Bioinformatics for Genomics in Malta

Informations projet

BioGeMT

N° de convention de subvention: 101086768

DOI

10.3030/101086768

Date de signature de la CE 24 Octobre 2022

Date de début 1 Decembre 2022

Date de fin 30 Novembre 2027

Financé au titre de

• Widening participation and spreading excellence

Coût total

€ 2 499 997,50

Contribution de l’UE

€ 2 499 997,50

Coordonné par

UNIVERSITA TA MALTA
Malta

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Other (2)

BT Recruitment completed

The recruitment of the BT will be coordinated by the ERA Chair assisted by the UM HRM&D following the protocol described in Section 1.2.1. It is expected that BT members will be recruited during the first 12 months of the project and proof or recruitment of team members will be submitted for this deliverable.

A letter confirming move of the ERA-Chair to a full-time post at the UM

The ERA-Chair will move to the UM to take up a full-time post within the University. The UM will provide confirmation that this move has taken place.

Documents, reports (6)

A list of BT members assigned to the UM research projects in D1.1

The BT will support bioinformatics requirements of multiple UM research groups. A member of the BT with the relevant skill set will be assigned to assist on each of the projects identified, spending a portion of their time on the assigned project working closely with researchers from the relevant UM group. This deliverable will be a list of the research groups/projects being supported and the BT member assigned to this role.

A report on training requirements and action plan

The needs of UM research groups will be surveyed to assess current background bioinformatics knowledge in areas that are fundamental for data analysis and interpretation, including: computer programming, Big Data processing and visualisation, awareness of publicly available resources and tools and knowledge of statistical methods. The need for professional training in grant and publication writing will also be assessed. A report will be drawn up summarising the information gathered from these activities and outlining a training action plan, and submitted as this deliverable

A plan for dissemination, exploitation and communication

A projected plan of dissemination activities to be held during the lifetime of the project will be drawn up.

A Scientific and Management Plan

Following a detailed internal assessment of the current infrastructure and genomic research at the UM the ERA Chair will develop a Scientific and Management plan that includes a strategy for the effective implementation of the BT. It is expected that the ERA Chair will include the relevant major -Omic and HTS projects currently underway at UM as described in Section 1.2.2.

Bioinformatics requirements (hardware and software) document

The ERA-Chair will set up one-to-one meetings with molecular biology research groups and identify local bioinformatics needs, and define computer storage and processing requirements of each project. The outcome of these meetings will generate the information required to satisfy this deliverable.

A consolidated ethics protocol for HTS work in a multi-Omic era

For this deliverable, an ethics protocol for high throughput sequencing work in a multi-Omic era approved by the University Research Ethics Committee will be set up with consent forms and information letters that can be readily adapted to multiple projects.

Websites, patent fillings, videos etc. (1)

Set-up of project website

A dedicated project website will be set up under the UM domain. This website will be maintained during the lifetime of the project.

Data Management Plan (1)

A Data Management Plan

A data management plan for bioinformatics projects at UM will be built and updated throughout the lifetime of the project.

Publications

Other (3)

Agentomics-ML: Autonomous Machine Learning Experimentation Agent for Genomic and Transcriptomic Data

Auteurs: Vlastimil Martinek, Andrea Gariboldi, Dimosthenis Tzimotoudis, Aitor Alberdi Escudero, Edward Blake, David Cechak, Luke Cassar, Alessandro Balestrucci, Panagiotis Alexiou
Publié dans: 2025
Éditeur: Arxiv
DOI: 10.48550/ARXIV.2506.05542

miRBench: novel benchmark datasets for microRNA binding site prediction that mitigate against prevalent microRNA Frequency Class Bias

Auteurs: Stephanie Sammut, Katarina Gresova, Dimosthenis Tzimotoudis, Eva Marsalkova, David Cechak, Panagiotis Alexiou
Publié dans: 2025, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.14.623628

Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics

Auteurs: Martinek, V; Martin, J; Belair, C; Payea, MJ; Malla, S; Alexiou, P; Maragkakis, M
Publié dans: bioRxiv, 2023, ISSN 2692-8205
Éditeur: bioRxiv
DOI: 10.1101/2023.11.17.567581

Peer reviewed articles (13)

An Automated Analysis of Homocoupling Defects Using MALDI-MS and Open-Source Computer Software

Auteurs: Maria Bochenek; Michał Aleksander Ciach; Sander Smeets; Omar Beckers; Jochen Vanderspikken; Błażej Miasojedow; Barbara Domżał; Dirk Valkenborg; Wouter Maes; Anna Gambin
Publié dans: Journal of the American Society for Mass Spectrometry, 2024, ISSN 1879-1123
Éditeur: ACS Publications
DOI: 10.1021/JASMS.4C00225

Multiomics tools for improved atherosclerotic cardiovascular disease management

Auteurs: Sopic, M; Vilne, B; Gerdts, E; Trindade, F; Uchida, S; Khatib, S; Bezzina Wettinger, S; Devaux, Y; Magni, P
Publié dans: Trends in Molecular Medicine, 2023, ISSN 1471-4914
Éditeur: Cell Press
DOI: 10.1016/j.molmed.2023.09.004

