Výpis publikací

HERREROS, David, Roy R. LEDERMAN, James M. KRIEGER, Amaya JIMÉNEZ-MORENO, Marta MARTÍNEZ, David MYŠKA, David STŘELÁK, Jiří FILIPOVIČ, Carlos O. S. SORZANO a José M. CARAZO. Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials. Nature Communications. 2023, roč. 14, č. 1, s. 1-10. ISSN 2041-1723.

PETROVIČ, Filip a Jiří FILIPOVIČ. Kernel Tuning Toolkit. SoftwareX. Elsevier, 2023, neuveden, č. 22, s. 1-6. ISSN 2352-7110. doi:10.1016/j.softx.2023.101385.

VÁVRA, Ondřej, Jakub BERANEK, Jan ŠTOURAČ, Martin SURKOVSKY, Jiří FILIPOVIČ, Jiří DAMBORSKÝ, Jan MARTINOVIC a 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, roč. 39, č. 8, s. 1-3. ISSN 1367-4803. doi:10.1093/bioinformatics/btad443.

TØRRING, Jacob O, van Werkhoven BEN, Filip PETROVIČ, Floris-Jan WILLEMSEN, Jiří FILIPOVIČ a Anne C ELSTER. Towards a Benchmarking Suite for Kernel Tuners. In 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). IEEE, 2023. s. 724-733. ISBN 979-8-3503-1200-3. doi:10.1109/IPDPSW59300.2023.00124.

STŘELÁK, David, David MYŠKA, Filip PETROVIČ, Jan POLÁK, Jaroslav OĽHA a Jiří FILIPOVIČ. Umpalumpa: a framework for efficient execution of complex image processing workloads on heterogeneous nodes. Computing. Springer, 2023. ISSN 0010-485X. doi:10.1007/s00607-023-01190-w.

HERREROS, David, Jakub KISKA, Erney RAMÍREZ-APORTELA, Jiří FILIPOVIČ, José María CARAZO a Carlos Oscar SORZANO. ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis. Journal of Molecular Biology. Elsevier, 2023, roč. 435, č. 9, s. 1-14. ISSN 0022-2836. doi:10.1016/j.jmb.2023.168088.

NĚMCOVÁ, Petra, Jana HOZZOVÁ a Jiří FILIPOVIČ. Improving ligand transport trajectory within flexible receptor in CaverDock. In SAC '22: Proceedings of the 37th ACM/SIGAPP Symposium on Applied Computing. USA: Association for Computing Machinery, 2022. s. 619-626. ISBN 978-1-4503-8713-2. doi: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 a 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, roč. 78, č. 4, s. 410-423. ISSN 2059-7983. doi:10.1107/S2059798322001978.

FILIPOVIČ, Jiří, Jana HOZZOVÁ, Amin NEZARAT, Jaroslav OĽHA a Filip PETROVIČ. Using hardware performance counters to speed up autotuning convergence on GPUs. Journal of Parallel and Distributed Computing. Elsevier, 2022, roč. 160, February, s. 16-35. ISSN 0743-7315. doi: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 a Carlos SORZANO. Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion. Molecules. Mayer und Muller, 2021, roč. 26, č. 20, s. 1-14. ISSN 1420-3049. doi: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 a 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, roč. 8, č. 6, s. 992-1005. ISSN 2052-2525. doi:10.1107/S2052252521008903.

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 a 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 a 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, roč. 213, č. 2, s. "107712", 14 s. ISSN 1047-8477. doi:10.1016/j.jsb.2021.107712.

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 a 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. s. 257-289. Methods in Molecular Biology. ISBN 978-1-0716-1405-1. doi:10.1007/978-1-0716-1406-8_13.

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

RANGEL PAMPLONA PIZARRO PINTO, José Gaspar, Ondřej VÁVRA, Sérgio Manuel MARQUES, Jiří FILIPOVIČ, David BEDNÁŘ a 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, roč. 19, May, s. 3187-3197. ISSN 2001-0370. doi:10.1016/j.csbj.2021.05.043.

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

HOZZOVÁ, Jana, Ondřej VÁVRA, David BEDNÁŘ a 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. s. 105-124. Methods in Molecular Biology, vol 2266. ISBN 978-1-0716-1208-8. doi:10.1007/978-1-0716-1209-5_6.

