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MGnify: the microbiome analysis resource in 2020.
Mitchell AL, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G, Crusoe MR, Kale V, Potter SC, Richardson LJ, Sakharova E, Scheremetjew M, Korobeynikov A, Shlemov A, Kunyavskaya O, Lapidus A, Finn RD. Mitchell AL, et al. Among authors: crusoe mr. Nucleic Acids Res. 2020 Jan 8;48(D1):D570-D578. doi: 10.1093/nar/gkz1035. Nucleic Acids Res. 2020. PMID: 31696235 Free PMC article.
Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics.
Baichoo S, Souilmi Y, Panji S, Botha G, Meintjes A, Hazelhurst S, Bendou H, Beste E, Mpangase PT, Souiai O, Alghali M, Yi L, O'Connor BD, Crusoe M, Armstrong D, Aron S, Joubert F, Ahmed AE, Mbiyavanga M, Heusden PV, Magosi LE, Zermeno J, Mainzer LS, Fadlelmola FM, Jongeneel CV, Mulder N. Baichoo S, et al. BMC Bioinformatics. 2018 Nov 29;19(1):457. doi: 10.1186/s12859-018-2446-1. BMC Bioinformatics. 2018. PMID: 30486782 Free PMC article.
Scalable Workflows and Reproducible Data Analysis for Genomics.
Strozzi F, Janssen R, Wurmus R, Crusoe MR, Githinji G, Di Tommaso P, Belhachemi D, Möller S, Smant G, de Ligt J, Prins P. Strozzi F, et al. Among authors: crusoe mr. Methods Mol Biol. 2019;1910:723-745. doi: 10.1007/978-1-4939-9074-0_24. Methods Mol Biol. 2019. PMID: 31278683 Free PMC article.
Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.
Ahmed AE, Mpangase PT, Panji S, Baichoo S, Souilmi Y, Fadlelmola FM, Alghali M, Aron S, Bendou H, De Beste E, Mbiyavanga M, Souiai O, Yi L, Zermeno J, Armstrong D, O'Connor BD, Mainzer LS, Crusoe MR, Meintjes A, Van Heusden P, Botha G, Joubert F, Jongeneel CV, Hazelhurst S, Mulder N. Ahmed AE, et al. Among authors: crusoe mr. AAS Open Res. 2019 Aug 7;1:9. doi: 10.12688/aasopenres.12847.2. eCollection 2018. AAS Open Res. 2019. PMID: 32382696 Free PMC article.
Recommendations for the packaging and containerizing of bioinformatics software.
Gruening B, Sallou O, Moreno P, da Veiga Leprevost F, Ménager H, Søndergaard D, Röst H, Sachsenberg T, O'Connor B, Madeira F, Dominguez Del Angel V, Crusoe MR, Varma S, Blankenberg D, Jimenez RC; BioContainers Community; Perez-Riverol Y. Gruening B, et al. Among authors: crusoe mr. F1000Res. 2018 Jun 14;7:ISCB Comm J-742. doi: 10.12688/f1000research.15140.2. eCollection 2018. F1000Res. 2018. PMID: 31543945 Free PMC article.
Enabling precision medicine via standard communication of HTS provenance, analysis, and results.
Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, Suresh A, Purkayastha A, King CH, Taylor D, Johanson E, Thompson EE, Donaldson E, Morizono H, Tsang H, Vora JK, Goecks J, Yao J, Almeida JS, Keeney J, Addepalli K, Krampis K, Smith KM, Guo L, Walderhaug M, Schito M, Ezewudo M, Guimera N, Walsh P, Kahsay R, Gottipati S, Rodwell TC, Bloom T, Lai Y, Simonyan V, Mazumder R. Alterovitz G, et al. Among authors: crusoe mr. PLoS Biol. 2018 Dec 31;16(12):e3000099. doi: 10.1371/journal.pbio.3000099. eCollection 2018 Dec. PLoS Biol. 2018. PMID: 30596645 Free PMC article.
Perspectives on automated composition of workflows in the life sciences.
Lamprecht AL, Palmblad M, Ison J, Schwämmle V, Al Manir MS, Altintas I, Baker CJO, Ben Hadj Amor A, Capella-Gutierrez S, Charonyktakis P, Crusoe MR, Gil Y, Goble C, Griffin TJ, Groth P, Ienasescu H, Jagtap P, Kalaš M, Kasalica V, Khanteymoori A, Kuhn T, Mei H, Ménager H, Möller S, Richardson RA, Robert V, Soiland-Reyes S, Stevens R, Szaniszlo S, Verberne S, Verhoeven A, Wolstencroft K. Lamprecht AL, et al. Among authors: crusoe mr. F1000Res. 2021 Sep 7;10:897. doi: 10.12688/f1000research.54159.1. eCollection 2021. F1000Res. 2021. PMID: 34804501 Free PMC article.
Using bio.tools to generate and annotate workbench tool descriptions.
Hillion KH, Kuzmin I, Khodak A, Rasche E, Crusoe M, Peterson H, Ison J, Ménager H. Hillion KH, et al. F1000Res. 2017 Nov 30;6:ELIXIR-2074. doi: 10.12688/f1000research.12974.1. eCollection 2017. F1000Res. 2017. PMID: 29333231 Free PMC article.
15 results