Publication Records

HRADISKÁ, Helena, Martin KUREČKA, Jan BERÁNEK, Guglielmo TEDESCHI, Vladimír VIŠŇOVSKÝ, Aleš KŘENEK and Vojtěch SPIWOK. Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics. The Journal of Physical Chemistry B. 2024. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/acs.jpcb.3c05669.

SLANINÁKOVÁ, Terézia, David PROCHÁZKA, Jakub ČILLÍK, Lucie NOVOTNÁ and Adrián ROŠINEC. AlphaFind. 2024. Available from: https://dx.doi.org/10.5281/zenodo.11085862.

SLANINÁKOVÁ, Terézia, David PROCHÁZKA, Jaroslav OĽHA, Adrián ROŠINEC, Katarína GREŠOVÁ, Jakub ČILLÍK, Miriama JÁNOŠOVÁ, Jana PORUBSKÁ, Radka SVOBODOVÁ, Vlastislav DOHNAL and Matej ANTOL. AlphaFind — discover structure similarity across the proteome in AlphaFold DB. In Elixir All-Hands 2024. 2024. Available from: https://dx.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 and 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 and Matej ANTOL. AlphaFind: Discover structure similarity across the entire known proteome. bioRxiv, 2024.

NOVOTNÁ, Lucie, Terézia SLANINÁKOVÁ, David PROCHÁZKA, Lukáš HEJTMÁNEK, Katarína GREŠOVÁ, Jaroslav OĽHA, Vlastislav DOHNAL, Adrián ROŠINEC and Matej ANTOL. AlphaFind: Discover structure similarity across the entire known proteome – data and model. 2024. Available from: https://dx.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 and Matej ANTOL. AlphaFind: discover structure similarity across the proteome in AlphaFold DB. Nucleic acids research. Oxford: Oxford University Press, 2024, vol. 52, July 5, p. W182-W186, 5 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkae397.

BERANEK, Jan, Aleš KŘENEK and Vojtěch SPIWOK. Analysis of metadynamics simulations by metadynminer.py. Bioinformatics. OXFORD: Oxford University Press, 2024, vol. 40, No 10, 4 pp. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btae614.

HÁJEK, Adam and Aleš HORÁK. CzeGPT-2 – Training New Model for Czech Generative Text Processing Evaluated with the Summarization Task. IEEE ACCESS. UNITED STATES: IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2024, vol. 2024, No 12, p. 34570-34581. ISSN 2169-3536. Available from: https://dx.doi.org/10.1109/ACCESS.2024.3371689.

SVOBODA, Tomáš, Jakub ČILLÍK, Michal MIKL, Tomáš SLAVÍČEK and Radka SVOBODOVÁ. Data Management and FAIRification in MAFIL. In Czech‐BioImaging Annual Scientific Conference 2024: Imaging Principles of Life. 2024.

SVOBODA, Tomáš, Adrián ROŠINEC, Tomáš RAČEK and Radka SVOBODOVÁ. Data Management of Biological Imaging Data. In ELIXIR CZ Annual Conference 2024: Data management. 2024.

SVOBODA, Tomáš and Adrián ROŠINEC. Data workflows at CEITEC MU. In Setkání OS metodiků MU. 2024.

SLANINÁKOVÁ, Terézia, Katarína GREŠOVÁ, David PROCHÁZKA, Viktória SPIŠAKOVÁ, Adrián ROŠINEC, Jakub ČILLÍK, Pavlína ŠPRINGEROVÁ, Aleš KŘENEK, Vlastislav DOHNAL, Radka SVOBODOVÁ and Matej ANTOL. Fast, structure-based searching in a large-scale protein data repository. In ELIXIR CZ Annual Conference. 2024. Available from: https://dx.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 and Matej ANTOL. GraSR: Protein structural embeddings of AlphaFold DB. 2024. Available from: https://dx.doi.org/10.48700/datst.br8aq-db495.

SVOBODA, Tomáš, Adrián ROŠINEC and Ondřej FILIP. Hands-on experience with big data transfer via iRODS and Onedata. In e-INFRA CZ CONFERENCE 2024. 2024.

ROŠINEC, Adrián. Introduction to the new generation EGI container execution platform. In EGI Webinar programme 2024. 2024. Available from: https://dx.doi.org/10.5281/zenodo.10566759.

NOVOTNÁ, Lucie, Terézia SLANINÁKOVÁ, David PROCHÁZKA, Lukáš HEJTMÁNEK, Adrián ROŠINEC, Jaroslav OĽHA, Katarína GREŠOVÁ, Vlastislav DOHNAL and Matej ANTOL. LMI-10: Protein structural embeddings of AlphaFold DB. 2024. Available from: https://dx.doi.org/10.48700/datst.t45hr-bcw17.

NOVOTNÁ, Lucie, Terézia SLANINÁKOVÁ, David PROCHÁZKA, Lukáš HEJTMÁNEK, Adrián ROŠINEC, Jaroslav OĽHA, Katarína GREŠOVÁ, Vlastislav DOHNAL and Matej ANTOL. LMI-30: Protein structural embeddings of AlphaFold DB. 2024. Available from: https://dx.doi.org/10.48700/datst.kgb8j-r5f84.

SVOBODA, Tomáš. MAFILDB - technická realizace (MAFILDB - technical implementation). In FAIR data pro uživatele CF MAFIL. 2024.

HECHT, Helge, Wudmir Yudy ROJAS VERASTEGUI, Zargham AHMAD, Aleš KŘENEK, Jana KLÁNOVÁ and Elliott James PRICE. Quantum Chemistry-Based Prediction of Electron Ionization Mass Spectra for Environmental Chemicals. Analytical chemistry. WASHINGTON: American Chemical Society, 2024, vol. 96, No 33, p. 13652-13662. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.4c02589.

BUČEKOVÁ, Gabriela, Viktoriia DOSHCHENKO, Aliaksei CHARESHNEU, Jana PORUBSKÁ, Michal PAJTINKA, Michal OLEKSIK, Tomáš SVOBODA, Vladimír HORSKÝ and Radka SVOBODOVÁ. Rare ring conformations in PDB: Facts or wishful thinking? bioRxiv. 2024. Available from: https://dx.doi.org/10.1101/2024.06.20.598822.

ROŠINEC, Adrián and Tomáš SVOBODA. Research Data Management at CEITEC MU. In Open Science Workshop 2024. 2024.

SVOBODA, Tomáš, Adrián ROŠINEC, Tomáš RAČEK, Josef HANDL, Aleš KŘENEK and Radka SVOBODOVÁ. Scientific Dataset Management System for the Research Institute Based on Onedata. In EGI Conference 2024. 2024.

