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2019 (9 publications)

  1. David Hoksza, Piotr Gawron, Marek Ostaszewski, Ewa Smula, Reinhard Schneider. MINERVA API and plugins: opening molecular network analysis and visualization to the community, Bioinformaics, Oxford Journals, ISSN: 1460-2059, 2019

  2. David Hoksza. Piotr Gawron, Marek Ostaszewski, Jan Hausenauer, Reinhard Schneider. Closing the gap between formats for storing layout information in systems biology, Briefings in Bioinformatics, Oxford Journals, ISSN: 1477-4054, 2019

  3. David Hoksza, Josef Pánek, Jan Jelínek. rPredictorDB: A predictive database of individual secondary structures of RNAs and their formatted plots, DATABASE, 2019, Oxford Journals, ISSN: 1758-0463, 2019

  4. Lukáš Jendele, Radoslav Krivák, Petr Škoda, Marian Novotný, David Hoksza. PrankWeb: a web server for ligand binding site prediction and visualization, Nucleic Acids Research, Oxford Journals, ISSN: 1362-4962, 2019

  5. David Bernhauer, Tomáš Skopal. Recommender system as the support for binaural audio, 4th International AR and VR Conference 2018, Manchester, UK, Springer, 2019

  6. T. Grosup, L. Peska, T. Skopal. Towards Augmented Database Schemes by Discovery of Latent Visual Attributes, EDBT 2019, 2019

  7. D. Bernhauer, T. Skopal. Approximate Search in Dissimilarity Spaces using GA, GECCO 2019, ACM, 2019

  8. Jakub Lokoč, Gregor Kovalčík, Tomáš Souček, Jaroslav Moravec, Jan Bodnár, Přemysl Čech. VIRET Tool Meets NasNet, MMM, pp.: 597-601, Springer, 2019

  9. I. Holubová, M. Svoboda, T. Skopal, D. Bernhauer, L. Peška. Advanced Behavioral Analyses Using Inferred Social Networks: a Vision, TIR 2019, Springer, 2019

2018 (11 publications)

  1. David Hoksza, Piotr Gawron, Marek Ostaszewski and Reinhard Schneider. MolArt: A molecular structure annotation and visualization tool, Bioinformatics, Oxford Journals, 2018

  2. Jan Kohout, Tomáš Komárek, Přemysl Čech, Jan Bodnár, Jakub Lokoč. Learning communication patterns for malware discovery in HTTPs data, Expert Systems with Applications, Elsevier, 2018

  3. Jakub Lokoc, Werner Bailer, Klaus Schoeffmann, Bernd Muenzer, George Awad. On Influential Trends in Interactive Video Retrieval: Video Browser Showdown 2015-2017, IEEE Transactions on Multimedia, IEEE, ISSN: 1520-9210, 2018

  4. Radoslav Krivák, David Hoksza. P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure, Journal of Cheminformatics, 10(39), Springer, ISSN: 1758-2946, 2018

  5. Klaus Schöffmann, Werner Bailer, Cathal Gurrin, George Awad, Jakub Lokoč. Interactive Video Search: Where is the User in the Age of Deep Learning?, ACM Multimedia, pp.: 2101-2103, ACM, 2018

  6. Radoslav Krivak, Lukáš Jendele, David Hoksza. Peptide-Binding Site Prediction From Protein Structure via points on the Solvent Accessible Surface, Computational Structural Bioinformatics Workshop, ACM-BCB, ACM, 2018

  7. Jakub Lokoč, Gregor Kovalčík, Tomáš Souček. Revisiting SIRET Video Retrieval Tool, International Conference on Multimedia Modeling, pp.: 419-424, Springer, 2018

  8. Jakub Lokoč, Tomáš Souček, Gregor Kovalčík. Using an Interactive Video Retrieval Tool for LifeLog Data, LSC@ICMR, pp.: 15-19, ACM, 2018

  9. Jakub Lokoč, Werner Bailer, Klaus Schöffmann. What Is the Role of Similarity for Known-Item Search at Video Browser Showdown?, SISAP, pp.: 96-104, Springer, 2018

  10. T. Skopal, L. Peska, T. Grosup. Interactive product search based on global and local visual-semantic features, SISAP 2018, Springer, 2018

  11. T. Skopal, L. Peska, I. Holubova, P. Pascenko, J. Hucin. Advanced Analytics of Large Connected Data Based on Similarity Modeling, SISAP 2018, Springer, 2018

2017 (16 publications)

  1. Radim Bača, Michal Krátký, Irena Holubová, Martin Nečaský, Tomáš Skopal, Martin Svoboda, Sherif Sakr. Structural XML Query Processing, ACM Computing Surveys, 50(5), pp.: 64:42, ACM, ISSN: 0360-0300, 2017

  2. Jan Jelínek, Petr Škoda, David Hoksza. Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites, BMC Bioinformatics, 18(Suppl. 15), Springer Nature, ISSN: 1471-2105, 2017

  3. Richard Eliáš, David Hoksza. TRAVeLer: a tool for Template-based RnA secondary structure visualization, BMC Bioinformatics, 18(847), Springer Nature, ISSN: 1471-2105, 2017

  4. C. Cobarzan, K. Schoeffmann, W. Bailer, W. Hurst, A. Blažek, J. Lokoč, S. Vrochidis, K. U. Barthel, L. Rossetto. Interactive Video Search Tools: A Detailed Analysis of the Video Browser Showdown 2015, Multimedia tools and applications, 76(4), pp.: 5539–5571, Springer, ISSN: 1380-7501, 2017

  5. Ivan Sipiran, Jakub Lokoč, Benjamin Bustos, Tomáš Skopal. Scalable 3D Shape Retrieval using Local Features and the Signature Quadratic Form Distance, The Visual Computer, 33(12), pp.: 1571–1585, Springer, ISSN: 0178-2789, 2017

  6. David Hoksza, Rastislav Galvánek. Template-based prediction of RNA tertiary structure using its predicted secondary structure, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp.: 2238-2240, IEEE, ISBN: 978-1-5090-3050-7, 2017

