Publications CRS4 - Equipe SCA

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Publications en 2024

Peer-reviewed publications in International Journals

[2-OCM24]

Linking the ECRIN Metadata Repository with the BBMRI-ERIC Directory to connect clinical studies with related biobanks and collections

Christian Ohmann, Steve Canham, Kurt Majcen, Vittorio Meloni, Luca Pireddu, Alessandro Sulis, Giovanni Delussu, Francesca Frexia, Petr Holub

Open Research Europe vol. 4 num. 50 - 2024 doi: 10.12688/openreseurope.17131.1

[2-LCR24]

Recording provenance of workflow runs with RO-Crate

Simone Leo, Michael R Crusoe, Laura Rodriguez Navas, Raül Sirvent, Alexander Kanitz, Paul De Geest, Rudolf Wittner, Luca Pireddu, Daniel Garijo, Jose Maria Fernandez, Iacopo Colonnelli, Matej Gallo, Tazro Ohta, Hirotaka Suetake, Salvador Capella-Gutierrez, Renske de Wit, Bruno P. Kinoshita, Stian Soiland-Reyes

PLoS ONE Public Library of Science pages e0309210 vol. 19 num. 9 - september 2024 doi: 10.1371/journal.pone.0309210

Publications en 2023

Peer-reviewed publications in International Journals

[2-DFM23]

Cohort Profile: the Turin Prostate Cancer Prognostication (TPCP) Cohort

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

Frontiers in Oncology Frontiers vol. 13 - october 2023
issn: 2234-943X doi: 10.3389/fonc.2023.1242639

[2-HMB23]

Privacy Risks of Whole-Slide Image Sharing in Digital Pathology

Petr Holub, Heimo Müeller, Tomáš Bíl, Luca Pireddu, Markus Plass, Fabian Prasser, Irene Schlünder, Kurt Zatloukal, Rudolf Nenutil, Tomáš Brázdil

Nature Communications Springer Nature pages 2577 vol. 14 - may 2023
issn: 2041-1723 doi: 10.1038/s41467-023-37991-y

Peer-reviewed publications in international events

[4-GBS23]

The EOSC-Life Workflow Collaboratory for the Life Sciences

Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Ignacio Eguinoa, Bert Droesbeke, Herve Menager, Laura Rodriguez Navas, Jose Maria Fernandez, Bjorn Gruning, Simone Leo, Luca Pireddu, Michael R Crusoe, Johan Gustafsson, Salvador Capella-Gutierrez, Frederik Coppens

Proceedings of the 1st Conference on Research Data Infrastructure (CoRDI) - Connecting Communities TIB Open Publishing vol. 1 York Sure-Vetter, Carole Goble - september 2023
issn: 2941-296X doi: 10.52825/cordi.v1i.352

Various talks, works and publications

[6-LCR23]

Recording provenance of workflow runs with RO-Crate

preprint - arXiv - december 2023

[6-LEO23]

RO-Crate and workflow execution provenance

Simone Leo

Invited talk - OSA2Micro – An Open Science Approach for Microbiology data integration - july 2023

[6-GBS23]

WorkflowHub – a fair registry for workflows

Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Ignacio Eguinoa, Bert Droesbeke, Herve Menager, Laura Rodriguez Navas, Jose Maria Fernandez, Salvador Capella-Gutierrez, Michael R Crusoe, Bjorn Gruning, Simone Leo, Luca Pireddu, Marco Enrico Piras, Johan Gustafson, Phil Ewels, WorkflowHub Community, Frederik Coppens

Poster - ELIXIR All Hands 2023 - june 2023

[6-LRF23]

Making workflow provenance FAIR across workflow systems with Workflow Run RO-Crate

Simone Leo, Laura Rodriguez Navas, Jose Maria Fernandez, Paul De Geest, Luca Pireddu, Michael R Crusoe, Daniel Garijo, Iacopo Colonnelli, Raül Sirvent, Stian Soiland-Reyes

Poster - ELIXIR All Hands 2023 - june 2023

[6-SLC23]

Sharing data as machine-actionable objects using RO-Crate, Bioschemas and Signposting

