Selected Publications

2024

• Draesslerová D., Ahmed O., Gagie T., Holub J., Langmead B., Manzini G., and Navarro G.: Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests. In Liberti L. (ed.): Proceedings of 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Vol. 301, pp. 10:1-10:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik, Dagstuhl Publishing, Germany, 2024

2023

• Procházka P., Cvacho O., Krčál L., Holub J.: Backward Pattern Matching on Elastic‐Degenerate Strings. SN Computer Science Vol. 4(5), Article No. 442, Springer Nature, Singapore, September 2023, ISSN: 2661-8907

2022

• Krčál L., Ho S.S., Holub J.: Hierarchical Bitmap Indexing for Range Queries on Multidimensional Arrays. In Bhattacharya A., Li J.L.M., Agrawal D., Reddy P.K., Mohania M., Mondal A., Goyal V., Kiran R.U. (eds.): Database Systems for Advanced Applications (DASFAA 2022), pp. 509-525, Springer Cham, 2022, ISBN: 978-3-031-00122-2, ISSN: 0302-9743

2021

• Boucher C., Cvacho O., Gagie T., Holub J., Manzini G., Navarro G., and Rossi M.: PFP Compressed Suffix Trees. In M. Farach-Colton and S. Storandt (eds.): Proceedings of the Symposium on Algorithm Engineering and Experiments (ALENEX 21), pp. 60-72, SIAM 2021, ISBN 978-1-61197-647-2.

• Chikhi R., Holub J., Medvedev P.: Data Structures to Represent a Set of k-long DNA Sequences. ACM Computing Surveys, Vol. 54(1), Article 17, 2021. ISSN: 0360-0300

• Procházka P., Cvacho, O., Krčál, L., Holub J.: Backward Pattern Matching on Elastic Degenerate Strings. In Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) - Volume 3: BIOINFORMATICS, pp. 50-59, 2021, ISBN: 978-989-758-490-9, ISSN: 2184-4305

2020

• Holub J. (editor): Special Issue: Stringology Algorithms. Discrete Applied Mathematics, Vol. 274, 2020. ISSN 0166-218X.

• Holub J., Žďárek J. (editors): Proceedings of the Prague Stringology Conference 2020. Czech Technical University in Prague, Prague, August 2020.

2019

• Holub J., Žďárek J. (editors)): Proceedings of the Prague Stringology Conference 2019. Czech Technical University in Prague, Prague, August 2019.

• Procházka P., Holub J.: On-line Searching in IUPAC nucleotide sequences. In Proceedings of 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019 pp. 66-77, 2019.

2018

• Cisłak A., Grabowski G., Holub J.: SOPanG: online text searching over a pan-genome. In Bioinformatics, Vol. 34(24), pp. 4290-4292, 2018.

• Cvacho O., Holub J.: Filtering Invalid Off-Targets in CRISPR/Cas9 Design Tools. In A. Bilgin, M. W. Marcellin, J. Serra-Sagrista, J. A. Storer (eds.): Proceedings of Data Compression Conference 2018, IEEE Computer Society Press, p. 403, 2018.

• Daykin J.W., Franěk F., Holub J., Islam A.S.M.S, Smyth W. F.: Reconstructing a String from its Lyndon Arrays. In Theoretical Computer Science, Vol. 710, pp. 44-51, Elsevier, 2018.

• Holub J., Žďárek J. (editors)): Proceedings of the Prague Stringology Conference 2018. Czech Technical University in Prague, Prague, August 2018.

• Šestáková E., Janoušek J.: Automata Approach to XML Data Indexing . Information, Vol. 9(1), 12, 2018.

2017

• Holub J., Žďárek J. (editors): Proceedings of the Prague Stringology Conference 2017. Czech Technical University in Prague, Prague, August 2017.

• Procházka P., Holub J.: Towards Efficient Positional Inverted Index. In Algorithms, Vol. 10(1), 30, 2017. ISSN 1999-4893.

• Procházka P., Holub J.: Byte-Aligned Pattern Matching in Encoded Genomic Sequences. In R. Schwartz and K. Reinert (eds.): Proceedings of 17th International Workshop on Algorithms in Bioinformatics (WABI 2017), pp. 20:1-20:13, Dagstuhl Publishing, Germany, 2017. ISBN 978-3-95977-050-7. ISSN 1868-8969.

• Šestáková E., Janoušek J.: Indexing XML Documents Using Tree Paths Automaton . In Proceedings of OASIcs-OpenAccess Series in Informatics. Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, pp. 10:1-10:14, 2017.

• Tarhio J., Holub J., Giaquinta E.: Technology Beats Algorithms (in Exact String Matching). In Software: Practice and Experience, Vol. 47(12), pp. 1877-1885, Wiley, December 2017. ISSN 1097-024X

2016

• Guth O.: Computing All Approximate Enhanced Covers with the Hamming Distance. In Proceedings of the Prague Stringology Conference 2016, pp. 146–157. ISBN 978-80-01-05996-8.

• Holub, J. (editor): Special Issue: Stringology Algorithms. Discrete Applied Mathematics, Vol. 212, 2016. ISSN 0166-218X.

• Holub J., Žďárek J. (editors): Proceedings of the Prague Stringology Conference 2016. Czech Technical University in Prague, Prague, August 2016.

• Hrbek, L., Holub, J.: Approximate String Matching for Self-Indexes. In A. Bilgin, M. W. Marcellin, J. Serra-Sagrista, J. A. Storer (eds.): Proceedings of Data Compression Conference 2016, IEEE Computer Society Press, p. 604, 2016.

