Bioinformatics for Genomics in Malta

Informazioni relative al progetto

BioGeMT

ID dell’accordo di sovvenzione: 101086768

DOI

10.3030/101086768

Data della firma CE 24 Ottobre 2022

Data di avvio 1 Dicembre 2022

Data di completamento 30 Novembre 2027

Finanziato da

• Widening participation and spreading excellence

Costo totale

€ 2 499 997,50

Contributo UE

€ 2 499 997,50

Coordinato da

UNIVERSITA TA MALTA
Malta

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 (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.

Pubblicazioni

Other (3)

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

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

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

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

Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics

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

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

Multiomics tools for improved atherosclerotic cardiovascular disease management

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

Autori: Victoria Stopa, Dimitra Dafou, Korina Karagianni, A. Yaël Nossent, Rosienne Farrugia, Yvan Devaux, Miron Sopic
Pubblicato in: Vascular Pharmacology, Numero 159, 2025, ISSN 1537-1891
Editore: 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

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

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

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

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

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

Autori: 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,
Pubblicato in: Briefings in Bioinformatics, Numero 26, 2025, ISSN 1477-4054
Editore: Oxford University Press (OUP)
DOI: 10.1093/BIB/BBAF526

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

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

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

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

Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics

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

On the Complexities of Enabling Demonstrated Consent

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

Identification of osteoporosis genes using family studies

Autori: Marichela Schembri; Melissa M. Formosa; Melissa M. Formosa
Pubblicato in: Frontiers in Endocrinology, 2024, ISSN 1664-2392
Editore: Frontiers Media
DOI: 10.3389/FENDO.2024.1455689

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

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

Book chapters (1)

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

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