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Page 1
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. Afgan E, et al. Among authors: van den beek m. Nucleic Acids Res. 2016 Jul 8;44(W1):W3-W10. doi: 10.1093/nar/gkw343. Epub 2016 May 2. Nucleic Acids Res. 2016. PMID: 27137889 Free PMC article.
ReGaTE: Registration of Galaxy Tools in Elixir.
Doppelt-Azeroual O, Mareuil F, Deveaud E, Kalaš M, Soranzo N, van den Beek M, Grüning B, Ison J, Ménager H. Doppelt-Azeroual O, et al. Among authors: van den beek m. Gigascience. 2017 Jun 1;6(6):1-4. doi: 10.1093/gigascience/gix022. Gigascience. 2017. PMID: 28402416 Free PMC article.
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.
Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Grüning BA, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D. Afgan E, et al. Among authors: van den beek m. Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544. doi: 10.1093/nar/gky379. Nucleic Acids Res. 2018. PMID: 29790989 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: van den beek m. 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.
No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics.
Baker D, van den Beek M, Blankenberg D, Bouvier D, Chilton J, Coraor N, Coppens F, Eguinoa I, Gladman S, Grüning B, Keener N, Larivière D, Lonie A, Kosakovsky Pond S, Maier W, Nekrutenko A, Taylor J, Weaver S. Baker D, et al. Among authors: van den beek m. PLoS Pathog. 2020 Aug 13;16(8):e1008643. doi: 10.1371/journal.ppat.1008643. eCollection 2020 Aug. PLoS Pathog. 2020. PMID: 32790776 Free PMC article.
NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy.
de Koning W, Miladi M, Hiltemann S, Heikema A, Hays JP, Flemming S, van den Beek M, Mustafa DA, Backofen R, Grüning B, Stubbs AP. de Koning W, et al. Among authors: van den beek m. Gigascience. 2020 Oct 17;9(10):giaa105. doi: 10.1093/gigascience/giaa105. Gigascience. 2020. PMID: 33068114 Free PMC article.
RNA-Seq Data Analysis in Galaxy.
Batut B, van den Beek M, Doyle MA, Soranzo N. Batut B, et al. Among authors: van den beek m. Methods Mol Biol. 2021;2284:367-392. doi: 10.1007/978-1-0716-1307-8_20. Methods Mol Biol. 2021. PMID: 33835453
Ready-to-use public infrastructure for global SARS-CoV-2 monitoring.
Maier W, Bray S, van den Beek M, Bouvier D, Coraor N, Miladi M, Singh B, De Argila JR, Baker D, Roach N, Gladman S, Coppens F, Martin DP, Lonie A, Grüning B, Kosakovsky Pond SL, Nekrutenko A. Maier W, et al. Among authors: van den beek m. Nat Biotechnol. 2021 Oct;39(10):1178-1179. doi: 10.1038/s41587-021-01069-1. Nat Biotechnol. 2021. PMID: 34588690 Free PMC article. No abstract available.
Expanding the Galaxy's reference data.
VijayKrishna N, Joshi J, Coraor N, Hillman-Jackson J, Bouvier D, van den Beek M, Eguinoa I, Coppens F, Davis J, Stolarczyk M, Sheffield NC, Gladman S, Cuccuru G, Grüning B, Soranzo N, Rasche H, Langhorst BW, Bernt M, Fornika D, de Lima Morais DA, Barrette M, van Heusden P, Petrillo M, Puertas-Gallardo A, Patak A, Hotz HR, Blankenberg D. VijayKrishna N, et al. Among authors: van den beek m. Bioinform Adv. 2022 Apr 29;2(1):vbac030. doi: 10.1093/bioadv/vbac030. eCollection 2022. Bioinform Adv. 2022. PMID: 35669346 Free PMC article.
26 results