| Year |
Citation |
Score |
| 2021 |
Policastro RA, McDonald DJ, Brendel VP, Zentner GE. Flexible analysis of TSS mapping data and detection of TSS shifts with TSRexploreR. Nar Genomics and Bioinformatics. 3: lqab051. PMID 34250478 DOI: 10.1093/nargab/lqab051 |
0.351 |
|
| 2021 |
Luo D, Huguet-Tapia JC, Raborn RT, White FF, Brendel VP, Yang B. The resistance gene guards the rice susceptibility gene against exploitation by the bacterial blight pathogen. Plant Communications. 2: 100164. PMID 34027391 DOI: 10.1016/j.xplc.2021.100164 |
0.746 |
|
| 2020 |
Policastro RA, Raborn RT, Brendel VP, Zentner GE. Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq. Genome Research. PMID 32660958 DOI: 10.1101/gr.261545.120 |
0.756 |
|
| 2019 |
McCarthy TW, Chou HC, Brendel VP. SRAssembler: Selective Recursive local Assembly of homologous genomic regions. Bmc Bioinformatics. 20: 371. PMID 31266441 DOI: 10.1186/s12859-019-2949-4 |
0.351 |
|
| 2019 |
Raborn RT, Brendel VP. Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes. Methods in Molecular Biology (Clifton, N.J.). 1858: 99-116. PMID 30414114 DOI: 10.1007/978-1-4939-8775-7_9 |
0.763 |
|
| 2017 |
Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, et al. The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiology. 175: 1499-1509. PMID 29208732 DOI: 10.1104/Pp.17.01490 |
0.331 |
|
| 2016 |
Raborn RT, Spitze K, Brendel VP, Lynch M. Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex. Genetics. PMID 27585846 DOI: 10.1534/Genetics.116.193334 |
0.749 |
|
| 2016 |
Duvick J, Standage DS, Merchant N, Brendel VP. xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud. The Plant Cell. 28: 840-54. PMID 27020957 DOI: 10.1105/Tpc.15.00933 |
0.336 |
|
| 2016 |
Raborn RT, Spitze K, Brendel V, Lynch M. Promoter architecture and sex-specific gene expression in the microcrustacean Daphnia pulex revealed by profiling of 5’-mRNA ends F1000research. 5. DOI: 10.7490/F1000Research.1112602.1 |
0.359 |
|
| 2014 |
Rauch HB, Patrick TL, Klusman KM, Battistuzzi FU, Mei W, Brendel VP, Lal SK. Discovery and expression analysis of alternative splicing events conserved among plant SR proteins. Molecular Biology and Evolution. 31: 605-13. PMID 24356560 DOI: 10.1093/Molbev/Mst238 |
0.383 |
|
| 2012 |
Standage DS, Brendel VP. ParsEval: parallel comparison and analysis of gene structure annotations. Bmc Bioinformatics. 13: 187. PMID 22852583 DOI: 10.1186/1471-2105-13-187 |
0.339 |
|
| 2009 |
Wilkerson MD, Ru Y, Brendel VP. Common introns within orthologous genes: Software and application to plants Briefings in Bioinformatics. 10: 631-644. PMID 19933210 DOI: 10.1093/bib/bbp051 |
0.336 |
|
| 2008 |
Sparks ME, Brendel V. MetWAMer: eukaryotic translation initiation site prediction. Bmc Bioinformatics. 9: 381. PMID 18801175 DOI: 10.1186/1471-2105-9-381 |
0.426 |
|
| 2008 |
Ru Y, Wang BB, Brendel V. Spliceosomal proteins in plants Current Topics in Microbiology and Immunology. 326: 1-15. PMID 18630744 DOI: 10.1007/978-3-540-76776-3_1 |
0.375 |
|
| 2008 |
Tasma IM, Brendel V, Whitham SA, Bhattacharyya MK. Expression and evolution of the phosphoinositide-specific phospholipase C gene family in Arabidopsis thaliana. Plant Physiology and Biochemistry : Ppb / SociéTé FrançAise De Physiologie VéGéTale. 46: 627-37. PMID 18534862 DOI: 10.1016/J.Plaphy.2008.04.015 |
0.38 |
|
| 2008 |
Wang BB, O'toole M, Brendel V, Young ND. Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes Bmc Plant Biology. 8. PMID 18282305 DOI: 10.1186/1471-2229-8-17 |
0.384 |
|
| 2008 |
Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V. PlantGDB: a resource for comparative plant genomics. Nucleic Acids Research. 36: D959-65. PMID 18063570 DOI: 10.1093/Nar/Gkm1041 |
