PlantGDB Publications

  • Lushbough, C.M., Jennewein, D.M., Brendel, V.P. (2011) The BioExtract Server: a web-based bioinformatic workflow platform Nucleic Acids Res. 39 (Web Server issue):W528-32. Epub 2011 May 5. [PubMed ID: PMC3125737]
  • Wilkerson, M.D., Ru, Y., Brendel, VP. (2009) Common introns within orthologous genes: software and application to plants. Brief Bioinform10(6):631-44. [PubMed ID 19933210]
  • Ru, Y, Wang, B.B., Brendel, V. (2008) Spliceosomal proteins in plants. Curr Top Microbiol Immunol. 2008;326:1-15.[[PubMed ID 18630744]
  • 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.

New & Noteworthy

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New Location for PlantGDB (July 23, 2012)
The Brendel Group is now located at Indiana University, and the PlangGDB server has been migrated as well, and it is now hosted at the Indiana University School of Informatics and Computing. We don't anticipate any disruption in service, but if you encounter any problems with the website we encourage you to contact us using our Feedback Form. (3-14-2012)
BrGDB - Brassica rapa chromosome-based genome browser (Mar. 16)
StGDB - Solanum tuberosum new genome browser (Mar. 16)
StGDB, a new genome database for the potato (Solanum tuberosum) is now available at PlantGDB (Genomes→Other→StGDB). Based on the JGI draft genome, VcGDB includes 14,971 protein-coding loci and 15,285 protein-coding transcripts on 413 scaffolds. Other data displayed include splice-aligned cDNAs, EST and PUTs, and splice-aligned related species proteins. (3-14-2012)
BrGDB - Brassica rapa chromosome-based genome browser (Mar. 16)
BrGDB, the genome browser for rapeseed (Brassica rapa) is now updated at PlantGDB (Genomes→Other→BrGDB). Based on the BRAD draft genome, BrGDB includes 41,019 protein-coding transcripts on 10 chromosomes plus unanchored scaffolds (concatenated with 200 N spacer as "chr11"). Other data displayed include splice-aligned cDNAs, EST and PUTs, and splice-aligned related species proteins. (3-16-2012)
VcGDB - Volvox carteri new genome browser (Mar. 14)
VcGDB, a new genome database for the multicellular green alga Volvox (Volvox carteri) is now available at PlantGDB (Genomes→Other→VcGDB). Based on the JGI draft genome, VcGDB includes 14,971 protein-coding loci and 15,285 protein-coding transcripts on 413 scaffolds. Other data displayed include splice-aligned cDNAs, EST and PUTs, and splice-aligned related species proteins. (3-14-2012)
Medicago genome updated (Feb 27)
The Medicago truncatula (barrel medic) genome browser MtGDB has been updated to the new assembly / annotation version 3.5 using data deposited at phytozome. New transcript / protein spliced alignments and gene quality estimates have been calculated as well.
Rice genome updated (Feb 27)
The Oryza sativa (rice) genome browser OsGDB has been updated to the new assembly / annotation version 7 using data deposited at phytozome. New transcript / protein spliced alignments and gene quality estimates have been calculated as well.
Cassava genome updated (Feb 27)
The Manihot esculenta (cassava) genome browser MeGDB has been updated to the v4 assembly / v4.1 annotation that is available at phytozome. New transcript / protein spliced alignments and gene quality estimates have been calculated as well.
Populus annotation updated (Feb 27)
The Populus trichocarpa (poplar) genome browser PtGDB has been updated to annotation version 2.2 using data deposited at phytozome. Genome assembly and spliced-alignments are unchanged.
Mimulus annotation updated (Feb 27)
The Mimulus guttatus genome browser MgGDB has been updated to annotation version 4.3 using data deposited at phytozome. Genome assembly and spliced-alignments are unchanged.
Chlamydomonas annotation updated (Feb 27)
The Chlamydomonas reinhardtii genome browser CrGDB has been updated to annotation version 4.3 using data deposited at phytozome. Genome assembly and spliced-alignments are unchanged.
Brachopodium annotation updated (Feb 13)
The Brachypodium distachyon genome browser BdGDB has been updated to annotation version Bradi1.2 using data deposited at phytozome. Genome assembly and spliced-alignments are unchanged.
PlantGDB NSF Grant (Jan 31)

The PlantGDB website is currently being managed under a new NSF Genome Research Grant, IOS-1126267 (IPGA: Characterization, Modeling, Prediction, and Visualization of the Plant Transcriptome.) Read more about IPGA.

PlantGDB at Maize Genetics Conf. (Jan 31)
PlantGDB will be represented at the 54th Annual Maize Genetics Conference, March 15-18, 2012, in Portland, Oregon USA. Check out poster P56 "Discovery, annotation and expression analysis of arginine/serine (SR) proteins in maize using the Plant Genome Database PlantGDB". (1-28-2012)
GenBank Release 187 (Jan 31)
GenBank Release 187.0 sequence data (close date 12-15-2011) have been processed and are available for downloading at PlantGDB. Twenty-three new or updated transcript assemblies have been created. Please note that indexing the new sequence data has been postponed due to infrastructure issues. (2-27-2012)
New Add Track feature for Genome Browsers Dec 15
Users can add their own genome features (aligned transcripts, gene models, etc) using our User Add Track tool. All that's needed is a properly formatted gff3 file. This feature is currently available at ZmGDB and AtGDB/ and will be available soon for all GDB. (12-15-2011).

What's Coming?

Genome updates (1-31-2012)
We are in the process of prioritizing genomes at PlantGDB for update. In addition, newly-available plant genomes are being prioritized for inclusion in PlantGDB's Genome Browser suite. Our goal is to maintain current data for at least 25 genomes.

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