. & Kothari, S. (2003) Space and time efficient parallel algorithms and software for EST clustering. IEEE Transactions on Parallel and Distributed Systems 14, 1209-1221.
• Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V. (2005) Comparative Plant Genomics Resources at PlantGDB. Plant Physiology, 139, 610-618.
• Dong,Q., Schlueter,S.D. and Brendel,V. (2004) PlantGDB, plant genome database and analysis tools. Nucleic Acids Res., 32, D354-D359.
• Schlueter,S.D., Dong,Q. and Brendel,V. (2003) GeneSeqer@PlantGDB: gene structure prediction in plant genomes. Nucleic Acids Res., 31, 3597-3600.
• Zhu,W. and Brendel,V. (2003) Identification, characterization, and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome. Nucleic Acids Res., 31, 4561-4572.
• Zhu,W., Schlueter,S.D. and Brendel,V. (2003) Refined annotation of the Arabidopsis thaliana genome by complete EST mapping. Plant Physiology, 132, 469-484.