Publication Records

KACOVÁ, Radoslava, Zdenka DUDOVÁ, Tomáš HOUFEK, Radovan TOMÁŠIK and Roman HRSTKA. Integration, Cataloguing and FAIRification of Biobank and Clinical Data. In Europe Biobank Week Congress 2024. 2024.

WITTNER, Rudolf, Petr HOLUB, Cecilia MASCIA, Francesca FREXIA, Heimo MÜLLER, Markus PLASS, Clare ALLOCCA, Fay BETSOU, Tony BURDETT, Ibon CANCIO, Adriane CHAPMAN, Martin CHAPMAN, Mélanie COURTOT, Vasa CURCIN, Johann EDER, Mark ELLIOT, Katrina EXTER, Carole GOBLE, Martin GOLEBIEWSKI, Bron KISLER, Andreas KREMER, Simone LEO, Sheng LIN-GIBSON, Anna MARSANO, Marco MATTAVELLI, Josh MOORE, Hiroki NAKAE, Isabelle PERSEIL, Ayat SALMAN, James SLUKA, Stian SOILAND-REYES, Caterina STRAMBIO-DE-CASTILLIA, Michael SUSSMAN, Jason R SWEDLOW, Kurt ZATLOUKAL and Jörg GEIGER. Toward a common standard for data and specimen provenance in life sciences. LEARNING HEALTH SYSTEMS. UNITED STATES: WILEY, 2024, vol. 8, No 1, p. 1-9. ISSN 2379-6146. Available from: https://dx.doi.org/10.1002/lrh2.10365.

DAUBNER, Lukáš, Raimundas MATULEVICIUS, Barbora BÜHNOVÁ, Matej ANTOL, Michal RŮŽIČKA and 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, p. 522-538. ISBN 978-3-031-34559-3. Available from: https://dx.doi.org/10.1007/978-3-031-34560-9_31.

DAVID, Romain, Arina RYBINA, Jean-Marie BUREL, Jean-Karim HERICHE, Pauline AUDERGON, Jan-Willem BOITEN, Frederik COPPENS, Sara CROCKETT, Exter KATRINA, Sven FAHRENER, Maddalena FRATELLI, Carole GOBLE, Philipp GORMANNS, Tobias GRANTNER, Bjorn GRUNING, Kim Tamara GURWITZ, John HANCOCK, Henriette HARMSE, Petr HOLUB, Nick JUTY, Geoffrey KARNBACH, Emma KAROUNE, Antje KEPPLER, Jessica KLEMEIER, Carla LANCELOTTI, Jean-Luc LEGRAS, L Allyson LISTER, Livio Longo DARIO, Rebecca LUDWIG, Benedicte MADON, Marzia MASSIMI, Vera MATSER, Rafaele MATTEONI, Michaela Th MAYRHOFER, Ohmann CHRISTIAN, Maria PANAGIOTOPOULOU, Helen PARKINSON, Isabelle PERSEIL, Claudia PFANDER, Roland PIERUSCHKA, Michael RAESS, Andreas RAUBER, Audrey S RICHARD, Paolo ROMANO, Antonio ROSATO, Alex SANCHEZ-PLA, Susanna-Assunta SANSONE, Ugis SARKANS, Beatriz SERRANO-SOLANO, Jing TANG, Ziaurrehman TANOLI, Jonathan TEDDS, Harald WAGENER, Martin WEISE, Hans V WESTERHOFF, Rudolf WITTNER, Jonathan EWBANK, Niklas BLOMBERG and Philip GRIBBON. "Be Sustainable Recommendations" for FAIR Resources in Life Sciences research: EOSC-Life's Lessons. EMBO Journal. 2023. ISSN 1460-2075.

PLASS, Markus, Rudolf WITTNER, Petr HOLUB, Francesca FREXIA, Cecilia MASCIA, Matej GALLO, Heimo MÜLLER and Jörg GEIGER. Provenance of specimen and data – A prerequisite for AI development in computational pathology. NEW BIOTECHNOLOGY. NETHERLANDS: ELSEVIER, 2023, vol. 78, DEC, p. 22-28. ISSN 1871-6784. Available from: https://dx.doi.org/10.1016/j.nbt.2023.09.006.