0.357 |
|
| 2007 |
Brendel V. Gene Structure Annotation at PlantGDB. Methods in Molecular Biology (Clifton, N.J.). 406: 521-33. PMID 18287710 DOI: 10.1007/978-1-59745-535-0_25 |
0.412 |
|
| 2007 |
Brendel V, Kurtz S, Pan X. Visualization of syntenic relationships with SynBrowse. Methods in Molecular Biology (Clifton, N.J.). 396: 153-63. PMID 18025692 DOI: 10.1007/978-1-59745-515-2_11 |
0.406 |
|
| 2007 |
Dong Q, Wilkerson MD, Brendel V. Tracembler--software for in-silico chromosome walking in unassembled genomes. Bmc Bioinformatics. 8: 151. PMID 17490482 DOI: 10.1186/1471-2105-8-151 |
0.431 |
|
| 2006 |
Schlueter SD, Wilkerson MD, Dong Q, Brendel V. xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features. Genome Biology. 7: R111. PMID 17116260 DOI: 10.1186/Gb-2006-7-11-R111 |
0.421 |
|
| 2006 |
Wilkerson MD, Schlueter SD, Brendel V. yrGATE: A web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes Genome Biology. 7. PMID 16859520 DOI: 10.1186/Gb-2006-7-7-R58 |
0.415 |
|
| 2006 |
Wang BB, Brendel V. Genomewide comparative analysis of alternative splicing in plants. Proceedings of the National Academy of Sciences of the United States of America. 103: 7175-80. PMID 16632598 DOI: 10.1073/Pnas.0602039103 |
0.374 |
|
| 2006 |
Wang BB, Brendel V. Molecular characterization and phylogeny of U2AF35 homologs in plants. Plant Physiology. 140: 624-36. PMID 16407443 DOI: 10.1104/Pp.105.073858 |
0.394 |
|
| 2005 |
Sparks ME, Brendel V. Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants. Bioinformatics (Oxford, England). 21: iii20-30. PMID 16306388 DOI: 10.1093/Bioinformatics/Bti1205 |
0.401 |
|
| 2005 |
Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V. Comparative plant genomics resources at PlantGDB. Plant Physiology. 139: 610-8. PMID 16219921 DOI: 10.1104/Pp.104.059212 |
0.527 |
|
| 2005 |
Pan X, Stein L, Brendel V. SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics (Oxford, England). 21: 3461-8. PMID 15994196 DOI: 10.1093/Bioinformatics/Bti555 |
0.414 |
|
| 2005 |
Dong Q, Kroiss L, Oakley FD, Wang BB, Brendel V. Comparative EST analyses in plant systems. Methods in Enzymology. 395: 400-18. PMID 15984049 DOI: 10.1016/S0076-6879(05)95022-2 |
0.493 |
|
| 2005 |
Lawrence CJ, Seigfried TE, Brendel V. The maize genetics and genomics database. The community resource for access to diverse maize data. Plant Physiology. 138: 55-8. PMID 15888678 DOI: 10.1104/Pp.104.059196 |
0.321 |
|
| 2005 |
Schlueter SD, Wilkerson MD, Huala E, Rhee SY, Brendel V. Community-based gene structure annotation. Trends in Plant Science. 10: 9-14. PMID 15642518 DOI: 10.1016/J.Tplants.2004.11.002 |
0.413 |
|
| 2005 |
Gremme G, Brendel V, Sparks ME, Kurtz S. Engineering a software tool for gene structure prediction in higher organisms Information and Software Technology. 47: 965-978. DOI: 10.1016/J.Infsof.2005.09.005 |
0.328 |
|
| 2004 |
Wang BB, Brendel V. The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing. Genome Biology. 5: R102. PMID 15575968 DOI: 10.1186/gb-2004-5-12-r102 |
0.324 |
|
| 2004 |
Fernandes J, Dong Q, Schneider B, Morrow DJ, Nan GL, Brendel V, Walbot V. Genome-wide mutagenesis of Zea mays L. using RescueMu transposons. Genome Biology. 5: R82. PMID 15461800 DOI: 10.1186/Gb-2004-5-10-R82 |
0.452 |
|
| 2004 |
Baran SB, Lawrence CJ, Brendel V. Plant genome research outreach portal. A gateway to plant genome research "outreach" programs and activities. Plant Physiology. 134: 889. PMID 15020751 DOI: 10.1104/Pp.103.038414 |
0.335 |
|
| 2004 |
