Publication Records

PROCHÁZKA, David, Terézia SLANINÁKOVÁ, Jaroslav OĽHA, Adrián ROŠINEC, Katarína GREŠOVÁ, Miriama JÁNOŠOVÁ, Jakub ČILLÍK, Jana PORUBSKÁ, Radka SVOBODOVÁ, Vlastislav DOHNAL and Matej ANTOL. AlphaFind: Discover structure similarity across the entire known proteome. bioRxiv, 2024.

PROCHÁZKA, David, Terézia SLANINÁKOVÁ, Jaroslav OĽHA, Adrián ROŠINEC, Katarína GREŠOVÁ, Miriama JÁNOŠOVÁ, Jakub ČILLÍK, Jana PORUBSKÁ, Radka SVOBODOVÁ, Vlastislav DOHNAL and Matej ANTOL. AlphaFind: discover structure similarity across the proteome in AlphaFold DB. Nucleic acids research. Oxford: Oxford University Press, 2024, Neuveden, May 15, p. 1-5. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkae397.

VOREL, Jiří, Nikol KMENTOVÁ, Christoph HAHN, Petr BUREŠ and Martin KAŠNÝ. An insight into the functional genomics and species classification of Eudiplozoon nipponicum (Monogenea, Diplozoidae), a haematophagous parasite of the common carp Cyprinus carpio. BMC Genomics. BioMed Central Ltd, 2023, vol. 24, No 1, p. 1-20. ISSN 1471-2164. Available from: https://dx.doi.org/10.1186/s12864-023-09461-8.

ŠREIBR, Sara, Jana ILGOVÁ, Pavel DOBEŠ, Jiří VOREL, Jacek MARCINIAK, Jana HURYCHOVÁ, Martin KAŠNÝ and Pavel HYRŠL. Bioactive molecules released by Heterorhabditis bacteriophora in response to various activation materials. In Virtual Nematology Conference 2023. 2023.

MACÁK, Martin, Tomáš REBOK, Matúš ŠTOVČIK, Mouzhi GE, Bruno ROSSI and Barbora BÜHNOVÁ. CopAS: A Big Data Forensic Analytics System. Online. In Proceedings of the 8th International Conference on Internet of Things, Big Data and Security IoTBDS - Volume 1. Setubal, Portugal: SciTePress, 2023, p. 150-161. ISBN 978-989-758-643-9. Available from: https://dx.doi.org/10.5220/0011929000003482.

REBOK, Tomáš and Ondřej MACHALA. CoPAS: the Modular Data Analytics Tool. 2023.

BULLA, Lukas, Kristian HJORTH, Oskar KOHOUT, Jan LANG, Sebastian ECKER, Sebastian NEUMANN, Julius BITTERMANN, Robert KINDLER, Marcus HUBER, Martin BOHMANN, Rupert URSIN and Matej PIVOLUSKA. Distribution of genuine high-dimensional entanglement over 10.2 km of noisy metropolitan atmosphere. PHYSICAL REVIEW A. UNITED STATES: AMER PHYSICAL SOC, 2023, vol. 107, L050402, p. 1-5. ISSN 2469-9926. Available from: https://dx.doi.org/10.1103/PhysRevA.107.L050402.

HERREROS, David, Roy R. LEDERMAN, James M. KRIEGER, Amaya JIMÉNEZ-MORENO, Marta MARTÍNEZ, David MYŠKA, David STŘELÁK, Jiří FILIPOVIČ, Carlos O. S. SORZANO and José M. CARAZO. Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials. Nature Communications. 2023, vol. 14, No 1, p. 1-10. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-023-35791-y.

PETROVIČ, Filip and Jiří FILIPOVIČ. Kernel Tuning Toolkit. SoftwareX. Elsevier, 2023, vol. 22, neuveden, p. 1-6. ISSN 2352-7110. Available from: https://dx.doi.org/10.1016/j.softx.2023.101385.

BULLA, Lukas, Matej PIVOLUSKA, Kristian HJORTH, Oskar KOHOUT, Jan LANG, Sebastian ECKER, Sebastian P NEUMANN, Julius BITTERMANN, Robert KINDLER, Marcus HUBER, Martin BOHMANN and Rupert URSIN. Nonlocal Temporal Interferometry for Highly Resilient Free-Space Quantum Communication. Physical Review X. College Park: American Physical Society, 2023, vol. 13, No 2, p. 1-12. ISSN 2160-3308. Available from: https://dx.doi.org/10.1103/PhysRevX.13.021001.

VÁVRA, Ondřej, Jakub BERANEK, Jan ŠTOURAČ, Martin SURKOVSKY, Jiří FILIPOVIČ, Jiří DAMBORSKÝ, Jan MARTINOVIC and David BEDNÁŘ. pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support. Bioinformatics. Oxford: Oxford University Press, 2023, vol. 39, No 8, p. 1-3. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btad443.

ARAUJO, Mateus, Marcus HUBER, Miguel NAVASCUES, Matej PIVOLUSKA and Armin TAVAKOLI. Quantum key distribution rates from semidefinite programming. QUANTUM. WIEN: VEREIN FORDERUNG OPEN ACCESS PUBLIZIERENS QUANTENWISSENSCHAF, 2023, vol. 7, No 1, p. 1-18. ISSN 2521-327X. Available from: https://dx.doi.org/10.22331/Q-2023-05-24-1019.

