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Recording provenance of workflow runs with RO-Crate.
Leo S, Crusoe MR, Rodríguez-Navas L, Sirvent R, Kanitz A, De Geest P, Wittner R, Pireddu L, Garijo D, Fernández JM, Colonnelli I, Gallo M, Ohta T, Suetake H, Capella-Gutierrez S, de Wit R, Kinoshita BP, Soiland-Reyes S. Leo S, et al. Among authors: pireddu l. PLoS One. 2024 Sep 10;19(9):e0309210. doi: 10.1371/journal.pone.0309210. eCollection 2024. PLoS One. 2024. PMID: 39255315 Free PMC article.
BioBlend.objects: metacomputing with Galaxy.
Leo S, Pireddu L, Cuccuru G, Lianas L, Soranzo N, Afgan E, Zanetti G. Leo S, et al. Among authors: pireddu l. Bioinformatics. 2014 Oct;30(19):2816-7. doi: 10.1093/bioinformatics/btu386. Epub 2014 Jun 12. Bioinformatics. 2014. PMID: 24928211 Free PMC article.
wft4galaxy: a workflow testing tool for galaxy.
Piras ME, Pireddu L, Zanetti G. Piras ME, et al. Among authors: pireddu l. Bioinformatics. 2017 Dec 1;33(23):3805-3807. doi: 10.1093/bioinformatics/btx461. Bioinformatics. 2017. PMID: 29036536 Free PMC article.
PhenoMeNal: processing and analysis of metabolomics data in the cloud.
Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JTM, Peluso A, Piras ME, Pireddu L, Reed MAC, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C. Peters K, et al. Among authors: pireddu l. Gigascience. 2019 Feb 1;8(2):giy149. doi: 10.1093/gigascience/giy149. Gigascience. 2019. PMID: 30535405 Free PMC article.
Interoperable and scalable data analysis with microservices: applications in metabolomics.
Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran AN, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O. Emami Khoonsari P, et al. Among authors: pireddu l. Bioinformatics. 2019 Oct 1;35(19):3752-3760. doi: 10.1093/bioinformatics/btz160. Bioinformatics. 2019. PMID: 30851093 Free PMC article.
The openEHR Genomics Project.
Mascia C, Frexia F, Uva P, Zanetti G, Pireddu L, Giacomelli G, Jaeger-Schmidt C, Tomczak A, Schumacher S, Kraecher F, Eils R, Ljosland Bakke S, Leslie H. Mascia C, et al. Among authors: pireddu l. Stud Health Technol Inform. 2020 Jun 16;270:443-447. doi: 10.3233/SHTI200199. Stud Health Technol Inform. 2020. PMID: 32570423
Experiences with workflows for automating data-intensive bioinformatics.
Spjuth O, Bongcam-Rudloff E, Hernández GC, Forer L, Giovacchini M, Guimera RV, Kallio A, Korpelainen E, Kańduła MM, Krachunov M, Kreil DP, Kulev O, Łabaj PP, Lampa S, Pireddu L, Schönherr S, Siretskiy A, Vassilev D. Spjuth O, et al. Among authors: pireddu l. Biol Direct. 2015 Aug 19;10:43. doi: 10.1186/s13062-015-0071-8. Biol Direct. 2015. PMID: 26282399 Free PMC article.
Privacy risks of whole-slide image sharing in digital pathology.
Holub P, Müller H, Bíl T, Pireddu L, Plass M, Prasser F, Schlünder I, Zatloukal K, Nenutil R, Brázdil T. Holub P, et al. Among authors: pireddu l. Nat Commun. 2023 May 4;14(1):2577. doi: 10.1038/s41467-023-37991-y. Nat Commun. 2023. PMID: 37142591 Free PMC article.
SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop.
Schumacher A, Pireddu L, Niemenmaa M, Kallio A, Korpelainen E, Zanetti G, Heljanko K. Schumacher A, et al. Among authors: pireddu l. Bioinformatics. 2014 Jan 1;30(1):119-20. doi: 10.1093/bioinformatics/btt601. Epub 2013 Oct 22. Bioinformatics. 2014. PMID: 24149054 Free PMC article.
18 results