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1.

Genetic variants regulating immune cell levels in health and disease.

Orrù, Valeria; Steri, Maristella; Sole, Gabriella; Sidore, Carlo; Virdis, Francesca; Dei, Mariano; Lai, Sandra; Zoledziewska, Magdalena; Busonero, Fabio; Mulas, Antonella; Floris, Matteo; Mentzen, Wieslawa I; Urru, Silvana A M; Olla, Stefania; Marongiu, Michele; Piras, Maria G; Lobina, Monia; Maschio, Andrea; Pitzalis, Maristella; Urru, Maria F; Marcelli, Marco; Cusano, Roberto; Deidda, Francesca; Serra, Valentina; Oppo, Manuela; Pilu, Rosella; Reinier, Frederic; Berutti, Riccardo; Pireddu, Luca; Zara, Ilenia; Porcu, Eleonora; Kwong, Alan; Brennan, Christine; Tarrier, Brendan; Lyons, Robert; Kang, Hyun M; Uzzau, Sergio; Atzeni, Rossano; Valentini, Maria; Firinu, Davide; Leoni, Lidia; Rotta, Gianluca; Naitza, Silvia; Angius, Andrea; Congia, Mauro; Whalen, Michael B; Jones, Chris M; Schlessinger, David; Abecasis, Gonçalo R; Fiorillo, Edoardo.

Cell ; 155(1): 242-56, 2013 Sep 26.

Article in English | MEDLINE | ID: mdl-24074872

2.

Interoperable and scalable data analysis with microservices: applications in metabolomics.

Emami Khoonsari, Payam; Moreno, Pablo; Bergmann, Sven; Burman, Joachim; Capuccini, Marco; Carone, Matteo; Cascante, Marta; de Atauri, Pedro; Foguet, Carles; Gonzalez-Beltran, Alejandra N; Hankemeier, Thomas; Haug, Kenneth; He, Sijin; Herman, Stephanie; Johnson, David; Kale, Namrata; Larsson, Anders; Neumann, Steffen; Peters, Kristian; Pireddu, Luca; Rocca-Serra, Philippe; Roger, Pierrick; Rueedi, Rico; Ruttkies, Christoph; Sadawi, Noureddin; Salek, Reza M; Sansone, Susanna-Assunta; Schober, Daniel; Selivanov, Vitaly; Thévenot, Etienne A; van Vliet, Michael; Zanetti, Gianluigi; Steinbeck, Christoph; Kultima, Kim; Spjuth, Ola.

Bioinformatics ; 35(19): 3752-3760, 2019 10 01.

Article in English | MEDLINE | ID: mdl-30851093

3.

wft4galaxy: a workflow testing tool for galaxy.

Piras, Marco Enrico; Pireddu, Luca; Zanetti, Gianluigi.

Bioinformatics ; 33(23): 3805-3807, 2017 Dec 01.

Article in English | MEDLINE | ID: mdl-29036536

4.

BioBlend.objects: metacomputing with Galaxy.

Leo, Simone; Pireddu, Luca; Cuccuru, Gianmauro; Lianas, Luca; Soranzo, Nicola; Afgan, Enis; Zanetti, Gianluigi.

Bioinformatics ; 30(19): 2816-7, 2014 Oct.

Article in English | MEDLINE | ID: mdl-24928211

5.

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop.

Schumacher, André; Pireddu, Luca; Niemenmaa, Matti; Kallio, Aleksi; Korpelainen, Eija; Zanetti, Gianluigi; Heljanko, Keijo.

Bioinformatics ; 30(1): 119-20, 2014 Jan 01.

Article in English | MEDLINE | ID: mdl-24149054

6.

Privacy risks of whole-slide image sharing in digital pathology.

Holub, Petr; Müller, Heimo; Bíl, Tomás; Pireddu, Luca; Plass, Markus; Prasser, Fabian; Schlünder, Irene; Zatloukal, Kurt; Nenutil, Rudolf; Brázdil, Tomás.

Nat Commun ; 14(1): 2577, 2023 05 04.

Article in English | MEDLINE | ID: mdl-37142591

7.

Cohort profile: the Turin prostate cancer prognostication (TPCP) cohort.

Destefanis, Nicolas; Fiano, Valentina; Milani, Lorenzo; Vasapolli, Paolo; Fiorentino, Michelangelo; Giunchi, Francesca; Lianas, Luca; Del Rio, Mauro; Frexia, Francesca; Pireddu, Luca; Molinaro, Luca; Cassoni, Paola; Papotti, Mauro Giulio; Gontero, Paolo; Calleris, Giorgio; Oderda, Marco; Ricardi, Umberto; Iorio, Giuseppe Carlo; Fariselli, Piero; Isaevska, Elena; Akre, Olof; Zelic, Renata; Pettersson, Andreas; Zugna, Daniela; Richiardi, Lorenzo.

Front Oncol ; 13: 1242639, 2023.

Article in English | MEDLINE | ID: mdl-37869094

8.

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

Pireddu, Luca; Leo, Simone; Zanetti, Gianluigi.