• Polách, R., Trávníček, J., Janoušek, J., Melichar, B.: Efficient Determinization of Visibly and Height-deterministic Pushdown Automata. Computer Languages, Systems & Structures, Vol. 46, pp. 91-105, 2016.

• Procházka, P., Holub, J.: Positional Inverted Self-index. In A. Bilgin, M. W. Marcellin, J. Serra-Sagrista, J. A. Storer (eds.): Proceedings of Data Compression Conference 2016, IEEE Computer Society Press, p. 627, 2016.

• Procházka, P., Holub, J.: Towards Efficient Positional Inverted Index. In B. Carpentieri, F. Palmieri (eds): Proceedings of International Conference on Data Compression, Communication, Processing and Security 2016, pp. 55-62, 2016.

2015

• Furletova E., Holub J., and Régnier M.: Minimized Compact Automaton for Clumps over Degenerate Patterns. In Denise A., Lespinet O., Régnier M. (eds): Actes du workshop pluridisciplinaire Algorithmique des séquences pour la bioinformatique (SeqBio) / Proceedings of String algorithms for bioinformatics, Orsay, France, 2015.

• Janoušek, J., Polách, R., Trávníček, J., Melichar, B.: New Algorithm for the Determinisation of Visibly Pushdown Automata. In Ganzha M., Maciaszek L.A., Paprzycki M. (Eds.): Proceedings of Federated Conference on Computer Science and Information Systems (FedCSIS 2015), pp. 915-922, 2015.

• Krčál, L., Holub, J.: Incremental Locality & Clustering-Based Compression. In A. Bilgin, M. W. Marcellin, J. Serra-Sagrista, J. A. Storer (eds.): Proceedings of Data Compression Conference 2015, IEEE Computer Society Press, pp. 203-212, 2015.

• Procházka, P., Holub, J.: Compression of a Set of Files with Natural Language Content. The Computer Journal, Vol. 58(5), pp. 1169-1185, 2015.

• Šestáková E., Janoušek J.: Tree String Path Subsequences Automaton and Its Use for Indexing XML Documents.. In Sierra-Rodríguez, J.-L., Leal, J., P., Simoes, A. (Eds.): Proceedings of International Symposium on Languages, Applications and Technologies. Springer, Cham, pp. 171-181, 2015.

• Trávníček, J., Janoušek, J., Melichar, B., Cleophas, L., G.: Backward Linearised Tree Pattern Matching. In Dediu, A.-H., Formenti, E., Martín-Vide, C., Truthe, B. (Eds.): Proceedings of the 9th International Conference on Language and Automata Theory and Applications (LATA 2015), LNCS Vol. 8977, pp. 599-610, 2015.

2014

• Holub, J. (editor): Special Issue: Stringology Algorithms. Discrete Applied Mathematics, Vol. 163, Part 3, 2014. ISSN 0166-218X.

• Janoušek, J., Málek, J.: Target Code Selection by Tilling AST with the Use of Tree Pattern Pushdown Automaton. In Proceedings of the 3rd Symposium on Languages, Applications and Technologies, pp. 159–165, 2014.

• Janoušek, J., Melichar, B., Polách, R., Poliak, M., Trávníček, J.: A Full and Linear Index of a Tree for Tree Patterns. In H. Jürgensen, J. Karhumäki, A. Okhotin (eds.): Proceedings of Descriptional Complexity of Formal Systems - 16th International Workshop, pp. 198–209, 2014.

• Lahoda, J., Žďárek, J.: Simple Tree Pattern Matching for Trees in the Prefix Bar Notation. In Discrete Applied Mathematics, Vol. 163, Part 3, pp. 343–351, Jan 2014.

• Procházka, P., Holub, J.: Compressing Similar Biological Sequences using FM-index. In A. Bilgin, M. W. Marcellin, J. Serra-Sagrista, J. A. Storer (eds.): Proceedings of Data Compression Conference 2014, IEEE Computer Society Press, pp. 312-321, 2014.

2013

• Christou, M., Flouri, T., Iliopoulos, C.S., Janoušek, J., Melichar, B., Pissis, S.P., Žďárek, J.: Tree template matching in unranked ordered trees. Journal of Discrete Algorithms, Vol. 20, StringMasters 2011 Special Issue, pp. 51–60, 2013.

• Holub, J., Žďárek, J. (editors): Proceedings of the Prague Stringology Conference 2013. Czech Technical University in Prague, Prague, August 2013.

• Janoušek, J.: Tree Indexing by Deteministic Automata. Dagstuhl Reports, Vol. 3, No. 5, Tree Transducers and Formal Methods (Dagstuhl Seminar 13192), p. 6, 2013.

• Na, J. C., Park, H., Crochemore, M., Holub, J., Iliopoulos C. S., Mouchard, L., Park, K.: Suffix Tree of Alignment: An Efficient Index for Similar Data. Proceedings of the 24th Workshop on Combinatorial Algorithms (IWOCA 2013), Rouen, July 2013, LNCS 8288, Springer-Verlag, pp. 337-348, 2013.

• Procházka, P., Holub, J.: Natural Language Compression Optimized for Large Set of Files. In A. Bilgin, M. W. Marcellin, J. Serra-Sagrista, J. A. Storer (eds.): Proceedings of Data Compression Conference 2013, IEEE Computer Society Press, p. 514, 2013.

• Procházka, P., Holub, J.: ODC: Frame for Definition of Dense Codes. European Journal of Combinatorics, Elsevier, Vol. 34, No. 1, pp. 52-68, 2013.