  7. Norman Meuschke, Moritz Schubotz, Felix Hamborg, Tomáš Skopal, Bela Gipp. Analyzing Mathematical Content to Detect Academic Plagiarism, CIKM, Singapore, pp.: 1-4, ACM, 2017

  8. Tomáš Skopal, Ladislav Peška, Gregor Kovalčík, Tomáš Grošup, Jakub Lokoč. Product exploration based on latent visual attributes, CIKM, Singapore, pp.: 1-4, ACM, 2017

  9. Radoslav Krivák, David Hoksza. Improving quality of ligand-binding site prediction with bayesian optimization, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE, 2017

  10. Petr Škoda, David Hoksza. Platform for ligand-based virtual screening, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE, 2017

  11. Rastislav Galánek, David Hoksza. Template-based prediction of RNA tertiary structure using its predicted secondary structure, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE, 2017

  12. Jakub Lokoč, Anh Nguyen Phuong, Marta Vomlelová , Chong-Wah Ngo. Color-sketch simulator: a guide for color-based visual known-item search, International Conference on Advanced Data Mining and Applications (ADMA 2017), Springer, 2017

  13. Přemysl Čech , Jakub Maroušek , Jakub Lokoč , Yasin N. Silva, Jeremy Starks. Comparing MapReduce-Based k-NN Similarity Joins On Hadoop For High-dimensional Data, International Conference on Advanced Data Mining and Applications (ADMA 2017), Springer, 2017

  14. Adam Blažek, Jakub Lokoč, David Kuboň. Video Hunter at VBS 2017, International Conference on MultiMedia Modeling, Reykjavík, Iceland, LNCS 10133, pp.: 493-498, Springer, 2017

  15. Jakub Lokoč, David Kuboň, Adam Blažek. A Comparative Study for Known Item Visual Search Using Position Color Feature Signatures, International Conference on MultiMedia Modeling, Reykjavík, Iceland, LNCS 10133, pp.: 3-14, Springer, 2017

  16. Jakub Lokoč, Tomáš Grošup, Přemysl Čech, Tomáš Pevný, Tomáš Skopal. Malware discovery using behaviour-based exploration of network traffic, SISAP, Munich, Germany, pp.: 1-8, Springer, 2017

2016 (14 publications)

  1. Jan Pešek, David Hoksza. Large RNA secondary structure conservation annotation using secondary structure-based MSA, International Journal of Bioscience, Biochemistry and Bioinformatics, 6(1), pp.: 18-25, International Academy Publishing, ISSN: 2010-3638, 2016

  2. Richard Eliáš, David Hoksza. RNA secondary structure visualization using tree edit distance, International Journal of Bioscience, Biochemistry and Bioinformatics, 6(1), pp.: 9-17, International Academy Publishing, ISSN: 2010-3638, 2016

  3. Jakub Velkoborsky, David Hoksza. Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization, Journal of Cheminformatics, 8(74), Springer, ISSN: 1758-2946, 2016

  4. M. Kruliš, J. Lokoč, T. Skopal. Efficient Extraction of Clustering-Based Feature Signatures Using GPU Architectures, Multimedia tools and applications, 75(13), pp.: 8071–8103, Springer, ISSN: 1380-7501, 2016

  5. David Hoksza, Petr Škoda. Using Bayesian Modeling on Molecular Fragments Features for Virtual Screening, IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2016), Chiang Mai, Thailand, IEEE, ISBN: 978-1-4673-9472-7, 2016

  6. Jakub Lokoč, Jan Kohout, Přemysl Čech, Tomáš Skopal, Tomáš Pevný. k-NN Classification of Malware in HTTPS Traffic Using the Metric Space Approach, 11th Pacific Asia Workshop, PAISI 2016, Auckland, New Zealand, LNCS 9650, pp.: 131-145, Springer, ISBN: 978-3-319-31862-2, ISSN: 0302-9743, 2016

  7. Miroslav Macík, Jakub Lokoč, Přemysl Čech and Tomáš Skopal. Particle Physics Model for Content-based 3D Exploration, 14th International Workshop on Content-Based Multimedia Indexing (CBMI), Bucharest, Romania, pp.: 1-6, IEEE, 2016

  8. Petr Škoda, David Hoksza. Benchmarking Platform for Ligand-Based Virtual Screening, BIBM Workshop on Health Informatics and Data Science (HI-DS), Shenzhen, China, pp.: 1225-1232, IEEE, ISBN: 978-1-5090-1610-5, 2016

  9. Rastislav Galvánek, David Hoksza, Josef Pánek. Template-based prediction of RNA tertiary structure, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shenzhen, 1902-1905, IEEE, ISBN: 978-1-5090-1610-5, 2016

  10. Jan Jelínek, Petr Škoda, David Hoksza. Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites, IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Atlanta, GA, USA, IEEE, ISBN: 978-1-5090-4199-2, 2016

  11. David Kuboň, Adam Blažek, Jakub Lokoč, Tomáš Skopal. Multi-sketch Semantic Video Browser, MMM 2016, Miami, USA, January 4-6, LNCS 9517, pp.: 406-411, Springer, ISBN: 978-3-319-27673-1, ISSN: 0302-9743, 2016

  12. Adam Blažek, David Kuboň and Jakub Lokoč. Known-Item Search in Video Databases with Textual Queries, SISAP 2016, Tokio, Japan, Springer, 2016

  13. Hasmik Osipyan, Jakub Lokoč and Stéphane Marchand-Maillet. Similarity Search of Sparse Histograms on GPU Architecture, SISAP 2016, Tokio, Japan, Springer, 2016

  14. Přemysl Čech, Jan Kohout, Jakub Lokoč, Tomáš Komárek, Jakub Maroušek and Tomáš Pevný. Feature Extraction and Malware Detection on Large HTTPS Data Using MapReduce, SISAP 2016, Tokio, Japan, Springer, 2016

2015 (15 publications)

  1. Petr Čech, David Hoksza, Daniel Svozil. MultiSETTER: web server for multiple RNA structure comparison, BMC Bioinformatics, 16(253), BioMed Central, ISSN: 1471-2105, 2015

  2. Radoslav Krivák, David Hoksza. Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features, Journal of Cheminformatics, 7(1), Chemistry Central, ISSN: 1758-2946, 2015

