What's New

Fresh off the press:

Morandin, C., Brendel, V.P., Sundström, L.; Helanterä, H. & Mikheyev, A. (2019) Changes in gene DNA methylation and expression networks accompany caste specialization and age-related physiological changes in a social insect methylation. Molecular Ecology, 28, 1975-1993. [PubMed ID: 30809873] [online article] [PDF]

The future of computational genomics:

  Brendel, V.P. (2018) From small RNA discoveries to a new paradigm in computational genomics? New Phytol. 220, 659-660. [PubMed ID: 30324739] [online article] [PDF]

  Check out our new bgRAMOSE Jetstream image!


TSRchitect is now available as a Bioconductor R package!

Brendel group in the Indiana Daily Student news (Dec. 12, 2016)

Volker Brendel elected AAAS Fellow (Oct. 2016); IU News Release (Nov. 21, 2016)

Check out our github site!


The Brendel Group provides domain expertise to advise the Jetstream national science and engineering cloud project.

V. Brendel serves on the CyVerse External Advisory Board.

V. Brendel serves as Consulting Editor of The Plant Cell.

PlantGDB News:

xGDBvm on YouTube

Volker Brendel - List of Publications

Google Scholar Profile


In the press


Published papers (most recent publications first)


121. Daniel S Standage, Tim Lai & Volker P Brendel (2022) iLoci: Robust evaluation of genome content and organization for provisional and mature genome assemblies. Nucleic Acids Research Genomics and Bioinformatics 4, Issue 1, March 2022, lqac013, [PubMed ID: 35211671] [online article] [PDF] [BioRxiv pre-print] posted Oct. 4, 2021.
[Complete workflow and data repository] - if you really wish to download (744G) ...


120. Claire Morandin & Volker P. Brendel (2021) Tools and applications for integrative analysis of DNA methylation in social insects. Molecular Ecology Resources 00, 1-19. [PubMed ID: 34861105] [online article] [PDF] [BioRxiv pre-print] posted Aug. 20, 2021.
[Complete workflow and data repository] - if you really wish to download (5.1T) ...

119. Policastro, R.A., McDonald, D.J., Brendel, V.P. & Zentner, G.E. (2021) Flexible analysis of TSS mapping data and detection of TSS shifts with TSRexploreR. NAR Genomics and Bioinformatics 3, Issue 2, June 2021, lqab051. [PubMed ID: 34250478] [online article] [PDF] [BioRxiv pre-print] posted Feb. 15, 2021.

118. Luo, D., Huguet-Tapia, J.C., Raborn, R.T., White, F.F., Brendel, V.P. & Yang, B. (2021) The Xa7 resistance gene guards the rice susceptibility gene SWEET14 against exploitation by the bacterial blight pathogen. Plant Communications 2, 100164. [PubMed ID: 34027391] [online article] [PDF]


117. Policastro, R.A., Raborn, R.T., Brendel, V.P. & Zentner, G.E. (2020) Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq. Genome Research 30, 910--823. [PubMed ID: 32660958] [online article] [PDF] [BioRxiv pre-print] posted Januay 16, 2021.


116. McCarthy, T.W., Chou, H.C. & Brendel, V.P. (2019) SRAssembler: Selective Recursive local Assembly of homologous genomic regions. BMC Bioinformatics 20, 371. [PubMed ID: 31266441] [online article] [PDF]

115. Morandin, C., Brendel, V.P., Sundström, L.; Helanterä, H. & Mikheyev, A. (2019) Changes in gene DNA methylation and expression networks accompany caste specialization and age-related physiological changes in a social insect methylation. Molecular Ecology 28, 1975-1993. [PubMed ID: 30809873] [online article] [PDF]

114. Raborn, R.T. & Brendel, V.P. (2019) Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes In Insect Genomics: Methods and Protocols, S.J. Brown & Michael E. Pfrender (eds.), Methods in Molecular Biology 1858, 99-116. [PubMed ID: 30414114]


113. Brendel, V.P. (2018) From small RNA discoveries to a new paradigm in computational genomics? New Phytol. 220, 659-660. [PubMed ID: 30324739] [online article] [PDF]


