Výpis publikací

SLANINÁKOVÁ, Terézia; Adrián ROŠINEC; Jakub ČILLÍK; Aleš KŘENEK; Katarína GREŠOVÁ; Jana PORUBSKÁ; Eva MARŠÁLKOVÁ; Jaroslav OĽHA; David PROCHÁZKA; Lukáš HEJTMÁNEK; Vlastislav DOHNAL; Karel BERKA; Radka SVOBODOVÁ a Matej ANTOL. AlphaFind v2: Similarity Search in AlphaFold DB and TED Domains across Structural Contexts - data. 2026. Dostupné z: https://doi.org/10.58074/mv1w-y227.

SLANINÁKOVÁ, Terézia; Adrián ROŠINEC; Tomáš PAVLÍK; Róbert RANDIAK; Tomáš SVOBODA; Tomáš RAČEK; Gabriela BUČEKOVÁ; Ondřej SCHINDLER; Matej ANTOL; Aleš KŘENEK; Karel BERKA a Radka SVOBODOVÁ. GROMACS MetaDump: A tool to describe molecular dynamics simulations with powerful metadata. 2026.

ROŠINEC, Adrián; Tomáš PAVLÍK; Terézia SLANINÁKOVÁ; Aleš KŘENEK; Matej ANTOL a Radka SVOBODOVÁ. MDFind: Federated search for molecular dynamics data. 2026. Dostupné z: https://doi.org/10.5281/zenodo.18740944.

SLANINÁKOVÁ, Terézia; Jaroslav OĽHA; David PROCHÁZKA; Matej ANTOL a Vlastislav DOHNAL. On the Costs and Benefits of Learned Indexing for Dynamic High-Dimensional Data. In Carson K. Leung, Anton Dignös, Gabriele Kotsis, A. Min Tjoa, Ismail Khalil. Big Data Analytics and Knowledge Discovery 27th International Conference, DaWaK 2025, Bangkok, Thailand, August 25–27, 2025, Proceedings. 1. vyd. Cham: Springer Cham, 2026, s. 251-258. ISBN 978-3-032-02214-1. Dostupné z: https://doi.org/10.1007/978-3-032-02215-8_20.

CAPANDOVÁ, Michaela; Jaroslav JURÁČEK; Veronika AMBROZOVÁ a Matej ANTOL. Advancing research by unlocking the full value of scientific data. In 3. Offsite Meeting of the Department of Histology and Embryology (ÚHE): Advancing Science and Collaboration; Pavlov, Czech Republic (June 4–6, 2025). 2025. ISBN 978-80-280-0733-1.

SLANINÁKOVÁ, Terézia; Jakub ČILLÍK; Adrián ROŠINEC; Katarína GREŠOVÁ; Aleš KŘENEK; Jana PORUBSKÁ; Radka SVOBODOVÁ a Matej ANTOL. AlphaFind 2.0 – Enhanced structural similarity search for AlphaFold database. In EOSC Long Live Research Data 2025, Ostrava, Czech Republic. 2025.

OĽHA, Jaroslav; Jana HOZZOVÁ; Matej ANTOL a Jiří FILIPOVIČ. Estimating resource budgets to ensure autotuning efficiency. PARALLEL COMPUTING. NETHERLANDS: ELSEVIER, 2025, roč. 2025, č. 123, s. 1-15. ISSN 0167-8191. Dostupné z: https://doi.org/10.1016/j.parco.2025.103126.

ROŠINEC, Adrián; Terézia SLANINÁKOVÁ; Tomáš PAVLÍK; Róbert RANDIAK; Tomáš SVOBODA; Tomáš RAČEK; Gabriela BUČEKOVÁ; Ondřej SCHINDLER; Matej ANTOL; Aleš KŘENEK; Karel BERKA a Radka SVOBODOVÁ. GROMACS MetaDump. 2025.

