Bioinformatics for Genomics in Malta

Project Information

BioGeMT

Grant agreement ID: 101086768

DOI

10.3030/101086768

EC signature date 24 October 2022

Start date 1 December 2022

End date 30 November 2027

Funded under

• Widening participation and spreading excellence

Total cost

€ 2 499 997,50

EU contribution

€ 2 499 997,50

Coordinated by

UNIVERSITA TA MALTA
Malta

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 (3)

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.

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

Author(s): Vlastimil Martinek, Andrea Gariboldi, Dimosthenis Tzimotoudis, Aitor Alberdi Escudero, Edward Blake, David Cechak, Luke Cassar, Alessandro Balestrucci, Panagiotis Alexiou
Published in: 2025
Publisher: Arxiv
DOI: 10.48550/ARXIV.2506.05542

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

Author(s): Stephanie Sammut, Katarina Gresova, Dimosthenis Tzimotoudis, Eva Marsalkova, David Cechak, Panagiotis Alexiou
Published in: 2025, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.14.623628

Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics

Author(s): Martinek, V; Martin, J; Belair, C; Payea, MJ; Malla, S; Alexiou, P; Maragkakis, M
Published in: bioRxiv, 2023, ISSN 2692-8205
Publisher: 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

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

Multiomics tools for improved atherosclerotic cardiovascular disease management

Author(s): Sopic, M; Vilne, B; Gerdts, E; Trindade, F; Uchida, S; Khatib, S; Bezzina Wettinger, S; Devaux, Y; Magni, P
Published in: Trends in Molecular Medicine, 2023, ISSN 1471-4914
Publisher: 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

Author(s): Victoria Stopa, Dimitra Dafou, Korina Karagianni, A. Yaël Nossent, Rosienne Farrugia, Yvan Devaux, Miron Sopic
Published in: Vascular Pharmacology, Issue 159, 2025, ISSN 1537-1891
Publisher: 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

Author(s): Stephanie Sammut, Katarina Gresova, Dimosthenis Tzimotoudis, Eva Marsalkova, David Cechak, Panagiotis Alexiou
Published in: Bioinformatics, Issue 41, 2025, ISSN 1367-4811
Publisher: Oxford University Press (OUP)
DOI: 10.1093/BIOINFORMATICS/BTAF233

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

Author(s): Piotr Radziński, Jakub Skrajny, Maurycy Moczulski, Michał A. Ciach, Dirk Valkenborg, Benjamin Balluff, Anna Gambin
Published in: Analytical Chemistry, Issue 97, 2025, ISSN 1520-6882
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.ANALCHEM.4C06913

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

Author(s): Roufou, Styliani; Griffin, Sholeem; Katsini, Lydia; Polanska, Monika; Van Impe, Jan F.M.; Alexiou, Panagiotis; Valdramidis, Vasilis P.
Published in: Gene Reports, 2024, ISSN 2452-0144
Publisher: 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

Author(s): 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,
Published in: Briefings in Bioinformatics, Issue 26, 2025, ISSN 1477-4054
Publisher: Oxford University Press (OUP)
DOI: 10.1093/BIB/BBAF526

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

Author(s): Vaculík, Ondřej; Chalupová, Eliška; Grešová, Katarína; Majtner, Tomáš; Alexiou, Panagiotis
Published in: Biology, 2023, ISSN 2079-7737
Publisher: MDPI
DOI: 10.3390/biology12101276

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

Author(s): Grešová, Katarína; Racek, Tomas; Martinek, Vlastimil; Cechak, David; Svobodova, Radka; Alexiou, Panagiotis
Published in: F1000Research, 2023, ISSN 2046-1402
Publisher: F1000 Research Ltd
DOI: 10.12688/f1000research.131014.1

Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics

Author(s): Vlastimil Martinek; Jessica Martin; Cedric Belair; Matthew J Payea; Sulochan Malla; Panagiotis Alexiou; Manolis Maragkakis
Published in: NAR Genomics and Bioinformatics, 2023, ISSN 2631-9268
Publisher: Oxford Academic
DOI: 10.1101/2023.11.17.567581

On the Complexities of Enabling Demonstrated Consent

Author(s): Panagiotis Alexiou, Joel Azzopardi, Claude Julien Bajada, Jean-Paul Ebejer, Gillian M. Martin, Nikolai Paul Pace
Published in: The American Journal of Bioethics, Issue 25, 2025, ISSN 1536-0075
Publisher: Informa UK Limited
DOI: 10.1080/15265161.2025.2470694

Identification of osteoporosis genes using family studies

Author(s): Marichela Schembri; Melissa M. Formosa; Melissa M. Formosa
Published in: Frontiers in Endocrinology, 2024, ISSN 1664-2392
Publisher: Frontiers Media
DOI: 10.3389/FENDO.2024.1455689

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

Author(s): Hejret, Vaclav; Varadarajan, Nandan Mysore; Klimentova, Eva; Gresova, Katarina; Giassa, Ilektra-Chara; Vanacova, Stepanka; Alexiou, Panagiotis
Published in: Scientific Reports, 2023, ISSN 2045-2322
Publisher: Nature Portfolio
DOI: 10.1038/s41598-023-49757-z

Book chapters (1)

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

Author(s): Panagiotis Alexiou, Aleksandra Gruca, José Basílio, Kanita Karaduzovic-Hadziabdic, David P. Kreil, Stephanie Bezzina Wettinger
Published in: Transcriptomics in Atherosclerosis, 2025
Publisher: Elsevier
DOI: 10.1016/B978-0-443-33064-3.00008-6