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Items: 1 to 50 of 103

1.

SRAssembler: Selective Recursive local Assembly of homologous genomic regions.

McCarthy TW, Chou HC, Brendel VP.

BMC Bioinformatics. 2019 Jul 2;20(1):371. doi: 10.1186/s12859-019-2949-4.

2.

Changes in gene DNA methylation and expression networks accompany caste specialization and age-related physiological changes in a social insect.

Morandin C, Brendel VP, Sundström L, Helanterä H, Mikheyev AS.

Mol Ecol. 2019 Apr;28(8):1975-1993. doi: 10.1111/mec.15062. Epub 2019 Apr 29.

PMID:
30809873
3.

Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes.

Raborn RT, Brendel VP.

Methods Mol Biol. 2019;1858:99-116. doi: 10.1007/978-1-4939-8775-7_9.

PMID:
30414114
4.

From small RNA discoveries to a new paradigm in computational genomics?

Brendel VP.

New Phytol. 2018 Nov;220(3):659-660. doi: 10.1111/nph.15478. No abstract available.

5.

The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology.

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, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM.

Plant Physiol. 2017 Dec;175(4):1499-1509. doi: 10.1104/pp.17.01490. No abstract available.

6.

Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex.

Raborn RT, Spitze K, Brendel VP, Lynch M.

Genetics. 2016 Oct;204(2):593-612. Epub 2016 Aug 31.

7.

xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.

Duvick J, Standage DS, Merchant N, Brendel VP.

Plant Cell. 2016 Apr;28(4):840-54. doi: 10.1105/tpc.15.00933. Epub 2016 Mar 28.

8.

Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect.

Standage DS, Berens AJ, Glastad KM, Severin AJ, Brendel VP, Toth AL.

Mol Ecol. 2016 Apr;25(8):1769-84. doi: 10.1111/mec.13578. Epub 2016 Mar 15.

PMID:
26859767
9.

Discovery and expression analysis of alternative splicing events conserved among plant SR proteins.

Rauch HB, Patrick TL, Klusman KM, Battistuzzi FU, Mei W, Brendel VP, Lal SK.

Mol Biol Evol. 2014 Mar;31(3):605-13. doi: 10.1093/molbev/mst238. Epub 2013 Dec 19.

PMID:
24356560
10.

Single nucleotide polymorphisms of human STING can affect innate immune response to cyclic dinucleotides.

Yi G, Brendel VP, Shu C, Li P, Palanathan S, Cheng Kao C.

PLoS One. 2013 Oct 21;8(10):e77846. doi: 10.1371/journal.pone.0077846. eCollection 2013.

11.

Development of p21 activated kinase-targeted multikinase inhibitors that inhibit thyroid cancer cell migration.

Ma Y, McCarty SK, Kapuriya NP, Brendel VJ, Wang C, Zhang X, Jarjoura D, Saji M, Chen CS, Ringel MD.

J Clin Endocrinol Metab. 2013 Aug;98(8):E1314-22. doi: 10.1210/jc.2012-3937. Epub 2013 May 24. Erratum in: J Clin Endocrinol Metab. 2016 Mar;101(3):1314.

12.

ParsEval: parallel comparison and analysis of gene structure annotations.

Standage DS, Brendel VP.

BMC Bioinformatics. 2012 Aug 1;13:187. doi: 10.1186/1471-2105-13-187.

13.

TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction.

Doyle EL, Booher NJ, Standage DS, Voytas DF, Brendel VP, Vandyk JK, Bogdanove AJ.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W117-22. doi: 10.1093/nar/gks608. Epub 2012 Jun 12.

14.

Sorafenib and Mek inhibition is synergistic in medullary thyroid carcinoma in vitro.

Koh YW, Shah MH, Agarwal K, McCarty SK, Koo BS, Brendel VJ, Wang C, Porter K, Jarjoura D, Saji M, Ringel MD.

Endocr Relat Cancer. 2012 Jan 9;19(1):29-38. doi: 10.1530/ERC-11-0155. Print 2012 Feb.

15.

Preclinical validation of AR42, a novel histone deacetylase inhibitor, as treatment for vestibular schwannomas.