ROŠINEC, Adrián; Terézia SLANINÁKOVÁ; Tomáš PAVLÍK; Róbert RANDIAK; Tomáš SVOBODA; Tomáš RAČEK; Gabriela BUČEKOVÁ; Ondřej SCHINDLER; Matej ANTOL; Aleš KŘENEK; Karel BERKA a Radka SVOBODOVÁ. Gromacs MetaDump: a tool for extracting GROMACS simulation metadata. Journal of Cheminformatics. BMC, 2025, roč. 17, č. 1, s. 160-169. ISSN 1758-2946. Dostupné z: https://doi.org/10.1186/s13321-025-01082-5.

SLANINÁKOVÁ, Terézia; Jaroslav OĽHA; David PROCHÁZKA; Matej ANTOL a Vlastislav DOHNAL. On the Costs and Benefits of Learned Indexing for Dynamic High-Dimensional Data: Extended Version. arXiv, 2025, 16 s. N/A. Dostupné z: https://doi.org/10.48550/arXiv.2507.05865.

SLANINÁKOVÁ, Terézia; Eva MARŠÁLKOVÁ; Katarína GREŠOVÁ; Aleš KŘENEK; Jaroslav OĽHA; Tomáš PAVLÍK; Pavlína ŠPRINGEROVÁ; David SEHNAL a Matej ANTOL. Refining Structure-Based Search in AlphaFold DB: Including confidence metrics into AlphaFind. In CZECH PHD BIOINFORMATICS CONFERENCE. 2025. Dostupné z: https://doi.org/10.5281/zenodo.15103129.

PROCHÁZKA, David; Terézia SLANINÁKOVÁ; Jozef ČERŇANSKÝ; Jaroslav OĽHA; Matej ANTOL a Vlastislav DOHNAL. Scaling Learned Metric Index to 100M Datasets. In Edgar Chávez, Benjamin Kimia, Jakub Lokoč, Marco Patella, Jan Sedmidubsky. SIMILARITY SEARCH AND APPLICATIONS, SISAP 2024. BERLIN: Springer, 2025, s. 266-273. ISBN 978-3-031-75822-5. Dostupné z: https://doi.org/10.1007/978-3-031-75823-2_22.

CAPANDOVÁ, Michaela; Veronika SEDLÁKOVÁ; Zbyněk VORÁČ; Hana KOTASOVÁ; Jana DUMKOVÁ; Lukáš MORÁŇ; Josef JAROŠ; Matej ANTOL; Dáša BOHAČIAKOVÁ a Aleš HAMPL. Using Polycaprolactone Nanofibers for the Proof-of-Concept Construction of the Alveolar-Capillary Interface. JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART A. Hoboken: WILEY, 2025, roč. 113, č. 1, s. 1-16. ISSN 1549-3296. Dostupné z: https://doi.org/10.1002/jbm.a.37824.

SLANINÁKOVÁ, Terézia; David PROCHÁZKA; Jaroslav OĽHA; Adrián ROŠINEC; Katarína GREŠOVÁ; Jakub ČILLÍK; Miriama JÁNOŠOVÁ; Jana PORUBSKÁ; Radka SVOBODOVÁ; Vlastislav DOHNAL a Matej ANTOL. AlphaFind — discover structure similarity across the proteome in AlphaFold DB. In Elixir All-Hands 2024. 2024. Dostupné z: https://doi.org/10.7490/f1000research.1119872.1.

GREŠOVÁ, Katarína; Pavlína ŠPRINGEROVÁ; Terézia SLANINÁKOVÁ; David PROCHÁZKA; Jaroslav OĽHA; Adrián ROŠINEC; Miriama JÁNOŠOVÁ; Jakub ČILLÍK; Jana PORUBSKÁ; Radka SVOBODOVÁ; Vlastislav DOHNAL a Matej ANTOL. AlphaFind — discover structure similarity across the proteome in AlphaFold DB. In ECCB2024. 2024.

PROCHÁZKA, David; Terézia SLANINÁKOVÁ; Jaroslav OĽHA; Adrián ROŠINEC; Katarína GREŠOVÁ; Miriama JÁNOŠOVÁ; Jakub ČILLÍK; Jana PORUBSKÁ; Radka SVOBODOVÁ; Vlastislav DOHNAL a Matej ANTOL. AlphaFind: Discover structure similarity across the entire known proteome. Cold Spring Harbor, USA: bioRxiv, 2024, 6 s. N/A. Dostupné z: https://doi.org/10.1101/2024.02.15.580465.

