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Page 1
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.
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.
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.
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.
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.
Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards.
Tollis M, Hutchins ED, Stapley J, Rupp SM, Eckalbar WL, Maayan I, Lasku E, Infante CR, Dennis SR, Robertson JA, May CM, Crusoe MR, Bermingham E, DeNardo DF, Hsieh ST, Kulathinal RJ, McMillan WO, Menke DB, Pratt SC, Rawls JA, Sanjur O, Wilson-Rawls J, Wilson Sayres MA, Fisher RE, Kusumi K. Tollis M, et al. Among authors: crusoe mr. Genome Biol Evol. 2018 Feb 1;10(2):489-506. doi: 10.1093/gbe/evy013. Genome Biol Evol. 2018. PMID: 29360978 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.
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.
13 results