Building Data Rich Clinical Trials

Project Information

CCE_DART

Grant agreement ID: 965397

DOI

10.3030/965397

Project closed

EC signature date 18 January 2021

Start date 1 February 2021

End date 31 December 2025

Funded under

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

Total cost

No data

EU contribution

€ 5 999 411,25

Coordinated by

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

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

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.

Publications

Non-peer reviewed articles (6)

Next generation clinical trials: Seamless designs and master protocols

Author(s): Burdon, Abigail; Jaki, Thomas; Chen, Xijin; Mozgunov, Pavel; Zheng, Haiyan; Baird, Richard
Published in: arXiv, 2024, ISSN 0000-0000
Publisher: arXiv
DOI: 10.48550/arxiv.241122345

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

Author(s): Olena Berkovska, Igor Schliemann, Georgios Mermelekas, Nazlı Ezgi Özkan, Mahnaz Nikpour, Vilde Drageset Haakensen, Åslaug Helland, Janne Lehtiö, Lukas M. Orre
Published in: BioRxiv Preprints, 2026, ISSN 0000-0000
Publisher: BioRxiv
DOI: 10.64898/2026.01.20.700495

Publishing FAIR datasets from Bioimaging repositories

Author(s): Stefan Dvoretskii, Philipp Schader, Josh Moore, Marco Nolden
Published in: BioHackrXiv series SWAT4HCLS 2024, 2024, ISSN 0000-0000
Publisher: BioHackrXiv
DOI: 10.37044/osf.io/7whtf

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

Author(s): Delmas, Maxime; Wysocka, Magdalena; Freitas, André
Published in: arXiv, Issue 3, 2023, ISSN 2331-8422
Publisher: Cornell Tech
DOI: 10.48550/arxiv.2311.06364

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

Author(s): Wysocka, Magdalena; Wysocki, Oskar; Delmas, Maxime; Mutel, Vincent; Freitas, Andre
Published in: Crossref, Issue 2, 2023, ISSN 2331-8422
Publisher: Cornell Tech
DOI: 10.48550/arxiv.2305.17819

Multivariate group sequential tests for global summary statistics

Author(s): Burdon, Abigail J.; Jaki, Thomas
Published in: arXiv, 2024, ISSN 0000-0000
Publisher: 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

Author(s): Orre et al
Published in: Nature Cancer, Issue 26621347, 2021, Page(s) 1224-1242, ISSN 2662-1347
Publisher: 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

Author(s): Oskar Wysocki; Jessica Katharine Davies; Markel Vigo; Anne Caroline Armstrong; Dónal Landers; Rebecca Lee; André Freitas
Published 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, Issue 4, 2023, ISSN 0004-3702
Publisher: Elsevier BV
DOI: 10.1016/j.artint.2022.103839

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

Author(s): Magdalena Wysocka, Oskar Wysocki, Maxime Delmas, Vincent Mutel, André Freitas
Published in: Journal of Biomedical Informatics, Issue 158, 2025, Page(s) 104724, ISSN 1532-0464
Publisher: 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

Author(s): 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
Published in: BMC Cancer, Vol 23, Iss 1, Pp 1-10 (2023), Issue 7, 2023, ISSN 1471-2407
Publisher: BioMed Central
DOI: 10.1186/s12885-023-11262-x

Engaging European society at the forefront of cancer research and care

Author(s): Celis, Julio E; Ringborg, Ulrik; heitor, manuel; Berns, Anton; Albreht, Tit; GARRALDA, Elena; Baumann, Michael
Published in: Scientia, Issue 2, 2023, ISSN 1574-7891
Publisher: Elsevier BV
DOI: 10.1002/1878-0261.13423

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

Author(s): Xijin Chen, Pavel Mozgunov, Richard D Baird, Thomas Jaki
Published in: Statistical Methods in Medical Research, Issue 34, 2025, Page(s) 1665-1683, ISSN 0962-2802
Publisher: SAGE Publications
DOI: 10.1177/09622802251350457

The Porto European cancer research summit 2021

Author(s): 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
Published in: Molecular Oncology, 2021, ISSN 1574-7891
Publisher: Elsevier BV
DOI: 10.1002/1878-0261.13078

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

Author(s): Abigail J Burdon, Richard D Baird, Thomas Jaki
Published in: Statistical Methods in Medical Research, Issue 33, 2025, Page(s) 2098-2114, ISSN 0962-2802
Publisher: SAGE Publications
DOI: 10.1177/09622802241287711

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

Author(s): 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
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-42668-7

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

Author(s): Tamborero et al
Published in: Nature Cancer, Issue 26621347, 2022, ISSN 2662-1347
Publisher: Springer Nature
DOI: 10.1038/s43018-022-00332-x

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

Author(s): Jaki, Thomas; Burdon, Abigail; Chen, Xijin; Mozgunov, Pavel; Zheng, Haiyan; Baird, Richard
Published in: Crossref, Issue 189, 2023, ISSN 0959-8049
Publisher: 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

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

Transformers and the Representation of Biomedical Background Knowledge

Author(s): Wysocki, Oskar; Zhou, Zili; O'Regan, Paul; Ferreira, Deborah; Wysocka, Magdalena; Landers, Dónal; Freitas, André
Published in: Crossref, Issue 2, 2023, ISSN 0891-2017
Publisher: MIT Press
DOI: 10.1162/coli_a_00462

Conference proceedings (2)

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

Author(s): Magdalena Wysocka, Danilo Carvalho, Oskar Wysocki, Marco Valentino, Andre Freitas
Published 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, Page(s) 7235-7258
Publisher: Association for Computational Linguistics
DOI: 10.18653/v1/2025.naacl-long.371

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

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