2012

• Christou, M., Crochemore, M., Flouri, T., Iliopoulos, C. S., Janoušek, J., Melichar, B., Pissis, S. P.: Computing all subtree repeats in ordered trees. Information Processing Letters, Elsevier, Vol. 112(24), pp. 958–962, 2012.

• Christou M., Crochemore M., Guth O., Iliopoulos C.S., Pissis, S.P.: On left and right seeds of a string. In Journal of Discrete Algorithms. Vol. 17, pp. 31–44. ISSN 1570-8667. 2012.

• Flouri, T., Iliopoulos, C. S., Janoušek, J., Melichar, B., Pissis, S. P.: Tree template matching in ranked ordered trees by pushdown automata. In B. Bouchou-Markhoff, P. Caron, J. M. Champarnaud, and D. Maurel (eds.): Implementation and Application of Automata - 16th International Conference, CIAA, Vol. 17, pp. 15–23, 2012.

• Holub, J.: The Finite Automata Approaches in Stringology. Kybernetika, Vol. 48 (3), pp. 386-401, 2012.

• Holub, J. (editor): Special Issue of International Journal of Foundations of Computer Science, Vol. 23, No. 2, 2012.

• Holub, J., Žďárek, J. (editors): Proceedings of the Prague Stringology Conference 2012. Czech Technical University in Prague, Prague, August 2012.

• Janoušek, J., Melichar, B., Poliak, M.: Tree compression pushdown automaton. Kybernetika, Vol. 48 (3), pp. 429-452, 2012.

• Melichar, B., Janoušek, J., Flouri, T.: Arbology: Trees and pushdown automata. Kybernetika, Vol. 48 (3), pp. 401-428, 2012.

• Trávníček, J., Janoušek, J., Melichar, B.: Indexing ordered trees for (nonlinear) tree pattern matching by pushdown automata. In M. Ivanovic (ed.): Comput. Sci. Inf. Syst., Vol. 9(3), pp. 1125–1153, 2012.

• Žďárek, J., Melichar, B.: Tree-Based 2D Indexing. In Domaratzki, M., Salomaa, K. (Eds.): International Journal of Foundations of Computer Science (IJFCS), Special Issue Implementation and Application of Automata (CIAA 2010), vol. 22, no. 8, World Scientific, pp. 1893–1907, Dec. 2011.

2011

• Antoš, J., Melichar, B.: Finite Automata for Generalized Approach to Backward Pattern Matching. In Domaratzki, M., Salomaa, K. (Eds.): Proceedings of CIAA 2010, LNCS 6482, Springer-Verlag, pp. 49–58, 2011.

• Christou, M., Crochemore, M., Flouri, T., Iliopoulos, C.S., Janoušek, J., Melichar, B., Pissis, S.P.: Computing all subtree repeats in ordered ranked trees. In Proceedings of the 18th International Symposium on String Processing and Information Retrieval (SPIRE 2011), LNCS 7024, Springer-Verlag, pp. 338-343.

• Christou, M., Crochemore, M., Guth, O., Iliopoulos, C.S., Pissis, S.P.: On the Right-seed Array of a String. In Proceedings of COCOON 2011, LNCS 6482, Springer-Verlag, pp. 492–502.

• Flouri, T., Frousios, K., Iliopoulos, C.S., Park, K., Pissis, S.P., Tischler, G.: Approximate string-matching with a single gap for sequence alignment. In Proceedings of the ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), 2011. ACM Digital Library, pp. 490-492, 2011.

• Flouri, T., Iliopoulos, C.S., Pissis, S.P.: DynMap: mapping short reads to multiple related genomes. In Proceedings of the ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), 2011. ACM Digital Library, pp. 330-334, 2011.

• Flouri, T., Iliopoulos, C.S., Pissis, S.P., Tischler, G.: Mapping short reads to a genomic sequence with circular structure. International Journal of Systems Biology and Biomedical Technologies, vol. 1, no. 1, IGI Global, pp. 26-34, Jan. 2012.

• Flouri, T., Janoušek, J., Melichar, B., Iliopoulos, C.S., Pissis, S.P.: Tree Indexing by Pushdown Automata and Repeats of Subtrees. In Ganzha M., Maciaszek L.A., Paprzycki M. (eds.) FedCSIS 2011, pp. 899-902.

• Flouri, T., Janoušek, J., Melichar, B., Iliopoulos, C.S., Pissis, S.P.: Tree Template Matching in Ranked Ordered Trees by Pushdown Automata. In Bouchou-Markhoff B., Caron P., Champarnaud J-M., Maurel D. (eds.): Proceedings of CIAA 2011, LNCS 6807, Springer-Verlag, pp. 273-281.

• Holub, J.: Finite Automata in Pattern Matching. In M. Elloumi, A. Y. Zomaya (eds.): Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Wiley, pp. 51-71, 2011.

• Holub, J., Řezníček, J., Šimek, F.: Lossless Data Compression Testbed: ExCom and Prague Corpus. In J. A. Storer, M. W. Marcellin (eds.): Proceedings of Data Compression Conference 2011, IEEE Computer Society Press, p. 457, 2011.

• Holub, J., Žďárek, J. (editors): Proceedings of the Prague Stringology Conference 2011. Czech Technical University in Prague, Prague, August 2011.

• Plicka, M., Janoušek, J., Melichar, B.: Subtree Oracle Pushdown Automata for Ranked and Unranked Ordered Trees. In Ganzha M., Maciaszek L.A., Paprzycki M. (eds.) FedCSIS 2011, pp. 903-906.