SLANINÁKOVÁ, Terézia, Matej ANTOL, Jaroslav OĽHA, Vlastislav DOHNAL, Susana LADRA and Miguel A. MARTÍNEZ-PRIETO. Reproducible experiments with Learned Metric Index Framework. Information systems. Elsevier, 2023, vol. 118, No 1, p. 102255-102270. ISSN 0306-4379. Available from: https://dx.doi.org/10.1016/j.is.2023.102255.

SLANINÁKOVÁ, Terézia, David PROCHÁZKA, Matej ANTOL, Jaroslav OĽHA and 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, p. 282-290. ISBN 978-3-031-46993-0. Available from: https://dx.doi.org/10.1007/978-3-031-46994-7_24.

MESSINA, Nicola, Jan SEDMIDUBSKÝ, Falchi FABRIZIO and Tomáš REBOK. Text-to-Motion Retrieval: Towards Joint Understanding of Human Motion Data and Natural Language. Online. In 46th International Conference on Research and Development in Information Retrieval (SIGIR). New York, NY, USA: Association for Computing Machinery, 2023, p. 2420-2425. ISBN 978-1-4503-9408-6. Available from: https://dx.doi.org/10.1145/3539618.3592069.

TØRRING, Jacob O, van Werkhoven BEN, Filip PETROVIČ, Floris-Jan WILLEMSEN, Jiří FILIPOVIČ and Anne C ELSTER. Towards a Benchmarking Suite for Kernel Tuners. Online. In 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). neuveden: IEEE, 2023, p. 724-733. ISBN 979-8-3503-1199-0. Available from: https://dx.doi.org/10.1109/IPDPSW59300.2023.00124.

STŘELÁK, David, David MYŠKA, Filip PETROVIČ, Jan POLÁK, Jaroslav OĽHA and Jiří FILIPOVIČ. Umpalumpa: a framework for efficient execution of complex image processing workloads on heterogeneous nodes. Computing. Springer, 2023, vol. 105, No 11, p. 2389-2417. ISSN 0010-485X. Available from: https://dx.doi.org/10.1007/s00607-023-01190-w.

HERREROS, David, Jakub KISKA, Erney RAMÍREZ-APORTELA, Jiří FILIPOVIČ, José María CARAZO and Carlos Oscar SORZANO. ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis. Journal of Molecular Biology. Elsevier, 2023, vol. 435, No 9, p. 1-14. ISSN 0022-2836. Available from: https://dx.doi.org/10.1016/j.jmb.2023.168088.

MIHÁLIKOVÁ, Ivana, Martin FRIÁK, Matej PIVOLUSKA, Martin PLESCH, Martin SAIP and Mojmír ŠOB. Best-Practice Aspects of Quantum-Computer Calculations: A Case Study of the Hydrogen Molecule. MOLECULES. SWITZERLAND: MDPI, 2022, vol. 27, No 3, p. 1-15. ISSN 1420-3049. Available from: https://dx.doi.org/10.3390/molecules27030597.

APPEL, Paul, Alexander J. HEILMAN, Ezekiel W. WERTZ, David W. LYONS, Marcus HUBER, Matej PIVOLUSKA and Giuseppe VITAGLIANO. Finite-Function-Encoding Quantum States. QUANTUM. WIEN: VEREIN FORDERUNG OPEN ACCESS PUBLIZIERENS QUANTENWISSENSCHAF, 2022, vol. 6, No 708, p. 1-34. ISSN 2521-327X. Available from: https://dx.doi.org/10.22331/q-2022-05-09-708.

PIVOLUSKA, Matej and Martin PLESCH. Implementation of quantum compression on IBM quantum computers. Nature Scientific Reports. USA: NATURE PUBLISHING GROUP, 2022, vol. 12, No 1, p. 5841-5849. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-022-09881-8.

NĚMCOVÁ, Petra, Jana HOZZOVÁ and Jiří FILIPOVIČ. Improving ligand transport trajectory within flexible receptor in CaverDock. Online. In SAC '22: Proceedings of the 37th ACM/SIGAPP Symposium on Applied Computing. USA: Association for Computing Machinery, 2022, p. 619-626. ISBN 978-1-4503-8713-2. Available from: https://dx.doi.org/10.1145/3477314.3506988.

SORZANO, Carlos, Amaya JIMÉNEZ-MORENO, David MALUENDA, Marta MARTÍNEZ, Erney RAMÍREZ-APORTELA, James KRIEGER, Roberto MELERO, Ana CUERVO, Javier CONESA, Jiří FILIPOVIČ, Pablo CONESA, Laura del CAÑO, Yunior FONSECA, Jorge Jiménez-de LA MORENA, Patricia LOSANA, Ruben SÁNCHEZ-GARCÍA, David STŘELÁK, Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, David HERREROS, Jose Luis VILAS, Roberto MARABINI and Jose Maria CARAZO. On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy. Acta Crystallographica Section D: Structural Biology. Chester: International Union of Crystallography, 2022, vol. 78, No 4, p. 410-423. ISSN 2059-7983. Available from: https://dx.doi.org/10.1107/S2059798322001978.

TRAPL, Dalibor, MArtin KRUPIČKA, Vladimír VIŠŇOVSKÝ, Jana HOZZOVÁ, Jaroslav OĽHA, Aleš KŘENEK and Vojtěch SPIWOK. Property Map Collective Variable as a Useful Tool for a Force Field Correction. Journal of Chemical Information and Modeling. American Chemical Society, 2022, vol. 62, No 3, p. 567-576. ISSN 1549-9596. Available from: https://dx.doi.org/10.1021/acs.jcim.1c00651.