Bioinformatics ; 27(15): 2159-60, 2011 Aug 01.

Article in English | MEDLINE | ID: mdl-21697132

9.

MMsINC: a large-scale chemoinformatics database.

Masciocchi, Joel; Frau, Gianfranco; Fanton, Marco; Sturlese, Mattia; Floris, Matteo; Pireddu, Luca; Palla, Piergiorgio; Cedrati, Fabian; Rodriguez-Tomé, Patricia; Moro, Stefano.

Nucleic Acids Res ; 37(Database issue): D284-90, 2009 Jan.

Article in English | MEDLINE | ID: mdl-18931373

10.

ISA API: An open platform for interoperable life science experimental metadata.

Johnson, David; Batista, Dominique; Cochrane, Keeva; Davey, Robert P; Etuk, Anthony; Gonzalez-Beltran, Alejandra; Haug, Kenneth; Izzo, Massimiliano; Larralde, Martin; Lawson, Thomas N; Minotto, Alice; Moreno, Pablo; Nainala, Venkata Chandrasekhar; O'Donovan, Claire; Pireddu, Luca; Roger, Pierrick; Shaw, Felix; Steinbeck, Christoph; Weber, Ralf J M; Sansone, Susanna-Assunta; Rocca-Serra, Philippe.

Gigascience ; 10(9)2021 09 16.

Article in English | MEDLINE | ID: mdl-34528664

11.

The openEHR Genomics Project.

Mascia, Cecilia; Frexia, Francesca; Uva, Paolo; Zanetti, Gianluigi; Pireddu, Luca; Giacomelli, Gideon; Jaeger-Schmidt, Christina; Tomczak, Aurelie; Schumacher, Simon; Kraecher, Florian; Eils, Roland; Ljosland Bakke, Silje; Leslie, Heather.

Stud Health Technol Inform ; 270: 443-447, 2020 Jun 16.

Article in English | MEDLINE | ID: mdl-32570423

12.

PhenoMeNal: processing and analysis of metabolomics data in the cloud.

Peters, Kristian; Bradbury, James; Bergmann, Sven; Capuccini, Marco; Cascante, Marta; de Atauri, Pedro; Ebbels, Timothy M D; Foguet, Carles; Glen, Robert; Gonzalez-Beltran, Alejandra; Günther, Ulrich L; Handakas, Evangelos; Hankemeier, Thomas; Haug, Kenneth; Herman, Stephanie; Holub, Petr; Izzo, Massimiliano; Jacob, Daniel; Johnson, David; Jourdan, Fabien; Kale, Namrata; Karaman, Ibrahim; Khalili, Bita; Emami Khonsari, Payam; Kultima, Kim; Lampa, Samuel; Larsson, Anders; Ludwig, Christian; Moreno, Pablo; Neumann, Steffen; Novella, Jon Ander; O'Donovan, Claire; Pearce, Jake T M; Peluso, Alina; Piras, Marco Enrico; Pireddu, Luca; Reed, Michelle A C; Rocca-Serra, Philippe; Roger, Pierrick; Rosato, Antonio; Rueedi, Rico; Ruttkies, Christoph; Sadawi, Noureddin; Salek, Reza M; Sansone, Susanna-Assunta; Selivanov, Vitaly; Spjuth, Ola; Schober, Daniel; Thévenot, Etienne A; Tomasoni, Mattia.

Gigascience ; 8(2)2019 02 01.

Article in English | MEDLINE | ID: mdl-30535405

13.

The Path-A metabolic pathway prediction web server.

Pireddu, Luca; Szafron, Duane; Lu, Paul; Greiner, Russell.

Nucleic Acids Res ; 34(Web Server issue): W714-9, 2006 Jul 01.

Article in English | MEDLINE | ID: mdl-16845105

14.

Recommendations on e-infrastructures for next-generation sequencing.

Spjuth, Ola; Bongcam-Rudloff, Erik; Dahlberg, Johan; Dahlö, Martin; Kallio, Aleksi; Pireddu, Luca; Vezzi, Francesco; Korpelainen, Eija.

Gigascience ; 5: 26, 2016 06 07.

Article in English | MEDLINE | ID: mdl-27267963

15.

Experiences with workflows for automating data-intensive bioinformatics.

Spjuth, Ola; Bongcam-Rudloff, Erik; Hernández, Guillermo Carrasco; Forer, Lukas; Giovacchini, Mario; Guimera, Roman Valls; Kallio, Aleksi; Korpelainen, Eija; Kandula, Maciej M; Krachunov, Milko; Kreil, David P; Kulev, Ognyan; Labaj, Pawel P; Lampa, Samuel; Pireddu, Luca; Schönherr, Sebastian; Siretskiy, Alexey; Vassilev, Dimitar.

Biol Direct ; 10: 43, 2015 Aug 19.

Article in English | MEDLINE | ID: mdl-26282399

16.

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

Michielan, Lisa; Pireddu, Luca; Floris, Matteo; Moro, Stefano.

Mol Inform ; 29(1-2): 51-64, 2010 Jan 12.

Article in English | MEDLINE | ID: mdl-27463848

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