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

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

NOVOTNÁ, Lucie, Terézia SLANINÁKOVÁ, David PROCHÁZKA, Lukáš HEJTMÁNEK, Adrián ROŠINEC, Jaroslav OĽHA, Katarína GREŠOVÁ, Vlastislav DOHNAL and Matej ANTOL. 3DZD: Protein structural embeddings of ESM Atlas. 2024. Available from: https://dx.doi.org/10.48700/datst.cd6zk-k0v44.

CALATRAVA, Amanda, Hernán ASOREY, Jan ASTALOS, Alberto AZEVEDO, Francesco BENINCASA, Ignacio BLANQUER, Martin BOBAK, Francisco BRASILEIRO, Laia CODÓ, Laura del CANO, Borja ESTEBAN, Meritxell FERRET, Josef HANDL, Tobias KERZENMACHER, Valentin KOZLOV, Aleš KŘENEK, Ricardo MARTINS, Manuel PAVESIO, Antonio Juan RUBIO-MONTERO and Juan SÁNCHEZ-FERRERO. A survey of the European Open Science Cloud services for expanding the capacity and capabilities of multidisciplinary scientific applications. COMPUTER SCIENCE REVIEW. NETHERLANDS: ELSEVIER, 2023, vol. 49. ISSN 1574-0137. Available from: https://dx.doi.org/10.1016/j.cosrev.2023.100571.

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

ROŠINEC, Adrián and Klára MORAVCOVÁ. Beskar Cloud: OpenStack Deployment on Top of Kubernetes. In 12th Iberian Grid Conference. 2023.

ROŠINEC, Adrián and Klára MORAVCOVÁ. Building OpenStack Cloud with Kubernetes as Undercloud. In EGI Conference 2023. 2023.

SVOBODA, Tomáš, Aleš KŘENEK, Łukasz OPIOŁA, Andrea MANZI and Josef HANDL. Cloudification of scientific experimental data using Onedata. In EGI Conference 2023. 2023.

HEJTMÁNEK, Lukáš, Adrián ROŠINEC and Sebastian LUNA-VALERO. Easy Deployment of Dask and Jupyter Notebooks on Managed Kubernetes. In EGI Conference 2023. 2023.

ROŠINEC, Adrián, Tomáš SVOBODA, Tomáš RAČEK, Aleš KŘENEK and Radka SVOBODOVÁ. Enhancing Data Accessibility: Strategies and Tools for Effective Metadata Management. In IBERGRID 2023. 2023.

SCHINDLER, Ondřej, Karel BERKA, Alessio CANTARA, Aleš KŘENEK, Dominik TICHÝ, Tomáš RAČEK and Radka SVOBODOVÁ. αCharges: partial atomic charges for AlphaFold structures in high quality. Nucleic Acids Research. Oxford: Oxford University Press, 2023, vol. 51, W1, p. "W11"-"W16", 6 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkad349.

SVOBODA, Tomáš, Radka SVOBODOVÁ, David ANTOŠ, Adrián ROŠINEC and Aleš KŘENEK. Introduction to Onedata at CEITEC MU and in Czech National Repository Platform. In MATECHat meeting. 2023.

RAČEK, Tomáš, Tomáš SVOBODA and Radka SVOBODOVÁ. Management of life-science data and their metadata. In XXII. setkání biochemiků a molekulárních biologů. 2023.

KUREČKA, Martin. Monte Carlo Tree Search with Function Approximation for Risk-constrained Planning and Reinforcement Learning. In The IJCAI-23 Joint Workshop on Artificial Intelligence Safety and Safe Reinforcement Learning. 2023.

SPIŠAKOVÁ, Viktória, Lukáš HEJTMÁNEK and Jakub HYNŠT. Nextflow in Bioinformatics: Executors Performance Comparison Using Genomics Data. FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE. NETHERLANDS: ELSEVIER, 2023, vol. 142, May 2023, p. 328-339. ISSN 0167-739X. Available from: https://dx.doi.org/10.1016/j.future.2023.01.009.

ROŠINEC, Adrián, Tomáš SVOBODA, Tomáš RAČEK, Josef HANDL, Jozef SABO, Aleš KŘENEK and Radka SVOBODOVÁ. Onedata4Sci: Life-science experimental datasets management system. In 3D-BioInfo | ISCB 3D-SIG | ELIXIR Czech Republic Structural Bioinformatics. 2023.

KLAŠKA, David, Antonín KUČERA, Martin KUREČKA, Vít MUSIL, Petr NOVOTNÝ and Vojtěch ŘEHÁK. Synthesizing Resilient Strategies for Infinite-Horizon Objectives in Multi-Agent Systems. Online. In Edith Elkind. Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence, IJCAI 2023,. Neuveden: International Joint Conferences on Artificial Intelligence, 2023, p. 171-179. ISBN 978-1-956792-03-4. Available from: https://dx.doi.org/10.24963/ijcai.2023/20.

SPIŠAKOVÁ, Viktória, Dalibor KLUSÁČEK and Lukáš HEJTMÁNEK. Using Kubernetes in Academic Environment : Problems and Approaches. In Dalibor Klusáček, Julita Corbalán, Gonzalo P. Rodrigo. Job Scheduling Strategies for Parallel Processing. 1st ed. Cham (Switzerland): Springer, 2023, p. 235-253. ISBN 978-3-031-22697-7. Available from: https://dx.doi.org/10.1007/978-3-031-22698-4_12.

SVOBODA, Tomáš, Aleš KŘENEK and Josef HANDL. Automatic storing, sharing and archiving datasets with Onedata. In EGI Conference 2022. 2022.

SVOBODA, Tomáš, Aleš KŘENEK and Josef HANDL. Automating scientific dataset management and processing using Onedata. In IBERGRID 2022. 2022.

SPIWOK, Vojtěch, Martin KUREČKA and Aleš KŘENEK. Collective Variable for Metadynamics Derived From AlphaFold Output. FRONTIERS IN MOLECULAR BIOSCIENCES. SWITZERLAND: FRONTIERS MEDIA SA, 2022, vol. 2022, No 9, p. 1-10. ISSN 2296-889X. Available from: https://dx.doi.org/10.3389/fmolb.2022.878133.

KUREČKA, Martin. Lower bound on the size of a quasirandom forcing set of permutations. COMBINATORICS PROBABILITY & COMPUTING. 2022, vol. 31, No 2, p. 304-319. ISSN 0963-5483. Available from: https://dx.doi.org/10.1017/S0963548321000298.

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

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.

PARDY, Filip, Jakub HYNŠT, Dana FIALOVÁ, Kristýna BRZOBOHATÁ, Lukáš HEJTMÁNEK and Šárka POSPÍŠILOVÁ. Reconstructing of the genome of Gregor Johann Mendel using state-of-the-art molecular and bioinformatics tools. In Mendel Genetics Conference 2022. 2022.