• Procházka, P., Holub, J.: Block-oriented Dense Compressor. In J. A. Storer, M. W. Marcellin (eds.): Proceedings of Data Compression Conference 2011, IEEE Computer Society Press, p. 472, 2011.

• Procházka, P., Holub, J.: Natural Language Compression per Blocks. The First International Conference on Data Compression, Communications and Processing, CCP 2011, Palinuro, Italy, IEEE 2011, ISBN 978-1-4577-1458-0, pp. 67-75.

• Trávníček, J., Janoušek, J., Melichar, B.: Nonlinear Tree Pattern Pushdown Automata. In Ganzha M., Maciaszek L.A., Paprzycki M. (eds.) FedCSIS 2011, pp. 871-878.

• Žďárek, J., Melichar, B.: A Note on a Tree-Based 2D Indexing. In Domaratzki, M., Salomaa, K. (Eds.): Proceedings of CIAA 2010, LNCS 6482, Springer-Verlag, pp. 300–309, 2011.

2010

• Antoš, J.: Automaton-based Backward Pattern Matching. Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, February 2010. Dissertation thesis.

• Flouri, T., Holub, J., Iliopoulos, C.S., Pissis, S.P.: An algorithm for mapping short reads to a dynamically changing genomic sequence. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2010), IEEE Computer Society, pp. 133-136, 2010.

• Ďurian B., Holub J., Peltola H., Tarhio J.: Improving Practical Exact String Matching. Information Processing Letters, Elsevier, Vol. 110, No. 4, pp. 148-152, 2010.

• Flouri, T., Janoušek , J., Melichar, B.: Aho-Corasick like multiple subtree matching by pushdown automata. In: ACM Symposium on Applied Computing 2010, pp. 2157-2158, ACM Press, 2010.

• Flouri, T., Janoušek , J., Melichar, B.: Subtree matching by deterministic pushdown automata.. In: COMSIS, Vol. 7, No.2, pp. 331-357, ComSIS Consortium, 2010.

• Guth, O., Melichar, B.: Using Finite Automata Approach for Searching Approximate Seeds of Strings. In Xu Huang, Sio-Iong Ao, and Oscar Castillo (eds.): Intelligent Automation and Computer Engineering, Springer Netherlands, ISBN 978-90-481-3517-2, pp. 347-360, 2010.

• Holub, J., Žďárek, J. (editors): Proceedings of the Prague Stringology Conference 2010. Czech Technical University in Prague, Prague, August 2010.

• Janoušek , J.: Algorithms on Trees and Pushdown Automata. Technical University Brno, Faculty of Information Technology, 161 pages, 2010. Habilitation thesis.

• Jaroš J., Holub J.: Semi-static Word-based Natural Language Compression. Proceedings of the 11th International PhD Workshop on Systems and Control A Young Generation Viewpoint, Veszprém, September 1, pp. 57-62, 2010.

• Lahoda, J., Žďárek, J.: Simple Tree Pattern Matching for Trees in the Prefix Bar Notation. In Holub, J., Žďárek, J. (Eds.) Proceedings of the Prague Stringology Conference 2010, CTU in Prague, pp. 25–36.

• Melichar, B.: Arbology: Trees and Pushdown Automata. In: LATA 2010 (LNCS 6031), Invited paper, pp. 32-49, Springer, 2010.

• Žďárek, J.: Two-dimensional Pattern Matching Using Automata Approach. Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, February 2010. Dissertation thesis.

• Žďárek, J., Melichar, B.: A Note on a Tree-based 2D Indexing. In Domaratzki, M., Salomaa, K. (Eds.) Pre-proceedings of the Fifteenth Conference on Implementation and Application of Automata 2011, pp. 269–277.

2009

• Ďurian B., Holub B., Peltola H, Tarhio J.: Tuning BNDM with q-Grams. Proceedings of the Tenth Workshop on Algorithm Engineering and Experiments (ALENEX09), New York City, January 3, pp. 29-37, 2009.

• Flouri, T., Janoušek, J., Melichar, B.: Subtree Matching by Deterministic Pushdown Automata. Proceedings of the IMCSIT, Vol. 4, IEEE Computer Society Press, 2009, pp. 659–666.

• Guth, O., Melichar, B.: Finite Automata Approach to Computing All Seeds of Strings with the Smallest Hamming Distance. International Journal of Computer Science 36 (2), 2009, pp. 137-146.

• Franěk, F., Holub J.: A Different Proof of the Crochemore-Ilie Lemma Concerning Microruns. London Algorithmics 2008: Theory and Practice, College Publications, pp. 1-9, 2009.

• Holub, J. (editor): Special Issue of Theoretical Computer Science: Implementation and Application of Automata (CIAA 2007), Elsevier, Vol. 410, No. 37, 2009.

• Holub, J. (editor): Special Issue of International Journal of Foundations of Computer Science, Vol. 20, No. 6, 2009.

• Holub J., Kadlec T.: NFA Simulation Using Deterministic State Cache. London Algorithmics 2008: Theory and Practice, College Publications, pp. 152-166, 2009.

• Holub J., Štekr S.: On Parallel Implementation of Deterministic Finite Automata. In S. Maneth (ed.): Proceedings of the 14^th International Conference on Implementation and Application of Automata (CIAA2009), University of New South Wales, Sydney, Australia, LNCS 5642, Springer-Verlag, pp. 54-64, 2009.

• Holub, J., Žďárek, J. (editors): Proceedings of the Prague Stringology Conference 2009. Czech Technical University in Prague, Prague, August 2009.

