Recent papers:
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, https://doi.org/10.1093/nargab/lqac013 [PubMed ID: 35211671] [online article] [PDF]
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 github site!
Group:
PlantGDB News:
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. https://doi.org/10.1111/1755-0998.13566
[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]
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]
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] [PDF]
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] [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] [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]
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.