ANTOL, Matej, Michal RŮŽIČKA, Luděk MATYSKA and 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, p. 51-66. Data Rulezzzz! ISBN 978-80-280-0392-0.

GALLO, Matej, Vojtěch KRAJŇANSKÝ, Rudolf NENUTIL, Petr HOLUB and Tomáš BRÁZDIL. Shedding light on the black box of a neural network used to detect prostate cancer in whole slide images by occlusion-based explainability. NEW BIOTECHNOLOGY. NETHERLANDS: ELSEVIER, 2023, vol. 78, December, p. 52-67. ISSN 1871-6784. Available from: https://dx.doi.org/10.1016/j.nbt.2023.09.008.

DAVID, Romain, Audrey RICHARD, Claire CONNELLAN, Katharina LAUER, Maria Luisa CHIUSANO, Carole GOBLE, Martin HOUDE, Isabel KEMMER, Antje KEPPLER, Philippe LIEUTAUD, Christian OHMANN, Maria PANAGIOTOPOULOU, Sara Raza KHAN, Arina RYBINA, Stian SOILAND-REYES, Charlotte WIT, Rudolf WITTNER, Rafael Andrade BUONO, Sarah Arnaud MARSH, Pauline AUDERGON, Dylan BONFILS, Carazo JOSE-MARIA, Remi CHARREL, Frederik COPPENS, Wolfgang FECKE, Claudia FILIPPONE, Eva Garcia ALVAREZ, Sheraz GUL, Henning HERMJAKOB, Katja HERZOG, Petr HOLUB, Lukasz KOZERA, Allyson LISTER, José LÓPEZ-CORONADO, Bénédicte MADON, Kurt MAJCEN, William MARTIN, Wolfgang MÜLLER, Elli PAPADOPOULOU, Christine M.A. PRAT, Paolo ROMANO, Sansone SUSANNA-ASSUNTA, Gary SAUNDERS, Niklas BLOMBERG and Jonathan EWBANK. Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness. Data Science Journal. Ubiquity Press, 2023. ISSN 1683-1470. Available from: https://dx.doi.org/10.5334/dsj-2023-035.

HORÁK, Jiří, Katarína FURMANOVÁ, Barbora KOZLÍKOVÁ, Tomáš BRÁZDIL, Petr HOLUB, Martin KAČENGA, Matej GALLO, Rudolf NENUTIL, Jan BYŠKA and Vít RUSŇÁK. xOpat: eXplainable Open Pathology Analysis Tool. COMPUTER GRAPHICS FORUM. England: Wiley, 2023, vol. 42, No 3, p. 63-73. ISSN 0167-7055. Available from: https://dx.doi.org/10.1111/cgf.14812.

WITTNER, Rudolf, Cecilia MASCIA, Matej GALLO, Francesca FREXIA, Heimo MÜLLER, Markus PLASS, Jörg GEIGER and Petr HOLUB. Lightweight Distributed Provenance Model for Complex Real–world Environments. Scientific Data. Berlin: Nature Research, 2022, vol. 2022, No 9, p. 1-19. ISSN 2052-4463. Available from: https://dx.doi.org/10.1038/s41597-022-01537-6.

PORTEŠOVÁ, Šárka, Eva NOVÁKOVÁ, Růžena BLAŽKOVÁ, Michal JABŮREK, Ondřej STRAKA, Michal RŮŽIČKA, Matěj SMETANA, Jaroslav TOČÍK, Jana UNČOVSKÁ, Kateřina KREPSOVÁ, Ondřej DVOŘÁK, Ondřej VORÁČ, Jan KOTTMAN, Zdeněk NOVÁK, Petra BUŠKOVÁ, Jindřiška SVOBODOVÁ, Eva MALACHOVÁ and Tereza HRSTKOVÁ. Podporujeme nadané prvňáčky (We support gifted pupils in the first grades). 2022.