  3. J. Lokoč. Approximating Adaptive Distance Measures Using Scalable Feature Signatures, Multimedia Tools and Applications, 74(24), pp.: 11569-11594, Springer, ISSN: 1380-7501, 2015

  4. J. Moško, J. Lokoč, T. Grošup, P. Čech, T. Skopal, J. Lánský. MLES: Multilayer Exploration Structure for Multimedia Exploration, ADBIS - Advances in Databases and Information Systems, Poitiers, France, 539, pp.: 135-144, Springer International Publishing, ISBN: 978-3-319-23200-3, 2015

  5. Radoslav Krivák, David Hoksza. P2RANK: knowledge-based ligand binding site prediction using aggregated local features, AlCoB, Mexico City, Mexico, pp.: 41-52, Springer, ISBN: 978-3-319-21232-6, 2015

  6. Petr Škoda, David Hoksza. Exploration of Topological Torsion Fingerprints, BIBM Workshop on Health Informatics and Data Science (HI-DS), Washington, USA, IEEE, 2015

  7. Přemysl Čech and Tomáš Grošup. Comparison of metric space browsing strategies for efficient image exploration, Content-Based Multimedia Indexing (CBMI), Prague, pp.: 6, IEEE, 2015

  8. T. Grošup, J. Moško, P. Čech. Continuous Hierarchical Exploration of Multimedia Collections, Content-Based Multimedia Indexing (CBMI), Prague, Czech republic, IEEE, ISBN: 978-1-4673-6870-4, 2015,
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  9. Martin Šícho, Daniel Svozil, David Hoksza. Activity-Driven Exploration of Chemical Space with Morphing, International Workshop on Biomedical and Health Informatics, IEEE, 2015

  10. J. Lokoč, B. Münzer, K. Schoeffmann, M. Del Fabro, M. J. Primus, T. Skopal, J. Lánský. What Are The Salient Keyframes In Short Casual Videos? An Extensive User Study Using A New Video Dataset, International Workshop on Mobile Multimedia Computing, IEEE, 2015

  11. J. Lokoč, K. Schoeffmann, M. del Fabro. Dynamic Hierarchical Visualization of Keyframes in Endoscopic Video, MMM, LNCS 8936, pp.: 291-294, Springer, ISBN: 978-3-319-14441-2, ISSN: 0302-9743, 2015

  12. T. Grošup, P. Čech, J. Lokoč, T. Skopal. A Web Portal For Effective Multi-model Exploration, MMM, LNCS 8936, pp.: 315-318, Springer, ISBN: 978-3-319-14441-2, ISSN: 0302-9743, 2015

  13. A. Blažek, J. Lokoč, F. Matzner, T. Skopal. Enhanced Signature-based Video Browser at Video Search Showcase 2015, MMM, LNCS 8936, pp.: 243-248, Springer, ISBN: 978-3-319-14441-2, ISSN: 0302-9743, 2015

  14. David Hoksza, Jan Jelínek. Using Neo4j for mining protein graphs: a case study, NoSQL-Net - International Workshop on NoSQL Databases, Emerging Database Technologies and Applications, DEXA, Valencia, Spain, pp.: 230-235, IEEE, ISBN: 978-1-4799-5722-4, 2015

  15. J. Moško, J. Lokoč, T. Grošup, P. Čech, T. Skopal, J. Lánský. Evaluating Multilayer Multimedia Exploration, SISAP, Glasgow, Scotland, UK, pp.: 162-169, Springer, ISBN: 978-3-319-25087-8, ISSN: 0302-9743, 2015

2014 (14 publications)

  1. David Hoksza, Daniel Svozil. Multiple 3D RNA Structure Superposition Using Neighbor Joining, IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics, PP(99), IEEE, ISSN: 1545-5963, 2014

  2. J. Lokoč, J. Moško, P. Čech, T. Skopal. On Indexing Metric Spaces using Cut-Regions, Information Systems, 43, pp.: 1-19, Elsevier, ISSN: 0306-4379, 2014

  3. J. M. Barrios, B. Bustos, T. Skopal. Analyzing and Dynamically Indexing the Query Set, Information Systems, 45, pp.: 37-47, Elsevier, ISSN: 0306-4379, 2014

  4. David Hoksza, Petr Škoda, Milan Voršilák and Daniel Svozil. Molpher: a software framework for systematic chemical space exploration, Journal of Cheminformatics, 6(7), Chemistry Central, ISSN: 1758-2946, 2014

  5. J. Lokoč, T. Grošup, P. Čech, T. Skopal. Towards Efficient Multimedia Exploration Using The Metric Space Approach, 12th International Workshop on Content-Based Multimedia Indexing (CBMI), pp.: 1-4, IEEE, ISBN: 978-1-4799-3990-9, 2014

  6. J. Moško, T. Skopal, T. Bartoš, J. Lokoč. Real-Time Exploration of Multimedia Collections, 25th Australasian Database Conference, ADC 2014, Brisbane, QLD, Australia, LNCS 8506, pp.: 198-205, Springer, ISBN: 978-3-319-08607-1, ISSN: 0302-9743, 2014

  7. J. Lokoč, A. Blažek, T. Skopal. On Effective Known Item Video Search Using Feature Signatures, ACM ICMR, Glasgow, UK, pp.: 524-526, ACM, ISBN: 978-1-4503-2782-4, 2014

  8. Petr Škoda, David Hoksza. Target-Oriented Generic Fingerprint-Based Molecular Representation, CSEIT, Computer Science & Information Technology (CS & IT), ISSN: 2231-5403, 2014

  9. David Hoksza, Petr Škoda. Scaffold-based chemical space exploration, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp.: 1-3, IEEE, 2014

  10. Josef Pánek, Jan Hajič jr., David Hoksza. Template-Based Prediction of Ribosomal RNA Secondary Structure, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Belfast, UK, pp.: 18-20, IEEE, 2014

  11. J. Lokoč, A. Blažek, T. Skopal. Signature-based Video Browser, International Conference on MultiMedia Modeling, LNCS 8326, pp.: 415-418, Springer, ISBN: 978-3-319-04116-2, ISSN: 0302-9743, 2014