112. Friesner, J., Assmann, S.M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., Buell, C.R., Bucksch, A., Busch, W., Demura, T., Dinneny, J.R., Doherty, C.J., Eveland, A.L., Falter-Braun, P., Gehan, M.A., Gonzales, M., Grotewold, E., Gutierrez, R., Kramer, U., Krouk, G., Ma, S., Markelz, R.J.C., Megraw, M., Meyers, B.C., Murray, J.A.H., Provart, N.J., Rhee, S., Smith, R., Spalding, E.P., Taylor, C., Teal, T.K., Torii, K.U., Town, C., Vaughn, M., Vierstra, R., Ware, D., Wilkins, O., Williams, C. & Brady, S.M. (2017) The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology Plant Physiology 175, 1499-1509. [PubMed ID: 29208732] [online article] [PDF]

111. Raborn, R.T., Sridharan, K. & Brendel, V.P. (2017). TSRchitect: Promoter identification from large-scale TSS profiling data. [doi: 10.18129/B9.bioc.TSRchitect]


110. Raborn, R.T., Spitze, K., Brendel, V.P. & Lynch, M. (2016) Promoter architecture and sex-specific gene expression in Daphnia pulex. Genetics 204, 593-612. [PubMed ID: 27585846] [online article] [PDF]

109. Duvick, J., Standage, D.S., Merchant, N. & Brendel, V.P. (2016) xGDBvm: A Web GUI-driven workflow for annotating eukaryotic genomes in the cloud. The Plant Cell 28, 840-854. [PubMed ID: 27020957] [online article] [PDF]

108. Standage, D.S., Berens, A.J., Glastad, K.M., Severin, A.J., Brendel, V.P. & Toth, A.L. (2016) Genome, transcriptom and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect. Molecular Ecology 25, 1769-1784. [PubMed ID: 26859767] [online article] [PDF]


107. Rauch, H.B., Patrick, T.L., Klusman, K.M., Battistuzzi, F.U., Mei, W., Brendel, V.P. & Lal, S.K. (2014) Discovery and Expression Analysis of Alternative Splicing Events Conserved among Plant SR Proteins. Mol. Biol. Evol. 31, 605-613. [PubMed ID: 24356560] [online article] [PDF]


106. Yi, G., Brendel, V.P., Shu, C., Li, P., Palanathan, S. & Kao, C.C. (2013) Single Nucleotide Polymorphisms of Human STING Can Affect Innate Immune Response to Cyclic Dinucleotides. PLoS One 8, e77846. [PubMed ID: 24204993] [online article] [PDF]


105. Standage, D.S. & Brendel, V.P. (2012) ParsEval: parallel comparison and analysis of gene structure annotations. BMC Bioinformatics 13, 187. [PubMed ID: 22852583] [online article] [PDF]

104. Doyle, E.L., Booher, N.J., Standage, D.S., Voytas, D.F., Brendel, V.P., VanDyk, J.K. & Bogdanove, A.J. (2012) TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucl. Acids Res. 40, W117-W122. [PubMed ID: 22693217] [online article] [PDF]


103. Bogdanove, A.J., Koebnik, R., Lu, H., Furutani, A. Angiuoli, S.V. Patil, P.B., Van Sluys, M.-A. Ryan, R.P., Meyer, D.F., Han, S., Aparna, G., Rajaram, M., Delcher, A.L., Phillippy, A.M., Puiu, D., Schatz, M.C., Shumway, M., Sommer, D.D., Trapnell, C., Benahmed, F., Dimitrov, G., Madupu, R., Radune, D., Sullivan, S., Jha, G., Ishihara, H., Lee, S.-W., Pandey, A., Sharma, V., Sriariyanun, M., Szurek, B., Vera-Cruz, C.M., Dorman, K.S., Ronald, P.C., Verdier, V., Dow, J.M., Sonti, R.V., Tsuge, S., Brendel, V.P., Rabinowicz, P.D., Leach, J.E., White, F.F. & Salzberg, S.L. (2011) Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. J. Bact. 193, 5450-5464. [PubMed ID: 21784931] [online article] [PDF]

102. Lushbough, C.M., Jennewein, D.M. & Brendel, V.P. (2011) The BioExtract Server: a Web-based bioinformatic workflow platform. Nucl. Acids Res., 2011; doi: 10.1093/nar/gkr286. [PubMed ID: 21546552] [online article] [PDF]