RAI, Ashutosh, Matej PIVOLUSKA, Souradeep SASMAL, Manik BANIK, Sibasish GHOSH and Martin PLESCH. Self-testing quantum states via nonmaximal violation in Hardy's test of nonlocality. PHYSICAL REVIEW A. UNITED STATES: AMER PHYSICAL SOC, 2022, vol. 105, No 5, p. 1-8. ISSN 2469-9926. Available from: https://dx.doi.org/10.1103/PhysRevA.105.052227.

MIHÁLIKOVÁ, Ivana, Matej PIVOLUSKA, Martin PLESCH, Martin FRIÁK, Daniel NAGAJ and Mojmír ŠOB. The Cost of Improving the Precision of the Variational Quantum Eigensolver for Quantum Chemistry. Nanomaterials. London: MDPI, 2022, vol. 12, No 2, p. 1-22. ISSN 2079-4991. Available from: https://dx.doi.org/10.3390/nano12020243.

FILIPOVIČ, Jiří, Jana HOZZOVÁ, Amin NEZARAT, Jaroslav OĽHA and Filip PETROVIČ. Using hardware performance counters to speed up autotuning convergence on GPUs. Journal of Parallel and Distributed Computing. Elsevier, 2022, vol. 160, February, p. 16-35. ISSN 0743-7315. Available from: https://dx.doi.org/10.1016/j.jpdc.2021.10.003.

STŘELÁK, David, Amaya JIMÉNEZ-MORENO, José VILAS, Erney RAMÍREZ-APORTELA, Ruben SÁNCHEZ-GARCÍA, David MALUENDA, Javier VARGAS, David HERREROS, Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, Jan HORÁČEK, David MYŠKA, Martin HORÁČEK, Pablo CONESA, Yunior FONSECA-REYNA, Jorge JIMÉNEZ, Marta MARTÍNEZ, Mohamad HARASTANI, Slavica JONIĆ, Jiří FILIPOVIČ, Roberto MARABINI, José CARAZO and Carlos SORZANO. Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion. Molecules. Mayer und Muller, 2021, vol. 26, No 20, p. 1-14. ISSN 1420-3049. Available from: https://dx.doi.org/10.3390/molecules26206224.

HERREROS, David, Roy R LEDERMAN, James KRIEGER, Amaya JIMENEZ-MORENO, Marta MARTINEZ, David MYŠKA, David STŘELÁK, Jiří FILIPOVIČ, Ivet BAHAR, Jose Maria CARAZO and Carlos Oscar S SANCHEZ. Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials. International Union of Crystallography Journals. online, 2021, vol. 8, No 6, p. 992-1005. ISSN 2052-2525. Available from: https://dx.doi.org/10.1107/S2052252521008903.

VIŠŇOVSKÝ, Vladimír, Viktória SPIŠAKOVÁ, Jana HOZZOVÁ, Jaroslav OĽHA, Dalibor TRAPL, Vojtěch SPIWOK, Lukáš HEJTMÁNEK and Aleš KŘENEK. Complex simulation workflows in containerized high-performance environment. In Armenia S., Geril P. Proc. ESM 2021. Brusel: EUROSIS, 2021, p. 42-45. ISBN 978-94-92859-18-1.

DAMBORSKÝ, Jiří, David BEDNÁŘ, Zbyněk PROKOP, Martin MAREK, Stanislav MAZURENKO, Jan ŠTOURAČ, Sérgio Manuel MARQUES, Gabriela Filipa FONSECA PINTO, Joan PLANAS IGLESIAS, Miloš MUSIL, Jiří HON, Ondřej VÁVRA, Rayyan Tariq KHAN, Jiří FILIPOVIČ and Barbora KOZLÍKOVÁ. Computational enzyme design for metabolic engineering. In The 45th FEBS Congress. 2021. ISSN 2211-5463.

JIMÉNEZ-MORENO, Amaya, David STŘELÁK, Jiří FILIPOVIČ, José María CARAZO and Carlos Óscar S. SORZANO. DeepAlign, a 3D Alignment Method based on Regionalized Deep Learning for Cryo-EM. Journal of Structural Biology. San Diego,USA: Academic Press, 2021, vol. 213, No 2, p. "107712", 14 pp. ISSN 1047-8477. Available from: https://dx.doi.org/10.1016/j.jsb.2021.107712.

RAI, A., Matej PIVOLUSKA, Martin PLESCH, S. SASMAL, M. BANIK and S. GHOSH. Device-independent bounds from Cabello's nonlocality argument. Physical review A. New York: The American Physical Society, 2021, vol. 103, No 6, p. 1-7. ISSN 2469-9926. Available from: https://dx.doi.org/10.1103/PhysRevA.103.062219.

DODA, M., Matej PIVOLUSKA and Martin PLESCH. Choice of mutually unbiased bases and outcome labeling affecting measurement outcome secrecy. Physical review A. New York: The American Physical Society, 2021, vol. 103, No 3, p. 032206-32213. ISSN 2469-9926. Available from: https://dx.doi.org/10.1103/PhysRevA.103.032206.

S. SORZANO, Carlos Oscar, Amaya JIMÉNEZ-MORENO, David MALUENDA, Erney RAMÍREZ-APORTELA, Marta MARTÍNEZ, Ana CUERVO, Roberto MELERO, Jose Javier CONESA, Ruben SÁNCHEZ-GARCÍA, David STŘELÁK, Jiří FILIPOVIČ, Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, David HERREROS, Pablo CONESA, Laura DEL CAÑO, Yunior FONSECA, Jorge JIMÉNEZ DE LA MORENA, Jose Ramon MACÍAS, Patricia LOSANA, Roberto MARABINI and Jose-Maria CARAZO. Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods. In Structural Proteomics. Clifton, N.J.: Springer US, 2021, p. 257-289. Methods in Molecular Biology. ISBN 978-1-0716-1405-1. Available from: https://dx.doi.org/10.1007/978-1-0716-1406-8_13.