Stian Soiland-Reyes, Simone Leo, Leyla Jael Castro, Peter Sefton, Carole Goble

Poster - ELIXIR All Hands 2023 - june 2023

[6-LEO23]

RO-Crate for workflow run provenance

Simone Leo

Talk - CWL Conference 2023 - february 2023

Publications en 2022

Books and Book Chapters

[1-AAB22]

The DeepHealth toolkit: a key European free and open-source software for Deep Learning and Computer Vision ready to exploit heterogeneous HPC and cloud architectures

Marco Aldinucci, David Atienza, Federico Bolelli, Mónica Caballero, Iacopo Colonnelli, José Flich, Jon A. Gómez, David González, Costantino Grana, Marco Grangetto, Simone Leo, Pedro López, Dana Oniga, Roberto Paredes, Luca Pireddu, Eduardo Quiñones, Tatiana Silva, Enzo Tartaglione, Marina Zapater

Springer, chap. , pages 183-202 Chapter - april 2022

Peer-reviewed publications in International Journals

[2-SSC22]

Packaging research artefacts with RO-Crate

Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, Jose Maria Fernandez, Daniel Garijo, Bjorn Gruning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble

Data Science IOS Press pages 97-138 vol. 5 num. 2 - july 2022 doi: 10.3233/DS-210053

[2-C.L22]

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

The Galaxy Community, ..., Simone Leo, . ...

Nucleic Acids Research - april 2022
issn: 0305-1048 doi: 10.1093/nar/gkac247

[2-ZGC22]

Prognostic Utility of the Gleason Grading System Revisions and Histopathological Factors Beyond Gleason Grade

Renata Zelic, Francesca Giunchi, Jessica Carlsson, Sabina Davidsson, Luca Lianas, Cecilia Mascia, Daniela Zugna, Luca Molinaro, Per Henrik Vincent, Gianluigi Zanetti, Ove Andrén, Lorenzo Richiardi, Olof Akre, Michelangelo Fiorentino, Andreas Pettersson

Clinical Epidemiology Dovepress pages 59-70 num. 14 - january 2022 doi: 10.2147/CLEP.S339140

Peer-reviewed publications in international events

[4-CBV22]

Estimating Peak-Hour Urban Traffic Congestion

Marco Cogoni, Giovanni Busonera, Francesco Versaci

Complex Networks 2022 Springer Complex Networks & Their Applications XI: Proceedings of The Eleventh International Conference on Complex Networks and their Applications: COMPLEX NETWORKS 2022 vol. 1 Hocine Cherifi, Rosario Nunzio Mantegna, Luis M. Rocha, Chantal Cherifi, Salvatore Miccichè - 2022

[4-DLA22]

AI support for accelerating histopathological slide examinations of prostate cancer in clinical studies

Mauro Del Rio, Luca Lianas, Oskar Aspegren, Giovanni Busonera, Francesco Versaci, Renata Zelic, Per Henrik Vincent, Simone Leo, Andreas Pettersson, Olof Akre, Luca Pireddu

ICIAP 2021 Proceedings Springer Image Analysis and Processing. ICIAP 2022 Workshops. ICIAP 2022. Lecture Notes in Computer Science pages 545-556 - 2022 doi: 10.1007/978-3-031-13321-3_48

Various talks, works and publications

[2-SSC22]

Creating lightweight FAIR Digital Objects with RO-Crate

Stian Soiland-Reyes, Peter Sefton, Leyla Jael Castro, Frederik Coppens, Daniel Garijo, Simone Leo, Marc Portier, Paul Groth

Research Ideas and Outcomes Pensoft Publishers pages e93937 vol. 8 - 2022 doi: 10.3897/rio.8.e93937

[2-DCS22]

Enhancing RDM in Galaxy by integrating RO-Crate

Paul De Geest, Frederik Coppens, Stian Soiland-Reyes, Ignacio Eguinoa, Simone Leo

Research Ideas and Outcomes Pensoft Publishers pages e95164 vol. 8 - 2022 doi: 10.3897/rio.8.e95164

[6-VB22]

Data loading in Digital Pathology image classification

Francesco Versaci, Giovanni Busonera

Invited talk - Scalperf'22, Bertinoro (FC), Italy - september 2022

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