Výpis publikací

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

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

KRÁSA, Filip; Adrián ROŠINEC; Adam ONDREJKA a Aleš KŘENEK. MDDash – one stop shop for MD simulations. 2026. Dostupné z: https://doi.org/10.5281/zenodo.18740266.

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

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

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

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

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

HÁJEK, Adam; Helge HECHT; Elliott James PRICE a Aleš KŘENEK. SpecTUS: Spectral Translator for Unknown Structures annotation from EI-MS spectra. 2025. Dostupné z: https://doi.org/10.48550/arXiv.2502.05114.

HRADISKÁ, Helena; Martin KUREČKA; Jan BERÁNEK; Guglielmo TEDESCHI; Vladimír VIŠŇOVSKÝ; Aleš KŘENEK a Vojtěch SPIWOK. Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics. The Journal of Physical Chemistry B. 2024, roč. 128, č. 4, s. 903-913. ISSN 1520-6106. Dostupné z: https://doi.org/10.1021/acs.jpcb.3c05669.

BERANEK, Jan; Aleš KŘENEK a Vojtěch SPIWOK. Analysis of metadynamics simulations by metadynminer.py. Bioinformatics. OXFORD: Oxford University Press, 2024, roč. 40, č. 10, s. 1-4. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btae614.

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

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

HECHT, Helge; Wudmir Yudy ROJAS VERASTEGUI; Zargham AHMAD; Aleš KŘENEK; Jana KLÁNOVÁ a Elliott James PRICE. Quantum Chemistry-Based Prediction of Electron Ionization Mass Spectra for Environmental Chemicals. Analytical chemistry. WASHINGTON: American Chemical Society, 2024, roč. 96, č. 33, s. 13652-13662. ISSN 0003-2700. Dostupné z: https://doi.org/10.1021/acs.analchem.4c02589.

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

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 a 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, roč. 49, August, s. 1-18. ISSN 1574-0137. Dostupné z: https://doi.org/10.1016/j.cosrev.2023.100571.

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

ROŠINEC, Adrián; Tomáš SVOBODA; Tomáš RAČEK; Aleš KŘENEK a 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 a Radka SVOBODOVÁ. αCharges: partial atomic charges for AlphaFold structures in high quality. Nucleic Acids Research. Oxford: Oxford University Press, 2023, roč. 51, W1, s. "W11"-"W16", 6 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkad349.

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

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

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

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

SPIWOK, Vojtěch; Martin KUREČKA a Aleš KŘENEK. Collective Variable for Metadynamics Derived From AlphaFold Output. FRONTIERS IN MOLECULAR BIOSCIENCES. SWITZERLAND: FRONTIERS MEDIA SA, 2022, roč. 2022, č. 9, s. 1-10. ISSN 2296-889X. Dostupné z: https://doi.org/10.3389/fmolb.2022.878133.

TRAPL, Dalibor; MArtin KRUPIČKA; Vladimír VIŠŇOVSKÝ; Jana HOZZOVÁ; Jaroslav OĽHA; Aleš KŘENEK a 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, roč. 62, č. 3, s. 567-576. ISSN 1549-9596. Dostupné z: https://doi.org/10.1021/acs.jcim.1c00651.

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 a Aleš KŘENEK. The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization. BMC Genomics. BioMed Central, 2022, roč. 23, č. 1, s. 1-11. ISSN 1471-2164. Dostupné z: https://doi.org/10.1186/s12864-022-08367-1.

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

MÍČ, Vladimír; Tomáš RAČEK; Aleš KŘENEK a 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, s. 265-279. ISBN 978-3-030-89656-0. Dostupné z: https://doi.org/10.1007/978-3-030-89657-7_20.

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

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 a Martyn WINN. West-Life: A Virtual Research Environment for structural biology. Journal of Structural Biology: X. 2019, roč. 1, January - March 2019, s. 1-8. ISSN 2590-1524. Dostupné z: https://doi.org/10.1016/j.yjsbx.2019.100006.

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

POPOVICI, Vlad; Aleš KŘENEK a Eva BUDINSKÁ. Identification of "BRAF-Positive" Cases Based on Whole-Slide Image Analysis. Biomed Research International. New York: HINDAWI LTD, 2017, Neuveden, April, s. nestránkováno, 7 s. ISSN 2314-6133. Dostupné z: https://doi.org/10.1155/2017/3926498.

PAZÚRIKOVÁ, Jana; Aleš KŘENEK; Vojtěch SPIWOK a 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, roč. 146, č. 11, s. "115101:1"-"115101:8", 8 s. ISSN 0021-9606. Dostupné z: https://doi.org/10.1063/1.4978296.

FILIPOVIČ, Jiří; Jana PAZÚRIKOVÁ; Aleš KŘENEK a 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, s. 278-280. ISBN 978-90-77381-95-3.

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

PAZÚRIKOVÁ, Jana; Aleš KŘENEK a 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, s. 267-274. ISBN 978-90-77381-95-3.

RAČEK, Tomáš; Radka SVOBODOVÁ VAŘEKOVÁ; Aleš KŘENEK; Jana PAZÚRIKOVÁ; Stanislav GEIDL a 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 a Jaroslav KOČA. NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2016, roč. 8, October, s. nestránkováno, 14 s. ISSN 1758-2946. Dostupné z: https://doi.org/10.1186/s13321-016-0171-1.

PAZÚRIKOVÁ, Jana; Tomáš RAČEK; Stanislav GEIDL; Radka SVOBODOVÁ VAŘEKOVÁ a Aleš KŘENEK. Parametrizace ekvalizace elektronegativity metodou diferenciální evoluce. In ENBIK 2016. 2016.