PETROVIČ, Filip, Jiří FILIPOVIČ, David STŘELÁK, Jana HOZZOVÁ and Richard TREMBECKÝ. Kernel Tuning Toolkit 2.0. 2021.

NEUMANN, S.P., T. SCHEIDL, M. SELIMOVIC, Matej PIVOLUSKA, B. LIU, M. BOHMANN and R. URSIN. Model for optimizing quantum key distribution with continuous-wave pumped entangled-photon sources. Physical review A. New York: The American Physical Society, 2021, vol. 104, No 2, p. 022406-22416. ISSN 2469-9926. Available from: https://dx.doi.org/10.1103/PhysRevA.104.022406.

HU, X.M., C. ZHANG, Y. GUO, F.X. WANG, W.B. XING, C.X. HUANG, B.H. LIU, Y.F. HUANG, C.F. LI, G.C. GUO, X.Q. GAO, Matej PIVOLUSKA and M. HUBER. Pathways for Entanglement-Based Quantum Communication in the Face of High Noise. Physical Review Letters. COLLEGE PK: The American Physical Society, 2021, vol. 127, No 11, p. 1-7. ISSN 0031-9007. Available from: https://dx.doi.org/10.1103/PhysRevLett.127.110505.

DODA, M., M. HUBER, G. MURTA, Matej PIVOLUSKA, Martin PLESCH and C. VLACHOU. Quantum Key Distribution Overcoming Extreme Noise: Simultaneous Subspace Coding Using High-Dimensional Entanglement. PHYSICAL REVIEW APPLIED. COLLEGE PK: AMER PHYSICAL SOC, 2021, vol. 15, No 3, p. 034003-34017. ISSN 2331-7019. Available from: https://dx.doi.org/10.1103/PhysRevApplied.15.034003.

RANGEL PAMPLONA PIZARRO PINTO, José Gaspar, Ondřej VÁVRA, Sérgio Manuel MARQUES, Jiří FILIPOVIČ, David BEDNÁŘ and Jiří DAMBORSKÝ. Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning. Computational and Structural Biotechnology Journal. Amsterdam: Elsevier, 2021, vol. 19, May, p. 3187-3197. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2021.05.043.

HOZZOVÁ, Jana, Jiří FILIPOVIČ, Amin NEZARAT, Jaroslav OĽHA and Filip PETROVIČ. Searching CUDA code autotuning spaces with hardware performance counters: data from benchmarks running on various GPU architectures. Data in Brief. Elsevier, 2021, vol. 39, December, p. 1-12. ISSN 2352-3409. Available from: https://dx.doi.org/10.1016/j.dib.2021.107631.

PIVOLUSKA, Matej, Martin PLESCH, M. FARKAS, Natália RUŽIČKOVÁ, C. FLEGEL, N.H. VALENCIA, W. MCCUTCHEON, M. MALIK and EA AGUILAR. Semi-device-independent random number generation with flexible assumptions. NPJ QUANTUM INFORMATION. BERLIN: NATURE RESEARCH, 2021, vol. 7, No 1, p. 1-12. ISSN 2056-6387. Available from: https://dx.doi.org/10.1038/s41534-021-00387-1.

HOZZOVÁ, Jana, Ondřej VÁVRA, David BEDNÁŘ and Jiří FILIPOVIČ. Simulation of Ligand Transport in Receptors Using CaverDock. In Flavio Ballante. Protein-Ligand Interactions and Drug Design. New York: Humana, New York, NY, 2021, p. 105-124. Methods in Molecular Biology, vol 2266. ISBN 978-1-0716-1208-8. Available from: https://dx.doi.org/10.1007/978-1-0716-1209-5_6.

BRÁZDIL, Tomáš, David PORTEŠ, Jiří FILIPOVIČ, Jana HOZZOVÁ, Thomas EVANGELIDIS and Konstantinos TRIPSIANES. 4D-GRAPHS. 2021.

PETROVIČ, Filip, David STŘELÁK, Jana HOZZOVÁ, Jaroslav OĽHA, Richard TREMBECKÝ, Siegfried BENKNER and Jiří FILIPOVIČ. A benchmark set of highly-efficient CUDA and OpenCL kernels and its dynamic autotuning with Kernel Tuning Toolkit. Future Generation Computer Systems. Elsevier, 2020, vol. 108, July, p. 161-177. ISSN 0167-739X. Available from: https://dx.doi.org/10.1016/j.future.2020.02.069.

REBOK, Tomáš, Michal BATKO, Milan ČERMÁK, Martin DRAŠAR, Daniel TOVARŇÁK, Pavel ZEZULA, Martin MACÁK, Matúš GUOTH, Matej BABEJ, Dávid BRILLA and Martin KAŽIMÍR. ANALYZA – Datový sklad (ANALYZA – Dara Warehouse). 2020.

REBOK, Tomáš, Michal BATKO, Milan ČERMÁK, Martin DRAŠAR, Jarešová MIROSLAVA, Barbora KOZLÍKOVÁ, Kristína ZÁKOPČANOVÁ, Pavel ZEZULA, Katarína FURMANOVÁ, Marko ŘEHÁČEK, Jozef BÁTRNA and Daniel PLAKINGER. ANALYZA – Vizualizační komponenta – Visilant (ANALYZA – Visualization Component – Visilant). 2020.