  12. David Hoksza, Petr Škoda. 2D Pharmacophore Query Generation, ISBRA, Central South University, Zhangjiajie, China, Springer, 2014

  13. J. Lokoč. Approximating the Signature Quadratic Form Distance Using Scalable Feature Signatures, MMM, LNCS 8325, pp.: 86-97, Springer, ISBN: 978-3-319-04113-1, ISSN: 0302-9743, 2014

  14. A. Blažek, J. Lokoč, T. Skopal. Video Retrieval with Feature Signature Sketches, SISAP, LNCS 8821, pp.: 25-36, Springer, ISBN: 978-3-319-11987-8, ISSN: 0302-9743, 2014

2013 (14 publications)

  1. M.L. Hetland, T. Skopal. J. Lokoč, Ch. Beecks. Ptolemaic Access Methods: Challenging the Reign of the Metric Space Model, Information Systems, 38(7), pp.: 989–1006, Elsevier, ISSN: 0306-4379, 2013

  2. J. Novák, T. Sachsenberg, D. Hoksza, T. Skopal, O. Kohlbacher. On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications, Journal of Integrative Bioinformatics, 10(3), 2013

  3. T. Bartoš, T. Skopal, J. Moško. Towards Efficient Indexing of Arbitrary Similarity, SIGMOD Record, 42(2), ACM, ISSN: 0163-5808, 2013,
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  4. J. Galgonek, M. Kruliš, D. Hoksza. On the Parallelization of the SProt Measure and the TM-score Algorithm, 3rd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB), Rhodes Island, Greece, 7640, pp.: 238-247, Lecture Notes in Computer Science, Springer, ISSN: 0302-9743, 2013

  5. J. Galgonek, T. Skopal, D. Hoksza. P3S: Protein Structure Similarity Search, 3rd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB), Rhodes Island, Greece, 7640, pp.: 228-237, Lecture Notes in Computer Science, Springer, ISSN: 0302-9743, 2013

  6. J. Novák, T. Sachsenberg, D. Hoksza, T. Skopal, O. Kohlbacher. A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, 7th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB), Salamanca, Spain, Advances in Intelligent and Soft-Computing (AISC), vol. 222, pp.: 101-109, Springer, 2013

  7. J. Lokoč, L. Navrátil, J. Toušek, T. Skopal. Dynamic Multimedia Exploration Using SIFT Matching, ACM ICMR, Dallas, Texas, USA, pp.: 305-306, ACM, ISBN: 978-1-4503-2033-7, 2013

  8. D. Hoksza, P. Szepe, D. Svozil. MultiSETTER - Multiple RNA Structure Similarity Algorithm, BSB (Brazilian Symposium on Bioinformatics), Recife, Brazil, pp.: 59-70, Springer, ISBN: 978-3-319-02623-7, 2013

  9. T. Bartoš, T. Skopal, J. Moško. Efficient Indexing of Similarity Models with Inequality Symbolic Regression, Genetic and Evolutionary Computation Conference (GECCO) 2013, ACM, ISBN: 978-1-4503-1963-8, 2013

  10. P. Škoda, D. Hoksza. Chemical Space Visualization Using ViFrame, International Conference on Computer and Information Science (ICIS 2013), Toki Messe, Niigata, Japan, pp.: 541 - 546, IEEE, ISBN: 978-147990174-6, 2013

  11. M. Kruliš, J. Lokoč, T. Skopal. Efficient Extraction of Feature Signatures Using Multi-GPU Architecture, MMM, LNCS 7733, pp.: 446-456, Springer, ISBN: 978-3-642-35727-5, ISSN: 0302-9743, 2013

  12. T. Bartoš. Universal Indexing of Arbitrary Similarity Models, Proceedings of the VLDB Endowment, 6(12), pp.: 1392-1397, ACM, ISSN: 2150-8097, 2013

  13. T. Bartoš, T. Skopal. Designing Similarity Indexes with Parallel Genetic Programming, SISAP, 8199, pp.: 294-299, Springer, ISBN: 978-3-642-41062-8, ISSN: 0302-9743, 2013

  14. J. Lokoč, T. Grošup, T. Skopal. On Scalable Approximate Search with the Signature Quadratic Form Distance, SISAP 2013, LNCS 8199, pp.: 312-318, Springer, ISBN: 978-3-642-41061-1, ISSN: 0302-9743, 2013

2012 (17 publications)

  1. David Hoksza, Daniel Svozil. Efficient RNA pairwise structure comparison by SETTER method, Bioinformatics, 28(14), pp.: 1858 - 1864, Oxford Journals, ISSN: 1460-2059, 1367-4803, 2012

  2. M. Kruliš, T. Skopal. J. Lokoč, Ch. Beecks. Combining CPU and GPU Architectures for Fast Similarity Search, Distributed and Parallel Databases, 30(3), pp.: 179-207, Springer, ISSN: 0926-8782, 2012

  3. T. Skopal, J. Lokoč, B. Bustos. D-cache: Universal Distance Cache for Metric Access Methods, IEEE Transactions on Knowledge and Data Engineering, 24(5), pp.: 868-881, IEEE, ISSN: 1041-4347, 2012

  4. J. Novák, T. Skopal, D. Hoksza, J. Lokoč. Non-metric Similarity Search of Tandem Mass Spectra Including Posttranslational Modifications, Journal of Discrete Algorithms, 13, pp.: 19-31, Elsevier, ISSN: 1570-8667, 2012

  5. B. Bustos, S. Kreft, T. Skopal. Adapting Metric Indexes for Searching in Multi-Metric Spaces, Multimedia Tools and Applications, 58(3), pp.: 467-496, Springer, ISSN: 1380-7501, 2012

  6. P. Čech, D. Svozil, D. Hoksza. SETTER Web Server - the Web Server for RNA Structure Comparison, Nucleid Acids Research, 40(W1), pp.: W42-W48, Oxford Journals, ISSN: 1362-4962, 1460-2059, 2012