FREXIA, Francesca, Cecilia MASCIA, Rudolf WITTNER, Markus PLASS, Heimo MÜLLER, Jörg GEIGER and Petr HOLUB. The Common Provenance Model: Capturing Distributed Provenance in Life Sciences Processes. In Challenges of Trustable AI and Added-Value on Health. 2022. Available from: https://dx.doi.org/10.3233/SHTI220489.

LÍŠKA, Martin, Dávid LUPTÁK, Vít STARÝ NOVOTNÝ, Michal RŮŽIČKA, Boris SHMINKE, Petr SOJKA, Michal ŠTEFÁNIK and Makarius WENZEL. CICM'21 Systems Entries. Online. In 978-3-030-81097-9. INTELLIGENT COMPUTER MATHEMATICS (CICM 2021). CHAM: SPRINGER INTERNATIONAL PUBLISHING AG, 2021, p. 245-248. ISBN 978-3-030-81096-2. Available from: https://dx.doi.org/10.1007/978-3-030-81097-9_20.

WITTNER, Rudolf, Jörg GEIGER, Cecilia MASCIA, Francesca FREXIA, Heimo MULLER and Petr HOLUB. Enabling Trustworthy and Traceable Research by Non-Repudiable Opaque Provenance in a Distributed Environment. In Provenance Week 2021; Workshop on Provenance for Transparent Research. 2021.

WITTNER, Rudolf, Petr HOLUB, Heimo MÜLLER, Joerg GEIGER, Carole GOBLE, Stian SOILAND-REYES, Luca PIREDDU, Francesca FREXIA, Cecilia MASCIA, Elliot FAIRWEATHER, Jason R SWEDLOW, Josh MOORE, Caterina STRAMBIO, David GRUNWALD and Hiroki NAKAE. ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen And Data. In Lecture Notes in Computer Science. Cham: Springer, 2021, p. 222-225. ISBN 978-3-030-80959-1. Available from: https://dx.doi.org/10.1007/978-3-030-80960-7_16.

FAIRWEATHER, Elliot, Rudolf WITTNER, Martin CHAPMAN, Petr HOLUB and Vasa CURCIN. Non-repudiable provenance for clinical decision support systems. In Lecture Notes in Computer Science. Cham: Springer, 2021, p. 165-182. ISBN 978-3-030-80959-1. Available from: https://dx.doi.org/10.1007/978-3-030-80960-7_10.

LHOTÁK, Marin, Martin DUDA, Andrea FOJTŮ, Jan HEJZL, Jan HUTAŘ, Filip KERSCH, Jana KŘÍŽOVÁ, Marek MELICHAR, Martina NEZBEDOVÁ, Miroslav PAVELKA, Eliška PAVLÁSKOVÁ, Jan POKORSKÝ, Michal PŠENIČKA, Ivana ŠLAPÁKOVÁ, Zdeněk TICHÝ, Miroslav BARTOŠEK, Jan BILWACHS, Lukáš HEJTMÁNEK, Zdeněk HRUŠKA, Václav JIROUŠEK, Pavlína KOČIŠOVÁ, Vlastimil KREJČÍŘ, Iveta LODROVÁ, Natalie OSTRÁKOVÁ, Michal RŮŽIČKA, Zdeněk VAŠEK and Petr ŽABIČKA. ARCLib. 2020.

RŮŽIČKA, Michal, Andrea MIRANDA, Lukáš HEJTMÁNEK, Zdeněk VAŠEK, Vlastimil KREJČÍŘ and Miroslav BARTOŠEK. Metodika bitové ochrany digitálních dat (The methodology for bit-level preservation of digital dat). 2019.