NOVOTNÁ, Lucie; Terézia SLANINÁKOVÁ; David PROCHÁZKA; Lukáš HEJTMÁNEK; Katarína GREŠOVÁ; Jaroslav OĽHA; Vlastislav DOHNAL; Adrián ROŠINEC a Matej ANTOL. AlphaFind: Discover structure similarity across the entire known proteome – data and model. 2024. Dostupné z: https://doi.org/10.48700/datst.d35zf-1ja47.

PROCHÁZKA, David; Terézia SLANINÁKOVÁ; Jaroslav OĽHA; Adrián ROŠINEC; Katarína GREŠOVÁ; Miriama JÁNOŠOVÁ; Jakub ČILLÍK; Jana PORUBSKÁ; Radka SVOBODOVÁ; Vlastislav DOHNAL a Matej ANTOL. AlphaFind: discover structure similarity across the proteome in AlphaFold DB. Nucleic acids research. Oxford: Oxford University Press, 2024, roč. 52, W1, s. "W182"-"W186", 5 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkae397.

ROŠINEC, Adrián; Tomáš PAVLÍK; Terézia SLANINÁKOVÁ; Aleš KŘENEK; Pavlína ŠPRINGEROVÁ; Matej ANTOL a Radka SVOBODOVÁ. Beyond Metadata: Leveraging Similarity Search in Molecular Dynamics Data. In 2nd BioExcel Conference on Advances in Biomolecular Simulations. 2024. Dostupné z: https://doi.org/10.5281/zenodo.14500696.

CAPANDOVÁ, Michaela; Veronika SEDLÁKOVÁ; Zbyněk VORÁČ; Hana KOTASOVÁ; Jana DUMKOVÁ; Lukáš MORÁŇ; Josef JAROŠ; Matej ANTOL; Dáša BOHAČIAKOVÁ a Aleš HAMPL. Cells, biomaterials, infrastructure; and the value of the data. In 2. Offsite Meeting of the Department of Histology and Embryology (ÚHE): Advancing Science and Collaboration. 2024. ISBN 978-80-280-0587-0.

ANTOL, Matej; Jiří MAREK; Michaela CAPANDOVÁ; Jaroslav JURÁČEK a Luděk MATYSKA. EOSC CZ: Towards the development of Czech national ecosystem for FAIR research data. arXiv, 2024, 2 s.

SLANINÁKOVÁ, Terézia; Katarína GREŠOVÁ; David PROCHÁZKA; Viktória SPIŠAKOVÁ; Adrián ROŠINEC; Jakub ČILLÍK; Pavlína ŠPRINGEROVÁ; Aleš KŘENEK; Vlastislav DOHNAL; Radka SVOBODOVÁ a Matej ANTOL. Fast, structure-based searching in a large-scale protein data repository. In ELIXIR CZ Annual Conference. 2024. Dostupné z: https://doi.org/10.13140/RG.2.2.31355.53281.

NOVOTNÁ, Lucie; Terézia SLANINÁKOVÁ; David PROCHÁZKA; Lukáš HEJTMÁNEK; Adrián ROŠINEC; Jaroslav OĽHA; Katarína GREŠOVÁ; Vlastislav DOHNAL a Matej ANTOL. GraSR: Protein structural embeddings of AlphaFold DB. 2024.

NOVOTNÁ, Lucie; Terézia SLANINÁKOVÁ; David PROCHÁZKA; Lukáš HEJTMÁNEK; Adrián ROŠINEC; Jaroslav OĽHA; Katarína GREŠOVÁ; Vlastislav DOHNAL a Matej ANTOL. LMI-10: Protein structural embeddings of AlphaFold DB. 2024.

NOVOTNÁ, Lucie; Terézia SLANINÁKOVÁ; David PROCHÁZKA; Lukáš HEJTMÁNEK; Adrián ROŠINEC; Jaroslav OĽHA; Katarína GREŠOVÁ; Vlastislav DOHNAL a Matej ANTOL. LMI-30: Protein structural embeddings of AlphaFold DB. 2024.