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

PETROVIČ, Filip, David STŘELÁK, Jana HOZZOVÁ, Jaroslav OĽHA, Richard TREMBECKÝ, Siegfried BENKNER a 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, roč. 108, July, s. 161-177. ISSN 0167-739X. doi:10.1016/j.future.2020.02.069.

FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA a 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, roč. 17, č. 5, s. 1625-1638. ISSN 1545-5963. doi:10.1109/TCBB.2019.2907492.

OĽHA, Jaroslav, Jana HOZZOVÁ, Jan FOUSEK a Jiří FILIPOVIČ. Exploiting historical data: Pruning autotuning spaces and estimating the number of tuning steps. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE. HOBOKEN: WILEY, 2020, roč. 32, č. 21, s. 1-15. ISSN 1532-0626. doi:10.1002/cpe.5962.

STŘELÁK, David, Jiří FILIPOVIČ, Amaya JIMÉNEZ-MORENO, Jose María CARAZO a Carlos Óscar SÁNCHEZ SORZANO. FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy. Electronics. Switzerland: MDPI, 2020, roč. 9, č. 6, s. 1-25. ISSN 2079-9292. doi:10.3390/electronics9061040.

STŘELÁK, David, Carlos Óscar S. SORZANO, José María CARAZO a Jiří FILIPOVIČ. A GPU acceleration of 3-D Fourier reconstruction in cryo-EM. The International Journal of High Performance Computing Applications. SAGE Publishing, 2019, roč. 33, č. 5, s. 948-959. ISSN 1094-3420. doi:10.1177/1094342019832958.

ŠTOURAČ, Jan, O. VAVRA, Piia Pauliina KOKKONEN, Jiří FILIPOVIČ, Gabriela Filipa FONSECA PINTO, Andrea SCHENKMAYEROVÁ, Jiří DAMBORSKÝ a David BEDNÁŘ. Caver web: identification of tunnels and channels in proteins and analysis of ligand transport. In European Biotechnology Congress. 2019. ISSN 0168-1656. doi: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 a 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, roč. 47, W1, s. 414-422. ISSN 0305-1048. doi:10.1093/nar/gkz378.

VÁVRA, Ondřej, Jiří FILIPOVIČ, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Jan ŠTOURAČ, Luděk MATYSKA a Jiří DAMBORSKÝ. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics. Oxford: Oxford University Press, 2019, roč. 35, č. 23, s. 4986-4993. ISSN 1367-4803. doi:10.1093/bioinformatics/btz386.

OĽHA, Jaroslav, Jana HOZZOVÁ, Jan FOUSEK a 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. s. 295-307. ISBN 978-3-030-48339-5. doi:10.1007/978-3-030-48340-1_23.

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

STŘELÁK, David a Jiří FILIPOVIČ. cuFFTAdvisor. 2018.

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

STŘELÁK, David a Jiří FILIPOVIČ. Performance analysis and autotuning setup of the cuFFT library. In ACM International Conference Proceeding Series. Limassol, Cyprus: ACM, 2018. s. nestránkováno, 6 s. ISBN 978-1-4503-6591-8. doi:10.1145/3295816.3295817.

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

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

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.

FILIPOVIČ, Jiří, Jan PLHÁK a 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. s. 47-54. ISBN 978-1-4673-7812-3. doi:10.1109/HPCSim.2015.7237020.

KŘENEK, Aleš, Karel KUBÍČEK, Richard ŠTEFL a Jiří FILIPOVIČ. Accurate Fitting SAXS Curves with NMR Structure Ensembles. 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.

FILIPOVIČ, Jiří a 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. s. 98-105. ISSN 1550-6533. doi:10.1109/SBAC-PAD.2015.29.

FILIPOVIČ, Jiří, Matúš MADZIN, Jan FOUSEK a Luděk MATYSKA. Optimizing CUDA code by kernel fusion: application on BLAS. The Journal of Supercomputing. Springer US, 2015, roč. 71, č. 10, s. 3934-3957. ISSN 0920-8542. doi:10.1007/s11227-015-1483-z.

FILIPOVIČ, Jiří, Jan FOUSEK, Bedřich LAKOMÝ a Matúš MADZIN. Automatically Optimized GPU Acceleration of Element Subroutines in Finite Element Method. In Symposium on Application Accelerators in High Performance Computing. LOS ALAMITOS, CA, USA: IEEE, 2012. s. 141-144. ISBN 978-1-4673-2882-1.