Jacob A, Oblinger J, Bush ML, Brendel V, Santarelli G, Chaudhury AR, Kulp S, La Perle KM, Chen CS, Chang LS, Welling DB.

Laryngoscope. 2012 Jan;122(1):174-89. doi: 10.1002/lary.22392. Epub 2011 Nov 22.

16.

Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.

Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, Schatz MC, Shumway M, Sommer DD, Trapnell C, Benahmed F, Dimitrov G, Madupu R, Radune D, Sullivan S, Jha G, Ishihara H, Lee SW, Pandey A, Sharma V, Sriariyanun M, Szurek B, Vera-Cruz CM, Dorman KS, Ronald PC, Verdier V, Dow JM, Sonti RV, Tsuge S, Brendel VP, Rabinowicz PD, Leach JE, White FF, Salzberg SL.

J Bacteriol. 2011 Oct;193(19):5450-64. doi: 10.1128/JB.05262-11. Epub 2011 Jul 22.

17.

AR42, a novel histone deacetylase inhibitor, as a potential therapy for vestibular schwannomas and meningiomas.

Bush ML, Oblinger J, Brendel V, Santarelli G, Huang J, Akhmametyeva EM, Burns SS, Wheeler J, Davis J, Yates CW, Chaudhury AR, Kulp S, Chen CS, Chang LS, Welling DB, Jacob A.

Neuro Oncol. 2011 Sep;13(9):983-99. doi: 10.1093/neuonc/nor072. Epub 2011 Jul 21.

18.

The BioExtract Server: a web-based bioinformatic workflow platform.

Lushbough CM, Jennewein DM, Brendel VP.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W528-32. doi: 10.1093/nar/gkr286. Epub 2011 May 5.

19.

An overview of the BioExtract Server: a distributed, Web-based system for genomic analysis.

Lushbough CM, Brendel VP.

Adv Exp Med Biol. 2010;680:361-9. doi: 10.1007/978-1-4419-5913-3_41.

PMID:
20865520
20.

Genome-wide distribution of transposed Dissociation elements in maize.

Vollbrecht E, Duvick J, Schares JP, Ahern KR, Deewatthanawong P, Xu L, Conrad LJ, Kikuchi K, Kubinec TA, Hall BD, Weeks R, Unger-Wallace E, Muszynski M, Brendel VP, Brutnell TP.

Plant Cell. 2010 Jun;22(6):1667-85. doi: 10.1105/tpc.109.073452. Epub 2010 Jun 25.

21.

BioExtract server--an integrated workflow-enabling system to access and analyze heterogeneous, distributed biomolecular data.

Lushbough C, Bergman MK, Lawrence CJ, Jennewein D, Brendel V.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar;7(1):12-24. doi: 10.1109/TCBB.2008.98.

PMID:
20150665
22.

Common introns within orthologous genes: software and application to plants.

Wilkerson MD, Ru Y, Brendel VP.

Brief Bioinform. 2009 Nov;10(6):631-44. doi: 10.1093/bib/bbp051.

PMID:
19933210
23.

Regional mutagenesis using Dissociation in maize.

Ahern KR, Deewatthanawong P, Schares J, Muszynski M, Weeks R, Vollbrecht E, Duvick J, Brendel VP, Brutnell TP.

Methods. 2009 Nov;49(3):248-54. doi: 10.1016/j.ymeth.2009.04.009. Epub 2009 Apr 24.

PMID:
19394430
24.

MaizeGDB becomes 'sequence-centric'.

Sen TZ, Andorf CM, Schaeffer ML, Harper LC, Sparks ME, Duvick J, Brendel VP, Cannon E, Campbell DA, Lawrence CJ.

Database (Oxford). 2009;2009:bap020. doi: 10.1093/database/bap020. Epub 2009 Dec 7.

25.

Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas.

Lu H, Patil P, Van Sluys MA, White FF, Ryan RP, Dow JM, Rabinowicz P, Salzberg SL, Leach JE, Sonti R, Brendel V, Bogdanove AJ.

PLoS One. 2008;3(11):e3828. doi: 10.1371/journal.pone.0003828. Epub 2008 Nov 27.

26.

MetWAMer: eukaryotic translation initiation site prediction.

Sparks ME, Brendel V.

BMC Bioinformatics. 2008 Sep 18;9:381. doi: 10.1186/1471-2105-9-381.

