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Items: 12

1.

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 A, 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.

Bioinformatics. 2019 Mar 9. pii: btz160. doi: 10.1093/bioinformatics/btz160. [Epub ahead of print]

PMID:
30851093
2.

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.

Gigascience. 2019 Feb 1;8(2). pii: giy149. doi: 10.1093/gigascience/giy149.

3.

wft4galaxy: a workflow testing tool for galaxy.

Piras ME, Pireddu L, Zanetti G.

Bioinformatics. 2017 Dec 1;33(23):3805-3807. doi: 10.1093/bioinformatics/btx461.

4.

Recommendations on e-infrastructures for next-generation sequencing.

Spjuth O, Bongcam-Rudloff E, Dahlberg J, Dahlö M, Kallio A, Pireddu L, Vezzi F, Korpelainen E.

Gigascience. 2016 Jun 7;5:26. doi: 10.1186/s13742-016-0132-7. Review.

5.

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.

Biol Direct. 2015 Aug 19;10:43. doi: 10.1186/s13062-015-0071-8.

6.

BioBlend.objects: metacomputing with Galaxy.

Leo S, Pireddu L, Cuccuru G, Lianas L, Soranzo N, Afgan E, Zanetti G.

Bioinformatics. 2014 Oct;30(19):2816-7. doi: 10.1093/bioinformatics/btu386. Epub 2014 Jun 12.

7.

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.

Bioinformatics. 2014 Jan 1;30(1):119-20. doi: 10.1093/bioinformatics/btt601. Epub 2013 Oct 22.

8.

Genetic variants regulating immune cell levels in health and disease.

Orrù V, Steri M, Sole G, Sidore C, Virdis F, Dei M, Lai S, Zoledziewska M, Busonero F, Mulas A, Floris M, Mentzen WI, Urru SA, Olla S, Marongiu M, Piras MG, Lobina M, Maschio A, Pitzalis M, Urru MF, Marcelli M, Cusano R, Deidda F, Serra V, Oppo M, Pilu R, Reinier F, Berutti R, Pireddu L, Zara I, Porcu E, Kwong A, Brennan C, Tarrier B, Lyons R, Kang HM, Uzzau S, Atzeni R, Valentini M, Firinu D, Leoni L, Rotta G, Naitza S, Angius A, Congia M, Whalen MB, Jones CM, Schlessinger D, Abecasis GR, Fiorillo E, Sanna S, Cucca F.

Cell. 2013 Sep 26;155(1):242-56. doi: 10.1016/j.cell.2013.08.041.

9.

SEAL: a distributed short read mapping and duplicate removal tool.

Pireddu L, Leo S, Zanetti G.

Bioinformatics. 2011 Aug 1;27(15):2159-60. doi: 10.1093/bioinformatics/btr325. Epub 2011 Jun 22.

10.

Support Vector Machine (SVM) as Alternative Tool to Assign Acute Aquatic Toxicity Warning Labels to Chemicals.

Michielan L, Pireddu L, Floris M, Moro S.

Mol Inform. 2010 Jan 12;29(1-2):51-64. doi: 10.1002/minf.200900005.

PMID:
27463848
11.

MMsINC: a large-scale chemoinformatics database.

Masciocchi J, Frau G, Fanton M, Sturlese M, Floris M, Pireddu L, Palla P, Cedrati F, Rodriguez-Tomé P, Moro S.

Nucleic Acids Res. 2009 Jan;37(Database issue):D284-90. doi: 10.1093/nar/gkn727. Epub 2008 Oct 17.

12.

The Path-A metabolic pathway prediction web server.

Pireddu L, Szafron D, Lu P, Greiner R.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W714-9.

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