DUDOVÁ, Zdenka, Nathalie CONTE, Jeremy MASON, Dalibor STUCHLÍK, Radim PEŠA, Csaba HALMAGYI, Zinaida PEROVA, Abayomi MOSAKU, Ross THORNE, Alex FOLLETTE, Ľuboslav PIVARČ, Radim ŠAŠINKA, Muhammad USMAN, Steven NEUHAUSER, Dale A BEGLEY, Debra M KRUPKE, Massimiliano FRASSÀ, Alessandro FIORI, Riccardo CORSI, Luca VEZZADINI, Claudio ISELLA, Andrea BERTOTTI, Carol BULT, Helen PARKINSON, Enzo MEDICO, Terrence MEEHAN and Aleš KŘENEK. The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization. BMC Genomics. BioMed Central, 2022, vol. 23, No 1, p. 1-11. ISSN 1471-2164. Available from: https://dx.doi.org/10.1186/s12864-022-08367-1.

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.

MÍČ, Vladimír, Tomáš RAČEK, Aleš KŘENEK and Pavel ZEZULA. Similarity Search for an Extreme Application: Experience and Implementation. In Nora Reyes, Richard Connor, Nils Kriege, Daniyal Kazempour, Ilaria Bartolini, Erich Schubert, Jian-Jia Chen. Similarity Search and Applications: 14th International Conference, SISAP 2021, Dortmund, Germany, September 29 - October 1, 2021, Proceedings. Cham: Springer, 2021, p. 265-279. ISBN 978-3-030-89656-0. Available from: https://dx.doi.org/10.1007/978-3-030-89657-7_20.

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.

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.

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.

MORRIS, Chris, Paolo ANDREETTO, Lucia BANCI, Alexandre M J J BONVIN, Grzegorz CHOJNOWSKI, Laura del CANO, José Marıa CARAZO, Pablo CONESA, Susan DAENKE, George DAMASKOS, Andrea GIACHETTI, Natalie E C HALEY, Maarten L HEKKELMAN, Philipp HEUSER, Robbie P JOOSTEN, Daniel KOUŘIL, Aleš KŘENEK, Tomáš KULHÁNEK, Victor S LAMZIN, Nurul NADZIRIN, Anastassis PERRAKIS, Antonio ROSATO, Fiona SANDERSON, Joan SEGURA, Joerg SCHAARSCHMIDT, Egor SOBOLEV, Sergio TRALDI, Mikael E TRELLET, Sameer VELANKAR, Marco VERLATO and Martyn WINN. West-Life: A Virtual Research Environment for structural biology. Journal of Structural Biology: X. 2019, vol. 1, January - March 2019, p. 1-8. ISSN 2590-1524. Available from: https://dx.doi.org/10.1016/j.yjsbx.2019.100006.

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.

KLUSÁČEK, Dalibor, Boris PARÁK, Václav CHLUMSKÝ and Lukáš HEJTMÁNEK. Real-life Experience with Private Cloud hosting Heterogeneous Scientific Workloads. Online. In 2018 IEEE/ACM INTERNATIONAL CONFERENCE ON UTILITY AND CLOUD COMPUTING COMPANION (UCC COMPANION). NEW YORK: IEEE, 2018, p. 115-120. ISBN 978-1-72810-359-4. Available from: https://dx.doi.org/10.1109/UCC-Companion.2018.00044.

POPOVICI, Vlad, Aleš KŘENEK and Eva BUDINSKÁ. Identification of "BRAF-Positive" Cases Based on Whole-Slide Image Analysis. Biomed Research International. New York: HINDAWI LTD, 2017, Neuveden, April, p. nestránkováno, 7 pp. ISSN 2314-6133. Available from: https://dx.doi.org/10.1155/2017/3926498.

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.

KLUSÁČEK, Dalibor, Boris PARÁK and Lukáš HEJTMÁNEK. Scheduling Challenges in a Shared Private Cloud Infrastructure. CGW Workshop'17 Proceedings. 2017, vol. 2017, No 1, p. 23-24.

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.

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.

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.

TÓTH, Šimon and Miroslav RUDA. Distributed job scheduling in MetaCentrum. Journal of Physics: Conference Series. Institute of Physics, 2015, vol. 608, No 1, p. 012025-12029. ISSN 1742-6596. Available from: https://dx.doi.org/10.1088/1742-6596/608/1/012025.

GEIDL, Stanislav, Tomáš BOUCHAL, Tomáš RAČEK, Radka SVOBODOVÁ VAŘEKOVÁ, Václav HEJRET, Aleš KŘENEK, Ruben ABAGYAN and Jaroslav KOČA. High-quality and universal empirical atomic charges for chemoinformatics applications. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2015, vol. 7, DEC, p. 1-10. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/s13321-015-0107-1.

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.

IŠTVÁNEK, Jan, Michal JAROŠ, Aleš KŘENEK and Jana ŘEPKOVÁ. Genome assembly and annotation for red clover (Trifolium pratense; Fabaceae). American Journal of Botany. St Louis: Botanical Soc Amer Inc, 2014, vol. 101, No 2, p. 327-337. ISSN 0002-9122. Available from: https://dx.doi.org/10.3732/ajb.1300340.

RAČEK, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ, Aleš KŘENEK, Tomáš BOUCHAL and Jaroslav KOČA. NEEMP – Tool for parameterization of empirical charge calculation method EEM. In Chemoinformatics Strasbourg Summer School 2014. 2014.

RAČEK, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ and Aleš KŘENEK. Advanced implementation of atomic charge calculation with electronegativity equalization. In SVOČ 2013 v Opavě. 2013.

BOUCHAL, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ, Tomáš RAČEK, Crina-Maria IONESCU, Stanislav GEIDL, Aleš KŘENEK and Jaroslav KOČA. Empirical charges for chemoinformatics applications. In GCC 2013 - 9th German Conference on Chemoinformatics. 2013. Available from: https://dx.doi.org/10.1186/1758-2946-6-S1-P60.

HEJTMÁNEK, Lukáš, David ANTOŠ and Luboš KOPECKÝ. Choice of Data Transfer Protocols in Remote Storage Applications. CESNET, z.s.p.o., 2013, 21 pp. CESNET Technical Report 1/2013.

ŠTĚPÁN, Jakub, Petr KULHÁNEK, Milan LENČO, Zora STŘELCOVÁ, Aleš KŘENEK and Jaroslav KOČA. Nemesis - a molecular modeling package. Online. In Uli Fechner. Journal of Cheminformatics 2013, 5(Suppl 1). Goslar (GER): Chemistry Central, 2013, p. 13-14. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/1758-2946-5-S1-P12.