  7. J. Lokoč, T. Grošup, T. Skopal. Image Exploration using Online Feature Extraction and Reranking, ACM ICMR, Hong Kong, China, ACM, ISBN: 978-1-4503-1329-2, 2012

  8. J. Lokoč, J. Wuenschmann, A. Rothermel, T. Skopal. Similarity Search in 3D Object-Based Video Data, CIKM, Maui, Hawaii, USA, pp.: 2655-2658, ACM, ISBN: 978-1-4503-1156-4, 2012

  9. J. Novák, D. Hoksza, J. Lokoč, T. Skopal. On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering, ISBRA, Dallas, TX, USA, LNBI 7292, pp.: 189-200, Springer, 2012

  10. J. Lokoč, T. Skopal, Ch. Beecks, T. Seidl. Nonmetric Earth Mover’s Distance for Efficient Similarity Search, MMEDIA, pp.: 50-55, IARIA Press, ISBN: 978-1-61208-195-3, 2012

  11. J. Novák, J. Galgonek, D. Hoksza, T. Skopal. SimTandem: Similarity Search in Tandem Mass Spectra, SISAP, Toronto, Ontario, Canada, LNCS 7404, pp.: 242-243, Springer, 2012

  12. J. M. Barrios, B. Bustos, T. Skopal. Snake Table: A Dynamic Pivot Table for Streams of k-NN Searches, SISAP, Toronto, Canada, LNCS 7404, Springer, 2012

  13. T. Bartoš, T. Skopal. Revisiting Techniques for Lowerbounding the Dynamic Time Warping Distance, SISAP, Toronto, Canada, LNCS 7404, Springer, 2012

  14. T. Skopal, T. Bartoš. Algorithmic exploration of axiom spaces for efficient similarity search at large scale, SISAP, Toronto, Canada, LNCS 7404, Springer, 2012

  15. J. Lokoč, P. Čech, J. Novák, T. Skopal. Cut-region: A Compact Building Block For Hierarchical Metric Indexing, SISAP, Toronto, Ontario, Canada, LNCS 7404, pp.: 85-100, Springer, ISBN: 978-3-642-32152-8, ISSN: 0302-9743, 2012

  16. J. Lokoč, D. Novák, M. Batko, T. Skopal. Visual Image Search: Feature Signatures or/and Global Descriptors, SISAP 2012, Toronto, Canada, LNCS 7404, pp.: 177-191, Springer, ISBN: 978-3-642-32152-8, ISSN: 0302-9743, 2012

  17. J. Lokoč, T. Grošup, T. Skopal. SIR: The Smart Image Retrieval Engine, SISAP 2012, Toronto, Canada, LNCS 7404, pp.: 240-241, Springer, ISBN: 978-3-642-32152-8, ISSN: 0302-9743, 2012

2011 (19 publications)

  1. T. Skopal, B. Bustos . On Nonmetric Similarity Search Problems in Complex Domains, ACM Computing Surveys, 43(4), pp.: 34:1-34:50, ACM, ISSN: 0360-0300, 2011

  2. J. Brocke, J. Becker, A. Braccini, R. Butleris, B. Hofreiter, K. Kapočius, M. Marco, G. Schmidt, S. Seidel, A. Simons, T. Skopal, A. Stein, S. Stieglitz, R. Suomi, G. Vossen, R. Winter, S. Wrycza. Current and Future Issues in BPM Research: A European Perspective from the ERCIS Meeting 2010, Communications of the Association for Information Systems, 28, AISeL, ISSN: 1529-3181, 2011

  3. V. Dohnal, T. Skopal. Preface, Information Systems, 36(4), pp.: 707, Elsevier, ISSN: 0306-4379, 2011

  4. J. Galgonek, D. Hoksza, T. Skopal. SProt: sphere-based protein structure similarity algorithm, Proteome Science, 9(Supplment 1), pp.: S20, BioMed Central, ISSN: 1477-5956, 2011,
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  5. J. Kasarda,T. Bartoš. Semi-Automatic Transformation of an XML Schema to XForms, 19th International Conference on Information Systems Development (ISD 2010), Prague, Czech Republic, pp.: 331-343, Springer, ISBN: 978-1-4419-9790-6, 2011

  6. Ch. Beecks, J. Lokoč, T. Seidl, T. Skopal. Indexing the Signature Quadratic Form Distance for Efficient Content-Based Multimedia Retrieval, ACM ICMR, Trento, Italy, ACM, ISBN: 978-1-4503-0336-1, 2011

  7. D. Hoksza, D. Svozil. Exploration of Chemical Space by Molecular Morphing, BIBE, Taichung, Taiwan, pp.: 201-208, IEEE, ISBN: 978-3-642-21259-8, 2011

  8. P. Vojtáš, J. Pokorný, M. Nečaský, T. Skopal, K. Matoušek, J. Kubalík, O. Novotný, M. Maryška. SoSIReČR - IT professional social network, CASoN, IEEE, 2011

  9. M. Kruliš, J. Lokoč, Ch. Beecks, T. Skopal, T. Seidl. Processing Signature Quadratic Form Distance on Many-Core GPU Architecture, CIKM, Glasgow, UK, pp.: 2373-2376, ACM, ISBN: 978-1-4503-0717-8, 2011

  10. Ch. Beecks, T. Skopal, K. Schöffmann, T. Seidl. Towards Large-Scale Multimedia Exploration, DBRank, VLDB, 2011

  11. T. Skopal, T. Bartoš, J. Lokoč. On (not) indexing quadratic form distance by metric access methods, EDBT, Uppsala, Sweden, pp.: 249-258, ACM, ISBN: 978-1-4503-0528-0, 2011

  12. T. Bartoš, A. Eckhardt, T. Skopal. Fuzzy Approach to Non-Metric Similarity Indexing, Fourth International Conference on SImilarity Search and APplications (SISAP 2011), Lipari, Italy, pp.: 115-116, ACM, ISBN: 978-1-4503-0795-6, 2011

  13. B. Bustos, T. Skopal. Nonmetric Similarity Search Problems in Very Large Collections, ICDE, Hannover, Germany, IEEE, ISBN: 978-1-4244-8958-9 , 2011