REBOK, Tomáš, Michal BATKO, Milan ČERMÁK, Barbora KOZLÍKOVÁ, Vladimír MÍČ, Filip NÁLEPA, David NOVÁK, Daniel TOVARŇÁK, Pavel ZEZULA, Jakub PESCHEL, Kasanič DENIS, Denisa ŠRÁMKOVÁ, Erik HRICIŠÁK, Vladimír LAZÁRIK and Kristián GUTIČ. ANALYZA – Výpočetní a orchestrační subsystém (ANALYZA – Computation and Orchestration Subsystem). 2020.

FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Los Alamitos: IEEE Computer Society, 2020, vol. 17, No 5, p. 1625-1638. ISSN 1545-5963. Available from: https://dx.doi.org/10.1109/TCBB.2019.2907492.

HU, Xiao-Min, WB. XING, C. ZHANG, BH. LIU, Matej PIVOLUSKA, M. HUBER, YF. HUANG, CF. LI and GC. GUO. Experimental creation of multi-photon high-dimensional layered quantum states. NPJ QUANTUM INFORMATION. BERLIN: NATURE RESEARCH, 2020, vol. 6, No 1, p. 1-5. ISSN 2056-6387. Available from: https://dx.doi.org/10.1038/s41534-020-00318-6.

OĽHA, Jaroslav, Jana HOZZOVÁ, Jan FOUSEK and Jiří FILIPOVIČ. Exploiting historical data: Pruning autotuning spaces and estimating the number of tuning steps. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE. HOBOKEN: WILEY, 2020, vol. 32, No 21, p. 1-15. ISSN 1532-0626. Available from: https://dx.doi.org/10.1002/cpe.5962.

KŘENEK, Aleš, Jana HOZZOVÁ, Jaroslav OĽHA, Dalibor TRAPL and Vojtěch SPIWOK. Exploring Protein Folding Space with Neural Network Guided Simulations. In Alexandre Nketsa. MODELLING AND SIMULATION 2020. Brusel: EUROSIS-ETI, 2020, p. 305-309. ISBN 978-94-92859-12-9.

STŘELÁK, David, Jiří FILIPOVIČ, Amaya JIMÉNEZ-MORENO, Jose María CARAZO and Carlos Óscar SÁNCHEZ SORZANO. FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy. Electronics. Switzerland: MDPI, 2020, vol. 9, No 6, p. 1-25. ISSN 2079-9292. Available from: https://dx.doi.org/10.3390/electronics9061040.

VALENCIA, N.H., V. SRIVASTAV, Matej PIVOLUSKA, M. HUBER, N. FRIIS, W. MCCUTCHEON and M. MALIK. High-Dimensional Pixel Entanglement: Efficient Generation and Certification. QUANTUM. WIEN: VEREIN FORDERUNG OPEN ACCESS PUBLIZIERENS QUANTENWISSENSCHAF, 2020, vol. 4, December, p. 376-394. ISSN 2521-327X. Available from: https://dx.doi.org/10.22331/q-2020-12-24-376.

FRIÁK, Martin, Dušan LAGO, Nikola KOUTNÁ, David HOLEC, Tomáš REBOK and Mojmír ŠOB. Multi-phase ELAStic Aggregates (MELASA) software tool for modeling anisotropic elastic properties of lamellar composites. Computer Physics Communications. Amsterdam: Elsevier, 2020, vol. 247, FEB 2020, p. 1-9. ISSN 0010-4655. Available from: https://dx.doi.org/10.1016/j.cpc.2019.106863.

VODÁK, Rostislav, Michal BÍL, Tomáš SVOBODA, Zuzana KŘIVÁNKOVÁ, Jan KUBEČEK, Tomáš REBOK and Petr HLINĚNÝ. A deterministic approach for rapid identification of the critical links in networks. PLOS ONE. United States: Public Library of Science, 2019, vol. 14, No 7, p. 1-18. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0219658.

STŘELÁK, David, Carlos Óscar S. SORZANO, José María CARAZO and Jiří FILIPOVIČ. A GPU acceleration of 3-D Fourier reconstruction in cryo-EM. The International Journal of High Performance Computing Applications. SAGE Publishing, 2019, vol. 33, No 5, p. 948-959. ISSN 1094-3420. Available from: https://dx.doi.org/10.1177/1094342019832958.

REBOK, Tomáš. Big Data - overview, basic concepts and practical use in research. In Alliance4Life 5th project meeting. 2019.

ŠTOURAČ, Jan, O. VAVRA, Piia Pauliina KOKKONEN, Jiří FILIPOVIČ, Gabriela Filipa FONSECA PINTO, Andrea SCHENKMAYEROVÁ, Jiří DAMBORSKÝ and David BEDNÁŘ. Caver web: identification of tunnels and channels in proteins and analysis of ligand transport. In European Biotechnology Congress. 2019. ISSN 0168-1656. Available from: https://dx.doi.org/10.1016/j.jbiotec.2019.05.251.

ŠTOURAČ, Jan, Ondřej VÁVRA, Piia Pauliina KOKKONEN, Jiří FILIPOVIČ, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Jan BREZOVSKÝ, Jiří DAMBORSKÝ and David BEDNÁŘ. Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic acids research. Oxford: Oxford University Press, 2019, vol. 47, W1, p. 414-422. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkz378.

VÁVRA, Ondřej, Jiří FILIPOVIČ, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Jan ŠTOURAČ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics. Oxford: Oxford University Press, 2019, vol. 35, No 23, p. 4986-4993. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btz386.