LHOTÁK, Martin, Zdeněk VAŠEK and Michal RŮŽIČKA. Projekt ARCLib – vývoj open-source řešení pro dlouhodobou archivaci digitálních dokumentů pro knihovny a další paměťové instituce – aktuální stav (ARCLib – development of open source system for long-term preservation for library digital collections). In LTP 2019: Nové trendy a východiská pri budovaní LTP archívov: zborník príspevkov zo 4. medzinárodnej konferencie o dlhodobej archivácii. Bratislava: Univerzitná knižnica v Bratislave, 2019, p. 53-63. ISBN 978-80-89303-77-9.

SOJKA, Petr, Michal RŮŽIČKA and Vít NOVOTNÝ. MIaS: Math-Aware Retrieval in Digital Mathematical Libraries. Online. In Proceedings of the 27th ACM International Conference on Information and Knowledge Management (CIKM '18). Torino, Italy: Association for Computing Machinery, 2018, p. 1923-1926. ISBN 978-1-4503-6014-2. Available from: https://dx.doi.org/10.1145/3269206.3269233.

RŮŽIČKA, Michal, Vít NOVOTNÝ, Petr SOJKA, Jan POMIKÁLEK and Radim ŘEHŮŘEK. Flexible Similarity Search of Semantic Vectors Using Fulltext Search Engines. Online. In CEUR Workshop Proceedings, Vol. 1923. Vienna, Austria: Neuveden, 2017, p. 1-12. ISSN 1613-0073.

RŮŽIČKA, Michal. Math Information Retrieval for Digital Libraries. Brno: Masaryk University, Faculty of Informatics, 2017, 144 pp. Doctoral Thesis.

BARTOŠEK, Miroslav, Michal RŮŽIČKA and Václav STUPKA. Nařízení GDPR a jeho implementace na vysokých školách v ČR – jak na to (GDPR Regulation and its Implementation at Universities in the Czech Republic - how to do it). In EUNIS-CZ. Dopad zavedení novely VŠ zákona do IS vysokých škol. 1st ed. Plzeň: Západočeská univerzita v Plzni, 2017, p. 5-14. ISBN 978-80-261-0713-2.

RYGL, Jan, Jan POMIKÁLEK, Radim ŘEHŮŘEK, Michal RŮŽIČKA, Vít NOVOTNÝ and Petr SOJKA. Semantic Vector Encoding and Similarity Search Using Fulltext Search Engines. Online. In Proceedings of the 2nd Workshop on Representation Learning for NLP, RepL4NLP 2017 c/o ACL 2017. Vancouver, Canada: Association for Computational Linguistics, ACL, 2017, p. 81-90. ISBN 978-1-945626-62-3. Available from: https://dx.doi.org/10.18653/v1/W17-2611.

RŮŽIČKA, Michal, Petr SOJKA and Martin LÍŠKA. Math Indexer and Searcher under the Hood: Fine-Tuning Query Expansion and Unification Strategies. Online. In Noriko Kando and Kazuaki Kishida and Makoto P. Kato and Shuhei Yamamoto. Proceedings of the 12th NTCIR Conference on Evaluation of Information Access Technologies. Tokyo: National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430 Japan, 2016, p. 331-337. ISBN 978-4-86049-071-3.

SOJKA, Petr and Michal RŮŽIČKA. Math-Aware Search Interfaces for Digital Mathematical Libraries (DML). 2016.

MELICHAR, Marek, Jan HUTAŘ, Michal RŮŽIČKA, Zdeněk HRUŠKA, Zdeněk VAŠEK, Miroslav BARTOŠEK and Martin LHOTÁK. Projekt ArcLib – budování systému pro dlouhodobou archivaci digitálních dat v českých knihovnách (ArcLib Project: Designing Solution for Long-term Preservation in Czech Libraries). IT lib. Bratislava: Centrum vedecko-technických informácií SR, 2016, vol. 20, No 2, p. 13-17. ISSN 1335-793X.

