16 entries / 5 as first or co-first author

Publications

Everything, newest first. Journal articles, preprints and reviews together — the label next to the venue says which is which.

Also on Google Scholar.

1. 2026

   miRBind2 enables sequence-only prediction of miRNA binding and transcript repression

   David Čechák, Dimosthenis Tzimotoudis, Stephanie Sammut, Katarína Grešová, Eva Maršálková, David Farrugia, Panagiotis Alexiou

   Bioinformatics42(Supplement_2)

2. 2026

   AlphaFind v2: similarity search in AlphaFold DB and TED domains across structural contexts

   Terézia Slanináková, Adrián Rošinec, Jakub Čillík, Aleš Křenek, Katarína Grešová, Jana Porubská, Eva Maršálková, Jaroslav Olha, David Procházka, Lukáš Hejtmánek, Vlastislav Dohnal, Karel Berka, Radka Svobodová, Matej Antol

   Nucleic Acids Research54(W1), W206–W210

3. 2026

   SenCat: cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types

   Carlos Anerillas, Gisela Altés, Katarína Grešová, Dimitrios Tsitsipatis, Krystyna Mazan-Mamczarz, et al., Manolis Maragkakis, Nathan Basisty, Myriam Gorospe

   Molecular Cell86(13), 2605–2616.e8Shared second author

4. 2026

   Senescence: an overlooked VSMC phenotype and therapeutic opportunity?

   Allison B. Herman, Katarína Grešová, Manolis Maragkakis, Michael V. Autieri

   Arteriosclerosis, Thrombosis, and Vascular Biology46(1), 119–131Review

5. 2025

   miRBench: novel benchmark datasets for microRNA binding site prediction that mitigate against prevalent microRNA frequency class bias

   Stephanie Sammut, Katarína Grešová, Dimosthenis Tzimotoudis, Eva Maršálková, David Čechák, Panagiotis Alexiou

   Bioinformatics41(Supplement_1), i542–i551Co-first author

6. 2025

   Cell-specific RNA isoform remodeling in the aging mouse brain

   Abid Rehman, Megan Duffy, Katarína Grešová, Cedric Belair, Na Yang, Lin Wang, Christopher T. Lee, Matthew Payea, Sulochan Malla, Showkat Ahmad Dar, Payel Sen, Mark R. Cookson, Manolis Maragkakis

   bioRxivPreprint

7. 2025

   Viral infection induces Alzheimer's disease-related pathways and senescence in iPSC-derived neuronal models

   Hana Hříbková, Veronika Pospíšilová, Kateřina Amruz Černá, Tereza Váňová, Jan Haviernik, et al., Katarína Grešová, Manolis Maragkakis, et al., Daniel Růžek, Dáša Bohačiaková

   bioRxivPreprint

8. 2024

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

   Katarína Grešová, Tomáš Racek, Vlastimil Martinek, David Čechák, Radka Svobodová, Panagiotis Alexiou

   F1000Research12, 755First author

9. 2024

   AlphaFind: discover structure similarity across the proteome in AlphaFold DB

   David Procházka, Terézia Slanináková, Jaroslav Olha, Adrián Rošinec, Katarína Grešová, Miriama Jánošová, Jakub Čillík, Jana Porubská, Radka Svobodová, Vlastislav Dohnal, Matej Antol

   Nucleic Acids Research52(W1), W182–W186

10. 2023

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

    Václav Hejret, Nandan Mysore Varadarajan, Eva Klimentová, Katarína Grešová, Ilektra-Chara Giassa, Štěpánka Vaňáčová, Panagiotis Alexiou

    Scientific Reports13, 22895

11. 2023

    Transfer learning allows accurate RBP target site prediction with limited sample sizes

    Ondřej Vaculík, Eliška Chalupová, Katarína Grešová, Tomáš Majtner, Panagiotis Alexiou

    Biology12(10), 1276

12. 2023

    Genomic benchmarks: a collection of datasets for genomic sequence classification

    Katarína Grešová, Vlastimil Martinek, David Čechák, Petr Šimeček, Panagiotis Alexiou

    BMC Genomic Data24, 25First author

13. 2023

    Using attribution sequence alignment to interpret deep learning models for miRNA binding site prediction

    Katarína Grešová, Ondřej Vaculík, Panagiotis Alexiou

    Biology12(3), 369First author

14. 2022

    Small RNA targets: advances in prediction tools and high-throughput profiling

    Katarína Grešová, Panagiotis Alexiou, Ilektra-Chara Giassa

    Biology11(12), 1798First authorReview

15. 2022

    miRBind: a deep learning method for miRNA binding classification

    Eva Klimentová, Václav Hejret, Ján Krčmář, Katarína Grešová, Ilektra-Chara Giassa, Panagiotis Alexiou

    Genes13(12), 2323

16. 2022

    Fine-tuning transformers for genomic tasks

    Vlastimil Martinek, David Čechák, Katarína Grešová, Panagiotis Alexiou, Petr Šimeček

    bioRxivPreprint