  14. D. Hoksza, D.Svozil. SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm, ISBRA, Changsha, China, pp.: 37-49, LNBI, Springer Verlag, ISBN: 978-0-7695-4391-8, ISSN: 0302-9743, 2011,
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  15. J. Moško, J. Lokoč, T. Skopal. Clustered pivot tables for I/O-optimized similarity search, SISAP, Lipari, Italy, pp.: 17-24, ACM, ISBN: 978-1-4503-0795-6, 2011

  16. J. Lokoč, M.L. Hetland, T. Skopal, Ch. Beecks. Ptolemaic Indexing of the Signature Quadratic Form Distance, SISAP, Lipari, Italy, pp.: 9-16, ACM, ISBN: 978-1-4503-0795-6, 2011

  17. J. Lokoč, Ch. Beecks, T. Seidl, T. Skopal. Parameterized Earth Mover’s Distance for Efficient Metric Space Indexing, SISAP, Lipari, Italy, pp.: 121-122, ACM, ISBN: 978-1-4503-0795-6, 2011

  18. J. Novák, T. Skopal, D. Hoksza, J. Lokoč, J. Galgonek. Protein Sequences Identification using NM-tree, SISAP, Lipari, Italy, pp.: 125-126, ACM, ISBN: 978-1-4503-0795-6, 2011

  19. J. Galgonek, D. Hoksza. On Metric Approximations of the SProt Measure, SISAP 2011: Fourth International Conference on Similarity Search and Applications, Lipari, Italy, pp.: 119-120, ACM, ISBN: 978-1-4503-0795-6, 2011

2010 (15 publications)

  1. D. Hoksza, J. Galgonek. Alignment-Based Extension to DDPIn Feature Extraction, International Journal of Computational Bioscience, (1), pp.: 79-87, Acta Press, ISSN: 1918-3909, 2010

  2. B. Bustos, T. Skopal. Beyond the Metric Space Model, SIGSPATIAL Special, 2(2), pp.: 20-23, ACM, ISSN: 1946-7729, 2010

  3. T. Bartoš. Native Indexing of Large XML Databases, 2010

  4. J. Lokoč. Tree-based Indexing Methods for Similarity Search in Metric and Nonmetric Spaces, 2010

  5. D. Hoksza. Similarity Search in Protein Databases, 2010

  6. J. Novák, D. Hoksza. Similarity Search and Posttranslational Modifications in Tandem Mass Spectra, BIBM, Hong Kong, China, pp.: 845-846, IEEE, ISBN: 978-1-4244-8302-0, 2010

  7. J. Galgonek, D. Hoksza. SProt - From Local to Global Protein Structure Similarity, BIBM'10 International Workshop on Computational Proteomics, Hong Kong, China, pp.: 124-129, IEEE, ISBN: 978-1-4244-8302-0, 2010

  8. T. Skopal, J. Lokoč. Answering Metric Skyline Queries by PM-tree, DATESO, Štědronín-Plazy, Czech Republic, 567, pp.: 22-37, CEUR, ISBN: 978-80-7378-116-3, 2010

  9. J. Novák, D. Hoksza. Parametrised Hausdorff Distance as a Non-Metric Similarity Model for Tandem Mass Spectrometry, DATESO, Štědronín - Plazy, Czech Republic, pp.: 1-12, CEUR proceedings, ISSN: 1613-0073, 2010

  10. T. Bartoš, J. Kasarda. iXUPT: Indexing XML Using Path Templates, Dateso 2010, Štedronín - Plazy, Czech Republic, pp.: 84 - 95, MatfyzPress, ISBN: 978-80-7378-116-3, ISSN: 1613-0073, 2010

  11. J. Kasarda, M. Nečaský,T. Bartoš. Generating XForms from an XML Schema, Networked Digital Technologies Second International Conference, NDT 2010, Prague, Czech Republic, pp.: 706-714, Springer, ISBN: 978-3-642-14305-2, ISSN: 1865-0929, 2010

  12. J. Galgonek, T. Knap, M. Kruliš, M. Nečaský. SMILE - A Framework for Semantic Applications, On the Move to Meaningful Internet Systems Workshops, Hersonissou, Crete, Greece, pp.: 53-54, Springer, ISBN: 978-3-642-16960-1, 2010

  13. T. Skopal. Where are you heading, metric access methods? A provocative survey, SISAP, Istanbul, Turkey, ACM, ISBN: 978-1-4503-0420-7, 2010

  14. J. Novák, T. Skopal, D. Hoksza, J. Lokoč. Improving the Similarity Search of Tandem Mass Spectra using Metric Access Methods, SISAP, Istanbul, Turkey, pp.: 85-92, ACM, ISBN: 978-1-4503-0420-7, 2010

  15. J. Lokoč, T. Skopal. On Applications of Parameterized Hyperplane Partitioning, SISAP, Istanbul, Turkey, pp.: 131-132, ACM, ISBN: 978-1-4503-0420-7, 2010

2009 (13 publications)

  1. T. Skopal, P. Zezula (Eds.). SISAP 2009, Proceedings of the 2nd International Workshop on Similarity Search and Applications, Prague, Czech Republic, IEEE, ISBN: 978-0-7695-3765-8, 2009

  2. T. Skopal, J. Lokoč. New Dynamic Construction Techniques for M-tree, Journal of Discrete Algorithms, 7(1), pp.: 62-77, Elsevier, ISSN: 1570-8667, 2009

  3. O. Danko, T. Skopal. Elliptic Indexing of Multidimensional Databases, ADC, Wellington, New Zealand, Australian Computer Society, 2009

  4. J. Novák, D. Hoksza. An Application of the Metric Access Methods to the Mass Spectrometry Data, CIBCB, Nashville, TN, USA, pp.: 220-227, IEEE, ISBN: 978-1-4244-2756-7, 2009

  5. D. Hoksza, J. Galgonek. Density-Based Classification of Protein Structures Using Iterative TM-score, CSBW 2009 (workshop at BIBM 2009), Wahsington, D.C., USA, pp.: 87-93, IEEE, ISBN: 978-1-4244-5121-0, 2009