RYGL, Jan, Petr SOJKA, Michal RŮŽIČKA and Radim ŘEHŮŘEK. ScaleText: The Design of a Scalable, Adaptable and User-Friendly Document System for Similarity Searches : Digging for Nuggets of Wisdom in Text. In Aleš Horák, Pavel Rychlý, Adam Rambousek. Proceedings of the Tenth Workshop on Recent Advances in Slavonic Natural Language Processing, RASLAN 2016. Brno: Tribun EU, 2016, p. 79-87. ISBN 978-80-263-1095-2.

LÍŠKA, Martin, Petr SOJKA and Michal RŮŽIČKA. Combining Text and Formula Queries in Math Information Retrieval: Evaluation of Query Results Merging Strategies. In Davood Rafiei, Katsumi Tanaka. NWSearch '15: Proceedings of the First International Workshop on Novel Web Search Interfaces and Systems. New York, NY, USA: ACM, 2015, p. 7-9. ISBN 978-1-4503-3789-2. Available from: https://dx.doi.org/10.1145/2810355.2810359.

RŮŽIČKA, Michal, Petr SOJKA and Martin LÍŠKA. Math Indexer and Searcher under the Hood: History and Development of a Winning Strategy. In Noriko Kando, Hideo Joho, Kazuaki Kishida. Proceedings of the 11th NTCIR Conference on Evaluation of Information Access Technologies. Tokyo: National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430 Japan, 2014, p. 127-134. ISBN 978-4-86049-065-2.

LÍŠKA, Martin, Petr SOJKA and Michal RŮŽIČKA. Math Indexer and Searcher Web Interface: Towards Fulfillment of Mathematicians' Information Needs. In Stephen M. Watt, James H. Davenport, Alan P. Sexton, Petr Sojka, Josef Urban. Intelligent Computer Mathematics CICM 2014. Proceedings of Calculemus, DML, MKM, and Systems and Projects. LNAI 8543. Zurich: Springer International Publishing Switzerland, 2014, p. 444-448. ISBN 978-3-319-08433-6. Available from: https://dx.doi.org/10.1007/978-3-319-08434-3_36.

SZALAI, Dominik, Robert ŠIŠKA, David FORMÁNEK, Jakub ADLER and Michal RŮŽIČKA. MathCanEval 1.0. 2014.

FORMÁNEK, David, Robert ŠIŠKA, Dominik SZALAI, Jakub ADLER, Michal RŮŽIČKA, Martin LÍŠKA and Petr SOJKA. MathML Canonicalizer 1.0.0. 2014.

RŮŽIČKA, Michal. Maths Information Retrieval for Digital Libraries. 2014. ISBN 978-3-319-08434-3.

LÍŠKA, Martin, Petr SOJKA and Michal RŮŽIČKA. WebMIaS 1.5. 2014.

SOJKA, Petr, Michal RŮŽIČKA, Maroš KUCBEL and Martin JARMAR. Accessibility Issues in Digital Mathematical Libraries. In Proceedings of the Conference Universal Learning Design 2013. Brno: Masaryk University, 2013, p. 89-97. ISBN 978-80-210-6270-2.

KREJČÍŘ, Vlastimil, Tomáš HOFMAN, Michal RŮŽIČKA and Miroslav BARTOŠEK. DML-CZ DSpace. 2013.

RŮŽIČKA, Michal. Masaryk University DOI Tools. 2013.

RŮŽIČKA, Michal, Petr KOVÁŘ and Vlastimil KREJČÍŘ. Metadata Editor FFdigi. 2013.

LÍŠKA, Martin, Petr SOJKA and Michal RŮŽIČKA. Similarity Search for Mathematics: Masaryk University team at the NTCIR-10 Math Task. In Noriko Kando, Kazuaki Kishida. Proceedings of the 10th NTCIR Conference on Evaluation of Information Access Technologies. Tokyo: National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430 Japan, 2013, p. 686-691. ISBN 978-4-86049-062-1.