KŘENEK, Aleš, Petr HOLUB, Vlastimil HOLER, Daniel KOUŘIL, Filip PROCHÁZKA, Zdeněk HEJNA, Miroslav GURIČAN and František MULLER. 3.5 Million Smartmeters in the Cloud. Online. In Simon Lin. Proceedings ISGC 2013. Trieste: PoS - Proceedings of Science, 2013, p. 180-189. ISSN 1824-8039.

FEIT, Josef, Lukáš HEJTMÁNEK, Michal PROCHÁZKA, Slávek LICEHAMMER and Luděk MATYSKA. Hypertext Atlases of Pathology. 2012. ISSN 0945-6317.

KREMSER, Jiří, Božena KOVÁČOVÁ, Marta PAVLOVSKÁ, Lukáš HEJTMÁNEK and David ANTOŠ. Long Term Preservation of Digital Data—Background Research. 2012.

KOTÁSEK, Zdeněk, Jan BOUDA, Ivana ČERNÁ, Lukáš SEKANINA, Tomáš VOJNAR and David ANTOŠ. Mathematical and Engineering Methods in Computer Science MEMICS 2011, Seventh International Doctoral Workshop, Revised Selected Papers. Springer-Verlag, 2012, 215 pp. ISBN 978-3-642-25928-9. Available from: https://dx.doi.org/10.1007/978-3-642-25929-6.

KLUSÁČEK, Dalibor, Hana RUDOVÁ and Miroslav RUDA. New Fairness and Performance Metrics for Current Grids. In Cracow Grid Workshop 2012. 2012. ISBN 978-83-61433-06-4.

CHLUMSKÝ, Václav, Dalibor KLUSÁČEK and Miroslav RUDA. Planning, Predictability and Optimization within the TORQUE Scheduler. In Antonín Kučera, Thomas Henzinger, Jaroslav Nešetřil, Tomáš Vojnar, David Antoš. MEMICS 2012. první. Brno: Novpress s.r.o., 2012, p. 96-97. ISBN 978-80-87342-15-2.

TÓTH, Šimon and Miroslav RUDA. Practical Experiences with Torque Meta-Scheduling in The Czech National Grid. Krakow, Poland: AGH University of Science and Technology Press, 2012, p. 33-45. ISSN 1508-2806.

KLUSÁČEK, Dalibor, Václav CHLUMSKÝ and Miroslav RUDA. THE EXTENSION OF TORQUE SCHEDULER ALLOWING THE USE OF PLANNING AND OPTIMIZATION IN GRIDS. Computer Science Journal. Krakow, Poland: AGH University of Science and Technology, 2012, vol. 13, No 2, p. 5-19. ISSN 1508-2806. Available from: https://dx.doi.org/10.7494/csci.2012.13.2.5.

KUČERA, Antonín, Thomas A. HENZINGER, Jaroslav NEŠETŘIL, Tomáš VOJNAR and David ANTOŠ. 8th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: NOVPRESS, 2012. ISBN 978-80-87342-15-2.

MATYSKA, Luděk and David ANTOŠ. Centrum CERIT-SC po roce příprav. ÚVT MU, 2011, 3 pp. Zpravodaj ÚVT MU, roč. XXI, č. 3. ISSN 1212-0901.

GOLEMBIOVSKÝ, Tomáš and Aleš KŘENEK. Compression of Vector Field Changing in Time. Online. In Ludek Matyska, Michal Kozubek, Tomas Vojnar and Pavel Zemcik, David Antos. Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Dagstuhl: Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, 2011, p. 40-46. ISBN 978-3-939897-22-4.

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.

KOTÁSEK, Zdeněk, Jan BOUDA, Ivana ČERNÁ, Lukáš SEKANINA, Tomáš VOJNAR and David ANTOŠ. MEMICS 2011, Seventh Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno University of Technology, Antonínská 548/1, Brno 601 90, 2011, 146 pp. ISBN 978-80-214-4305-1.

MATYSKA, Luděk, Miroslav RUDA and Šimon TÓTH. Peer-to-peer Cooperative Scheduling Architecture for National Grid Infrastructure. In Simon C.Lin, Eric Yen. Data Driven e-Science. Academia Sinica Grid Computing Centre, 2011, p. 105-118. ISBN 978-1-4419-8014-4.

MATYSKA, Luděk, Michal KOZUBEK, Tomáš VOJNAR, Pavel ZEMČÍK and David ANTOŠ. Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS'10) -- Selected Papers. Dagstuhl, Germany: Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, 2011. ISBN 978-3-939897-22-4.

CHLUMSKÝ, Václav, Dalibor KLUSÁČEK and Miroslav RUDA. The Extension of TORQUE Scheduler Allowing the Use of Planning and Optimization Algorithms in Grids. In Cracow Grid Workshop. 2011.

TÓTH, Šimon, Miroslav RUDA and Luděk MATYSKA. Towards Peer-to-Peer Scheduling Architecture for the Czech National Grid. Krakow, Poland: Academic Computer Centre CYFRONET AGH, 2011, p. 92-101. ISBN 978-83-61433-03-3.

GOLEMBIOVSKÝ, Tomáš and Aleš KŘENEK. Compression of Vector Field Changing in Time. In MEMICS 2010: Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: NOVPRESS, s.r.o., 2010, p. 76-83. ISBN 978-80-87342-10-7.

MATYSKA, Luděk, Michal KOZUBEK, Tomáš VOJNAR, Pavel ZEMČÍK and David ANTOŠ. MEMICS 2010: Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: NOVPRESS s.r.o., 2010, 213 pp. ISBN 978-80-87342-10-7.

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.

ANTOŠ, David, Martin OSOVSKÝ, Marek SAITL and Václav LORENC. Ráno Eduroamisto, večer takisto. 2010, 6 pp. Zpravodaj ÚVT MU, roč. XXI, č. 2. ISSN 1212-0901.

COLLING, David, Janusz MARTYNIAK, Andrew MCGOUGH, Aleš KŘENEK, Jiří SITERA, Miloš MULAČ and František DVOŘÁK. Real Time Monitor of Grid job executions. Journal of Physics: Conference Series. 2010, vol. 219, No 6, 9 pp. ISSN 1742-6596.

ŠUSTR, Zdeněk, Jiří SITERA, František DVOŘÁK, Jiří FILIPOVIČ, Daniel KOUŘIL, Aleš KŘENEK, Luděk MATYSKA, Miloš MULAČ, Jan POSPÍŠIL, Miroslav RUDA, Zdeněk SALVET and Michal VOCŮ. Something you may have wanted to know about L&B. Journal of Physics: Conference Series. 2010, vol. 219, No 6, 10 pp. ISSN 1742-6596.

