Building Data Rich Clinical Trials

Informazioni relative al progetto

CCE_DART

ID dell’accordo di sovvenzione: 965397

DOI

10.3030/965397

Progetto chiuso

Data della firma CE 18 Gennaio 2021

Data di avvio 1 Febbraio 2021

Data di completamento 31 Dicembre 2025

Finanziato da

• SOCIETAL CHALLENGES - Health, demographic change and well-being

Costo totale

Nessun dato

Contributo UE

€ 5 999 411,25

Coordinato da

FUNDACIO PRIVADA INSTITUT D'INVESTIGACIO ONCOLOGICA DE VALL-HEBRON (VHIO)
Spain

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

Documents, reports (4)

Molecular standardization

[This Deliverable is co-lead by UCAM/KI]Technical specifications for non-invasive molecular monitoring approaches, including decision making thresholds for specific clinical trial scenarios.

Quality assurance guidelines and procedures

A set of quality assurance scientific and clinical principles to be applied in all work to be developed during the project

Imaging response

[This Deliverable is co-lead by UCAM/KI]Definition of new imaging and molecular markers, based on single or combination of measurements, for patient stratification and as early readouts for tumour progression and drug response.

Imaging standardization

[this Deliverable is co-lead by UCAM/KI]Development of a pipeline for multi-scanner image data standardization, processing and radiomics feature extraction.

Websites, patent fillings, videos etc. (1)

Project website

Creation of a public project website

Demonstrators, pilots, prototypes (1)

Initial workshop

Convene Workshop 1 between academic / pharma / regulatory stakeholders and publish workshop report.

Other (1)

BoB biorepository of data (front end)

[This Deliverable is co-lead by KI/HYVE]Deployment of a cBioPortal instance to navigate the generated data adapted to the CCE-DART clinical needs.

Pubblicazioni

Non-peer reviewed articles (6)

Next generation clinical trials: Seamless designs and master protocols

Autori: Burdon, Abigail; Jaki, Thomas; Chen, Xijin; Mozgunov, Pavel; Zheng, Haiyan; Baird, Richard
Pubblicato in: arXiv, 2024, ISSN 0000-0000
Editore: arXiv
DOI: 10.48550/arxiv.241122345

Mass spectrometry-based proteomics delivers in-depth proteome profiling of FFPE lung cancer biopsies from single glass slides

Autori: Olena Berkovska, Igor Schliemann, Georgios Mermelekas, Nazlı Ezgi Özkan, Mahnaz Nikpour, Vilde Drageset Haakensen, Åslaug Helland, Janne Lehtiö, Lukas M. Orre
Pubblicato in: BioRxiv Preprints, 2026, ISSN 0000-0000
Editore: BioRxiv
DOI: 10.64898/2026.01.20.700495

Publishing FAIR datasets from Bioimaging repositories

Autori: Stefan Dvoretskii, Philipp Schader, Josh Moore, Marco Nolden
Pubblicato in: BioHackrXiv series SWAT4HCLS 2024, 2024, ISSN 0000-0000
Editore: BioHackrXiv
DOI: 10.37044/osf.io/7whtf

Relation Extraction in underexplored biomedical domains: A diversity-optimised sampling and synthetic data generation approach

Autori: Delmas, Maxime; Wysocka, Magdalena; Freitas, André
Pubblicato in: arXiv, Numero 3, 2023, ISSN 2331-8422
Editore: Cornell Tech
DOI: 10.48550/arxiv.2311.06364

Large Language Models, scientific knowledge and factuality: A systematic analysis in antibiotic discovery

Autori: Wysocka, Magdalena; Wysocki, Oskar; Delmas, Maxime; Mutel, Vincent; Freitas, Andre
Pubblicato in: Crossref, Numero 2, 2023, ISSN 2331-8422
Editore: Cornell Tech
DOI: 10.48550/arxiv.2305.17819