101. Lushbough, C.M. & Brendel, V.P. (2010) An overview of the BioExtract Server: a distributed, Web-based system for genomic analysis. In Advances in Computational Biology, H.R. Arabnia (ed.), Advances in Experimental Medicine and Biology 680, 361-369. [PubMed ID: 20865520] [online abstract] [reprint request]

100. Vollbrecht, E., Duvick, J., Schares, J.P., Ahern, K.R., Deewatthanawong, P., Xu, L., Conrad, L.J., Kikuchi, K., Kubinec, T.A., Hall, B.D., Weeks, R., Unger-Wallace, E., Muszynski, M., Brendel, V.P. & Brutnell, T.P. (2010) Genome-wide distribution of transposed Dissociation elements in maize. Plant Cell 22, 1667-1685. [PubMed ID: 20581308] [online article] [PDF] [commentary]

99. Lushbough, C., Bergman, M.K., Lawrence, C.J., Jennewein, D. & Brendel, V. (2010) BioExtract Server - an integrated workflow-enabling system to access and analyze heterogeneous, distributed biomolecular data. IEEE/ACM Transactions Comp. Biol. Bioinformatics 7, 7-24. [PubMed ID: 20150665] [online abstract] [reprint request]


98. Sen, T.Z., Andorf, C.M., Schaeffer, M.L., Harper, L.C., Sparks, M.E., Duvick, J., Brendel, V.P., Cannon, E., Campbell, D.A. & Lawrence, C.J. (2009) MaizeGDB becomes ‘sequence-centric’. Database 2009, bap020. [PubMed ID: not yet available] [online article] [PDF]

97. Wilkerson, M.D., Ru, Y. & Brendel, V.P. (2009) Common introns within orthologous genes: software and application to plants. Briefings Bioinformatics 10, 631-644. [PubMed ID: 19933210] [online article] [PDF]

96. Ahern, K.R., Deewatthanawong, P., Schares, J., Muszynski, M., Weeks, R., Vollbrecht, E., Duvick, J., Brendel, V.P. & Brutnell, T.P. (2009) Regional mutagenesis using Dissociation in maize. Methods 49, 248-254. [PubMed ID: 19394430] [online abstract] [reprint request]


95. Agrawal, A., Brendel, V.P. & Huang, X. (2008) Pairwise statistical significance and empirical determination of effective gap opening penalties for protein local sequence alignment. Int. J. of Computational Biol. and Drug Design 1, 347-367. [PubMed ID: 20063463] [online abstract] [reprint request]

94. 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 3, e3828. [PubMed ID: 19043590] [online article] [PDF] [cited in PMC]

93. Sparks, M.E. & Brendel, V. (2008) MetWAMer: eukaryotic translation initiation site prediction. BMC Bioinformatics 9, 381. [PubMed ID: 18801175] [online article] [PDF] [cited in PMC]

92. 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, 627-637. [PubMed ID: 18534862] [online abstract] [reprint request] [cited in PMC]

91. Agrawal, A., Brendel, V. & Huang, X. (2008) Pairwise statistical significance versus database statistical significance for local alignment of protein sequences. In I.I. Măndoiu, 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] [reprint request]

90. 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. [PubMed ID: 18630744] [PDF]

89. 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] [PDF] [cited in PMC]

88. 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] [PDF] [cited in PMC]


87. 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, 302-312. [PubMed ID: 20054995] [online abstract] [reprint request]

86. 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] [reprint request] [cited in PMC]

85. 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] [reprint request]

84. 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] [reprint request]

83. 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 article] [PDF] [cited in PMC]


82. 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, R111. [PubMed ID: 17116260] [online article] [PDF] [cited in PMC]

81. 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] [online article] [PDF] [cited in PMC]

80. 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] [online article] [PDF] [cited in PMC]

79. Wang, B.-B. & Brendel, V. (2006) Molecular characterization and phylogeny of U2AF1 homologs in plants. Plant Physiol. 140, 624-636. [PubMed ID: 16407443] [online article] [PDF] [cited in PMC]


78. 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] [reprint request]

77. 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]

76. 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] [online abstract] [PDF] [cited in PMC]

75. 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] [online article] [PDF [cited in PMC]

74. Pan, X., Stein, L. & Brendel, V. (2005) SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics 21, 3461-3468. [PubMed ID: 15994196] [online article] [PDF] [cited in PMC]

73. Lawrence, C.J., Seigfried, T.E. & Brendel, V. (2005) The maize genetics and genomics database. The community resource for access to diverse maize data. Plant Physiol. 138, 55-58. [PubMed ID: 15888678] [online article] [PDF] [cited in PMC]

72. 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] [cited in PMC]

71. 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. [online abstract] [PDF]

70. 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]

69. 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] [online abstract] [reprint request] [cited in PMC]


68. 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] [PDF] [cited in PMC]

67. 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] [online article] [PDF] [cited in PMC]

66. 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.

