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ParsEval: parallel comparison and analysis of gene structure annotations.
Standage DS, Brendel VP. Standage DS, et al. BMC Bioinformatics. 2012 Aug 1;13:187. doi: 10.1186/1471-2105-13-187. BMC Bioinformatics. 2012. PMID: 22852583 Free PMC article.
xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.
Duvick J, Standage DS, Merchant N, Brendel VP. Duvick J, et al. Among authors: standage ds. Plant Cell. 2016 Apr;28(4):840-54. doi: 10.1105/tpc.15.00933. Epub 2016 Mar 28. Plant Cell. 2016. PMID: 27020957 Free PMC article.
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. Doyle EL, et al. Among authors: standage ds. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W117-22. doi: 10.1093/nar/gks608. Epub 2012 Jun 12. Nucleic Acids Res. 2012. PMID: 22693217 Free PMC article.
The khmer software package: enabling efficient nucleotide sequence analysis.
Crusoe MR, Alameldin HF, Awad S, Boucher E, Caldwell A, Cartwright R, Charbonneau A, Constantinides B, Edvenson G, Fay S, Fenton J, Fenzl T, Fish J, Garcia-Gutierrez L, Garland P, Gluck J, González I, Guermond S, Guo J, Gupta A, Herr JR, Howe A, Hyer A, Härpfer A, Irber L, Kidd R, Lin D, Lippi J, Mansour T, McA'Nulty P, McDonald E, Mizzi J, Murray KD, Nahum JR, Nanlohy K, Nederbragt AJ, Ortiz-Zuazaga H, Ory J, Pell J, Pepe-Ranney C, Russ ZN, Schwarz E, Scott C, Seaman J, Sievert S, Simpson J, Skennerton CT, Spencer J, Srinivasan R, Standage D, Stapleton JA, Steinman SR, Stein J, Taylor B, Trimble W, Wiencko HL, Wright M, Wyss B, Zhang Q, Zyme E, Brown CT. Crusoe MR, et al. F1000Res. 2015 Sep 25;4:900. doi: 10.12688/f1000research.6924.1. eCollection 2015. F1000Res. 2015. PMID: 26535114 Free PMC article.
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. Standage DS, et al. Mol Ecol. 2016 Apr;25(8):1769-84. doi: 10.1111/mec.13578. Epub 2016 Mar 15. Mol Ecol. 2016. PMID: 26859767
Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants.
Standage DS, Brown CT, Hormozdiari F. Standage DS, et al. iScience. 2019 Aug 30;18:28-36. doi: 10.1016/j.isci.2019.07.032. Epub 2019 Jul 23. iScience. 2019. PMID: 31377530 Free PMC article.