Bioinformatics for Genomics in Malta

Informacje na temat projektu

BioGeMT

Identyfikator umowy o grant: 101086768

DOI

10.3030/101086768

Data podpisania przez KE 24 Października 2022

Data rozpoczęcia 1 Grudnia 2022

Data zakończenia 30 Listopada 2027

Finansowanie w ramach

• Widening participation and spreading excellence

Koszt całkowity

€ 2 499 997,50

Wkład UE

€ 2 499 997,50

Koordynowany przez

UNIVERSITA TA MALTA
Malta

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Rezultaty

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.

Publikacje

Other (3)

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

Autorzy: Vlastimil Martinek, Andrea Gariboldi, Dimosthenis Tzimotoudis, Aitor Alberdi Escudero, Edward Blake, David Cechak, Luke Cassar, Alessandro Balestrucci, Panagiotis Alexiou
Opublikowane w: 2025
Wydawca: Arxiv
DOI: 10.48550/ARXIV.2506.05542

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

Autorzy: Stephanie Sammut, Katarina Gresova, Dimosthenis Tzimotoudis, Eva Marsalkova, David Cechak, Panagiotis Alexiou
Opublikowane w: 2025, ISSN 2692-8205
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.14.623628

Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics

Autorzy: Martinek, V; Martin, J; Belair, C; Payea, MJ; Malla, S; Alexiou, P; Maragkakis, M
Opublikowane w: bioRxiv, 2023, ISSN 2692-8205
Wydawca: 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

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

Multiomics tools for improved atherosclerotic cardiovascular disease management

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

Autorzy: Victoria Stopa, Dimitra Dafou, Korina Karagianni, A. Yaël Nossent, Rosienne Farrugia, Yvan Devaux, Miron Sopic
Opublikowane w: Vascular Pharmacology, Numer 159, 2025, ISSN 1537-1891
Wydawca: 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

Autorzy: Stephanie Sammut, Katarina Gresova, Dimosthenis Tzimotoudis, Eva Marsalkova, David Cechak, Panagiotis Alexiou
Opublikowane w: Bioinformatics, Numer 41, 2025, ISSN 1367-4811
Wydawca: Oxford University Press (OUP)
DOI: 10.1093/BIOINFORMATICS/BTAF233

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

Autorzy: Piotr Radziński, Jakub Skrajny, Maurycy Moczulski, Michał A. Ciach, Dirk Valkenborg, Benjamin Balluff, Anna Gambin
Opublikowane w: Analytical Chemistry, Numer 97, 2025, ISSN 1520-6882
Wydawca: American Chemical Society (ACS)
DOI: 10.1021/ACS.ANALCHEM.4C06913

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

Autorzy: Roufou, Styliani; Griffin, Sholeem; Katsini, Lydia; Polanska, Monika; Van Impe, Jan F.M.; Alexiou, Panagiotis; Valdramidis, Vasilis P.
Opublikowane w: Gene Reports, 2024, ISSN 2452-0144
Wydawca: 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

Autorzy: 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,
Opublikowane w: Briefings in Bioinformatics, Numer 26, 2025, ISSN 1477-4054
Wydawca: Oxford University Press (OUP)
DOI: 10.1093/BIB/BBAF526

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

Autorzy: Vaculík, Ondřej; Chalupová, Eliška; Grešová, Katarína; Majtner, Tomáš; Alexiou, Panagiotis
Opublikowane w: Biology, 2023, ISSN 2079-7737
Wydawca: MDPI
DOI: 10.3390/biology12101276

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

Autorzy: Grešová, Katarína; Racek, Tomas; Martinek, Vlastimil; Cechak, David; Svobodova, Radka; Alexiou, Panagiotis
Opublikowane w: F1000Research, 2023, ISSN 2046-1402
Wydawca: F1000 Research Ltd
DOI: 10.12688/f1000research.131014.1

Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics

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

On the Complexities of Enabling Demonstrated Consent

Autorzy: Panagiotis Alexiou, Joel Azzopardi, Claude Julien Bajada, Jean-Paul Ebejer, Gillian M. Martin, Nikolai Paul Pace
Opublikowane w: The American Journal of Bioethics, Numer 25, 2025, ISSN 1536-0075
Wydawca: Informa UK Limited
DOI: 10.1080/15265161.2025.2470694

Identification of osteoporosis genes using family studies

Autorzy: Marichela Schembri; Melissa M. Formosa; Melissa M. Formosa
Opublikowane w: Frontiers in Endocrinology, 2024, ISSN 1664-2392
Wydawca: Frontiers Media
DOI: 10.3389/FENDO.2024.1455689

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

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

Book chapters (1)

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

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