65. 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] [online article] [PDF] [cited in PMC]

64. 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] [online abstract] [PDF] [cited in PMC]

63. 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] [online article] [PDF] [cited in PMC]

62. Dong, Q., Schlueter, S.D. & Brendel, V. (2004) PlantGDB, plant genome database and analysis tools. Nucl. Acids Res. 32, D354-D359. [PubMed ID: 14681433] [online article] [PDF] [cited in PMC]


61. 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. [online abstract] [reprint request]

60. Zhu, W. & Brendel, V. (2003) Identification, characterization, and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome. Nucl. Acids Res. 31, 4561-4572. [PubMed ID: 12888517] [online article] [PDF] [cited in PMC]

59. Schlueter, S.D., Dong, Q. & Brendel, V. (2003) GeneSeqer@PlantGDB - gene structure prediction in plant genomes. Nucl. Acids Res. 31, 3597-3600. [PubMed ID: 12824374] [online article] [PDF] [cited in PMC]

58. Zhu, W., Schlueter, S.D. & Brendel, V. (2003) Refined annotation of the Arabidopsis thaliana genome by complete EST mapping. Plant Physiol. 132, 469-484. [PubMed ID: 12805580] [online article] [PDF] [cited in PMC]

57. Kalyanaraman, A., Aluru, S., Kothari, S. & Brendel, V. (2003) Efficient clustering of large EST data sets on parallel computers. Nucl. Acids Res. 31, 2963-2974. [PubMed ID: 12771222] [online article] [PDF] [cited in PMC]

56. Lal, S.K., Giroux, M.J., Brendel, V., Vallejos, C.E. & Hannah, L.C. (2003) The maize genome contains a Helitron insertion. Plant Cell 15, 381-391. [PubMed ID: 12566579] [online article] [PDF] [commentary] [cited in PMC]

55. Dong, Q., Roy, L., Freeling, M., Walbot, V. & Brendel, V. (2003) ZmDB, an integrated database for maize genome research. Nucl. Acids Res. 31, 244-247. [PubMed ID: 12519992] [online article] [PDF] [cited in PMC]


54. Chandler, V.L. & Brendel, V. (2002) The maize genome sequencing project. Plant Physiol. 130, 1594-1597. [PubMed ID: 12481042] [online article] [PDF] [cited in PMC]

53. Brendel, V. (2002) Integration of data management and analysis for genome research. In S. Schubert, B. Reusch and N. Jesse (eds.), "Informatik bewegt". Lecture Notes in Informatics (LNI) - Proceedings P-20, 10-21. [PDF]

52. Zhu, W. & Brendel, V. (2002) Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions. Bioinformatics 18, 761-762. [PubMed ID: 12050073] [online abstract] [PDF] [cited in PMC]

51. Fernandes, J., Brendel, V., Gai, X., Lal, S., Chandler, V.L., Elumalai, R.P., Galbraith, D.W., Pierson, E.A. & Walbot, V. (2002) Comparison of RNA expression profiles based on maize EST frequency analysis and microarray hybridization. Plant Physiol. 128, 896-910. [PubMed ID: 11891246] [online article] [PDF] [cited in PMC]

50. Shoemaker, R., Keim, P., Vodkin, L., Retzel, E., Clifton, S.W., Waterston, R., Smoller, D., Coryell, V., Khanna, A., Erpelding, J., Gai, X., Brendel, V., Raph-Schmidt, C., Shoop, E.G., Vielweber, C.J., Schmatz, M., Pape, D., Bowers, Y., Theising, B., Martin, J., Dante, M., Wylie, T. & Granger, C. (2002) A compilation of soybean ESTs: Generation and analysis. Genome 45, 329-338. [PubMed ID: 11962630] [online abstract] [PDF] [cited in PMC]

