Publications CRS4 - Equipe SCA

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Publications en 2018

Peer-reviewed publications in International Journals

[2-HKP18]

Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health

Petr Holub, Floriant Kohlmayer, Fabian Prasser, Michaela Th. Mayrhofer, Irene Schlünder, Gillian M. Martin, Sara Casati, Lefteris Koumakis, Andrea Wutte, Lukasz Kozera, Dominik Strapagiel, Gabriele Anton, Gianluigi Zanetti, Osman Ugur Sezerman, Maimuna Mendy, Dalibor Valik, Marialuisa Lavitrano, Georges Dagher, Kurt Zatloukal, GertJan B. van Ommen, Jan-Eric Litton

Biopreservation and Biobanking vol. 16 num. 2 - april 2018 doi: 10.1089/bio.2017.0110

Peer-reviewed publications in international events

[4-VPZ18]

Kafka Interfaces for Composable Streaming Genomics Pipelines

Francesco Versaci, Luca Pireddu, Gianluigi Zanetti

IEEE Conference on Biomedical and Health Informatics (BHI) - 2018

Various talks, works and publications

[2-MPR18]

Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

Pablo Moreno, Luca Pireddu, Pierrick Roger, Nuwan Goonasekera, Enis Afgan, Marius van den Beek, Sijin He, Anders Larsson, Christoph Ruttkies, Daniel Schober, David Johnson, Philippe Rocca-Serra, Ralf Weber, Bjoern Gruening, Reza M. Salek, Namrata Kale, Yasset Perez-Riverol, Irene Papatheodorou, Ola Spjuth, Steffen Neumann

bioRxiv Cold Spring Harbor Laboratory - december 2018 doi: 10.1101/488643

[2-PBB18]

PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud

Kristian Peters, James Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Timothy Ebbels, Carles Foguet, Robert Glen, Alejandra N. Gonzalez-Beltran, Evangelos Handakas, Thomas Hankemeier, Stephanie Herman, Kenneth Haug, Petr Holub, Massimiliano Izzo, Daniel Jacob, David Johnson, Fabien Jourdan, Namrata Kale, Ibrahim Karaman, Bita Khalili, Payam Emami Khoonsari, Kim Kultima, Samuel Lampa, Anders Larsson, Pablo Moreno, Steffen Neumann, Jon Ander Novella, Claire O Donovan, Jake TM Pearce, Alina Peluso, Luca Pireddu, Marco Enrico Piras, Michelle AC Reed, Philippe Rocca-Serra, Pierrick Roger, Antonio Rosato, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Vitaly Selivanov, Ola Spjuth, Daniel Schober, Etienne A. Thévenot, Mattia Tomasoni, merlijn van Rijswijk, Michael van Vliet, Mark Viant, Ralf Weber, Gianluigi Zanetti, Christoph Steinbeck

bioRxiv Cold Spring Harbor Laboratory - september 2018 doi: 10.1101/409151

[6-RJW18]

ISAcreate: a Galaxy tool for Prospective Data Management with ISA format support

Philippe Rocca-Serra, David Johnson, Ralf Weber, Pierrick Roger, Luca Pireddu, Massimiliano Izzo, Alejandra N. Gonzalez-Beltran, Susanna-Assunta Sansone

2018 Galaxy Community Conference - june 2018

Publications en 2017

Peer-reviewed publications in International Journals

[2-PPZ17]

wft4galaxy: A Workflow Testing Tool for Galaxy

Marco Enrico Piras, Luca Pireddu, Gianluigi Zanetti

Bioinformatics Oxford University Press - july 2017 doi: 10.1093/bioinformatics/btx461

[2-WML17]

Image Data Resource: a bioimage data integration and publication platform

Eleanor Williams, Josh Moore, Simon W. Li, Gabriella Rustici, Aleksandra Tarkowska, Anatole Chessel, Simone Leo, Bálint Antal, Richard K. Ferguson, Ugis Sarkans, Alvis Brazma, Rafael E. Carazo Salas, Jason R. Swedlow

Nature Methods Nature Publishing Group pages 775--781 vol. 14 - june 2017 doi: 10.1038/nmeth.4326