Epitranscriptomics in atherosclerosis: Unraveling RNA modifications, editing and splicing and their implications in vascular disease

Auteurs: Victoria Stopa, Dimitra Dafou, Korina Karagianni, A. Yaël Nossent, Rosienne Farrugia, Yvan Devaux, Miron Sopic
Publié dans: Vascular Pharmacology, Numéro 159, 2025, ISSN 1537-1891
Éditeur: Elsevier BV
DOI: 10.1016/J.VPH.2025.107496

miRBench: novel benchmark datasets for microRNA binding site prediction that mitigate against prevalent microRNA frequency class bias

Auteurs: Stephanie Sammut, Katarina Gresova, Dimosthenis Tzimotoudis, Eva Marsalkova, David Cechak, Panagiotis Alexiou
Publié dans: Bioinformatics, Numéro 41, 2025, ISSN 1367-4811
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/BIOINFORMATICS/BTAF233

Efficient Compression of Mass Spectrometry Images via Contrastive Learning-Based Encoding

Auteurs: Piotr Radziński, Jakub Skrajny, Maurycy Moczulski, Michał A. Ciach, Dirk Valkenborg, Benjamin Balluff, Anna Gambin
Publié dans: Analytical Chemistry, Numéro 97, 2025, ISSN 1520-6882
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.ANALCHEM.4C06913

Identification of genes used by Escherichia coli to mitigate climatic stress conditions

Auteurs: Roufou, Styliani; Griffin, Sholeem; Katsini, Lydia; Polanska, Monika; Van Impe, Jan F.M.; Alexiou, Panagiotis; Valdramidis, Vasilis P.
Publié dans: Gene Reports, 2024, ISSN 2452-0144
Éditeur: Elsevier BV
DOI: 10.1016/J.GENREP.2024.101998

Bottlenecks in advancing and applying multiomic data integration—common data resources as rate-limiting drivers—the high-impact use case of atherosclerotic cardiovascular disease

Auteurs: Stephanie Bezzina Wettinger, Kanita Karaduzovic-Hadziabdic, Ritienne Attard, Rosienne Farrugia, Brooke N Wolford, Marco Chierici, Giuseppe Jurman, Panagiotis Alexiou, José L Peñalvo, Rafael S Costa,
Publié dans: Briefings in Bioinformatics, Numéro 26, 2025, ISSN 1477-4054
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/BIB/BBAF526

Transfer Learning Allows Accurate RBP Target Site Prediction with Limited Sample Sizes

Auteurs: Vaculík, Ondřej; Chalupová, Eliška; Grešová, Katarína; Majtner, Tomáš; Alexiou, Panagiotis
Publié dans: Biology, 2023, ISSN 2079-7737
Éditeur: MDPI
DOI: 10.3390/biology12101276

RBP-Tar – a searchable database for experimental RBP binding sites

Auteurs: Grešová, Katarína; Racek, Tomas; Martinek, Vlastimil; Cechak, David; Svobodova, Radka; Alexiou, Panagiotis
Publié dans: F1000Research, 2023, ISSN 2046-1402
Éditeur: F1000 Research Ltd
DOI: 10.12688/f1000research.131014.1

Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics

Auteurs: Vlastimil Martinek; Jessica Martin; Cedric Belair; Matthew J Payea; Sulochan Malla; Panagiotis Alexiou; Manolis Maragkakis
Publié dans: NAR Genomics and Bioinformatics, 2023, ISSN 2631-9268
Éditeur: Oxford Academic
DOI: 10.1101/2023.11.17.567581

On the Complexities of Enabling Demonstrated Consent

Auteurs: Panagiotis Alexiou, Joel Azzopardi, Claude Julien Bajada, Jean-Paul Ebejer, Gillian M. Martin, Nikolai Paul Pace
Publié dans: The American Journal of Bioethics, Numéro 25, 2025, ISSN 1536-0075
Éditeur: Informa UK Limited
DOI: 10.1080/15265161.2025.2470694

Identification of osteoporosis genes using family studies

Auteurs: Marichela Schembri; Melissa M. Formosa; Melissa M. Formosa
Publié dans: Frontiers in Endocrinology, 2024, ISSN 1664-2392
Éditeur: Frontiers Media
DOI: 10.3389/FENDO.2024.1455689

Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation

Auteurs: Hejret, Vaclav; Varadarajan, Nandan Mysore; Klimentova, Eva; Gresova, Katarina; Giassa, Ilektra-Chara; Vanacova, Stepanka; Alexiou, Panagiotis
Publié dans: Scientific Reports, 2023, ISSN 2045-2322
Éditeur: Nature Portfolio
DOI: 10.1038/s41598-023-49757-z

Book chapters (1)

Integrating genomics, transcriptomics, proteomics, metabolomics, and other omics

Auteurs: Panagiotis Alexiou, Aleksandra Gruca, José Basílio, Kanita Karaduzovic-Hadziabdic, David P. Kreil, Stephanie Bezzina Wettinger
Publié dans: Transcriptomics in Atherosclerosis, 2025
Éditeur: Elsevier
DOI: 10.1016/B978-0-443-33064-3.00008-6