OĽHA, Jaroslav, Jana HOZZOVÁ, Jan FOUSEK and Jiří FILIPOVIČ. Exploiting historical data: pruning autotuning spaces and estimating the number of tuning steps. In Ulrich Schwardmann, Christian Boehme, Dora B. Heras, Valeria Cardellini, Emmanuel Jeannot, Antonio Salis, Claudio Schifanella, Ravi Reddy Manumachu, Dieter Schwamborn, Laura Ricci, Oh Sangyoon, Thomas Gruber, Laura Antonelli, Stephen L. Scott. Lecture Notes in Computer Science. Cham, Switzerland: Springer, Cham, 2019, p. 295-307. ISBN 978-3-030-48339-5. Available from: https://dx.doi.org/10.1007/978-3-030-48340-1_23.

RANGEL PAMPLONA PIZARRO PINTO, José Gaspar, Ondřej VÁVRA, Jiří FILIPOVIČ, Jan ŠTOURAČ, David BEDNÁŘ and Jiří DAMBORSKÝ. Fast Screening of Inhibitor Binding/Unbinding using Novel Software Tool CaverDock. FRONTIERS IN CHEMISTRY. LAUSANNE: FRONTIERS MEDIA SA, 2019, vol. 7, OCT 29 2019, p. 1-14. ISSN 2296-2646. Available from: https://dx.doi.org/10.3389/fchem.2019.00709.

ČELEDA, Pavel, Jakub ČEGAN, Martin DRAŠAR, Ivo NUTÁR, Jiří RÁJA, Tomáš REBOK, Andrej TOMČI and Daniel TOVARŇÁK. Nástroje pro ověřování bezpečnosti SW/HW a simulaci útoků na prvky kritické informační infrastruktury (Tools for verification of SW/HW security and simulation of attacks on critical information infrastructure). 2019.

ČELEDA, Pavel, Jakub ČEGAN, Kamil ANDONIADIS, Milan ČERMÁK, Jan DUDA, Vlastimil HOLER, Ľuboš HYŽÁK, Boris JADUŠ, Jakub KADAŠI, David LEŠKA, Martin MACHÁČ, Ivo NUTÁR, Radek OŠLEJŠEK, Dominik PILÁR, Tomáš PLESNÍK, Michal PROCHÁZKA, Tomáš REBOK, Vít RUSŇÁK, Miloslav STANĚK, Pavel ŠEDA, Valdemar ŠVÁBENSKÝ, Daniel TOVARŇÁK, Petr VELAN, Martin VIZVÁRY, Jan VYKOPAL and Tatiana ZBONČÁKOVÁ. Software pro simulaci obecných i kritických informačních infrastruktur (Software for simulation of generic and critical information infrastructures). 2019.

PAZÚRIKOVÁ, Jana, Jaroslav OĽHA, Aleš KŘENEK and Vojtěch SPIWOK. Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations. arXiv, 2018, 22 pp. arXiv:1801.02362.

STŘELÁK, David and Jiří FILIPOVIČ. cuFFTAdvisor. 2018.

PETROVIČ, Filip, Jiří FILIPOVIČ, David STŘELÁK and Jana PAZÚRIKOVÁ. Kernel Tuning Toolkit. 2018.

PIVOLUSKA, Matej, Marcus HUBER and Mehul MALIK. Layered quantum key distribution. Physical Review A. 2018, vol. 97, No 3, p. "032312:1"-"032312:10", 10 pp. ISSN 2469-9926. Available from: https://dx.doi.org/10.1103/PhysRevA.97.032312.

PLESCH, Martin and Matej PIVOLUSKA. Loss of information in quantum guessing game. New Journal of Physics. IOP publishing, 2018, vol. 20, 07 02 2018, p. "023018:1"-"023018:10", 10 pp. ISSN 1367-2630. Available from: https://dx.doi.org/10.1088/1367-2630/aaa5f8.

BAVARESCO, Jessica, Natalia Herrera VALENCIA, Claude KLÖCKL, Matej PIVOLUSKA, Paul ERKER, Nicolai FRIIS, Mehul MALIK and Marcus HUBER. Measurements in two bases are sufficient for certifying high-dimensional entanglement. Nature Physics. Nature Publishing Group, 2018, vol. 14, No 10, p. 1032-1040. ISSN 1745-2473. Available from: https://dx.doi.org/10.1038/s41567-018-0203-z.

STŘELÁK, David and Jiří FILIPOVIČ. Performance analysis and autotuning setup of the cuFFT library. Online. In ACM International Conference Proceeding Series. Limassol, Cyprus: ACM, 2018, p. nestránkováno, 6 pp. ISBN 978-1-4503-6591-8. Available from: https://dx.doi.org/10.1145/3295816.3295817.

FILIPOVIČ, Jiří, Filip PETROVIČ and Siegfried BENKNER. Autotuning of OpenCL Kernels with Global Optimizations. Online. In 1st Workshop on Autotuning and Adaptivity Approaches for Energy Efficient HPC Systems (ANDARE'2017). Portland (USA): ACM, 2017, p. nestránkováno, 6 pp. ISBN 978-1-4503-5363-2. Available from: https://dx.doi.org/10.1145/3152821.3152877.

FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock 1.0. 2017.

PAZÚRIKOVÁ, Jana, Aleš KŘENEK, Vojtěch SPIWOK and Mária ŠIMKOVÁ. Reducing the number of mean-square deviation calculations with floating close structure in metadynamics. Journal of Chemical Physics. Melville: American Institute of Physics, 2017, vol. 146, No 11, p. "115101:1"-"115101:8", 8 pp. ISSN 0021-9606. Available from: https://dx.doi.org/10.1063/1.4978296.