RUDA, Miroslav, Zdeněk ŠUSTR, Jiří SITERA, David ANTOŠ, Lukáš HEJTMÁNEK and Petr HOLUB. Virtual Clusters as a New Service of MetaCentrum, the Czech NGI. In Cracow Grid Workshop '09. Krakow: Academic Computer Centre CYFRONET AGH, 2010, p. 64-71. ISBN 978-83-61433-01-9.

HEJTMÁNEK, Lukáš and Josef FEIT. Distribuované zpracování obrazu pro virtuální mikroskop (Distributed Workflow for Virtual Microscope). Brno: Masarykova univerzita, 2009. Mefanet 2009. ISBN 978-80-7392-118-7.

HOLUB, Petr and David ANTOŠ. e-Infrastruktury - komplexní nástroje pro podporu vědy, výzkumu i výuky (e-Infrastructures--tools for science and education support). Masarykova univerzita, 2009, 7 pp. Zpravodaj ÚVT MU, 19, 4, 1-6. ISSN 1212-0901.

VOJNAR, Tomáš, Petr HLINĚNÝ, Václav MATYÁŠ and David ANTOŠ. MEMICS 2009, Fifth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. first. Brno: NOVPRESS s.r.o., nám. Republiky 725/15, 614 00 Brno, 2009, 258 pp. ISBN 978-80-87342-04-6.

ANTOŠ, David, Jiří SITERA, Luděk MATYSKA and Petr HOLUB. MetaCenter Virtual Networks. In Cracow Grid Workshop 2008. Cracow, Poland: Cyfronet AGH, Kraków, Poland, 2009, p. 86-93. ISBN 978-83-61433-00-2.

ŠUSTR, Zdeněk, Jiří SITERA, Miloš MULAČ, Miroslav RUDA, David ANTOŠ, Lukáš HEJTMÁNEK, Petr HOLUB, Zdeněk SALVET and Luděk MATYSKA. MetaCentrum, the Czech Virtualized NGI. 2009.

ANTOŠ, David, Lukáš HEJTMÁNEK, Jiří CHUDOBA, Daniel KOUŘIL, Luděk MATYSKA and Michal PROCHÁZKA. Správa dat v gridových systémech (Data Management in Grid Systems). In Proceedings of the Annual Database Conference DATAKON 2009. 1st ed. Praha: Oeconomica, Praha, 2009, p. 251-265. ISBN 978-80-245-1568-7.

LIŠKA, Miloš, Jiří MATELA and Lukáš HEJTMÁNEK. UltraGrid2K. 2009.

ANTOŠ, David, Luděk MATYSKA, Petr HOLUB and Jiří SITERA. VirtCloud: Virtual Network for User-controlled Virtual Clusters. 2009.

ANTOŠ, David, Luděk MATYSKA, Petr HOLUB and Jiří SITERA. VirtCloud: Virtualising Network for Grid Environments--First Experiences. In The 23rd IEEE International Conference on Advanced Information Networking and Applications AINA 2009. Bradford, UK: IEEE Comp. Soc., 2009, p. 876-883. ISBN 978-1-4244-4000-9.

RUDA, Miroslav, Zdeněk ŠUSTR, Jiří SITERA, David ANTOŠ, Lukáš HEJTMÁNEK, Petr HOLUB and Miloš MULAČ. Virtual Clusters as a New Service of MetaCentrum, the Czech NGI; CESNET technical report 17/2009. 2009.

ANTOŠ, David. Virtualizace v gridových infrastrukturách. 2009.

SITERA, Jiří and David ANTOŠ. Virtuální grid: virtualizace krátí cestu do MetaCentra (Virtual Grid). Brno: CPress Media, a. s., 2009, 2 pp. Connect! 7-8/2009, roč. XIV. ISSN 1211-3085.

ANTOŠ, David, Jiří DENEMARK and Jan FOUSEK. Effects of Virtualisation on Behaviour and Performance Characteristics of Network Processing. 2008.

SCHOVANCOVÁ, Jaroslava, Jiří CHUDOBA, František DVOŘÁK, Jiří FILIPOVIČ, Jan KMUNÍČEK, Aleš KŘENEK, Luděk MATYSKA, Miloš MILAČ, Miroslav RUDA, Zdeněk SALVET, Jiří SITERA, Zdeněk ŠUSTR and Petr TRÁVNÍČEK. Experience with Large Scale Simulations on the EGEE Grid for the AUGER collaboration. In Proceedings of the Third Conference of the EELA Project. Catania, Itálie: CIEMAT, 2008, p. 283-291, 8 pp. ISBN 978-84-7834-565-6.

KŘENEK, Aleš, Jiří SITERA, Jiří CHUDOBA, František DVOŘÁK, Jiří FILIPOVIČ, Jan KMUNÍČEK, Luděk MATYSKA, Miloš MULAČ, Miroslav RUDA, Zdeněk ŠUSTR, Simone CAMPANA, Elizabetta MOLINARI and David REBATTO. Experimental evaluation of job provenance in ATLAS environment. In Journal of Physics: Conference Series. Bristol, Great Britain, 2008, p. 1-9.

KŘENEK, Aleš, Jiri SITERA, Luděk MATYSKA, Frantisek DVORAK, Miloš MULAČ, Miroslav RUDA and Zdeněk SALVET. gLite Job Provenance - a job-centric view. Concurrency and Computation: Practice and Experience. John Wiley & Sons, Inc, 2008, vol. 20, No 5, p. 453-462. ISSN 1532-0626. Available from: https://dx.doi.org/10.1002/cpe.1252.

ANTOŠ, David, Jiří SITERA and Daniel KOUŘIL. IPv6 in METACenter. 2008.

RUDA, Miroslav, Jiri SITERA, Aleš KŘENEK, Luděk MATYSKA, Zdenek SUSTR and Michal VOCŮ. Job Centric Monitoring on the Grid 7 years of experience with L&B and JP services. In CESNET CONFERENCE 2008-SECURITY, MIDDLEWARE, AND VIRTUALIZATION-GLUE OF FUTURE NETWORKS. Praha: CESNET, 2008, p. 3-12. ISBN 978-80-904173-0-4.

KŘENEK, Aleš, Luděk MATYSKA, Jiří SITERA, Miroslav RUDA, František DVOŘÁK, Jiří FILIPOVIČ, Zdeněk ŠUSTR and Zdeněk SALVET. Job Provenance - Insight into Very Large Provenance Datasets. In Provenance and Annotation of Data and Processes. Second International Provenance and Annotation Workshop, IPAW 2008; LNCS. Berlin: Springer Berlin / Heidelberg, 2008, p. 144-151. ISBN 978-3-540-89964-8.

ČEŠKA, Milan, Zdeněk KOTÁSEK, Mojmír KŘETÍNSKÝ, Luděk MATYSKA, Tomáš VOJNAR and David ANTOŠ. MEMICS 2008, Fourth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. 2008.

