Mgr. Eva Maršálková

2025

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

  SAMMUT Stephanie GREŠOVÁ Katarína TZIMOTOUDIS Dimosthenis MARŠÁLKOVÁ Eva ČECHÁK David ALEXIOU Panagiotis

  Article in Periodical

  Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference, year: 2025, volume: 41, edition: 1, DOI

• Refining Structure-Based Search in AlphaFold DB: Including confidence metrics into AlphaFind

  SLANINÁKOVÁ Terézia MARŠÁLKOVÁ Eva GREŠOVÁ Katarína KŘENEK Aleš OĽHA Jaroslav PAVLÍK Tomáš ŠPRINGEROVÁ Pavlína SEHNAL David ANTOL Matej

  Conference abstract

  Year: 2025, type: Conference abstract

2024

• Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model

  SIKORA Maciej KLIMENTOVÁ Eva UCHAL Dawid ŠRÁMKOVÁ Denisa PERLINSKA Agata P NGUYEN Mai Lan KORPACZ Marta MALINOWSKA Roksana NOWAKOWSKI Szymon RUBACH Pawel ŠIMEČEK Petr SULKOWSKA Joanna I

  Article in Periodical

  Protein Science, year: 2024, volume: 33, edition: 7, DOI

2023

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

  HEJRET Václav VARADARAJAN Nandan Mysore KLIMENTOVÁ Eva GREŠOVÁ Katarína GIASSA Ilektra-Chara VAŇÁČOVÁ Štěpánka ALEXIOU Panagiotis

  Article in Periodical

  Scientific Reports, year: 2023, volume: 13, edition: 1, DOI

• The SAP domain of Ku facilitates its efficient loading onto DNA ends

  FULNEČEK Jaroslav KLIMENTOVÁ Eva CAIRO CALZADA Albert BUKOVČÁKOVÁ Soňa ALEXIOU Panagiotis PROKOP Zbyněk ŘÍHA Karel

  Article in Periodical

  Nucleic Acids Research, year: 2023, volume: 51, edition: 21, DOI

2022

• miRBind: a Deep Learning method for miRNA binding classification

  KLIMENTOVÁ Eva HEJRET Václav GREŠOVÁ Katarína GIASSA Ilektra-Chara ALEXIOU Panagiotis

  Conference abstract

  Year: 2022, type: Conference abstract

• miRBind: A Deep Learning Method for miRNA Binding Classification

  KLIMENTOVÁ Eva HEJRET Václav KRČMÁŘ Ján GREŠOVÁ Katarína GIASSA Ilektra-Chara ALEXIOU Panagiotis

  Article in Periodical

  GENES, year: 2022, volume: 13, edition: 12, DOI

• Noncanonical small RNA chimeras identified by AGO2-CLASH

  HEJRET Václav VARADARAJAN Nandan Mysore KLIMENTOVÁ Eva GIASSA Ilektra-Chara VAŇÁČOVÁ Štěpánka ALEXIOU Panagiotis

  Conference abstract

  Year: 2022, type: Conference abstract

2020

• PENGUINN: Precise Exploration of Nuclear G-Quadruplexes Using Interpretable Neural Networks

  KLIMENTOVÁ Eva POLÁČEK Jakub ŠIMEČEK Petr ALEXIOU Panagiotis

  Article in Periodical

  Frontiers in Genetics, year: 2020, volume: 11, edition: OCT, DOI