• Janoušek, J., Melichar, B.: On Regular Tree Languages and Deterministic Pushdown Automata. Acta Informatica, Vol. 46, No. 7, Springer, 2009, pp. 533–547.

• Janoušek, J.: String Suffix Automata and Subtree Pushdown Automata. Proceedings of the Prague Stringology Conference 2009, Czech Technical University in Prague, Prague, September 2009, pp. 160–172.

• Lahoda, J., Melichar, B., Žďárek, J.: Pattern Matching in DCA Coded Text. In Ibarra, O. H., Ravikumar, B. (Eds.) Proceedings of the Thirteenth Conference on Implementation and Application of Automata, LNCS 5148, Springer-Verlag 2008, pp. 151–160.

• Melichar, B., Hanuš, M.: Repetitions and Factor Automata. In Chan, J., Daykin, J. W., Rahman, M. S. (Eds.): London Algorithmics 2008: Theory and Practice, KCL Publications, King's College London, England, 2009, pp. 167–183.
• Procházka P., Holub J.: New Word-based Adaptive Dense Compressors. Proceedings of the 20th Workshop on Combinatorial Algorithms (IWOCA09), Hradec nad Moravici, June 2009, LNCS 5874, Springer-Verlag 2009, pp. 420-431.

2008

• Jaroš J., Procházka P., Holub J.: On Implementation of Word-Based Compression Methods. In 4th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, Brno, 2008, pp. 76–83, 978-80-7355-082-0.

• Šimůnek, M., Melichar, B.: Approximate Periods with Levenshtein Distance. In Ibarra, O. H., Ravikumar, B. (Eds.) Proceedings of the Thirteenth Conference on Implementation and Application of Automata, LNCS 5148, Springer-Verlag 2008, pp. 286–287.

• Flouri T., Voráček M., Vagner L.: Indexing factors in DNA/RNA Sequences. In Bioinformatics Research and Developement. Berlin: Springer, 2008, pp. 436–445. ISBN 3-540-70598-8.

• Guth, O., Melichar, B., Balík, M.: Searching All Approximate Covers and Their Distance using Finite Automata. In Vojtáš, P. (Ed.) Information Technologies – Applications and Theory, pp. 21–26, ISBN 978-80-969184-9-2.

• Holub, J., Žďárek, J. (editors): Proceedings of the Prague Stringology Conference 2008. Czech Technical University in Prague, Prague, September 2008.

• Lahoda, J., Melichar, B., Žďárek, J.: Pattern Matching in DCA Coded Text. In Ibarra, O. H., Ravikumar, B. (Eds.) Proceedings of the Thirteenth Conference on Implementation and Application of Automata, LNCS 5148, Springer-Verlag 2008, pp. 151–160.

• Holub, J., Smyth, W. F., Wang, S.: Fast Pattern-Matching on Indeterminate Strings. Journal of Discrete Algorithms, Vol. 6, No. 1, 2008, pp. 37-50.

• Holub, J. (editor): Special Issue of International Journal of Foundations of Computer Science, Vol. 19, No. 1, 2008.

• Fiala, M., Holub, J.: DCA using Suffix Arrays. In J. A. Storer, M. W. Marcellin (eds.): Proceedings of Data Compression Conference 2008, IEEE Computer Society Press, p. 516, 2008.

2007

• Flouri T., Voráček M., Vagner L.: Indexing Degenerate Strings. In Proceedings of International Conference of Computational Methods in Sciences and Engineering 2007, American Institute of Physics, Melville, New York, pp. 1400–1403, 2007.

• Voráček M., Vagner L., Rahman S.M., Iliopoulos C.S.: Computing Constrained Longest Common Subsequence for Degenerate Strings using Finite Automata. 2007, In Algorithms and Complexity in Durham 2007. London: King's College, 2007, vol. 1, pp. 94–106. ISBN 978-1-904987-55-0.

• Voráček M., Vagner L., Rahman S.M., Iliopoulos C.S.: The Constrained Longest Common Subsequence Problem for Degenerate Strings. In Twelfth International Conference on Implementation and Application of Automata. Berlin: Springer-Verlag, 2007, pp. 309–311. ISBN 978-3-540-76335-2.

• Holub, J., Smyth, W. F., Wang, S.: Hybrid Pattern-Matching Algorithms on Indeterminate Strings. In Daykin, J., Mohamed, M., Steinhoefel, K. (eds.): London Stringology Day + London Algorithmic Workshop 2006, King's College London Series Texts in Algorithmics, 2007, pp. 115-133.

• Holub, J., Žďárek, J. (editors): Pre-proceedings of CIAA 2007. Czech Technical University in Prague, Prague, July 2007, 284 pages, ISBN 978-80-01-03764-5.

• Holub, J., Žďárek, J. (editors): Implementation and Application of Automata, The proceedings of CIAA2007. Czech Technical University in Prague, Prague, July 16-18, 2007, 324 pages, ISBN 978-3-540-76335-2, LNCS 4783, SpringerLink, Springer-Verlag, 2007.

• Šimůnek, M., Melichar, B.: Borders and Finite Automata. International Journal of Foundations of Computer Science, Vol. 18, Number 4, August 2007, pp. 859-871.

• Šupol, J.: Significant Subpatterns Matching. In Holub, J., Žďárek, J. (eds.): Implementation and Application of Automata, 12th International Conference, CIAA 2007, Prague, Czech Republic, 2007, Revised Selected Papers, LNCS 4783, Springer-Verlag, pp. 317-319.