FOUSEK, Jan, Jiří FILIPOVIČ a Matúš MADZIN. Automatic Fusions of CUDA-GPU Kernels for Parallel Map. Computer architecture news. New York: ACM Press., 2011, roč. 39, č. 4, s. 98-99. ISSN 0163-5964.

FOUSEK, Jan, Jiří FILIPOVIČ a Matúš MADZIN. Automatic Fusions of CUDA-GPU Kernels for Parallel Map. In Hideharu Amano and Wayne Luk. Second International workshop on highly-efficient accelerators and reconfigurable technologies (HEART). London (UK), 2011. s. 42-47.

PETERLÍK, Igor a Jiří FILIPOVIČ. Distributed Construction of Configuration Spaces for Real-Time Haptic Deformation Modeling. IEEE Transactions on Industrial Electronics. 2011, roč. 58, č. 8, s. 3205-3212. ISSN 0278-0046. doi:10.1109/TIE.2009.2032438.

FOUSEK, Jan, Tomáš GOLEMBIOVSKÝ, Jiří FILIPOVIČ a Igor PETERLÍK. Haptic Rendering Based on RBF Approximation from Dynamically Updated Data. In Luděk Matyska and Michal Kozubek and Tomáš Vojnar and Pavel Zemčík and David Antoš. Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS'10) -- Selected Papers. 16. vyd. Leibniz: Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, 2011. s. 26-31. ISBN 978-3-939897-22-4.

OLŠÁK, Marek, Jiří FILIPOVIČ a Martin PROKOP. FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking. Computing and Informatics. Bratislava: Slovak Academy of Sciences, 2010, roč. 29, 6+, s. 1325-1336, 11 s. ISSN 1335-9150.

MATELA, Jiří a Jiří FILIPOVIČ. GPU work at FI MUNI and results. In Grid Computing Seminar 2010. 2010.

PETERLÍK, Igor, Luděk MATYSKA a Jiří FILIPOVIČ. Haptic Interaction with Complex Models Based on Precomputations. In Advances in Haptics. Vukovar (Croatia): IN-TECH, 2010. s. 333-356. ISBN 978-953-307-093-3.

FOUSEK, Jan, Tomáš GOLEMBIOVSKÝ, Jiří FILIPOVIČ a Igor PETERLÍK. Haptic Rendering Based on RBF Approximation from Dynamically Updated Data. In MEMICS 2010: Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno (Czech Republic): NOVPRESS, 2010. s. 53-59. ISBN 978-80-87342-10-7.

FILIPOVIČ, Jiří a Jan FOUSEK. Medium-grained functions mapping using modern GPUs. In Symposium on Application Accelerators in High Performance Computing 2010. 2010.

FILIPOVIČ, Jiří, Igor PETERLÍK a Matúš MADZIN. Parallel Real-time Deformation Simulator. 2010.

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.

OLŠÁK, Marek, Jiří FILIPOVIČ a Martin PROKOP. FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking. In MEMICS 2009: Fifth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno, Czech Republic: Masaryk University and Technical University of Brno, 2009. s. 160-167. ISBN 978-80-87342-04-6.

OLŠÁK, Marek, Jiří FILIPOVIČ a Martin PROKOP. FastGrid -- The Accelerated Computation of Potential Maps for Molecular Docking. 2009.

FILIPOVIČ, Jiří, Igor PETERLÍK a Jan FOUSEK. GPU Acceleration of Equations Assembly in Finite Elements Method -- Preliminary Results. In Symposium on Application Accelerators in High Performance Computing 2009. 2009.

FILIPOVIČ, Jiří. Obecné výpočty na grafických procesorech. In 35. konference EurOpen.cz. 2009.

FILIPOVIČ, Jiří, Igor PETERLÍK a Luděk MATYSKA. On-Line Precomputation Algorithm for Real-Time Haptic Interaction with Non-Linear Deformable Bodies. In Third Joint EuroHaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems. Salt Lake City, Utah, USA: The Institute of Electrical and Electronics Engineers, 2009. s. 24 - 29. ISBN 978-1-4244-3858-7.

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, 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.

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.

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