Publications CRS4 - Equipe SCA

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Publications en 2013

Peer-reviewed publications in International Journals

[2-OSC13]

Genetic Variants Regulating Immune Cell Levels in Health and Disease

Valeria Orrú, Maristella Steri, Sidore Carlo, Francesca Virdis, Mariano Dei, Sandra Lai, Magdalena Zoledziewska, Fabio Busonero, Antonella Mulas, Matteo Floris, Wieslawa Mentzen, Silvana Urru, michele marongiu, Stefania Olla, MG Piras, Lobina M., Andrea Maschio, Maristella Pitzalis, Maria Francesca Urru, Marco Marcelli, Roberto Cusano, Francesca Deidda, Manuela Oppo, Rosella Pilu, Frederic Reinier, Riccardo Berutti, Luca Pireddu, Ilenia Zara, Eleonora Porcu, Alan Kwong , Christine Brennan , Brendan Tarrier, Hyun Kang , Robert Lyons, Sergio Uzzau, Rossano Atzeni, Maria Valentini, Firinu D., Lidia Leoni, Gianluca Rotta, Silvia Naitza, Andrea Angius, Mauro Congia, Michael Whalen, Christopher M. S. Jones, David Schlessinger, Gonçalo R. Abecasis, Edoardo Fiorillo, Serena Sanna, Francesco Cucca

Cell Elsevier Inc pages 242-256 vol. 155 num. 1 - september 2013 doi: 10.1016/j.cell.2013.08.041

[2-BML13]

Lentiviral Hematopoietic Stem Cell Gene Therapy Benefits Metachromatic Leukodystrophy

Alessandra Biffi, Eugenio Montini, Laura Lorioli, Martina Cesani, Francesca Fumagalli, Tiziana Plati, Cristina Baldoli, Sabata Martino, Andrea Calabria, Sabrina Canale, Fabrizio Benedicenti, Giuliana Vallanti, Luca Biasco, Simone Leo, Nabil Kabbara, Gianluigi Zanetti, William B. Rizzo, Nalini A. L. Mehta, Maria Pia Cicalese, Miriam Casiraghi, Jaap J. Boelens, Ubaldo Del Carro, David J. Dow, Manfred Schmidt, Andrea Assanelli, Victor Neduva, Clelia Di Serio, Elia Stupka, Jason Gardner, Christof von Kalle, Claudio Bordignon, Fabio Ciceri, Attilio Rovelli, Maria Grazia Roncarolo, Alessandro Aiuti, Maria Sessa, Luigi Naldini

Science AAAS pages 1233158 vol. 341 num. 6148 - august 2013 doi: 10.1126/science.1233158

[2-PCL13]

Automated and traceable processing for large-scale high-throughput sequencing facilities

Luca Pireddu, Gianmauro Cuccuru, Luca Lianas, Matteo Vocale, Giorgio Fotia, Gianluigi Zanetti

EMBnet.journal pages 23--24 vol. 19 Supplement A - june 2013
issn: 2226-6089 doi: 10.14806/ej.19.A.626

Peer-reviewed publications in international events

[4-CFM13]

Reproducible and automated processing in high-throughput NGS facilities

Gianmauro Cuccuru, Giorgio Fotia, Josh Moore, Luca Lianas, Luca Pireddu, Jason R. Swedlow, Gianluigi Zanetti

Contributed presentation at the Galaxy Community Conference 2013, Oslo,Norway - 30 June, 2 July - 201 - 2013

[4-CFL13]

Scalability, Reproducibility and Traceability in Large Scale NGS Facilities

Gianmauro Cuccuru, Giorgio Fotia, Simone Leo, Luca Lianas, Massimiliano Orsini, Andrea Pinna, Luca Pireddu, Andrea Sbardellati, Nicola Soranzo, Paolo Uva, Gianluigi Zanetti

Contributed presentation to Clinical Genomics & Informatics Europe, Lisbon, Portugal - 4, 6 December - 2013

Various talks, works and publications

[6-COS13]

Engaging Galaxy in Microbiology

Gianmauro Cuccuru, Massimiliano Orsini, Nicola Soranzo, Andrea Pinna, Andrea Sbardellati, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia

Poster presentation at the Galaxy Community Conference 2013, Oslo,Norway - 30 June, 2 July - 2013

[6-MPL13]

Dynamic Hadoop clusters on HPC scheduling systems

Michele Muggiri, Luca Pireddu, Simone Leo, Gianluigi Zanetti

Contributed presentation to the 2013 Workshop on Middleware for HPC and Big Data Systems (part of Euro-Par 2013) - august 2013

[6-PLZ13]