• Šupol, J., Melichar, B.: Suffix Automata and Parallel String Matching. In Daykin, J., Mohamed, M., Steinhoefel, K. (eds.): London Stringology Day + London Algorithmic Workshop 2006, King's College London Series Texts in Algorithmics, 2007, pp. 149-176.

• Vagner, L., Melichar, B.: Parallel LL Parsing. In Acta Informatica 2007, vol. 44, no. 1, p. 1-21.

• Vagner, L., Melichar, B.: Formal Translation Directed by Paralllel LLP Parsing In Lecture Notes in Computer Science 4362 - SOFSEM 2007: Theory and Practice of Computer Science. Berlin: Springer-Verlag, 2007, p. 532-543.

• Iliopoulos, C., Jayasekera, I., Melichar, B., Šupol, J.,: Weighted Degenerated Approximate Pattern Matching. In Pre-proceedings of the 1st International Conference on Language and Automata Theory and Applications. Tarragona: Universitat Rovira i Virgili, 2007, pp. 285-296.

2006

• Antoniou, P., Holub, J., Iliopoulos, C.S., Melichar, B., Peterlongo, P.: Finding Common Motifs with Gaps using Finite Automata. In O. H. Ibarra, Hsu-Chun Yen (eds.): Proceedings of the 11^th International Conference on Implementation and Application of Automata (CIAA2006), National Taiwan University, Taipei, Taiwan, 2006, LNCS 4094, Springer-Verlag, pp. 69-77.

• Holub, J. (editor): Special Issue of International Journal of Foundations of Computer Science, Vol. 17, No. 6, 2006.

• Holub, J., Žďárek, J. (editors): Proceedings of the Prague Stringology Conference '06. Czech Technical University in Prague, Prague, September 2006.

• Šimůnek, M., Melichar, B.: Borders and Finite Automata. In Ibarra, O. H., Ravikumar, B. (Eds.) Proceedings of the 11th Conference on Implementation and Application of Automata, LNCS 4094, Springer-Verlag, pp. 58–68.

• Šupol, J., Melichar, B.: A New Approach to Determinisation Using Bit-Parallelism. In Barkaoui, K., Cavalcanti, A., Cerone, A. (Eds.) Proceedings of the Third International Colloquium on Theoretical Aspects of Computing, (ICTAC 2006), Tunis, Tunisia, 2006, LNCS 4281, Springer-Verlag, pp. 228-241.

• Žďárek, J.: Automata and 2D pattern matching. In Anselmo, M., Giammarresi, D. (Eds.) Extended abstracts from European Science Foundation meeting, University of Salerno, Salerno, Italy 2006.

• Žďárek, J., Melichar, B.: On Two-Dimensional Pattern Matching By Finite Automata. In Farré, J., Litovsky, I., Schmitz, S. (Eds.) Proceedings of the Tenth Conference on Implementation and Application of Automata, LNCS 3845, Springer-Verlag, pp. 329–340.

2005

• Voráček M., Melichar B.: Searching for Regularities in Generalized Strings using Finite Automata. In ICNAAM 2005 – International Conference on Numerical Analysis and Applied Mathematics 2005. Weinheim: WILEY-VCH Verlag Gmb, 2005, pp. 809–812. ISBN 3-527-40652-2.

• Antoš, J., Melichar, B.: Backward Pattern Matching Automaton. Proceedings of the Prague Stringology Conference '05, Czech Technical University in Prague, Prague, September 2005, pp. 81-94.

• Holub, J. (editor): Special Issue of International Journal of Foundations of Computer Science, Vol. 16, No. 6, 2005.

• Holub, J., Smyth, W. F., Wang, S.: Fast Pattern-Matching on Indeterminate Strings. In J. Ryan, P. Manyem, K. Sugeng, M. Miller (eds.): Proceedings of the 16^th Australasian Workshop on Combinatorial Algorithms AWOCA'05, University of Ballarat, Victoria, Australia, 2005, pp. 415-428.

• Holub, J., Šimánek, M. (editors): Proceedings of the Prague Stringology Conference '05. Czech Technical University in Prague, Prague, September 2005.
• Lahoda, J., Melichar, B.: General Pattern Matching on Regular Collage System. Proceedings of the Prague Stringology Conference '05, Czech Technical University in Prague, Prague, September 2005, pp. 153-162.

• Polcar, T., Melichar, B.: Two-dimensional Pattern Matching by Two-dimensional Online Tessellation Automata. Proceedings of the 9th International Conference on Implementation and Application of Automata, CIAA 2004, Lecture Notes in Computer Science, Vol. 3317, 2005, pp. 327-328.
• Žďárek, J., Melichar, B.: On Two-Dimensional Pattern Matching By Finite Automata. In J. Farré, I. Litovsky, S. Schmitz (eds): Proceedings of the 10th International Conference on Implementation and Application of Automata, CIAA 2005, pp. 185-194.