49. Brendel, V., Kurtz, S. & Walbot, V. (2002) Comparative genomics of Arabidopsis and maize: prospects and limitations. Genome Biol. 3, reviews1005.1-1005.6. [PubMed ID: 11897028] [online article] [PDF] [cited in PMC]

48. Brendel, V. & Zhu, W. (2002) Computational modeling of gene structure in Arabidopsis thaliana. Plant Mol. Biol. 48, 49-58. [PubMed ID: 11860212] [online abstract] [PDF] [cited in PMC]


47. Xing, L. & Brendel, V. (2001) Multi-query sequence BLAST output examination with MuSeqBox. Bioinformatics 17, 744-745. [PubMed ID: 11524378] [online abstract] [PDF] [cited in PMC]


46. Usuka, J. & Brendel, V. (2000) Gene structure prediction by spliced alignment of genomic DNA with protein sequences: Increased accuracy by differential splice site scoring. J. Mol. Biol. 297, 1075-1085. [PubMed ID: 10764574] [online abstract] [reprint request] [cited in PMC]

45. Usuka, J., Zhu, W. & Brendel, V. (2000) Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics 16, 203-211. [PubMed ID: 10869013] [PDF] [online abstract] [PDF] [cited in PMC]

44. Gai, X., Lal, S., Xing, L., Brendel, V. & Walbot, V. (2000) Gene discovery using the maize genome database ZmDB. Nucl. Acids Res. 28, 94-96. [PubMed ID: 10592191] [online article] [PDF] [cited in PMC]


43. Chopra, S., Brendel, V., Zhang, J., Axtell, J.D. & Peterson, T. (1999) Molecular characterization of a mutable pigmentation phenotype and isolation of the first active transposable element from Sorghum bicolor. Proc. Natl. Acad. Sci. USA 96, 15330-15335. [PubMed ID: 10611384] [online article] [PDF] [cited in PMC]

42. Latijnhouwers, M.J., Pairoba, C.F., Brendel, V., Walbot, V. & Carle-Urioste, J.C. (1999) Test of the combinatorial model of intron recognition in a native maize gene. Plant Mol. Biol. 41, 637-644. [PubMed ID: 10645723] [online abstract] [PDF] [cited in PMC]

41. Shafer, R.W., Hsu, P., Patick, A.K., Craig, C. & Brendel, V. (1999) Identification of biased amino acid substitution patterns in human immunodeficiency virus type I isolates from patients treated with protease inhibitors. J. Virol. 73, 6197-6202. [PubMed ID: 10364383] [online abstract] [PDF] [cited in PMC]


40. Brendel, V. & Kleffe, J. (1998) Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA. Nucl. Acids Res. 26, 4748-4757. [PubMed ID: 9753745] [online article] [PDF] [cited in PMC]

39. Kleffe, J., Hermann, K., Vahrson, W., Wittig, B. & Brendel, V. (1998) GeneGenerator - a flexible algorithm for gene prediction and its application to maize sequences. Bioinformatics 14, 232-243. [PubMed ID: 9614266] [online abstract] [PDF] [cited in PMC]

38. Brendel, V., Carle-Urioste, J.C. & Walbot, V. (1998) Intron recognition in plants. In J. Bailey-Serres and D.R. Gallie (eds.), A look beyond transcription: Mechanisms determining mRNA stability and translation in plants, pp. 20-28. Am. Soc. Plant Physiol., Rockville, MD, U.S.A.

37. Ko, C.H., Brendel, V., Taylor, R.D. & Walbot, V. (1998) U-richness is a defining feature of plant introns and may function as an intron recognition signal in maize. Plant Mol. Biol. 36, 573-583. [PubMed ID: 9484452] [online abstract] [PDF] [cited in PMC]

36. Brendel, V., Kleffe, J., Carle-Urioste, J.C. & Walbot, V. (1998) Prediction of splice sites in plant pre-mRNA from sequence properties. J. Mol. Biol. 276, 85-104. [PubMed ID: 9514728] [online abstract] [reprint request] [cited in PMC]


35. Carle-Urioste, J.C., Brendel, V. & Walbot, V. (1997) A combinatorial role for exon, intron and splice site sequences in splicing in maize. Plant J. 11, 1253-1263. [PubMed ID: 9225466] [online abstract] [PDF] [cited in PMC]