ČEŠKA, Milan, Zdeněk KOTÁSEK, Mojmír KŘETÍNSKÝ, Luděk MATYSKA, Tomáš VOJNAR and David ANTOŠ. MEMICS 2008, Fourth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. 1st ed. Brno: Ing. Zdeněk Novotný CSc., Ondráčkova 105, 628 00 Brno, 2008, p. 1-286. ISBN 978-80-7355-082-0.

ANTOŠ, David, Jiří SITERA, Luděk MATYSKA and Petr HOLUB. MetaCenter Virtual Networks. In Cracow Grid Workshop 2008. 2008.

HEJTMÁNEK, Lukáš. Secure and Fault Tolerant Distributed Framework with Mobility Support. In Grid Middleware and Services - Challenges and Solutions. New York, NY, USA: Springer Science + Business Media, 2008, p. 289-304. ISBN 978-0-387-78445-8.

ANTOŠ, David. Služby ÚVT pro vědu a výzkum (ICS Services for Science and Research). Brno: Masarykova univerzita, 2008. ISSN 1212-0901.

MOREAU, Luc, Bertram LUDASCHER, Ilkay ALTINTAS, Roger BARGA, Shawn BOWERS, Steven CALLAHAN, George CHIN, Ben CLIFFORD, Shirley COHEN, Sarah COHEN-BOULAKIA, Susan DAVIDSON, Ewa DEELMAN, Luciano DIGIAMPIETRI, Ian FOSTER, Juliana FREIRE, James FREW, Joe FUTRELLE, Tara GIBSON, Yolanda GIL, Carole GOBLE, Jennifer GOLBECK, Paul GROTH, David HOLLAND, Sheng JIANG, Jihie KIM, David KOOP, Aleš KŘENEK, Timothy MCPHILLIPS, Gaurang MEHTA, Simon MILES, Dominic METZGER, Steve MUNROE, Jim MYERS, Beth PLALE, Norbert PODHORSZKI, Varun RATNAKAR, Emanuele SANTOS, Carlos SCHEIDEGGER, Karen SCHUCHARDT, Margo SELTZER, Yogesh SIMMHAN, Claudio SILVA, Peter SLAUGHTER, Eric STEPHAN, Robert STEVENS, Daniele TURI, Huy VO, Mike WILDE, Jun ZHAO and Yong ZHAO. Special issue: The first provenance challenge. Concurrency and Computation: Practice and Experience. John Wiley & Sons, Inc, 2008, vol. 20, No 5, p. 409-418. ISSN 1532-0626. Available from: https://dx.doi.org/10.1002/cpe.1233.

ANTOŠ, David. Úvod do IPv6 (IPv6 Introduction). Brno: Masarykova univerzita, 2008, 4 pp. Zpravodaj ÚVT MU, XIX, 2, 2-5.

FEIT, Josef, Luděk MATYSKA, Vladimír ULMAN, Lukáš HEJTMÁNEK, Hana JEDLIČKOVÁ, Marta JEŽOVÁ, Mojmír MOULIS and Věra FEITOVÁ. Virtual microscope interface to high resolution histological images. In Diagnostic Pathology. (3)Suppl 1). http://www.diagnosticpathology.org: 2006 Kayser; licensee BioMed Central Ltd., 2008, p. NA, 1 pp.

DENEMARK, Jiří, Miroslav RUDA and Luděk MATYSKA. Virtualizing METACentrum Resources Using Magrathea. In Networking Studies II: Selected Technical Reports. 1st ed. Praha: CESNET, 2008, p. 129-145. ISBN 978-80-254-2151-2.

HEJTMÁNEK, Lukáš, Luděk MATYSKA and Michal PROCHÁZKA. Bezpečný distribuovaný úložný prostor (Secure distributed data storage). In Širokopásmové sítě a jejich aplikace. Olomouc: CESNET, z.s.p.o. a UP Olomouc, 2007, p. 60-65. ISBN 978-80-244-1687-8.

KRAJÍČEK, Ondřej, Andrea CECCANTI, Miroslav RUDA and Aleš KŘENEK. Designing a distributed mediator for the C-GMA monitoring architecture. In Distributed and Parallel Systems: From Cluster to Grid Computing. Innsbruck, Austria: Springer, 2007, p. 155-164. ISBN 978-0-387-69857-1.

HEJTMÁNEK, Lukáš and Luděk MATYSKA. Distributed Data Storage with Strong Offline Access Support. In The Second International Multi-Conference on Computing in the Global Information Technology Challanges for the Next Generation of IT & C. Gosier, Guadeloupe, French Caribbean: IEEE Computer Society Press, 2007, p. 1-6. ISBN 0-7695-2798-1.

HEJTMÁNEK, Lukáš. Distributed Storage Framework with Offline Support. Brno: Faculty of Informatics, Masaryk University, 2007, 110 pp. Ph.D Thesis.

RUDA, Miroslav and Jiří DENEMARK. Grid Deployment Using Virtual Machines: METACenter Use-Case. DESY, Hamburg, Germany, 2007. Virtualization users workshop.

RUDA, Miroslav and Hana RUDOVÁ. Grid Simulator with Production Scheduling Algorithms (abstract). Cracow, Poland, 2007. Cracow Grid Workshop '07.

FEIT, Josef, Lukáš HEJTMÁNEK, Luděk MATYSKA, Vladimír ULMAN, Marta JEŽOVÁ, Mojmír MOULIS, Věra FEITOVÁ, Sylva HOTÁRKOVÁ, Ondřej SOUČEK, Katarína MÚČKOVÁ and Pavel VLAŠÍN. Hypertextové atlasy patologie 2007 (Hypertext atlases of pathology 2007). In MEFANET 2007. Brno: MSD, 2007. ISBN 978-80-739-2007-4.

ANTOŠ, David, Zdeněk SALVET, Jiří SITERA and Daniel KOUŘIL. IPv6 in METACenter. 2007.

DENEMARK, Jiří, Miroslav RUDA and Luděk MATYSKA. Magrathea -- Grid Management Using Virtual Machine. In Cracow Grid Workshop '06. Krakow, Polsko: Academic Computer Centre CYFRONET AGH, 2007, p. 138-145. ISBN 83-915141-7-X.

MATYSKA, Luděk, David ANTOŠ, Milan ČEŠKA, Mojmír KŘETÍNSKÝ and Petr HLINĚNÝ. MEMICS 2007: Third Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. 2007.

MATYSKA, Luděk, David ANTOŠ, Milan ČEŠKA, Mojmír KŘETÍNSKÝ and Petr HLINĚNÝ. MEMICS 2007: Third Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. 1st ed. Brno: Ing. Zdeněk Novotný CSc., Ondráčkova 105, 62800 Brno, 2007, 290 pp. ISBN 978-80-7355-077-6.