2004

• Antoš, J.: Finite Automata and Backward Pattern Matching. Proceedings of the Sixth International Scientific Conference Electronic Computers and Informatics, ECI 2004, Department of Computers and Informatics of FEI, Technical University Košice, Košice, 2004, pp. 75-80.
• Franěk, F., Holub, J., Rosa, A.: Two factorizations of small complete graphs II: The case of 13 vertices. Journal of Combinatorial Mathematics and Combinatorial Computing, Vol. 51, 2004, pp. 89-94.
• Holub, J., Šimánek, M. (editors): Proceedings of the Prague Stringology Conference '04. Czech Technical University in Prague, Prague, September 2004.
• Holub, J., Špiller, P.: Practical Experiments with NFA Simulation. In L. Cleophas, B. W. Watson (eds): Proceedings of the Eindhoven FASTAR Days 2004, invited talk, Technical University of Eindhoven, 2004, pp. 73-95.
• Lahoda, J., Melichar, B.: Pattern Matching in Text Coded by Finite Translation Automaton. In: M. Heričko et al. (eds): Proceedings of the 7th International Multiconference Information Society IS'2004, Vol. D, Institut "Jožef Stefan", Ljubljana, Slovenia, 2004, pp. 212--214, ISBN 961-6303-65-1.
• Polcar, T., Melichar, B.: A Two-dimensional Online Tessellation Automata Approach to Two-dimensional Pattern Matching. In L. Cleophas, B. W. Watson (eds): Proceedings of the Eindhoven FASTAR Days 2004, invited talk, Technical University of Eindhoven, 2004.
• Šupol J., Melichar B.: Arithmetic Coding in Parallel. In: Holub, J., Šimánek M. (eds.): Proceedings of the 9th Prague Stringology Conference 2004. Department of Computer Science and Engineering, FEE CTU Prague, 2004, pp. 168-178.
• Troníček, Z.: Episode Directed Acyclic Subsequence Graph. Nordic Journal of Computing. Vol. 11, No. 1, 2004, pp. 35-40.
• Voráček M., Melichar B., Christodoulakis M.: Generalized and Weighted Strings: Repetitions and Pattern Matching. In String Algorithmics, C. Iliopoulos and T. Lecroq (eds), KCL Publications, King's College London, England, 2004, pp. 225-248.
• Žďárek, J., Melichar, B.: Finite automata and two-dimensional pattern matching. In M. Heričko et al. (eds): Proceedings of the 7th International Multiconference Information Society IS'2004, Vol. D, Institut "Jožef Stefan", Ljubljana, Slovenia, 2004, pp. 185-188, ISBN 961-6303-65-1.

2003

• Crochemore, M., Melichar, B., Troníček, Z.: Directed Acyclic Subsequence Graph - overview. Journal of Discrete Algorithms. Vol. 1/3-4 pp. 255-280.
• Franek, F., Holub, J., Smyth, W. F., Xiao, X.: Computing Quasi Suffix Arrays. In Journal of Automata, Languages and Combinatorics, Vol. 8, No. 4, Otto-von-Guericke University, Magdeburg, 2003, pp. 593-606.
• Holub, J. (editor): Special Issue of Nordic Journal of Computing, Vol. 10(1), 2003.
• Holub, J., Smyth, W. F.: Algorithms on Indeterminate Strings. In Miller, M., Park, K. (eds.): Proceedings of the 14th Australasian Workshop on Combinatorial Algorithms AWOCA'03, Seoul National University, Seoul, Korea, pp. 36-45.
• Melichar, B., Polcar, T.: The Longest Common Subsequence Problem - A Finite Automata Approach. Proceedings of the 8th International Conference on Implementation and Application of Automata, CIAA 2003, Lecture Notes in Computer Science, Vol. 2759, 2003, pp. 294-296.
• Troníček, Z., Shinohara, A.: The Size of Subsequence Automaton. 10th Symposium on String Processing and Information Retrieval 2003, Manaus, Brasil, October 2003. LNCS 2857, Springer-Verlag, Berlin, pp. 304-310.

2002

• Crochemore, M., Troníček, Z.: On the size of DASG for multiple texts. 9th Symposium on String Processing and Information Retrieval 2002, Lisbon, September 2002. LNCS 2476, Springer-Verlag, Berlin, pp. 58-64.
• Holub, J.: Dynamic Programming - NFA Simulation. Proceedings of the 7^th Conference on Implementation and Application of Automata, University of Tours, Tours, France, July 2002, LNCS 2608, Springer-Verlag, pp. 295-300.
• Holub, J.: Dynamic Programming for Reduced NFAs for Approximate String and Sequence Matching. Kybernetika, Vol. 38(1), 2002, pp. 81-90.
• Holub, J., Crochemore, M.: On the Implementation of Compact DAWG's. Proceedings of the 7^th Conference on Implementation and Application of Automata, University of Tours, Tours, France, July 2002, LNCS 2608, Springer-Verlag, pp. 289-294.
• Troníček, Z.: Common Subsequence Automaton. 7th International Conference on Implementation and Application of Automata 2002, Tours, France, July 2002. Springer-Verlag, Berlin.
• Troníček, Z.: Common Subsequence Automaton. Research report DC-2002-02. Department of Computer Science and Engineering, FEE CTU Prague, April 2002.

2001

• Holub, J.: Bit Parallelism - NFA Simulation. Proceedings of the 6^th Conference on Implementations and Applications of Automata, University of Pretoria, Pretoria, South Africa, July 2001, LNCS 2494, Springer-Verlag, pp. 149-160.
• Holub, J., Iliopoulos, C.S., C.S., Melichar, B., Mouchard, L.: Distributed Pattern Matching Using Finite Automata. Journal of Automata, Languages and Combinatorics, Vol. 6(2), Otto-von-Guericke University, Magdeburg, 2001, pp. 191-204.
• Troníček, Z.: Episode matching. 12th Annual Symposium, Combinatorial Pattern Matching 2001, Jerusalem, July 2001. LNCS 2089, Springer-Verlag, Berlin, pp. 143-146.
• Troníček, Z.: Searching subsequences. PhD thesis. Department of Computer Science and Engineering, FEE CTU Prague, December 2001.