34. Brendel, V., Brocchieri, L., Sandler, S.J., Clark, A.J. & Karlin, S. (1997) Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms. J. Mol. Evol. 44, 528-541. [PubMed ID: 9115177] [online abstract] [PDF] [cited in PMC]


33. Kleffe, J., Hermann, K., Vahrson, W., Wittig, B. & Brendel, V. (1996) Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences. Nucl. Acids Res. 24, 4709-4718. [PubMed ID: 8972857] [online article] [PDF] [cited in PMC]

32. Karlin, S. & Brendel, V. (1996) New directions in education: Computational tools for the molecular biologist and biological sources for the mathematician. In K.J. Arrow, R.W. Cottle, B.C. Eaves, and I. Olkin (eds.), Education in a Research University, Stanford University Press, Stanford, CA, pp. 407-427.

31. Brendel, V. (1996) Statistical analysis of protein sequences. In H. Villar (ed.), Advances in Computational Biology, Vol.~2, JAI Press, Greenwich, CT, USA, pp. 121-160.


30. Karlin, S., Weinstock, G. & Brendel, V. (1995) Bacterial classifications derived from RecA protein sequence comparisons. J. Bacteriol. 177, 6881-6893. [PubMed ID: 7592482] [online abstract] [PDF] [cited in PMC]


29. Brendel, V. & Karlin, S. (1994) Applications of statistical criteria in protein sequence analysis: case study of yeast RNA polymerase II subunits. Computers & Chemistry 18, 251-253. [PubMed ID: 7952895] [online abstract] [reprint request] [cited in PMC]


28. Sapolsky, R.J., Brendel, V. & Karlin, S. (1993) A comparative analysis of distinctive features of yeast protein sequences. Yeast 9, 1287-1298. [PubMed ID: 8154180] [cited in PMC]

27. Brendel, V. & Perelson, A.S. (1993) Quantitative model of ColE1 plasmid copy number control. J. Mol. Biol. 229, 860-872. [PubMed ID: 7680381] [online abstract] [reprint request] [cited in PMC]

26. Karlin, S. & Brendel, V. (1993) Patchiness and correlations in DNA sequences. Science 259, 677-680. [PubMed ID: 8430316] [online abstract] [reprint request] [cited in PMC]


25. Karlin, S. & Brendel, V. (1992) Chance and statistical significance in protein and DNA sequence analysis. Science 257, 39-49. [PubMed ID: 1621093] [online abstract] [reprint request] [cited in PMC]

24. Brendel, V. (1992) PROSET - a fast procedure to create non-redundant sets of protein sequences. Mathl. Comput. Modelling 16, No. 6/7, 37-43.

23. Brendel, V., Bucher, P., Nourbakhsh, I.R., Blaisdell, B.E. & Karlin, S. (1992) Methods and algorithms for statistical analysis of protein sequences. Proc. Natl. Acad. Sci. USA 89, 2002-2006. [PubMed ID: 1549558] [online abstract] [PDF] [cited in PMC]

22. Karlin, S., Brendel, V. & Bucher, P. (1992) Significant similarity and dissimilarity in homologous proteins. Mol. Biol. Evol. 9, 152-167. [PubMed ID: 1552837] [online abstract] [PDF] [cited in PMC]


21. Brendel, V. & Levine, H. (1991) In defence of Fourier. Nature 351, 528. [reprint request]

20. Karlin, S., Bucher, P., Brendel, V. & Altschul, S.F. (1991) Statistical methods and insights for protein and DNA sequences. Annu. Rev. Biophys. Biophys. Chem. 20, 175-203. [PubMed ID: 1867715] [cited in PMC]

19. Brendel, V., Dohlman, J., Blaisdell, B.E. & Karlin, S. (1991) Very long charge runs in systemic lupus erythematosus associated autoantigens. Proc. Natl. Acad. Sci. USA 88, 1536-1540. [PubMed ID: 1996354] [online abstract] [PDF] [cited in PMC]


18. Karlin, S., Blaisdell, B.E. & Brendel, V. (1990) Identification of significant sequence patterns in proteins. Methods Enzymol. 183, 388-402. [PubMed ID: 2179677] [cited in PMC]