27.

Spliceosomal proteins in plants.

Ru Y, Wang BB, Brendel V.

Curr Top Microbiol Immunol. 2008;326:1-15. Review.

PMID:
18630744
28.

Expression and evolution of the phosphoinositide-specific phospholipase C gene family in Arabidopsis thaliana.

Tasma IM, Brendel V, Whitham SA, Bhattacharyya MK.

Plant Physiol Biochem. 2008 Jul;46(7):627-37. doi: 10.1016/j.plaphy.2008.04.015. Epub 2008 Apr 26.

PMID:
18534862
29.

Gene Structure Annotation at PlantGDB.

Brendel V.

Methods Mol Biol. 2007;406:521-33.

PMID:
18287710
30.

Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes.

Wang BB, O'Toole M, Brendel V, Young ND.

BMC Plant Biol. 2008 Feb 19;8:17. doi: 10.1186/1471-2229-8-17.

31.

Pairwise statistical significance and empirical determination of effective gap opening penalties for protein local sequence alignment.

Agrawal A, Brendel VP, Huang X.

Int J Comput Biol Drug Des. 2008;1(4):347-67. Review.

PMID:
20063463
32.

Implementing bioinformatic workflows within the bioextract server.

Lushbough CM, Bergman MK, Lawrence CJ, Jennewein D, Brendel V.

Int J Comput Biol Drug Des. 2008;1(3):302-12.

PMID:
20054995
33.

PlantGDB: a resource for comparative plant genomics.

Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V.

Nucleic Acids Res. 2008 Jan;36(Database issue):D959-65. Epub 2007 Dec 6.

34.

Visualization of syntenic relationships with SynBrowse.

Brendel V, Kurtz S, Pan X.

Methods Mol Biol. 2007;396:153-63.

PMID:
18025692
35.

Tracembler--software for in-silico chromosome walking in unassembled genomes.

Dong Q, Wilkerson MD, Brendel V.

BMC Bioinformatics. 2007 May 9;8:151.

36.
37.
38.

Genomewide comparative analysis of alternative splicing in plants.

Wang BB, Brendel V.

Proc Natl Acad Sci U S A. 2006 May 2;103(18):7175-80. Epub 2006 Apr 21.

39.

Molecular characterization and phylogeny of U2AF35 homologs in plants.

Wang BB, Brendel V.

Plant Physiol. 2006 Feb;140(2):624-36. Epub 2006 Jan 11.

40.
41.

Comparative plant genomics resources at PlantGDB.

Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V.

Plant Physiol. 2005 Oct;139(2):610-8.

42.

SynBrowse: a synteny browser for comparative sequence analysis.

Pan X, Stein L, Brendel V.

Bioinformatics. 2005 Sep 1;21(17):3461-8. Epub 2005 Jun 30.

PMID:
15994196
43.

Comparative EST analyses in plant systems.

Dong Q, Kroiss L, Oakley FD, Wang BB, Brendel V.

Methods Enzymol. 2005;395:400-18. Review.

PMID:
15984049
44.

The maize genetics and genomics database. The community resource for access to diverse maize data.

Lawrence CJ, Seigfried TE, Brendel V.

Plant Physiol. 2005 May;138(1):55-8.

45.

Community-based gene structure annotation.

Schlueter SD, Wilkerson MD, Huala E, Rhee SY, Brendel V.

Trends Plant Sci. 2005 Jan;10(1):9-14.

PMID:
15642518
46.
47.

Genome-wide mutagenesis of Zea mays L. using RescueMu transposons.

Fernandes J, Dong Q, Schneider B, Morrow DJ, Nan GL, Brendel V, Walbot V.

Genome Biol. 2004;5(10):R82. Epub 2004 Sep 23.

48.

Plant genome research outreach portal. A gateway to plant genome research "outreach" programs and activities.

Baran SB, Lawrence CJ, Brendel V.

Plant Physiol. 2004 Mar;134(3):889. No abstract available.

49.

Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.

Brendel V, Xing L, Zhu W.

Bioinformatics. 2004 May 1;20(7):1157-69. Epub 2004 Feb 5.

PMID:
14764557
50.

MaizeGDB, the community database for maize genetics and genomics.

Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D393-7.

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