Brendel V, Xing L, Zhu W. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics (Oxford, England). 20: 1157-69. PMID 14764557 DOI: 10.1093/Bioinformatics/Bth058 |
0.487 |
|
| 2004 |
Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V. MaizeGDB, the community database for maize genetics and genomics. Nucleic Acids Research. 32: D393-7. PMID 14681441 DOI: 10.1093/Nar/Gkh011 |
0.418 |
|
| 2004 |
Dong Q, Schlueter SD, Brendel V. PlantGDB, plant genome database and analysis tools. Nucleic Acids Research. 32: D354-9. PMID 14681433 DOI: 10.1093/Nar/Gkh046 |
0.485 |
|
| 2003 |
Zhu W, Brendel V. Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome. Nucleic Acids Research. 31: 4561-72. PMID 12888517 DOI: 10.1093/Nar/Gkg492 |
0.38 |
|
| 2003 |
Schlueter SD, Dong Q, Brendel V. GeneSeqer@PlantGDB: Gene structure prediction in plant genomes. Nucleic Acids Research. 31: 3597-600. PMID 12824374 DOI: 10.1093/Nar/Gkg533 |
0.471 |
|
| 2003 |
Zhu W, Schlueter SD, Brendel V. Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping. Plant Physiology. 132: 469-84. PMID 12805580 DOI: 10.1104/Pp.102.018101 |
0.487 |
|
| 2003 |
Kalyanaraman A, Aluru S, Kothari S, Brendel V. Efficient clustering of large EST data sets on parallel computers Nucleic Acids Research. 31: 2963-2974. PMID 12771222 DOI: 10.1093/Nar/Gkg379 |
0.321 |
|
| 2003 |
Lal SK, Giroux MJ, Brendel V, Vallejos CE, Hannah LC. The maize genome contains a helitron insertion. The Plant Cell. 15: 381-91. PMID 12566579 DOI: 10.1105/Tpc.008375 |
0.465 |
|
| 2003 |
Dong Q, Roy L, Freeling M, Walbot V, Brendel V. ZmDB, an integrated database for maize genome research. Nucleic Acids Research. 31: 244-7. PMID 12519992 DOI: 10.1093/Nar/Gkg082 |
0.503 |
|
| 2003 |
Kalyanaraman A, Aluru S, Brendel V, Kothari S. Space and time efficient parallel algorithms and software for EST clustering Ieee Transactions On Parallel and Distributed Systems. 14: 1209-1221. DOI: 10.1109/Tpds.2003.1255634 |
0.315 |
|
| 2002 |
Chandler VL, Brendel V. The Maize Genome Sequencing Project. Plant Physiology. 130: 1594-7. PMID 12481042 DOI: 10.1104/Pp.015594 |
0.377 |
|
| 2002 |
Zhu W, Brendel V. Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions. Bioinformatics (Oxford, England). 18: 761-2. PMID 12050073 DOI: 10.1093/Bioinformatics/18.5.761 |
0.413 |
|
| 2002 |
Shoemaker R, Keim P, Vodkin L, Retzel E, Clifton SW, Waterston R, Smoller D, Coryell V, Khanna A, Erpelding J, Gai X, Brendel V, Raph-Schmidt C, Shoop EG, Vielweber CJ, et al. A compilation of soybean ESTs: Generation and analysis Genome. 45: 329-338. PMID 11962630 DOI: 10.1139/G01-150 |
0.484 |
|
| 2002 |
Brendel V, Kurtz S, Walbot V. Comparative genomics of Arabidopsis and maize: prospects and limitations. Genome Biology. 3: REVIEWS1005. PMID 11897028 DOI: 10.1186/Gb-2002-3-3-Reviews1005 |
0.424 |
|
| 2002 |
Fernandes J, Brendel V, Gai X, Lal S, Chandler VL, Elumalai RP, Galbraith DW, Pierson EA, Walbot V. Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization. Plant Physiology. 128: 896-910. PMID 11891246 DOI: 10.1104/Pp.010681 |
0.424 |
|
| 2002 |
Brendel V, Zhu W. Computational modeling of gene structure in Arabidopsis thaliana. Plant Molecular Biology. 48: 49-58. PMID 11860212 DOI: 10.1007/978-94-010-0448-0_4 |
0.471 |
|
| 2001 |
Xing L, Brendel V. Multi-query sequence BLAST output examination with MuSeqBox Bioinformatics. 17: 744-745. PMID 11524378 DOI: 10.1093/Bioinformatics/17.8.744 |
0.345 |
|
| 2000 |
Usuka J, Zhu W, Brendel V. Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics (Oxford, England). 16: 203-11. PMID 10869013 DOI: 10.1093/Bioinformatics/16.3.203 |
0.469 |
|
| 2000 |