ŠUSTR, Zdeněk, Aleš KŘENEK, Martin PETŘEK, Jiří FILIPOVIČ, Jan KMUNÍČEK, Jiří WIESNER, Jiří SITERA, František DVOŘÁK and Luděk MATYSKA. Multiple Ligand Trajectory Docking Study: Semiautomatic Analysis of Molecular Dynamics Simulations Using EGEE gLite Services. In Proceedings of the 16th Euromicro Conference on Parallel, Distributed and Network-based Processing. Toulouse, France: IEEE CPS, 2007, p. 447-454. ISBN 978-0-7695-3089-5.

DENEMARK, Jiří and David ANTOŠ. Network Overhead in Virtual Machines. Lyngby, Denmark: TERENA Networking Conference TNC2007, 2007.

HEJTMÁNEK, Lukáš and Luděk MATYSKA. Nonblocking Distributed Replication of Versioned Files. JOURNAL OF SOFTWARE (JSW). 2007, vol. 2, No 5, p. 16-23. ISSN 1796-217X.

HEJTMÁNEK, Lukáš, Luděk MATYSKA and Michal PROCHÁZKA. Secure Logistical Networking in Virtual Organizations. In Cracow'06 Grid Workshop. Krakow, Polsko: Academic Computer Centre CYFRONET AGH, 2007, p. 450-458. ISBN 83-915141-7-X.

HEJTMÁNEK, Lukáš, Luděk MATYSKA and Michal PROCHÁZKA. Secure Logistical Networking in Virtual Organizations. CESNET z.s.p.o., 2007, 16 pp. 2/2007.

RUDA, Miroslav, Jiří DENEMARK and Luděk MATYSKA. Scheduling Virtual Grids: the Magrathea System. In Second International Workshop on Virtualization Technology in Distributed Computing. USA: ACM digital library, 2007, p. 1-7. ISBN 978-1-59593-897-8.

ANTOŠ, David, Igor PETERLÍK, Jiří DENEMARK and Luděk MATYSKA. Virtualizace rozsáhlé výpočetní infrastruktury (Virtualisation of Large Computation Infrastructure). In Širokopásmové sítě a jejich aplikace. Olomouc: CESNET, z. s. p. o. a Univerzita Palackého Olomouc, 2007, p. 51-54. ISBN 978-80-244-1687-8.

DENEMARK, Jiří, Michał JANKOWSKI, Aleš KŘENEK, Luděk MATYSKA, Norbert MEYER, Miroslav RUDA and Paweł WOLNIEWICZ. Best Practices of User Account Management with Virtual Organization Based Access to Grid. Lecture Notes in Computer Science. Springer Berlin/Heidelberg, 2006, vol. 3911, -, p. 633-642. ISSN 0302-9743.

KRAJÍČEK, Ondřej, Aleš KŘENEK, Luděk MATYSKA, Miroslav RUDA and Jiří SITERA. Capability languages in C-GMA. In Proceedings of the Cracow Grid Workshop 2005. April 2006. Cracow: Academic Computer Center CYFRONET AGH, Cracow, Poland, 2006, p. 131-138. ISBN 83-915141-5-3.

KRAJÍČEK, Ondřej, Andrea CECCANTI, Aleš KŘENEK, Luděk MATYSKA and Miroslav RUDA. Designing a Distributed Mediator for the C-GMA Monitoring Architecture. In Proceedings of the Austrian Hungarian Workshop on Parallel and Distributed Systems 2006. 1st ed. Innsbruck, 2006, p. TO APPEAR, 10 pp.

KŘENEK, Aleš and Jiří FILIPOVIČ. Haptický model interakce molekul (Haptic model of interaction of molecules). 2006.

ANTOŠ, David. Hardware-constrained Packet Classification. Faculty of Informatics, Masaryk University, 2006, 148 pp.

ANTOŠ, David, Vojtěch ŘEHÁK and Petr HOLUB. Packet Filtering for FPGA-Based Routing Accelerator. In CESNET Conference 2006 Proceedings. Prague: CESNET, z. s. p. o., 2006, p. 161--173. ISBN 80-239-6533-6.

MATYSKA, Luděk, Antonín KUČERA, Tomáš VOJNAR, Zdeněk KOTÁSEK, David ANTOŠ and Ondřej KRAJÍČEK. Proceedings of the Second Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS 2006). Mikulov: FIT BUT, 2006, 281 pp. Proceedings. ISBN 80-214-3287-X.

ANTOŠ, David and Vojtěch ŘEHÁK. Routing and Level 2 Addressing in a Hardware Accelerator for Network Applications. In ICT 2006, 13th International Conference on Telecommunications. Funchal, Madeira: University of Aveiro, Portugal, 2006, p. 1-4. ISBN 972-98368-4-1.

ANTOŠ, David and Vojtěch ŘEHÁK. Routing, L2 Addressing, and Packet Filtering in a Hardware Engine. In Proceedings of MEMICS 2006. Mikulov: FIT BUT, 2006, p. 1-8. ISBN 80-214-3287-X.

DENEMARK, Jiří, Michał JANKOWSKI, Luděk MATYSKA, Norbert MEYER, Miroslav RUDA and Paweł WOLNIEWICZ. User Management for Virtual Organizations. In CoreGRID Integration Workshop. EU: CoreGRID, 2006.

CHUDOBA, Jiří, Lukáš FIALA, Jan KMUNÍČEK, Jiří KOSINA, Daniel KOUŘIL, Miloš LOKAJÍČEK, Luděk MATYSKA, Miroslav RUDA and Jan ŠVEC. VOCE---A Grid Environment for Central Europe. In Proceedings of the Cracow Grid Workshop 2005. Cracow: Academic Computer Center CYFRONET AGH, Cracow, Poland, 2006, p. 322-328. ISBN 83-915141-5-3.

SITERA, Jiří, Luděk MATYSKA, Aleš KŘENEK, Miroslav RUDA, Michal VOCŮ, Zdeněk SALVET and Miloš MULAČ. Capability and Attribute Based GRID Monitoring Architecture. In Proc. Cracow Grid Workshop'04. Krakow, Polsko: Academic Computing Centre CYFRONET AGH, 2005, p. 176-183. ISBN 83-9151414-4-5.

KŘENEK, Aleš and Igor PETERLÍK. Distribuované výpočty složitých stavových prostorů (Distributed computation of complex state spaces). In Širokopásmové sítě a jejich aplikace. Olomouc: CESNET, z.s.p.o., 2005, p. 176-185. ISBN 80-244-1035-4.