  6. J. Galgonek. Tequila - a query language for the Semantic Web, DATESO 2009, Spindleruv Mlyn, Czech Republic, pp.: 105-118, Czech Technical University in Prague, ISBN: 978-80-01-04323-3, ISSN: 1613-0073, 2009

  7. T. Skopal, B. Bustos. On Index-free Similarity Search in Metric Spaces, DEXA, Linz, Austria, LNCS 5690, Springer, ISBN: 978-3-642-03572-2, 2009

  8. A. Eckhardt, T. Skopal, P. Vojtas . On fuzzy vs. metric similarity search in complex databases, FQAS 2009, Roskilde, Denmark, LNAI 5822, Springer, ISBN: 978-3-642-04956-9, 2009

  9. D. Hoksza. DDPIn - Distance and Density Based Protein Indexing, IEEE CIBCB, Nashville, TN, USA, pp.: 263-270, IEEE, ISBN: 978-1-4244-2783-3, 2009

  10. J. Lokoč. Parallel dynamic batch loading in the M-tree, SISAP, Prague, Czech Republic, pp.: 117-123, IEEE, ISBN: 978-0-7695-3765-8, 2009

  11. J. Galgonek, D. Hoksza. On the Effectiveness of Distances Measuring Protein Structure Similarity, SISAP 2009: Second international workshop on similarity search and applications, Prague, Czech Republic, pp.: 165-166, IEEE, ISBN: 978-0-7695-3765-8, 2009

  12. T. Skopal, V. Dohnal, M. Batko, P. Zezula. Distinct Nearest Neighbors Queries for Similarity Search in Very Large Multimedia Databases, WIDM, Hong Kong, China, ACM, ISBN: 978-1-60558-808-7, 2009

  13. T. Skopal, J. Lokoč, . On Metric Skyline Processing by PM-tree, SIRET technical report 1-09, arXiv.org>cs> arXiv:0910.0983, 2009

2008 (7 publications)

  1. J. Galgonek. Query languages for the Semantic web, 2008

  2. D. Hoksza, T. Skopal. Native Multidimensional Indexing in Relational Databases, COMAD, Mumbai, India, pp.: 251-261, Computer Society of India, 2008

  3. D. Hoksza. Methods of Protein Structure Alignment, DATAKON, Brno, Czech Republic, ISBN: 978-80-7355-081-3, 2008

  4. T. Skopal, J. Lokoč. NM-tree: Flexible Approximate Similarity Search in Metric and Non-metric Spaces, DEXA, Turin, Italy, LNCS 5181, pp.: 312-325, Springer, ISBN: 978-3-540-85653-5, 2008

  5. D. Hoksza. Improved Alignment of Protein Sequences Based on Common Parts, ISBRA, Atlanta, GA, USA, pp.: 87-99, LNBI, Springer Verlag, ISSN: 0302-9743, 2008

  6. J. Lokoč, T. Skopal. On reinsertions in M-tree, SISAP, Cancun, Mexiko, pp.: 121-128, IEEE, ISBN: 978-0-7695-3101-4, 2008

  7. J. Lokoč. On M-tree Variants in Metric and Non-metric Spaces, WDS, Prague, Czech Republic, Matfyzpress, 2008

2007 (6 publications)

  1. T. Skopal. Unified Framework for Fast Exact and Approximate Search in Dissimilarity Spaces, ACM Transactions on Database Systems, 32(4), pp.: 29:1-29:47, ACM, ISSN: 1557-4644, 2007

  2. T. Skopal, D. Hoksza. Improving the Performance of M-tree Family by Nearest-Neighbor Graphs, ADBIS, Varna, Bulgaria, LNCS 4690, Springer, 2007

  3. T. Skopal, D. Hoksza, J. Pokorný. Construction of Tree-based Indexes for Level-Contiguous Buffering Support, DASFAA, Bangkok, Thailand, LNCS 4443, Springer, 2007

  4. J. Klíma, T. Skopal. Shape Extraction Framework for Similarity Search in Image Databases, DATESO, Desná-Černá Říčka, Czech Republic, CEUR proceedings volume 235, 2007

  5. D. Hoksza, T. Skopal. Index-based approach to similarity search in protein and nucleotide databases, DATESO, Desná-Èerná Øíèka, Czech Republic, CEUR proceedings, ISSN: 1613-0073, 2007

  6. D. Hoksza. Metric indexing of protein databases and promising approaches, WDS, Prague, Czech Republic, pp.: 91-98, Matfyzpress, 2007

2006 (6 publications)

  1. P. Vojtáš, T. Skopal (Eds.). DATAKON 2006, Proceedings of the annual Database Conference, Brno, Czech Republic, Masaryk University in Brno, 2006

  2. T. Skopal. Similarity Search in Multimedia Databases, Faculty of Mathematics and Physics, Charles University in Prague, 2006

  3. T. Skopal, M. Krátký, J. Pokorný, V. Snášel. A New Range Query Algorithm for Universal B-trees, Information Systems, 31(6), pp.: 489-511, Elsevier, ISBN: 0306-4379, 2006

  4. David Hoksza. Multidimensional indexing for relation databases, 2006

  5. T. Skopal. On Fast Non-Metric Similarity Search by Metric Access Methods, EDBT, Munich, Germany, LNCS 3896, Springer, ISBN: 978-3-540-32960-2, 2006

  6. B. Bustos, T. Skopal. Dynamic Similarity Search in Multi-Metric Spaces, MIR, Santa Barbara, CA, USA, ACM, ISBN: 1-59593-495-2 , 2006

2005 (3 publications)

  1. T. Skopal, J. Pokorný, V. Snášel. Nearest Neighbours Search using the PM-tree, DASFAA, Beijing, China, LNCS 3453, Springer, ISBN: 978-3-540-25334-1, 2005

  2. T. Skopal, P. Moravec. Modified LSI Model for Efficient Search by Metric Access Methods, ECIR, Santiago de Compostela, Spain, LNCS 3408, Springer, ISBN: 978-3-540-25295-5, 2005

  3. T. Skopal, M. Kolovrat, V. Snášel. An Application of LSI and M-tree in Image Retrieval, ZNALOSTI, Stará Lesná, Slovakia, 2005

2004 (8 publications)