FILIPOVIČ, Jiří, Jana PAZÚRIKOVÁ, Aleš KŘENEK and Vojtěch SPIWOK. Accelerated RMSD Calculation for Molecular Metadynamics. In José Évora-Gómez and José Juan Hernandéz-Cabrera. Proceedings of the 2016 European Simulation and Modelling Conference. Ghent, Belgie: EUROSIS - ETI, 2016, p. 278-280. ISBN 978-90-77381-95-3.

KŘENEK, Aleš, Tomáš RAČEK and Jana PAZÚRIKOVÁ. Direct SAXS Curve Fitting with an Ensable of Conformations. In Molecular Machines 2016. 2016.

PAZÚRIKOVÁ, Jana, Aleš KŘENEK and Luděk MATYSKA. Guided Optimization Method for Fast and Accurate Atomic Charges Computation. In José Évora-Gómez and José Juan Hernandéz-Cabrera. Proceedings of the 2016 European Simulation and Modelling Conference. Ghent, Belgicko: EUROSIS - ETI, 2016, p. 267-274. ISBN 978-90-77381-95-3.

RAČEK, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ, Aleš KŘENEK, Jana PAZÚRIKOVÁ, Stanislav GEIDL and Jaroslav KOČA. NEEMP – nástroj pro parametrizaci EEM. In ENBIK2016. 2016. ISBN 978-80-7080-960-0.

RAČEK, Tomáš, Jana PAZÚRIKOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Stanislav GEIDL, Aleš KŘENEK, Francesco Luca FALGINELLA, Vladimír HORSKÝ, Václav HEJRET and Jaroslav KOČA. NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2016, vol. 8, October, p. nestránkováno, 14 pp. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/s13321-016-0171-1.

SEDLÁŘ, Milan, Bin JI, Tomáš KRÁTKÝ, Tomáš REBOK and Rostislav HUZLÍK. Numerical and experimental investigation of three-dimensional cavitating flow around the straight NACA2412 hydrofoil. Ocean Engineering. Elsevier Ltd., 2016, vol. 123, No 123, p. 357-382. ISSN 0029-8018. Available from: https://dx.doi.org/10.1016/j.oceaneng.2016.07.030.

PAZÚRIKOVÁ, Jana, Tomáš RAČEK, Stanislav GEIDL, Radka SVOBODOVÁ VAŘEKOVÁ and Aleš KŘENEK. Parametrizace ekvalizace elektronegativity metodou diferenciální evoluce (Parametrization of Electronegativity Equalization Method through Differential Evolution). In ENBIK 2016. 2016.

FILIPOVIČ, Jiří, Jan PLHÁK and David STŘELÁK. Acceleration of dRMSD Calculation and Efficient Usage of GPU Caches. In Waleed Smari. Proceedings of IEEE International Conference on High Performance Computing & Simulation. neuveden: IEEE, 2015, p. 47-54. ISBN 978-1-4673-7812-3. Available from: https://dx.doi.org/10.1109/HPCSim.2015.7237020.

KŘENEK, Aleš, Karel KUBÍČEK, Richard ŠTEFL and Jiří FILIPOVIČ. Accurate Fitting SAXS Curves with NMR Structure Ensembles. Online. In Simon Lin, Vicky Huang. Proceedings of International Symposium on Grids and Clouds 2015. Pissa: Proceedings of Science, 2015, p. nestránkováno, 9 pp. ISSN 1824-8039.

TOMÁŠ, Martin, Tomáš REBOK and Christos EFSTATHIOU. Iterative Optimization of a Multi-compartmental Air Quality Modelling System. In Jan Kofroň and Tomáš Vojnar. Tenth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS 2015). první. Brno: MEMICS 2015, 2015, p. 70-81. ISBN 978-80-214-5254-1.

ČEGAN, Jakub, Pavel ČELEDA, Tomáš JIRSÍK, Tomáš PLESNÍK, Michal PROCHÁZKA, Petr VELAN, Jan VYKOPAL, Martin VIZVÁRY, Radek OŠLEJŠEK, Zdenek EICHLER, Dalibor TOTH, Milan ČERMÁK, Jan SOUKAL, Tomáš REBOK, Václav RAČANSKÝ, Ivo NUTÁR and Dušan LAGO. KYPO - Kybernetický polygon (KYPO - Cybernetic Proving Ground). 2015.

SPIWOK, Vojtěch, Pavel OBORSKÝ, Jana PAZÚRIKOVÁ, Aleš KŘENEK and Blanka KRÁLOVÁ. Nonlinear vs. linear biasing in Trp-cage folding simulations. Journal of the chemical society. Faraday transactions II, Journal of chemical physics. London: Chemical society, 2015, vol. 142, No 11, p. nestránkováno, 8 pp. ISSN 0021-9606. Available from: https://dx.doi.org/10.1063/1.4914828.

FILIPOVIČ, Jiří and Siegfried BENKNER. OpenCL Kernel Fusion for GPU, Xeon Phi and CPU. In Proceedings of IEEE International Symposium on Computer Architecture and High Performance Computing. Florianópolis: IEEE, 2015, p. 98-105. ISSN 1550-6533. Available from: https://dx.doi.org/10.1109/SBAC-PAD.2015.29.

FILIPOVIČ, Jiří, Matúš MADZIN, Jan FOUSEK and Luděk MATYSKA. Optimizing CUDA code by kernel fusion: application on BLAS. The Journal of Supercomputing. Springer US, 2015, vol. 71, No 10, p. 3934-3957. ISSN 0920-8542. Available from: https://dx.doi.org/10.1007/s11227-015-1483-z.