Multivariate group sequential tests for global summary statistics

Autori: Burdon, Abigail J.; Jaki, Thomas
Pubblicato in: arXiv, 2024, ISSN 0000-0000
Editore: arXiv
DOI: 10.48550/arxiv.2405.05139

Peer reviewed articles (13)

Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms

Autori: Orre et al
Pubblicato in: Nature Cancer, Numero 26621347, 2021, Pagina/e 1224-1242, ISSN 2662-1347
Editore: Springer Nature
DOI: 10.1038/s43018-021-00259-9

Assessing the communication gap between AI models and healthcare professionals: Explainability, utility and trust in AI-driven clinical decision-making

Autori: Oskar Wysocki; Jessica Katharine Davies; Markel Vigo; Anne Caroline Armstrong; Dónal Landers; Rebecca Lee; André Freitas
Pubblicato in: Wysocki , O , Davies , J K , Vigo , M , Armstrong , A C , Landers , D , Lee , R & Freitas , A 2023 , ' Assessing the communication gap between AI models and healthcare professionals : Explainability, utility and trust in AI-driven clinical decision-making ' , Artificial Intelligence , vol. 316 , 103839 . https://doi.org/10.1016/j.artint.2022.103839, Numero 4, 2023, ISSN 0004-3702
Editore: Elsevier BV
DOI: 10.1016/j.artint.2022.103839

Large Language Models, scientific knowledge and factuality: A framework to streamline human expert evaluation

Autori: Magdalena Wysocka, Oskar Wysocki, Maxime Delmas, Vincent Mutel, André Freitas
Pubblicato in: Journal of Biomedical Informatics, Numero 158, 2025, Pagina/e 104724, ISSN 1532-0464
Editore: Academic Press
DOI: 10.1016/j.jbi.2024.104724

Public and patient involvement: a survey on knowledge, experience and opinions among researchers within a precision oncology European project

Autori: Paola Mosconi; Cinzia Colombo; Pasquale Paletta; Laura Gangeri; Chiara Pellegrini; Elena Garralda; Rosalba Miceli; Cinzia Brunelli; Irene Braña; Jordi Rodon; Guillermo Villacampa; Anna Pedrola; Rodrigo Dienstmann; Bianca Pont; Júlia Lostes; Alejandro Piris; Elena Chavarria; Xenia Villalobos; Berta Colldeforns; Raquel Pérez-López; Paolo Nuciforo; David Tamborero; Janne Lehtiö; Ali Razzak; Mari
Pubblicato in: BMC Cancer, Vol 23, Iss 1, Pp 1-10 (2023), Numero 7, 2023, ISSN 1471-2407
Editore: BioMed Central
DOI: 10.1186/s12885-023-11262-x

Engaging European society at the forefront of cancer research and care

Autori: Celis, Julio E; Ringborg, Ulrik; heitor, manuel; Berns, Anton; Albreht, Tit; GARRALDA, Elena; Baumann, Michael
Pubblicato in: Scientia, Numero 2, 2023, ISSN 1574-7891
Editore: Elsevier BV
DOI: 10.1002/1878-0261.13423

Using circulating tumor DNA as a novel biomarker of efficacy for dose-finding designs in oncology

Autori: Xijin Chen, Pavel Mozgunov, Richard D Baird, Thomas Jaki
Pubblicato in: Statistical Methods in Medical Research, Numero 34, 2025, Pagina/e 1665-1683, ISSN 0962-2802
Editore: SAGE Publications
DOI: 10.1177/09622802251350457

The Porto European cancer research summit 2021

Autori: Ulrik Ringborg , Anton Berns , Julio E Celis , Manuel Heitor , Josep Tabernero , Joachim Schüz , Michael Baumann , Rui Henrique , Matti Aapro , Partha Basu 8, Regina Beets-Tan , Benjamin Besse , Fátima Cardoso , Fátima Carneiro , Guy van den Eede , Alexander Eggermont , Stefan Fröhling , Susan Galbraith , Elena Garralda , Douglas Hanahan , Thomas Hofmarc
Pubblicato in: Molecular Oncology, 2021, ISSN 1574-7891
Editore: Elsevier BV
DOI: 10.1002/1878-0261.13078