WOJCIECHOWSKI, Krzys, Petr SOJKA, Nicolas HOUILLON, Michal RŮŽIČKA, Radim HATLAPATKA, Vlastimil KREJČÍŘ, Miroslav HRDINA, Jiří SOCHOR, Pavel RYCHLÝ, Aleš HORÁK, Alan SEXTON, Gilberto PEDROSA, Franck LONTIN, Thierry BOUCHE and Maciej KOŁUDA. Toolset for Image and Text Processing and Metadata Enhancements — Final Release: Deliverable 7.4 of project EuDML. 1 as of 9th February 2013. EU CIP-ICT-PSP project 250503 EuDML: The European Digital Mathematics Library, 2013, 24 pp. Deliverable D7.4.

RŮŽIČKA, Michal, Petr SOJKA and Vlastimil KREJČÍŘ. Towards Machine-Actionable Modules of a Digital Mathematics Library: The Example of DML-CZ. In J. Carette et al. CICM 2013, LNAI 7961. Berlin / Heidelberg: Springer, 2013, p. 263-277. ISBN 978-3-642-39319-8. Available from: https://dx.doi.org/10.1007/978-3-642-39320-4_17.

LÍŠKA, Martin, David FORMÁNEK, Michal RŮŽIČKA and Petr SOJKA. MathML Canonicalizer. 2012.

FORMÁNEK, David, Martin LÍŠKA, Michal RŮŽIČKA and Petr SOJKA. Normalization of Digital Mathematics Library Content. In Petr Sojka, Michael Kohlhase. DML 2012: Towards a Digital Mathematics Library. Brno: Masaryk University, 2012, p. 91-103. ISSN 1613-0073.

FORMÁNEK, David, Martin LÍŠKA, Michal RŮŽIČKA and Petr SOJKA. Normalization of Digital Mathematics Library Content. In CEUR Workshop Proceedings, Volume 921. Aachen: Neuveden, 2012, p. 91-103, 12 pp. ISSN 1613-0073.

SOJKA, Petr, Krzysztof WOJCIECHOWSKI, Nicolas HOUILLON, Michal RŮŽIČKA and Radim HATLAPATKA. Toolset for Image and Text Processing and Metadata Enhancements — Value release: Deliverable 7.3 of project EuDML. 1.01 as of 8th March 2012. EU CIP-ICT-PSP project 250503 EuDML: The European Digital Mathematics Library, 2012, 32 pp. Deliverable D7.3.

SOJKA, Petr, Martin LÍŠKA and Michal RŮŽIČKA. Building Corpora of Technical Texts : Approaches and Tools. In Aleš Horák, Pavel Rychlý. Fifth Workshop on Recent Advances in Slavonic Natural Languages Processing, RASLAN 2011. první. Brno: Tribun EU, 2011, p. 71--82, 11 pp. ISBN 978-80-263-0077-9.

RŮŽIČKA, Michal. Použití Subversion pro verzování TeXových dokumentů (Version Control of TeX Documents Using Subversion). Zpravodaj CSTUG. Brno: CSTUG, 2011, vol. 2011, No 1, p. 21–64. ISSN 1211-6661. Available from: https://dx.doi.org/10.5300/2011-1/21.

RŮŽIČKA, Michal and Petr SOJKA. Redakční systém odborného časopisu s podporou exportu do digitální knihovny (A Scientific Journal Processing System with the Capability of Exporting to a Digital Library). Zpravodaj CSTUG. Brno: CSTUG, 2011, vol. 2011, No 1, p. 4–20. ISSN 1211-6661. Available from: https://dx.doi.org/10.5300/2011-1/4.

RŮŽIČKA, Michal and Petr SOJKA. Scientific Journal Processing System with the Capability of Exporting to a Digital Library using MathML. 2011.

LÍŠKA, Martin, Petr SOJKA, Michal RŮŽIČKA and Peter MRAVEC. Web Interface and Collection for Mathematical Retrieval : WebMIaS and MREC. In Petr Sojka, Thierry Bouche. DML 2011: Towards a Digital Mathematics Library. Brno: Masaryk University, 2011, p. 77-84. ISBN 978-80-210-5542-1.