Usuka J, Brendel V. Gene structure prediction by spliced alignment of genomic DNA with protein sequences: increased accuracy by differential splice site scoring. Journal of Molecular Biology. 297: 1075-1085. PMID 10764574 DOI: 10.1006/Jmbi.2000.3641 |
0.494 |
|
| 2000 |
Gai X, Lal S, Xing L, Brendel V, Walbot V. Gene discovery using the maize genome database ZmDB Nucleic Acids Research. 28: 94-96. PMID 10592191 DOI: 10.1093/Nar/28.1.94 |
0.498 |
|
| 1999 |
Latijnhouwers MJ, Pairoba CF, Brendel V, Walbot V, Carle-Urioste JC. Test of the combinatorial model of intron recognition in a native maize gene Plant Molecular Biology. 41: 637-644. PMID 10645723 DOI: 10.1023/A:1006329517740 |
0.387 |
|
| 1999 |
Chopra S, Brendel V, Zhang J, Axtell JD, Peterson T. Molecular characterization of a mutable pigmentation phenotype and isolation of the first active transposable element from Sorghum bicolor. Proceedings of the National Academy of Sciences of the United States of America. 96: 15330-5. PMID 10611384 DOI: 10.1073/Pnas.96.26.15330 |
0.411 |
|
| 1998 |
Brendel V, Kleffe J. Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA. Nucleic Acids Research. 26: 4748-57. PMID 9753745 DOI: 10.1093/Nar/26.20.4748 |
0.413 |
|
| 1998 |
Kleffe J, Hermann K, Vahrson W, Wittig B, Brendel V. GeneGenerator - A flexible algorithm for gene prediction and its application to maize sequences Bioinformatics. 14: 232-243. PMID 9614266 DOI: 10.1093/bioinformatics/14.3.232 |
0.329 |
|
| 1998 |
Brendel V, Kleffe J, Carle-Urioste JC, Walbot V. Prediction of splice sites in plant pre-mRNA from sequence properties Journal of Molecular Biology. 276: 85-104. PMID 9514728 DOI: 10.1006/Jmbi.1997.1523 |
0.362 |
|
| 1998 |
Ko CH, Brendel V, Taylor RD, Walbot V. U-richness is a defining feature of plant introns and may function as an intron recognition signal in maize. Plant Molecular Biology. 36: 573-83. PMID 9484452 DOI: 10.1023/A:1005932620374 |
0.4 |
|
| 1997 |
Carle-Urioste JC, Brendel V, Walbot V. A combinatorial role for exon, intron and splice site sequences in splicing in maize Plant Journal. 11: 1253-1263. PMID 9225466 DOI: 10.1046/J.1365-313X.1997.11061253.X |
0.418 |
|
| 1997 |
Brendel V, Brocchieri L, Sandler SJ, Clark AJ, Karlin S. Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms. Journal of Molecular Evolution. 44: 528-41. PMID 9115177 DOI: 10.1007/Pl00006177 |
0.561 |
|
| 1996 |
Kleffe J, Hermann K, Vahrson W, Wittig B, Brendel V. Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences Nucleic Acids Research. 24: 4709-4718. PMID 8972857 DOI: 10.1093/Nar/24.23.4709 |
0.367 |
|
| 1995 |
Karlin S, Weinstock GM, Brendel V. Bacterial classifications derived from recA protein sequence comparisons. Journal of Bacteriology. 177: 6881-93. PMID 7592482 DOI: 10.1128/Jb.177.23.6881-6893.1995 |
0.567 |
|
| 1994 |
Brendel V, Karlin S. Applications of statistical criteria in protein sequence analysis: case study of yeast RNA polymerase II subunits. Computers & Chemistry. 18: 251-3. PMID 7952895 DOI: 10.1016/0097-8485(94)85020-8 |
0.571 |
|
| 1993 |
Karlin S, Brendel V. Patchiness and correlations in DNA sequences. Science (New York, N.Y.). 259: 677-80. PMID 8430316 DOI: 10.1126/Science.8430316 |
0.495 |
|
| 1993 |
Sapolsky RJ, Brendel V, Karlin S. A comparative analysis of distinctive features of yeast protein sequences. Yeast (Chichester, England). 9: 1287-98. PMID 8154180 DOI: 10.1002/Yea.320091202 |
0.592 |
|
| 1992 |
Karlin S, Brendel V. Chance and statistical significance in protein and DNA sequence analysis. Science (New York, N.Y.). 257: 39-49. PMID 1621093 DOI: 10.1126/Science.1621093 |
0.581 |
|
| 1992 |