17. Karlin, S. & Brendel, V. (1990) Charge configurations in oncogene products and transforming proteins. Oncogene 5, 85-95. [PubMed ID: 2181379] [cited in PMC]


16. Brendel, V. & Karlin, S. (1989) Too many leucine zippers? Nature 341, 574-575. [PubMed ID: 2797188] [reprint request] [cited in PMC]

15. Perelson, A.S. & Brendel, V. (1989) Kinetics of complementary RNA-RNA interaction involved in plasmid ColE1 copy number control. J. Mol. Biol. 208, 245-255. [PubMed ID: 2475639] [online abstract] [reprint request] [cited in PMC]

14. Brendel, V. & Karlin, S. (1989) Association of charge clusters with functional domains of cellular transcription factors. Proc. Natl. Acad. Sci. USA 86, 5698-5702. [PubMed ID: 2569737] [online abstract] [PDF] [cited in PMC]

13. Karlin, S., Blaisdell, B.E., Mocarski, E.S. & Brendel, V. (1989) A method to identify distinctive charge configurations in protein sequences, with application to human herpesvirus polypeptides. J. Mol. Biol. 205, 165-177. [PubMed ID: 2538622] [online abstract] [reprint request] [cited in PMC]


12. Karlin, S. & Brendel, V. (1988) Charge configurations in viral proteins. Proc. Natl. Acad. Sci. USA 85, 9396-9400. [PubMed ID: 2849101] [online abstract] [PDF] [cited in PMC]


11. Brendel, V. & Perelson, A.S. (1987) Kinetic analysis of adsorption processes. SIAM J. Appl. Math. 47, 1306-1319.

10. Brendel, V. & Perelson, A.S. (1987) A note on stochastic models for bacterial adhesion. J. Theor. Biol. 126, 247-249. [online abstract]

9. Brendel, V. & Segel, L.A. (1987) On modes of recombination, replication & segregation of the higher plant mitochondrial genome. J. Theor. Biol. 125, 163-176. [online abstract]


8. Beckmann, J.S., Brendel, V. & Trifonov, E.N. (1986) Intervening sequences exhibit distinct vocabulary. J. Biomol. Struct. Dynam. 4, 391-400. [PubMed ID: 2482751] [cited in PMC]

7. Brendel, V., Beckmann, J.S. & Trifonov, E.N. (1986) Linguistics of nucleotide sequences: morphology and comparison of vocabularies. J. Biomol. Struct. Dynam. 4, 11-21. [PubMed ID: 3078230] [cited in PMC]

6. Brendel, V., Hamm, G.H. & Trifonov, E.N. (1986) Terminators of transcription with RNA polymerase from Escherichia coli: What they look like and how to find them. J. Biomol. Struct. Dynam. 3, 705-723. [PubMed ID: 3078109] [cited in PMC]


5. Konopka, A.K. & Brendel, V. (1985) The missense errors in protein can be controlled by selective synonymous codon usage at the level of transcription. Biochimie 67, 469-473. [PubMed ID: 2992612]

4. Brendel, V. (1985) Mapping of transcription terminators of bacteriophages Φx174 and G4 by sequence analysis. J. Virol. 53, 340-342. [PubMed ID: 3155555] [online abstract] [PDF] [cited in PMC]


3. Brendel, V. & Trifonov, E.N. (1984) Computer-aided mapping of DNA-protein interaction sites. CODATA Bulletin 56, 17-20; reproduced in P.S. Glaeser (ed.), The Role of Data in Scientific Progress, pp. 115-118. ElsevierNorth-Holland Publishing Co., Amsterdam, 1985.

2. Brendel, V. & Trifonov, E.N. (1984) A computer algorithm for testing potential prokaryotic terminators. Nucl. Acids Res. 12, 4411-4427. [PubMed ID: 6374619] [online abstract] [scanned PDF from PMC] [cited in PMC]

1. Brendel, V. & Busse, H.G. (1984) Genome structure described by formal languages. Nucl. Acids Res. 12, 2561-2568. [PubMed ID: 6200832] [online abstract] [scanned PDF from PMC] [cited in PMC]


Trifonov, E.N. & Brendel, V. GNOMIC - Dictionary of Genetic Codes. Balaban Publishers, Rehovot, Philadelphia, 1986; reprint 1987, VCH, Weinheim, Deerfield Beach.