NOVOTNÁ, Lucie; Terézia SLANINÁKOVÁ; David PROCHÁZKA; Lukáš HEJTMÁNEK; Adrián ROŠINEC; Jaroslav OĽHA; Katarína GREŠOVÁ; Vlastislav DOHNAL a Matej ANTOL. 3D-af-Surfer: Protein structural embeddings of AlphaFold DB. 2024. Dostupné z: https://doi.org/10.48700/datst.tbws0-hj147.

NOVOTNÁ, Lucie; Terézia SLANINÁKOVÁ; David PROCHÁZKA; Lukáš HEJTMÁNEK; Adrián ROŠINEC; Jaroslav OĽHA; Katarína GREŠOVÁ; Vlastislav DOHNAL a Matej ANTOL. 3DZD: Protein structural embeddings of AlphaFold DB v4. 2024. Dostupné z: https://doi.org/10.48700/datst.t45hr-bcw17.

NOVOTNÁ, Lucie; Terézia SLANINÁKOVÁ; David PROCHÁZKA; Lukáš HEJTMÁNEK; Adrián ROŠINEC; Jaroslav OĽHA; Katarína GREŠOVÁ; Vlastislav DOHNAL a Matej ANTOL. 3DZD: Protein structural embeddings of ESM Atlas. 2024.

DAUBNER, Lukáš; Raimundas MATULEVICIUS; Barbora BÜHNOVÁ; Matej ANTOL; Michal RŮŽIČKA a Tomáš PITNER. A Case Study on the Impact of Forensic-Ready Information Systems on the Security Posture. Online. In Advanced Information Systems Engineering. Cham: Springer Nature Switzerland, 2023, s. 522-538. ISBN 978-3-031-34559-3. Dostupné z: https://doi.org/10.1007/978-3-031-34560-9_31.

LAMOTHE, Lucie; Jennifer R B JENSEN; Hans IENASESCU; Ove J R GUSTAFSSON; Alban GAIGNARD; Dmitry REPCHEVSKY; Radka SVOBODOVÁ; Tomáš RAČEK; Adrián ROŠINEC; Matej ANTOL a Hervé MÉNAGER. An Evaluation of EDAM Coverage in the Tools Ecosystem and Prototype Integration of Galaxy and Workflowhub Systems. BioHackrXiv. 2023, s. 1-10. Dostupné z: https://doi.org/10.37044/osf.io/79kje.

CAPANDOVÁ, Michaela; Veronika SEDLÁKOVÁ; Dáša BOHAČIAKOVÁ; Hana KOTASOVÁ; Vendula PELKOVÁ; Zbyněk VORÁČ; Matej ANTOL a Aleš HAMPL. By leaps and bounds: From in vitro lung tissue models to fostering collaboration in science. In The Annual PhD Conference in Biomedical Sciences. 2023.

ANTOL, Matej; Michal RŮŽIČKA; Luděk MATYSKA a Jiří MAREK. Public (Health) Sector and Academia. In Martin Komenda. Data-Driven Decision-Making in Medical Education and Healthcare. First edition. Brno: Masaryk University, 2023, s. 51-66. Data Rulezzzz! ISBN 978-80-280-0392-0.

SLANINÁKOVÁ, Terézia; Matej ANTOL; Jaroslav OĽHA; Vlastislav DOHNAL; Susana LADRA a Miguel A. MARTÍNEZ-PRIETO. Reproducible experiments with Learned Metric Index Framework. Information systems. Elsevier, 2023, roč. 118, č. 1, s. 102255-102270. ISSN 0306-4379. Dostupné z: https://doi.org/10.1016/j.is.2023.102255.

SLANINÁKOVÁ, Terézia; David PROCHÁZKA; Matej ANTOL; Jaroslav OĽHA a Vlastislav DOHNAL. SISAP 2023 Indexing Challenge – Learned Metric Index. In Pedreira, O., Estivill-Castro, V. Similarity Search and Applications. SISAP 2023. Lecture Notes in Computer Science, vol 14289. Cham: Springer, 2023, s. 282-290. ISBN 978-3-031-46993-0. Dostupné z: https://doi.org/10.1007/978-3-031-46994-7_24.

