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.,
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Query Tool for Relational Databases. In H.R. Arabnia, M.Q.
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Nevada, USA. CSREA Press, ISBN x-xxxxx-xxx-x. [conference
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Lushbough, C.M. & Brendel, V. (2008) An overview of the
BioExtract Server - a distributed, Web based application for
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Yang (eds.), Proceedings of the International Conference on
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Press, ISBN x-xxxxx-xxx-x. [conference
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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.
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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
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Tasma, I.M., Brendel, V., Whitman, S.A. & Bhattacharyya,
M.K. (2008) Expression and evolution of the
phosphoinositide-specific phospholipase C gene family in
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statistical significance versus database statistical significance
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Ru, Y., Wang, B.-B. & Brendel, V. (2008) Spliceosomal
proteins in plants. In
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Wang, B.-B., O'Toole, M., Brendel, V. & Young, N.D. (2008)
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alternative splicing events in legumes.BMC Plant Biol.8:17. [PubMed ID:
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Duvick, J., Fu, A., Muppirala, U., Sabharwal, M., Wilkerson,
M.D., Lawrence, C.J., Lushbough, C. & Brendel, V. (2008)
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Lushbough, C.M., Bergman, M.K., Lawrence, C.J., Jennewein, D.
& Brendel, V. (2007)
Brendel, V., Kurtz, S. & Pan, X. (2007) Visualization of
syntenic relationships with SynBrowse. In N.H Bergman (ed.),
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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
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Dong, Q., Wilkerson, M.D. & Brendel, V. (2007)
Tracembler - software for in silico chromosome walking in
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Schlueter S.D., Wilkerson M.D., Dong Q., & Brendel V.
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integrated evaluation and analysis of genome features.Genome Biol.7(11): R111. [PubMed
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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
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Wang, B.-B. & Brendel, V. (2006) Genome-wide comparative
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Gremme, G., Brendel, V., Sparks, M.E. & Kurtz, S. (2005)
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higher organisms.Information Software Technol.47, 965-978. [online
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Brendel, V. (2005) Novel tools for plant genome annotation
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Sparks, M.E. & Brendel, V. (2005) Incorporation of
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Dong, Q., Lawrence, C.J., Schlueter, S.D., Wilkerson, M.D.,
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plant genomics resources at PlantGDB.Plant Physiol.139, 610-618. [PubMed
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Pan, X., Stein, L. & Brendel, V. (2005) SynBrowse: a
synteny browser for comparative sequence analysis.Bioinformatics21, 3461-3468. [PubMed
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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
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Dong, Q., Kroiss, L., Oakley, F.D., Wang, B.-B. & Brendel,
V. (2005) Comparative EST analyses in plant systems. In
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Brendel, V. (2005) Gene structure prediction in plant
genomes. In M.J. Dunn, L.B. Jorde, P.F.R. Little and S.
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Dong, Q. & Brendel, V. (2005) Computational
identification of related proteins: BLAST, PSI-BLAST, and other
tools. In J.M. Walker (ed.), The Proteomics Protocols
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Schlueter, S.D., Wilkerson, M.D., Huala, E., Rhee, S.Y. &
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the Arabidopsis thaliana genome.Trends Plant Sci. 10,
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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
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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.
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Genomics, pp. 255-266. Am. Oil Chem. Soc. Press, Champaign, IL,
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Baran, S., Lawrence, C.J. & Brendel, V. (2004) PGROP - A
gateway to plant genome research 'outreach' programs and
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Brendel, V., Xing, L. & Zhu, W. (2004) Gene structure
prediction from consensus spliced alignment of multiple ESTs
matching the same genomic locus.Bioinformatics20, 1157-1169. [PubMed
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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.
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ID: 14681441]
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., 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.