[2-CBZ17]

Ultrametricity of optimal transport substates for multiple interacting paths over a square lattice network

Marco Cogoni, Giovanni Busonera, Gianluigi Zanetti

Physical Review E Rapid Communications American Physical Society pages 030108 vol. 95 - march 2017 doi: 10.1103/PhysRevE.95.030108

Peer-reviewed publications in international events

[4-VPZ17]

Leveraging stream processing technology for genomics

Francesco Versaci, Luca Pireddu, Gianluigi Zanetti

14th Annual Meeting of the Bioinformatics Italian Society - 2017

[4-PPZ17]

Automating Galaxy Workflow Testing

Marco Enrico Piras, Luca Pireddu, Gianluigi Zanetti

14th Annual Meeting of the Bioinformatics Italian Society - 2017

Various talks, works and publications

[4-KMB17]

Interoperable and scalable metabolomics data analysis with microservices

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

bioRxiv Cold Spring Harbor Laboratory - november 2017 doi: 10.1101/213603

[6-VPZ17]

Distributed stream processing for genomics pipelines

Francesco Versaci, Luca Pireddu, Gianluigi Zanetti

poster - NETTAB 2017 Workshop on Methods, tools & platforms for Personalized Medicine in the Big Data Era - october 2017

[6-VPZ17]

Flink in genomics: Integrating Flink and Kafka in the standard genomic pipeline

Francesco Versaci, Luca Pireddu, Gianluigi Zanetti

Presentation at workshop FlinkForward 2017 - FlinkForward 2017 - september 2017

[2-PPZ17]

wft4galaxy: A Workflow Tester for Galaxy

Marco Enrico Piras, Luca Pireddu, Gianluigi Zanetti

bioRxiv Cold Spring Harbor Labs Journals - july 2017 doi: 10.1101/132001

[6-ACL17]

Integration, processing, and data analysis in the operational support of a large scale NGS core facility

Rossano Atzeni, Gianmauro Cuccuru, Luca Lianas, Ricardo Medda, Luca Pireddu, Paolo Uva, Ilenia Zara, Gianluigi Zanetti, Giorgio Fotia

Poster presentation at 14th Annual Meeting of the Bioinformatics Italian Society, July 5-7, 2017, Cagliari - july 2017

[6-UCA17]

Impact of sample size in variant identification from exome sequencing data

Paolo Uva, Gianmauro Cuccuru, Rossano Atzeni, Gianluigi Zanetti, Giorgio Fotia

Poster presentation at 14th Annual Meeting of the Bioinformatics Italian Society, July 5-7, 2017, Cagliari - july 2017

Contractual reports

[7-VPZ17]

Kafka Interfaces for Composable Streaming Genomics Pipelines

Francesco Versaci, Luca Pireddu, Gianluigi Zanetti

bioRxiv, Cold Spring Harbor Laboratory Publishing - august 2017

Publications en 2016

Peer-reviewed publications in International Journals

[2-SFM16]

Traceability Based Description of Clinical Processes: Extension of IHE Guidelines for Phlebotomy Workflows

Alessandro Sulis, Francesca Frexia, Vittorio Meloni, Massimo Gaggero, Mauro Del Rio, Riccardo Triunfo, Daniela Ghironi, Federico Caboni, Gianluigi Zanetti

EJBI - European Journal for Biomedical Informatics EuroMISE sr.o. pages en36--en44 vol. 12 - 2016

[2-CBZ16]

Transition to congestion in communication/computation networks for near-optimal and sub-optimal resource management via Montecarlo simulations

Marco Cogoni, Giovanni Busonera, Gianluigi Zanetti

Journal of Network and Computer Applications Elsevier - 2016 doi: 10.1016/j.jnca.2016.12.029

[2-DLF16]

A Scalable Data Access Layer to Manage Structured Heterogeneous Biomedical Data

Giovanni Delussu, Luca Lianas, Francesca Frexia, Gianluigi Zanetti

PLoS ONE plos one - december 2016 doi: 10.1371/journal.pone.0168004

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