OĽHA, Jaroslav; Terézia SLANINÁKOVÁ; Martin GENDIAR; Matej ANTOL a Vlastislav DOHNAL. Learned Indexing in Proteins: Extended Work on Substituting Complex Distance Calculations with Embedding and Clustering Techniques. arXiv, 2022. Dostupné z: https://doi.org/10.48550/ARXIV.2208.08910.

OĽHA, Jaroslav; Terézia SLANINÁKOVÁ; Martin GENDIAR; Matej ANTOL a Vlastislav DOHNAL. Learned Indexing in Proteins: Substituting Complex Distance Calculations with Embedding and Clustering Techniques. In Tomáš Skopal, Fabrizio Falchi, Jakub Lokoč, Maria Luisa Sapino, Ilaria Bartolini, Marco Patella. Similarity Search and Applications, 15th International Conference, SISAP 2022, Bologna, Italy, October 5–7, 2022, Proceedings. 1. vyd. Cham: Springer Cham, 2022, s. 274-282. ISBN 978-3-031-17848-1. Dostupné z: https://doi.org/10.1007/978-3-031-17849-8_22.

SPIŠAKOVÁ, Viktória; Adrián ROŠINEC; Lukáš HEJTMÁNEK a Matej ANTOL. Managed Kubernetes — Next Gen Academic Infrastructure? In EGI Conference 2022. 2022.

SLANINÁKOVÁ, Terézia; Matej ANTOL; Jaroslav OĽHA a Vlastislav DOHNAL. Data-driven Learned Metric Index: an Unsupervised Approach. In 14th International Conference on Similarity Search and Applications (SISAP 2021). Cham: Springer, 2021, s. 81-94. ISBN 978-3-030-89656-0. Dostupné z: https://doi.org/10.1007/978-3-030-89657-7_7.

ANTOL, Matej; Jaroslav OĽHA; Terézia SLANINÁKOVÁ a Vlastislav DOHNAL. Learned metric index - proposition of learned indexing for unstructured data. Information Systems. Elsevier, 2021, roč. 100, č. 101774, s. 1-12. ISSN 0306-4379. Dostupné z: https://doi.org/10.1016/j.is.2021.101774.

ANTOL, Matej; Miriama JÁNOŠOVÁ a Vlastislav DOHNAL. Metric hull as similarity-aware operator for representing unstructured data. Pattern Recognition Letters. Amsterdam: Elsevier, 2021, roč. 149, September 2021, s. 91-98. ISSN 0167-8655. Dostupné z: https://doi.org/10.1016/j.patrec.2021.05.011.

ANTOL, Matej a Vlastislav DOHNAL. BM-index: Balanced Metric Space Index based on Weighted Voronoi Partitioning. In Lecture Notes in Computer Science. Advances in Databases and Information Systems, 23th East European Conference, ADBIS 2019. LNCS 11695. Cham: Springer International Publishing, 2019, s. 337-353. ISBN 978-3-030-28729-0. Dostupné z: https://doi.org/10.1007/978-3-030-28730-6_21.

ANTOL, Matej a Vlastislav DOHNAL. Towards Artificial Priority Queues for Similarity Query Execution. Online. In 2018 IEEE 34th International Conference on Data Engineering Workshops (ICDEW). Paris, France: IEEE, 2018, s. 78-83. ISBN 978-1-5386-6306-6. Dostupné z: https://doi.org/10.1109/ICDEW.2018.00020.

ANTOL, Matej a Vlastislav DOHNAL. Popularity-Based Ranking for Fast Approximate kNN Search. Informatica. Lithuanian Academy of Sciences, 2017, roč. 28, č. 1, s. 1-21. ISSN 0868-4952. Dostupné z: https://doi.org/10.15388/Informatica.2017.118.

ANTOL, Matej a Vlastislav DOHNAL. Optimizing Query Performance with Inverted Cache in Metric Spaces. In Lecture Notes in Computer Science. Advances in Databases and Information Systems, 20th East European Conference, ADBIS 2016. Cham: Springer, 2016, s. 60-73. ISBN 978-3-319-44038-5. Dostupné z: https://doi.org/10.1007/978-3-319-44039-2_5.