RUDA, Miroslav and Hana RUDOVÁ. Grid Scheduling and Monitoring. Workshop of the UK Planning and Scheduling Special Interest Group. London, UK: City University, UK, 2005, vol. 2005, -, p. 98-99. ISSN 1368-5708.

PETERLÍK, Igor and Aleš KŘENEK. Haptically Driven Travelling Through Conformational Space. In First Joint EUROHAPTICS CONFERENCE and SYMPOSIUM ON HAPTIC INTERFACES FOR VIRTUAL ENVIRONMENT AND TELEOPERATOR SYSTEMS. Pisa: IEEE Computer Society, 2005, p. 342-347. ISBN 0-7695-2310-2.

KŘENEK, Aleš and Zora SEBESTIANOVÁ. Perun -- Fault-Tolerant Management of Grid Resources. In Krakow Grid Workshop 2004. Krakow: Academic Computer Centre CYFRONET AGH, 2005, p. 133-140. ISBN 83-915141-4-5.

CECCANTI, Andrea, Ondřej KRAJÍČEK, Aleš KŘENEK, Luděk MATYSKA and Miroslav RUDA. Towards Scalable and Interoperable Grid Monitoring Infrastructure. In Proceedings of the first CoreGRID Integration Workshop. Pisa: University of Pisa, Italy, 2005, p. 237-246.

MATYSKA, Luděk, Miroslav RUDA, Jiří DENEMARK, Norbert MEYER, Paweł WOLNIEWICZ and Michał JANKOWSKI. User Management for Virtual Organizations. EU: CoreGRID, 2005. TR-0012.

KOUŘIL, Daniel, Aleš KŘENEK, Luděk MATYSKA, Miloš MULAČ, Jan POSPÍŠIL, Miroslav RUDA, Zdeněk SALVET, Jiří SITERA, Jiří ŠKRABAL and Michal VOCŮ. Distributed Tracking, Storage, and Re-use of Job State Information on the Grid. 2004, 4 pp.

HOLUB, Petr, Martin KUBA, Luděk MATYSKA and Miroslav RUDA. Grid Infrastructure Monitoring as Reliable Information Service. In Grid Computing, Second European AcrossGrids Conference, AxGrids 2004, Lecture Notes in Computer Science 3165. Berlin / Heidelberg: Springer-Verlag, 2004, p. 220-229. ISBN 3-540-22888-8.

ANDREETTO, P., Valentina BORGIA, A. DORIGO, A. GIANELLE, M. MORDACCHINI, M. SGARAVATTO, L. ZANGRANDO, S. ANDREOZZI, V. CIASCHINI, C. DI GIUSTO, F. GIACOMINI, V. MEDICI, E. RONCHIERI, V. VENTURI, G. AVELLINO, S. BECO, A. MARASCHINI, F. PACINI, A. GUARISE and G. PATANIA. Practical approaches to Grid workload and resource management in the EGEE project. 2004, 4 pp.

KŘENEK, Aleš, Igor PETERLÍK and Luděk MATYSKA. Building 3D State Spaces of Virtual Environments with a TDS-based Algorithm (Haptic rendering of complex force fields). In Recent Advances in Parallel Virtual Machine and Message Passing Interface. Berlin: Springer-Verlag, 2003, p. 529-536. ISBN 3-540-20149-1.

KŘENEK, Aleš. Haptic rendering of complex force fields. In Proc. 9th Eurographics Workshop on Virtual Environments. Zurich: ACM Press, 2003, p. 231-240. ISBN 3-905673-00-2.

HLADKÁ, Eva and Zdeněk SALVET. An Active Network Architecture: Distributed Computer or Transport Medium. Lecture Notes in Computer Science. Berlin Heidelberg New York: Springer, 2001, vol. 2093, p. 612-620. ISSN 0302-9743.

KŘENEK, Aleš. Haptic Rendering of Molecular Conformations. In Proc. Eurohaptics 2001. Birmingham: The University of Birmingham, 2001, p. 142-145. Educational Tchnology Research Paper Series. ISSN: 1463-9394.

KŘENEK, Aleš and Luděk MATYSKA. Haptic Rendering of Molecular Properties. Francie: ERCIM, 2001. ERCIM News, 44. ISBN 0926-4981.

MATYSKA, Luděk, Michal VOCŮ and Aleš KŘENEK. MetaCenter -- Building a Virtual Supercomputer. Francie: ERCIM, 2001. ERCIM News, 45. ISBN 0926-4981.

MATYSKA, Luděk and Miroslav RUDA. Conformational Analysis as a Testbed for MetaComputer. In ISThmus 2000 - Research and Development for the Information Society. Poznan: Politechnika Poznanska, 2000, p. 279-564. ISBN 83-913639-0-2.

KŘENEK, Aleš. Handling Cycles in Conformational Behaviour Visualization. In Proceedings WSCG'2000. Plzeň: Západočeská univerzita, 2000, p. 48-54. ISBN 80-7082-614-6.

KŘENEK, Aleš. Haptic Rendering of Molecular Flexibility. In Proceedings PURS2000. 1st ed. Konstanz, CH: Swiss Federal Institute of Technology, 2000, p. 19-26. Selected Readings in Vison and Graphics, 8. ISBN 3-89649-579-8.

HLADKÁ, Eva and Zdeněk SALVET. Jak se domluvit s Evropou (How to videoconference in Europe). Zpravodaj Ústavu výpočetní techniky Masarykovy univerzity v Brně. Brno: Masarykova univerzita v Brně, 2000, vol. 11, No 2, p. 12-15. ISSN 1212-0901.

MATYSKA, Luděk and Miroslav RUDA. Security Infrastructure ot the MetaCenter. In ISThmus 2000 - Research and Development for the Information Society. Poznan: Politechnika Poznanska, 2000, p. 419-844. ISBN 83-913639-0-2.

HLADKÁ, Eva, David KOŠŤÁL and Zdeněk SALVET. Videokonference v aktivních sítích (Videoconferencing in Active Networks). In Sborník příspěvků Širokopásmové sítě a jejich aplikace. Olomouc, 2000, p. 31-33. ISBN 80-244-0095-2.

KŘENEK, Aleš, Martin ČERNOHORSKÝ and Zdeněk KABELÁČ. Haptic Visualization of Molecular Data. In Proceedings WSCG'99. Plzeň: Západočeská univerzita, 1999, p. 132-139. ISBN 80-7082-490-5.

KŘENEK, Aleš and Zdeněk KABELÁČ. Studying Conformational Behaviour with PHANToM device(s). In Proceedings PURS'99. Heidelberg: Deutsches Krebsforschungszentrum, 1999, p. 3-6.

MATYSKA, Luděk and Miroslav RUDA. Meta Computing - New Direction in High Performance Computing. In ITAB´97. Praha: IEEE EMB, 1997, p. 106. ISBN 0-7803-4318-2.