An Update on the Seal Hadoop-based Sequencing Processing Toolbox

Luca Pireddu, Simone Leo, Gianluigi Zanetti

Contributed presentation to the 14th Bioinformatics Open Source Conference - july 2013

[2-MBC13]

Integration Site Analysis in a Clinical Trial of Lentiviral Vector Based Hematopoietic Stem Cell Gene Therapy for Metachromatic Leukodystrophy. An 18 Months Follow-Up

Eugenio Montini, Alessandra Biffi, Andrea Calabria, Luca Biasco, Martina Cesani, Fabrizio Benedicenti, Tiziana Plati, Simone Leo, Victor Neduva, Gianluigi Zanetti, Alessandro Aiuti, David J. Dow, Christof von Kalle, Manfred Schmidt, Maria Sessa, Luigi Naldini

Molecular Therapy Nature Publishing Group pages S119 vol. 21 num. S1 - june 2013

[6-PIR13]

Data-intensive computing in NGS

Luca Pireddu

Contributed presentation to the Workshop on "ICT needs and challenges for Big Data in the Life Sciences" - june 2013

[2-RPM13]

ICT needs and challenges for Big Data in the Life Sciences

Babette Regierer, Luca Pireddu, Martijn Moné, Andreas Gisel

EMBnet.journal vol. 19 num. 1 - june 2013 doi: 10.14806/ej.19.1.699

[6-SHP13]

Scripting for large-scale sequencing based on Hadoop

André Schumacher, Keijo Heljanko, Luca Pireddu, Gianluigi Zanetti, Aleksi Kallio, Eija Korpelainen

poster - The Next NGS Challenge Conference: Data Processing and Integration 14-16 May 2013, Valencia, Spain - may 2013

Contractual reports

[7-BCZ13]

Quality assessment for different haplotyping methods and GWAS sensitivity to phasing errors

Giovanni Busonera, Marco Cogoni, Gianluigi Zanetti

CRS4 - 2013

Publications en 2012

Books and Book Chapters

[1-GAV12]

PaaSSOA: An Open PaaS Architecture for Service Oriented Applications

Claudio Guidi, Paolo Anedda, Tullio Vardanega

Service-Oriented and Cloud Computing, Springer Berlin Heidelberg Paoli, Flavio and Pimentel, Ernesto and Zavattaro, Gianluigi pages 208-209 vol. 7592 Lecture Notes in Computer Science - 2012

Peer-reviewed publications in International Journals

[2-ABM12]

OMERO: flexible, model-driven data management for experimental biology

Chris Allan, Jean-Marie Burel, Josh Moore, Colin Blackburn, Melissa Linkert, Scott Loynton, Donald MacDonald, William J. Moore, Carlos Neves, Andrew Patterson, Michael Porter, Aleksandra Tarkowska, Brian Loranger, Jerome Avondo, Ingvar Lagerstedt, Luca Lianas, Simone Leo, Katherine Hands, Ron T. Hay, Ardan Patwardhan, Christoph Best, Gerard J. Kleywegt, Gianluigi Zanetti, Jason R. Swedlow

Nature Methods pages 245--253 vol. 9 num. 3 - march 2012
issn: 1548-7091 doi: 10.1038/nmeth.1896

Peer-reviewed publications in international events

[4-ACL12]

Scalable data management and computable framework for large scale longitudinal studies

Chris Allan, Gianmauro Cuccuru, Simone Leo, Luca Lianas, Josh Moore, Maristella Pitzalis, Serena Sanna, Ilenia Zara, Jason R. Swedlow, Gianluigi Zanetti

Contributed presentation to Galaxy Community Conference 2012, Chicago (IL), United States - July 25 - 27 - 2012

[4-LPZ12]

SNP genotype calling with MapReduce

Simone Leo, Luca Pireddu, Gianluigi Zanetti

Proceedings of the third international workshop on MapReduce and its Applications ACM MapReduce '12 pages 49--56 - 2012
isbn: 978-1-4503-1343-8 doi: 10.1145/2287016.2287026

[4-SBB12]

The microwave holography system for the Sardinia Radio Telescope

Giampaolo Serra, Pietro Bolli, Giovanni Busonera, Tonino Pisanu, Sergio Poppi, Francesco Gaudiomonte, Giampaolo Zacchiroli, J. Roda, M. Morsiani, J.A. Lopez-Perez

Proceedings of SPIE: Ground-based and Airborne Telescopes IV - 2012

[4-GAV12]

Towards a new paas architecture generation

Claudio Guidi, Paolo Anedda, Tullio Vardanega

CLOSER 2012 - Proceedings of the 2nd International Conference on Cloud Computing and Services Science pages 279–282 ScitePress - april 2012

Various talks, works and publications

[5-DEL12]