Adaptive enrichment trial designs using joint modelling of longitudinal and time-to-event data

Autori: Abigail J Burdon, Richard D Baird, Thomas Jaki
Pubblicato in: Statistical Methods in Medical Research, Numero 33, 2025, Pagina/e 2098-2114, ISSN 0962-2802
Editore: SAGE Publications
DOI: 10.1177/09622802241287711

Development of mesothelioma-specific oncolytic immunotherapy enabled by immunopeptidomics of murine and human mesothelioma tumors

Autori: Jacopo Chiaro, Gabriella Antignani, Sara Feola, Michaela Feodoroff, Beatriz Martins, Hanne Cojoc, Salvatore Russo, Manlio Fusciello, Firas Hamdan, Valentina Ferrari, Daniele Ciampi, Ilkka Ilonen, Jari Räsänen, Mikko Mäyränpää, Jukka Partanen, Satu Koskela, Jarno Honkanen, Jussi Halonen, Lukasz Kuryk, Maria Rescigno, Mikaela Grönholm, Rui M. Branca, Janne Lehtiö, Vincenzo Cerullo
Pubblicato in: Nature Communications, Numero 14, 2023, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-42668-7

The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology

Autori: Tamborero et al
Pubblicato in: Nature Cancer, Numero 26621347, 2022, ISSN 2662-1347
Editore: Springer Nature
DOI: 10.1038/s43018-022-00332-x

Early phase clinical trials in oncology: Realising the potential of seamless designs

Autori: Jaki, Thomas; Burdon, Abigail; Chen, Xijin; Mozgunov, Pavel; Zheng, Haiyan; Baird, Richard
Pubblicato in: Crossref, Numero 189, 2023, ISSN 0959-8049
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.ejca.2023.05.005

A systematic review of biologically-informed deep learning models for cancer: fundamental trends for encoding and interpreting oncology data

Autori: Wysocka, Magdalena; Wysocki, Oskar; Zufferey, Marie; Landers, Dónal; Freitas, André
Pubblicato in: BMC Bioinformatics, Vol 24, Iss 1, Pp 1-31 (2023), Numero 1, 2023, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.21203/rs.3.rs-1970036/v1

Transformers and the Representation of Biomedical Background Knowledge

Autori: Wysocki, Oskar; Zhou, Zili; O'Regan, Paul; Ferreira, Deborah; Wysocka, Magdalena; Landers, Dónal; Freitas, André
Pubblicato in: Crossref, Numero 2, 2023, ISSN 0891-2017
Editore: MIT Press
DOI: 10.1162/coli_a_00462

Conference proceedings (2)

SylloBio-NLI: Evaluating Large Language Models on Biomedical Syllogistic Reasoning

Autori: Magdalena Wysocka, Danilo Carvalho, Oskar Wysocki, Marco Valentino, Andre Freitas
Pubblicato in: Proceedings of the 2025 Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers), 2025, Pagina/e 7235-7258
Editore: Association for Computational Linguistics
DOI: 10.18653/v1/2025.naacl-long.371

An LLM-based Knowledge Synthesis and Scientific Reasoning Framework for Biomedical Discovery

Autori: Oskar Wysocki, [e-mail] [e-mail], Danilo Carvalho, Alex Bogatu, [e-mail] [e-mail], [e-mail] [e-mail], [e-mail] [e-mail], Andre Freitas
Pubblicato in: Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (Volume 3: System Demonstrations), 2024, Pagina/e 355-364
Editore: Association for Computational Linguistics
DOI: 10.18653/v1/2024.acl-demos.34