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The anatomy of successful computational biology software.
Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. Altschul S, et al. Among authors: nekrutenko a. Nat Biotechnol. 2013 Oct;31(10):894-7. doi: 10.1038/nbt.2721. Nat Biotechnol. 2013. PMID: 24104757 Free PMC article. No abstract available.
Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.
Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP. Qu K, et al. Among authors: nekrutenko a. Nat Methods. 2016 Mar;13(3):245-247. doi: 10.1038/nmeth.3732. Epub 2016 Jan 18. Nat Methods. 2016. PMID: 26780094 Free PMC article.
Practical Computational Reproducibility in the Life Sciences.
Grüning B, Chilton J, Köster J, Dale R, Soranzo N, van den Beek M, Goecks J, Backofen R, Nekrutenko A, Taylor J. Grüning B, et al. Among authors: nekrutenko a. Cell Syst. 2018 Jun 27;6(6):631-635. doi: 10.1016/j.cels.2018.03.014. Cell Syst. 2018. PMID: 29953862 Free PMC article.
NGS analyses by visualization with Trackster.
Goecks J, Coraor N; Galaxy Team; Nekrutenko A, Taylor J. Goecks J, et al. Among authors: nekrutenko a. Nat Biotechnol. 2012 Nov;30(11):1036-9. doi: 10.1038/nbt.2404. Nat Biotechnol. 2012. PMID: 23138293 Free PMC article. No abstract available.
Ten simple rules for reproducible computational research.
Sandve GK, Nekrutenko A, Taylor J, Hovig E. Sandve GK, et al. Among authors: nekrutenko a. PLoS Comput Biol. 2013 Oct;9(10):e1003285. doi: 10.1371/journal.pcbi.1003285. Epub 2013 Oct 24. PLoS Comput Biol. 2013. PMID: 24204232 Free PMC article. No abstract available.
Harnessing cloud computing with Galaxy Cloud.
Afgan E, Baker D, Coraor N, Goto H, Paul IM, Makova KD, Nekrutenko A, Taylor J. Afgan E, et al. Among authors: nekrutenko a. Nat Biotechnol. 2011 Nov 8;29(11):972-4. doi: 10.1038/nbt.2028. Nat Biotechnol. 2011. PMID: 22068528 Free PMC article. No abstract available.
Using Galaxy to Perform Large-Scale Interactive Data Analyses-An Update.
Ostrovsky A, Hillman-Jackson J, Bouvier D, Clements D, Afgan E, Blankenberg D, Schatz MC, Nekrutenko A, Taylor J, Team TG, Lariviere D. Ostrovsky A, et al. Among authors: nekrutenko a. Curr Protoc. 2021 Feb;1(2):e31. doi: 10.1002/cpz1.31. Curr Protoc. 2021. PMID: 33583104
101 results