2000

• Holub, J.: Simulation of Nondeterministic Finite Automata in Pattern Matching. Ph.D. thesis, Czech Technical University, Prague, February 2000, p. 118.

• Holub, J., Melichar, B.: Approximate String Matching using Factor Automata. Theoretical Computer Science, Vol. 249 (2), Elsevier Science, 2000, pp. 305-311.

1999

• Crochemore, M., Troníček, Z.: Directed Acyclic Subsequence Graph for multiple texts. Rapport I.G.M. 99-13, Universite de Marne-la-Vallee, June 1999.
• Holub J., Iliopoulos, C.S., Melichar, B., Mouchard, L.: Distributed String Matching using Finite Automata. In Raman, R., Simpson, J., (eds.) Proceedings of the Tenth Australasian Workshop on Combinatorial Algorithms AWOCA'99, Curtin University of Technology, Perth, Australia, pp. 114-128.
• Holub, J., Melichar, B.: Implementation of Nondeterministic Finite Automata for Approximate Pattern Matching. In Proceedings of Third International Workshop on Implementing Automata WIA'98, University of Rouen, France, LNCS 1660, Springer-Verlag, Berlin, pp. 92-99, 1999.
• Holub, J., Šimánek, M. (editors): Proceedings of the Prague Stringology Club Workshop '99. CTU Prague, July 1999.
• Melichar, B., Holub, J.: Algorithms for Pattern Matching. Proceedings of Summer School of Information Systems and Their Applications 1999, Ruprechtov, Czech Republic, September 1999, pp. 69-78.
• Troníček, Z.: Problems related to subsequences and supersequences. 6th Symposium on String Processing and Information Retrieval'99, Cancun, Mexico, September 1999. IEEE CS Press, pp. 199-205.

1998

• Balik, M.: Implementation of DAWG. Proceedings of DATASEM'98, Brno, October 1998, pp. 295-305.
• Balik, M.: Implementation of DAWG. Proceedings of the Prague Stringology Club Workshop '98, September 1998, CTU Prague, pp. 26-35.
• Holub, J.: Simulation of NFA in Approximate String and Sequence Matching. Proceedings of the Prague Stringology Club Workshop '98, September 1998, CTU Prague, pp. 73-82.
• Holub, J.: Simulation of Nondeterministic Finite Automata in Approximate String and Sequence Matching. Research Report DC-98-04, April 1998, CTU Prague, 28 pages.
• Holub, J., Melichar, B.: Approximate String Matching Using Factor Automata. In Costas S. Iliopoulos (ed.): Proceedings of Ninth Australasian Workshop on Combinatorial Algorithms AWOCA'98, Curtin University of Technology, Perth, West Australia, July 1998, pp. 28-39.
• Holub, J., Šimánek, M. (editors): Proceedings of the Prague Stringology Club Workshop '98. CTU Prague, September 1998.
• Melichar, B., Holub, J.: Pattern Matching and Finite Automata. In Proceedings of Summer School of Information Systems and Their Applications 1998, Ruprechtov, Czech Republic, September 1998, pp. 154-183.
• Šimánek, M.: The Factor Automaton. Proceedings of the Prague Stringology Club Workshop '98, September 1998, CTU Prague, pp. 102-106.
• Troníček, Z.: Operations on DASG. In Proceedings of Third International Workshop on Implementing Automata WIA'98, University of Rouen, France, September 1998, pp. 65-73.
• Troníček, Z., Melichar, B.: Directed Acyclic Subsequence Graph. Proceedings of the Prague Stringology Club Workshop '98, September 1998, CTU Prague, pp. 107-118.

1997

• Holub, J. (editor): Proceedings of the Prague Stringology Club Workshop '97. CTU, Prague, July 1997, 68 pages.
• Holub, J.: Simulation of NFA in Approximate String and Sequence Matching. Proceedings of the Prague Stringology Club Workshop '97, July 1997, pp. 39-46.
• Melichar, B.: A Simple Method of Complete Indexing. Proceedings of DATASEM '97, Brno, October 1997, pp. 183-188.
• Melichar, B., Holub, J.: 6D Classification of Pattern Matching Problems. Proceedings of the Prague Stringology Club Workshop '97, July 1997, pp. 25-33.
• Melichar, B., Holub, J., Muzatko, P.: Languages and Translations. Czech Technical University, November 1997, 143 pages, textbook.

1996

• Bloch, M.: Efficiency of AC-Machine and SNFA in Practical String Matching. Proceedings of the Prague Stringology Club Workshop '96, August 1996, pp. 15-18.
• Holub, J. (editor): Proceedings of the Prague Stringology Club Workshop '96. CTU, Prague, August 1996, 83 pages.
• Holub, J.: Reduced Nondeterministic Finite Automata for Approximate String Matching. Proceedings of the Prague Stringology Club Workshop '96, August 1996, pp. 19-27.
• Melichar, B.: Space Complexity of Linear Time Approximate String Matching. Proceedings of the Prague Stringology Club Workshop '96, August 1996, pp. 28-36.
• Melichar, B.: String Matching with k Differences by Finite Automata. Proceedings of the 13^th ICPR, Vol II., Vienna 1996, pp. 256-260.
• Muzatko, P.: Approximate Regular Expression Matching. Proceedings of the Prague Stringology Club Workshop '96, August 1996, pp. 37-41.

1995

• Melichar, B.: Approximate String Matching by Finite Automata. CAIP '95, Prague 1995, Computer Analysis of Images and Patterns, LNCS 970, Springer-Verlag, pp. 342–349.

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