  1. M. Krátký, T. Skopal, V. Snášel. Multidimensional Term Indexing for Efficient Processing of Complex Queries, Kybernetika, 40(3), pp.: 381-396, ASCR, ISSN: 0023-5954, 2004

  2. T. Skopal. Metric Indexing in Information Retrieval, VŠB-Technical University of Ostrava, 2004

  3. T. Skopal, J. Pokorný, V. Snášel. PM-tree: Pivoting Metric Tree for Similarity Search in Multimedia Databases, ADBIS, research communications, Budapest, Hungary, Hungarian Academy of Sciences, 2004

  4. T. Skopal. Pivoting M-tree: A Metric Access Method for Efficient Similarity Search, DATESO, Desná-černá Øíčka, Czech Republic, 98, CEUR, ISSN: 1613-0073, 2004

  5. T. Skopal, P. Moravec, J. Pokorný, V. Snášel. Metric Indexing for the Vector Model in Text Retrieval, SPIRE, Padova, Italy, LNCS 3246, Springer, ISBN: 978-3-540-23210-0, 2004

  6. M. Krátký, V. Snášel, P. Zezula, J. Pokorný, T. Skopal. Efficient Processing of Narrow Range Queries in the R-Tree, technical report, Amphora Research Group (ARG), 2004

  7. M. Krátký, J. Pokorný, T. Skopal, V. Snášel. Implementation of XPath Axes in the Multidimensional Approach to Indexing XML Data, ZNALOSTI, Brno, Czech Republic, 2004

  8. T. Skopal, M. Krátký, V. Snášel. Metric and Semi-metric Indexing of Vector Models in Information Retrieval Systems, ZNALOSTI, Brno, Czech Republic, 2004

2003 (14 publications)

  1. J.Dvorský, T.Skopal, V.Snášel. Word-based Compression Methods - Survey Report, Transactions of the VŠB-Technical University of Ostrava, Computer Science and Mathematics Series, 2, 2003

  2. D. Barashev, M. Krátký, T. Skopal. Modern Approaches to Indexing XML Data, Transactions of the VŠB-Technical University of Ostrava, Computer Science and Mathematics Series, 2, 2003

  3. T.Skopal, J.Pokorný, M.Krátký, V.Snášel. Revisiting M-tree Building Principles, ADBIS, Dresden, Germany, LNCS 2798, Springer, 2003

  4. T.Skopal, M.Krátký, V.Snášel. An Efficient Implementation of the Vector Model for Information Retrieval, DATAKON, Brno, Czech Republic, 2003

  5. M. Krátký, T. Skopal, V. Snášel. Efficient Searching in Face Collections, DATAKON, Brno, Czech Republic, 2003

  6. J. Dvorský, M. Krátký, T. Skopal, V. Snášel. Benchmarking the Multidimensional Approach for Term Indexing, DATESO, Desná-Černá Říčka, Czech Republic, 2003

  7. M. Krátký, T. Skopal. Benchmarking the UB-tree, DATESO, Desná-černá Øíčka, Czech Republic, 2003

  8. M.Krátký, T.Skopal, V.Snášel. Image Compression Using Space-Filling Curves, ITAT, High Tatras, Slovakia, 2003

  9. J.Dvorský, M.Krátký, T.Skopal, V.Snášel. Term Indexing in Information Retrieval Systems, PSMP, Las Vegas, Nevada, USA, CSREA Press, 2003

  10. T.Skopal, V.Snášel, M.Krátký, V.Svátek. Searching the Internet Using Topological Analysis of Web Pages, PSMP, Las Vegas, Nevada, USA, CSREA Press, 2003

  11. T.Skopal, P.Moravec, J.Pokorný, M.Krátký, V.Snášel. An Efficient Implementation of the Vector Model in Information Retrieval, RCDL, St. Petersburg, Russia, 2003

  12. T. Skopal. Neural networks in Information Retrieval, technical report, VŠB-Technical University of Ostrava, 2003

  13. T. Skopal. Metric Indexing of Vector Models in Information Retrieval, WOFEX, 2003

  14. M.Krátký, T.Skopal, V.Snášel, . Multidimensional Approach for Non-trivial Term Searching, ZNALOSTI, Ostrava, Czech Republic, 2003

2002 (9 publications)

  1. V.Snášel, T.Skopal, D.Ïuráková,. Navigation Through Query Result Using Concept Order, ADBIS, research communications, Bratislava, Slovakia, 2002

  2. M.Krátký, J.Pokorný, T.Skopal, V.Snášel, . The Geometric Approach for Indexing XML Data, DATAKON, Brno, Czech Republic, 2002

  3. T.Skopal, M.Krátký, V.Snášel, . Geometric Indexing and Querying of Multimedia Data, DATAKON, Brno, Czech Republic, 2002

  4. T.Skopal. ACB Compression Method and Query Preprocessing in Text Retrieval Systems, DATESO, Desná, Czech Republic, 2002

  5. M.Krátký, J.Pokorný, T.Skopal, V.Snášel, . The Geometric Framework for Exact and Similarity Querying XML Data, EurAsia ICT, Shiraz, Iran, LNCS 2510, Springer, 2002

  6. T.Skopal . A Data Flow Based GIS Architecture, GIS OSTRAVA, Ostrava, Czech Republic, 2002

  7. T. Skopal, M. Krátký, V. Snášel, . Properties Of Space Filling Curves And Usage With UB-trees, ITAT, Malino Brdo, Slovakia, 2002

  8. M.Krátký, T.Skopal, V.Snášel.. On Comparison of Several Indexing Methods for Similarity Search in Multimedia Databases, Kybernetika - história, perspektívy, teória a prax, Žilina, Slovakia, 2002

  9. T.Skopal, V.Snášel, M.Krátký,. Image Recognition Using Finite Automata, Prague Stringology Conference, Prague, Czech Republic, 2002

2001 (2 publications)

  1. T.Skopal . Data processing - Piped GIS, Olomouc, Czech Republic, KMI UPOL, 2001

  2. T.Skopal . A data flow driven information system, OBJEKTY, Prague, Czech Republic, 2001



by Dr. Radut.