PROCHÁZKA, Filip, Tomáš REBOK and Aleš FARDA. První návrh cílové infrastruktury pro provoz systému IRIS (First draft of the target infrastructure for the IRIS system operation). 2015.

NGUYEN, Filip, Tomáš REBOK, Richard LUDVIGH and Václav TUNKA. Ruby Benchmark Suite using Docker. Online. In M. Ganzha, L. Maciaszek, M. Paprzycki. Annals of Computer Science and Information Systems, Volume 5. 2015th ed. Poland: IEEE, 2015, p. 947-952. ISBN 978-83-60810-66-8. Available from: https://dx.doi.org/10.15439/2015F99.

ČEGAN, Jakub, Pavel ČELEDA, Tomáš JIRSÍK, Tomáš PLESNÍK, Michal PROCHÁZKA, Petr VELAN, Jan VYKOPAL, Martin VIZVÁRY, Milan ČERMÁK, Jan SOUKAL, Tomáš REBOK, Ivo NUTÁR and Dušan LAGO. Software pro konfiguraci a monitorování virtuálního prostředí KYPO (Software for configuration and monitoring of KYPO environment). 2015.

KOUŘIL, Daniel, Tomáš REBOK, Tomáš JIRSÍK, Jakub ČEGAN, Martin DRAŠAR, Martin VIZVÁRY and Jan VYKOPAL. Cloud-based Testbed for Simulation of Cyber Attacks. In Hanan Lutfiyya and Piotr Cholda. Proceedings of the Network Operations and Management Symposium (NOMS 2014). Krakow, Poland: IEEE Xplore Digital Library, 2014, p. 1-6. ISBN 978-1-4799-0913-1. Available from: https://dx.doi.org/10.1109/NOMS.2014.6838298.

PAZÚRIKOVÁ, Jana and Luděk MATYSKA. Convergence of Parareal Algorithm Applied on Molecular Dynamics Simulations. In Petr Hliněný, Zdeněk Dvořák, Jiří Jaroš, Jan Kofroň, Jan Kořenek, Petr Matula, Karel Pala. MEMICS 2014. Brno: NOVPRESS, 2014, p. 101-111. ISBN 978-80-214-5022-6.

BÍL, Michal, Rostislav VODÁK, Jan KUBEČEK, Tomáš REBOK, Tomáš SVOBODA and Petr HLINĚNÝ. Vulnerability analysis methods for road networks. In European Geosciences Union General Assembly 2014 (EGU 2014). 2014.

SLOUP, Petr and Tomáš REBOK. Automatic reconstruction of Norway spruce tree models from LiDAR data. In ISPRS2013-SSG. 2013.

SLOUP, Petr, Tomáš REBOK and Jan HANUŠ. Automatic Tree Reconstruction from its Laser Scan [poster]. In Global Change and Resilience. 2013.

PAZÚRIKOVÁ, Jana and Luděk MATYSKA. Electrostatics' calculation parallel in time. In CECAM workshop on Fast Methods for Long Range Interactions in Complex Particle Systems. 2013.

SLOUP, Petr, Tomáš REBOK and Jan HANUŠ. Fully-automated Occlusion-insensitive Norway Spruce Tree Reconstructions from 3D Point Cloud Data [poster]. In ISPRS2013-SSG. 2013.

PAZÚRIKOVÁ, Jana and Luděk MATYSKA. Parallel methods for calculation of long-range electrostatic interactions. arXiv, 2013, 18 pp.

REBOK, Tomáš, Petr SLOUP, Jan HANUŠ and Věroslav KAPLAN. Three-dimensional Tree Reconstructions from Terrestrial LiDAR Scans. In National Grid Infrastructure Yearbook 2011-12. 2013, p. 91-95. ISBN 978-80-904689-7-9.

ANTOŠ, David, Petr HOLUB and Ivana KŘENKOVÁ. Kterak posluchárny spojovati a ještě záznam poříditi aneb audiovizuální technika na MU. ÚVT MU, 2011, 5 pp. Zpravodaj ÚVT MU, roč. XXI, č. 3. ISSN 1212-0901.

KŘENKOVÁ, Ivana, David ANTOŠ and Luděk MATYSKA. MetaCentrum Yearbook 2009. first. Prague: CESNET, z. s. p. o., 2010, 172 pp. ISBN 978-80-904173-7-3.

KMUNÍČEK, Jan, Martin KUBA, Ivana KŘENKOVÁ and David ANTOŠ. MetaCentrum—e-Infrastructure for Computational and Data Challenges. Nové Hrady, 2010.

HRBATÝ, Dušan, Jakub MAREČEK, Michal VÁVRA, Tomáš REBOK, Eva HLADKÁ, Jan DOLEČEK, Martin JANTOŠOVIČ, František KOBZÍK, Michal KOHUT, Vít RUSŇÁK, Martin SKALA, Daniel STIBOR and Jiří ŠKROBÁK. Testy softwarových VoIP klientů (Evaluation of Software VoIP clients). Brno: Laboratoř pokročilých síťových technologií FI MU, 2010.

REBOK, Tomáš. DiProNN: Distributed Programmable Network Node. Brno: Faculty of Informatics, Masaryk University, 2009, 200 pp. Ph.D. Thesis.

PÚDELKA, Ivan and Tomáš REBOK. Enhanced UDP Packet Reflector -- Erum. 2009.

REBOK, Tomáš, Martin BENEŠ and Milan KABÁT. Robust Audio Tool (RAT) Supporting Separate Recording and Playback Audio Devices Selection. 2009.