Karlin S, Brendel V, Bucher P. Significant similarity and dissimilarity in homologous proteins. Molecular Biology and Evolution. 9: 152-67. PMID 1552837 DOI: 10.1093/Oxfordjournals.Molbev.A040704 |
0.549 |
|
| 1992 |
Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S. Methods and algorithms for statistical analysis of protein sequences. Proceedings of the National Academy of Sciences of the United States of America. 89: 2002-6. PMID 1549558 DOI: 10.1073/Pnas.89.6.2002 |
0.573 |
|
| 1992 |
Brendel V. PROSET—a fast procedure to create non-redundant sets of protein sequences Mathematical and Computer Modelling. 16: 37-43. DOI: 10.1016/0895-7177(92)90150-J |
0.397 |
|
| 1991 |
Brendel V, Dohlman J, Blaisdell BE, Karlin S. Very long charge runs in systemic lupus erythematosus-associated autoantigens. Proceedings of the National Academy of Sciences of the United States of America. 88: 1536-40. PMID 1996354 DOI: 10.1073/Pnas.88.4.1536 |
0.513 |
|
| 1991 |
Karlin S, Bucher P, Brendel V, Altschul SF. Statistical methods and insights for protein and DNA sequences. Annual Review of Biophysics and Biophysical Chemistry. 20: 175-203. PMID 1867715 DOI: 10.1146/annurev.bb.20.060191.001135 |
0.477 |
|
| 1990 |
Brendel V, Beckmann JS, Trifonov EN. Linguistics of nucleotide sequences: morphology and comparison of vocabularies. Journal of Biomolecular Structure & Dynamics. 4: 11-21. PMID 3078230 DOI: 10.1080/07391102.1986.10507643 |
0.342 |
|
| 1990 |
Karlin S, Blaisdell BE, Brendel V. Identification of significant sequence patterns in proteins Methods in Enzymology. 183: 388-402. PMID 2179677 DOI: 10.1016/0076-6879(90)83026-6 |
0.538 |
|
| 1989 |
Karlin S, Brendel V. Charge configurations in viral proteins. Proceedings of the National Academy of Sciences of the United States of America. 85: 9396-400. PMID 2849101 DOI: 10.1073/Pnas.85.24.9396 |
0.51 |
|
| 1989 |
Brendel V, Karlin S. Too many leucine zippers? Nature. 341: 574-5. PMID 2797188 DOI: 10.1038/341574A0 |
0.44 |
|
| 1989 |
Brendel V, Karlin S. Association of charge clusters with functional domains of cellular transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 86: 5698-702. PMID 2569737 DOI: 10.1073/Pnas.86.15.5698 |
0.525 |
|
| 1989 |
Karlin S, Blaisdell BE, Mocarski ES, Brendel V. A method to identify distinctive charge configurations in protein sequences, with application to human herpesvirus polypeptides Journal of Molecular Biology. 205: 165-177. PMID 2538622 DOI: 10.1016/0022-2836(89)90373-2 |
0.533 |
|
| 1987 |
Brendel V, Segel LA. On modes of recombination, replication, and segregation of the higher plant mitochondrial genome Journal of Theoretical Biology. 125: 163-176. DOI: 10.1016/S0022-5193(87)80038-3 |
0.34 |
|
| 1986 |
Brendel V, Hamm GH, Trifonov EN. Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them. Journal of Biomolecular Structure & Dynamics. 3: 705-23. PMID 3078109 DOI: 10.1080/07391102.1986.10508457 |
0.416 |
|
| 1986 |
Beckmann S, Brendel V, Trifonov EN. Intervening sequences exhibit distinct vocabularyjacques Journal of Biomolecular Structure and Dynamics. 4: 391-400. PMID 2482751 DOI: 10.1080/07391102.1986.10506357 |
0.388 |
|
| 1985 |
Konopka AK, Brendel V. The missense errors in protein can be controlled by selective synonymous codon usage at the level of transcription. Biochimie. 67: 469-73. PMID 2992612 DOI: 10.1016/S0300-9084(85)80265-0 |
0.308 |
|
| 1984 |
Brendel V, Trifonov EN. A computer algorithm for testing potential prokaryotic terminators. Nucleic Acids Research. 12: 4411-27. PMID 6374619 DOI: 10.1093/Nar/12.10.4411 |
0.409 |
|
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