Bioinformatics for Genomics in Malta

Projektinformationen

BioGeMT

ID Finanzhilfevereinbarung: 101086768

DOI

10.3030/101086768

EK-Unterschriftsdatum 24 Oktober 2022

Startdatum 1 Dezember 2022

Enddatum 30 November 2027

Finanziert unter

• Widening participation and spreading excellence

Gesamtkosten

€ 2 499 997,50

EU-Beitrag

€ 2 499 997,50

Koordiniert durch

UNIVERSITA TA MALTA
Malta

CORDIS bietet Links zu öffentlichen Ergebnissen und Veröffentlichungen von HORIZONT-Projekten.

Links zu Ergebnissen und Veröffentlichungen von RP7-Projekten sowie Links zu einigen Typen spezifischer Ergebnisse wie Datensätzen und Software werden dynamisch von OpenAIRE abgerufen.

Leistungen

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.

Veröffentlichungen

Other (3)

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

Autoren: Vlastimil Martinek, Andrea Gariboldi, Dimosthenis Tzimotoudis, Aitor Alberdi Escudero, Edward Blake, David Cechak, Luke Cassar, Alessandro Balestrucci, Panagiotis Alexiou
Veröffentlicht in: 2025
Herausgeber: Arxiv
DOI: 10.48550/ARXIV.2506.05542

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

Autoren: Stephanie Sammut, Katarina Gresova, Dimosthenis Tzimotoudis, Eva Marsalkova, David Cechak, Panagiotis Alexiou
Veröffentlicht in: 2025, ISSN 2692-8205
Herausgeber: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.14.623628

Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics

Autoren: Martinek, V; Martin, J; Belair, C; Payea, MJ; Malla, S; Alexiou, P; Maragkakis, M
Veröffentlicht in: bioRxiv, 2023, ISSN 2692-8205
Herausgeber: 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

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

Multiomics tools for improved atherosclerotic cardiovascular disease management

Autoren: Sopic, M; Vilne, B; Gerdts, E; Trindade, F; Uchida, S; Khatib, S; Bezzina Wettinger, S; Devaux, Y; Magni, P
Veröffentlicht in: Trends in Molecular Medicine, 2023, ISSN 1471-4914
Herausgeber: 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

Autoren: Victoria Stopa, Dimitra Dafou, Korina Karagianni, A. Yaël Nossent, Rosienne Farrugia, Yvan Devaux, Miron Sopic
Veröffentlicht in: Vascular Pharmacology, Ausgabe 159, 2025, ISSN 1537-1891
Herausgeber: 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

Autoren: Stephanie Sammut, Katarina Gresova, Dimosthenis Tzimotoudis, Eva Marsalkova, David Cechak, Panagiotis Alexiou
Veröffentlicht in: Bioinformatics, Ausgabe 41, 2025, ISSN 1367-4811
Herausgeber: Oxford University Press (OUP)
DOI: 10.1093/BIOINFORMATICS/BTAF233

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

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

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

Autoren: Roufou, Styliani; Griffin, Sholeem; Katsini, Lydia; Polanska, Monika; Van Impe, Jan F.M.; Alexiou, Panagiotis; Valdramidis, Vasilis P.
Veröffentlicht in: Gene Reports, 2024, ISSN 2452-0144
Herausgeber: 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

Autoren: 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,
Veröffentlicht in: Briefings in Bioinformatics, Ausgabe 26, 2025, ISSN 1477-4054
Herausgeber: Oxford University Press (OUP)
DOI: 10.1093/BIB/BBAF526

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

Autoren: Vaculík, Ondřej; Chalupová, Eliška; Grešová, Katarína; Majtner, Tomáš; Alexiou, Panagiotis
Veröffentlicht in: Biology, 2023, ISSN 2079-7737
Herausgeber: MDPI
DOI: 10.3390/biology12101276

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

Autoren: Grešová, Katarína; Racek, Tomas; Martinek, Vlastimil; Cechak, David; Svobodova, Radka; Alexiou, Panagiotis
Veröffentlicht in: F1000Research, 2023, ISSN 2046-1402
Herausgeber: F1000 Research Ltd
DOI: 10.12688/f1000research.131014.1

Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics

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

On the Complexities of Enabling Demonstrated Consent

Autoren: Panagiotis Alexiou, Joel Azzopardi, Claude Julien Bajada, Jean-Paul Ebejer, Gillian M. Martin, Nikolai Paul Pace
Veröffentlicht in: The American Journal of Bioethics, Ausgabe 25, 2025, ISSN 1536-0075
Herausgeber: Informa UK Limited
DOI: 10.1080/15265161.2025.2470694

Identification of osteoporosis genes using family studies

Autoren: Marichela Schembri; Melissa M. Formosa; Melissa M. Formosa
Veröffentlicht in: Frontiers in Endocrinology, 2024, ISSN 1664-2392
Herausgeber: Frontiers Media
DOI: 10.3389/FENDO.2024.1455689

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

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

Book chapters (1)

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

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