Research

Publications

Alexiou, P., Azzopardi, J., Bajada, C. J., Ebejer, J. P., & Pace, N. P. (2025, April). On the Complexities of Enabling Demonstrated Consent. The American Journal of Bioethics, 25(4), 115-118. doi:https://doi.org/10.1080/15265161.2025.2470694

Bochenek, M., Ciach, M. A., Smeets, S., Beckers, O., Vanderspikken, J., Miasojedow, B., . . . Gambin, A. (2024, September). An Automated Analysis of Homocoupling Defects Using MALDI-MS and Open-Source Computer Software. Journal of the American Society for Mass Spectrometry, 35(10), 2256-2546. doi:10.1021/jasms.4c00225

Grešová, K., Racek, T., Martinek, V., Cechak, D., Svobodova, R., & Alexiou, P. (2023, June). RBP-Tar – a searchable database for experimental RBP binding sites. F1000Research, 12, 1-20. doi:https://doi.org/10.12688/f1000research.131014.1

Hejret, V., Varadarajan, N. M., Klimentova, E., Gresova, K., Giassa, I.-C., Vanacova, S., & Alexiou, P. (2023, December). Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation. Scientific Reports, 13, 1-9. doi:https://doi.org/10.1038/s41598-023-49757-z

Martinek, V., Martin, J., Belair, C., Payea, M., Malla, S., Alexiou, P., & Maragkakis, M. (2023, November). Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics. bioRxiv, 1-22. doi:https://doi.org/10.1101/2023.11.17.567581

Martinek, V., Martin, J., Belair, C., Payea, M., Malla, S., Alexiou, P., & Maragkakis, M. (2024, September). Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics. NAR Genomics and Bioinformatics, 6(3), 1-9. doi:https://doi.org/10.1093/nargab/lqae116

Sammut, S., Gresova, K., Tzimotoudis, D., Marsalkova, E., Cechak, D., & Alexiou, P. (2025, January). miRBench: A Comprehensive microRNA Binding Site Prediction Training and Benchmarking Dataset. bioRxiv, 1-12. doi:https://doi.org/10.1101/2024.11.14.623628

Sopic, M., Vilne, B., Gerdts, E., Trindade, F., Uchida, S., Khatib, S., . . . Magni, P. (2023, December). Multiomics tools for improved atherosclerotic cardiovascular disease management. Trends in Molecular Medicine, 29(12), 983-995. doi:https://doi.org/10.1016/j.molmed.2023.09.004

Stopa, V., Dafou, D., Karagianni, K., Nossent, A. Y., Farrugia, R., evaux, Y., & Sopic, M. o. (2025, June). Epitranscriptomics in atherosclerosis: Unraveling RNA modifications, editing and splicing and their implications in vascular disease. Vascular Pharmacology, 159, 1-15. doi:https://doi.org/10.1016/j.vph.2025.107496

Vaculík, O., Chalupová, E., Grešová, K., Majtner, T., & Alexiou, P. (2023, September). Transfer Learning Allows Accurate RBP Target Site Prediction with Limited Sample Sizes. Biology, 12(10), 1276. doi:10.3390/biology12101276

 

Grants

MALTAomics (IPAS+ from MCST Malta)

Security-first Federated Quantum Machine Learning for Genomics (Innovate, UK)

Women Molecular Biology of Atheromatosis (MINISTERIO DE CIENCIA E INNOVACIÓN, SPAIN)

Research Networking Scheme (RNS) Call 1 2024 (from Xjenza Malta in collaboration with the Central European Institute of Technology (CEITEC))

Data Integrity and Stewardship Cluster (DISC) (University of Malta)

MCST-TÜBİTAK (Sabanaci University, Turkey)

HORIZON-TMA-MSCA Postdoctoral Fellowship (University of Malta)


https://www.um.edu.mt/projects/biogemt/research/