KŘENEK, Aleš; Karel KUBÍČEK; Richard ŠTEFL a 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, s. nestránkováno, 9 s. ISSN 1824-8039.

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

SPIWOK, Vojtěch; Pavel OBORSKÝ; Jana PAZÚRIKOVÁ; Aleš KŘENEK a 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, roč. 142, č. 11, s. nestránkováno, 8 s. ISSN 0021-9606. Dostupné z: https://doi.org/10.1063/1.4914828.

IŠTVÁNEK, Jan; Michal JAROŠ; Aleš KŘENEK a Jana ŘEPKOVÁ. Genome assembly and annotation for red clover (Trifolium pratense; Fabaceae). American Journal of Botany. St Louis: Botanical Soc Amer Inc, 2014, roč. 101, č. 2, s. 327-337. ISSN 0002-9122. Dostupné z: https://doi.org/10.3732/ajb.1300340.

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

RAČEK, Tomáš; Radka SVOBODOVÁ VAŘEKOVÁ a 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 a Jaroslav KOČA. Empirical charges for chemoinformatics applications. In GCC 2013 - 9th German Conference on Chemoinformatics. 2013. Dostupné z: https://doi.org/10.1186/1758-2946-6-S1-P60.

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

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

GOLEMBIOVSKÝ, Tomáš a 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, s. 40-46. ISBN 978-3-939897-22-4.

GOLEMBIOVSKÝ, Tomáš a 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, s. 76-83. ISBN 978-80-87342-10-7.

COLLING, David; Janusz MARTYNIAK; Andrew MCGOUGH; Aleš KŘENEK; Jiří SITERA; Miloš MULAČ a František DVOŘÁK. Real Time Monitor of Grid job executions. Journal of Physics: Conference Series. 2010, roč. 219, č. 6, 9 s. 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 a Michal VOCŮ. Something you may have wanted to know about L&B. Journal of Physics: Conference Series. 2010, roč. 219, č. 6, 10 s. ISSN 1742-6596.

SCHOVANCOVÁ, Jaroslava; Jiří CHUDOBA; František DVOŘÁK; Jiří FILIPOVIČ; Jan KMUNÍČEK; Aleš KŘENEK; Luděk MATYSKA; Miloš MILAČ; Miroslav RUDA; Zdeněk SALVET; Jiří SITERA; Zdeněk ŠUSTR a 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, s. 283-291, 8 s. 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 a David REBATTO. Experimental evaluation of job provenance in ATLAS environment. In Journal of Physics: Conference Series. Bristol, Great Britain, 2008, s. 1-9.

KŘENEK, Aleš; Jiri SITERA; Luděk MATYSKA; Frantisek DVORAK; Miloš MULAČ; Miroslav RUDA a Zdeněk SALVET. gLite Job Provenance - a job-centric view. Concurrency and Computation: Practice and Experience. John Wiley & Sons, Inc, 2008, roč. 20, č. 5, s. 453-462. ISSN 1532-0626. Dostupné z: https://doi.org/10.1002/cpe.1252.

RUDA, Miroslav; Jiri SITERA; Aleš KŘENEK; Luděk MATYSKA; Zdenek SUSTR a 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, s. 3-12. ISBN 978-80-904173-0-4.

KŘENEK, Aleš; Luděk MATYSKA; Jiří SITERA; Miroslav RUDA; František DVOŘÁK; Jiří FILIPOVIČ; Zdeněk ŠUSTR a 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, s. 144-151. ISBN 978-3-540-89964-8.

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 a Yong ZHAO. Special issue: The first provenance challenge. Concurrency and Computation: Practice and Experience. John Wiley & Sons, Inc, 2008, roč. 20, č. 5, s. 409-418. ISSN 1532-0626. Dostupné z: https://doi.org/10.1002/cpe.1233.

KRAJÍČEK, Ondřej; Andrea CECCANTI; Miroslav RUDA a 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, s. 155-164. ISBN 978-0-387-69857-1.

ŠUSTR, Zdeněk; Aleš KŘENEK; Martin PETŘEK; Jiří FILIPOVIČ; Jan KMUNÍČEK; Jiří WIESNER; Jiří SITERA; František DVOŘÁK a 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, s. 447-454. ISBN 978-0-7695-3089-5.

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

KRAJÍČEK, Ondřej; Aleš KŘENEK; Luděk MATYSKA; Miroslav RUDA a 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, s. 131-138. ISBN 83-915141-5-3.

KRAJÍČEK, Ondřej; Andrea CECCANTI; Aleš KŘENEK; Luděk MATYSKA a 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. 1. vyd. Innsbruck, 2006, s. TO APPEAR, 10 s.

KŘENEK, Aleš a Jiří FILIPOVIČ. Haptický model interakce molekul. 2006.

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

KŘENEK, Aleš a Igor PETERLÍK. Distribuované výpočty složitých stavových prostorů. In Širokopásmové sítě a jejich aplikace. Olomouc: CESNET, z.s.p.o., 2005, s. 176-185. ISBN 80-244-1035-4.

PETERLÍK, Igor a 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, s. 342-347. ISBN 0-7695-2310-2.

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

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

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

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 a G. PATANIA. Practical approaches to Grid workload and resource management in the EGEE project. 2004, 4 s.

KŘENEK, Aleš; Igor PETERLÍK a Luděk MATYSKA. Building 3D State Spaces of Virtual Environments with a TDS-based Algorithm. In Recent Advances in Parallel Virtual Machine and Message Passing Interface. Berlin: Springer-Verlag, 2003, s. 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, s. 231-240. ISBN 3-905673-00-2.

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

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

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

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

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

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

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