Jan Holub

 english
profesor

Katedra teoretické informatiky
Fakulta informačních technologií
České vysoké učení technické v Praze
Thákurova 2700/9
160 00 Praha 6
Česká republika

tel.: (+420) 224 359 814, (+420) 224 359 876 (sekretářka)
fax: (+420) 224 353 600
e-mail: Jan.Holub@fit.cvut.cz
rozvrh na ČVUT FIT kancelář: A-1235 pozice na mapě

online konzultační hodiny: Pouze po předchozí domluvě.

Vzdělání

Témata vědeckého výzkumu

Výuka

Garance studijního programu/oboru

Právě probíhá

Všechny

Vedení studentů

Několik doporučení pro vytváření závěrečných prací.

Doktorandi

Diplomanti

Bakalanti

Další aktivity

CPM 2025

PSC 2024, IT SPY 2024 (informace o průběhu na ČVUT FIT)

Konference:

Jiné:

Stáže

Vybrané publikace

Scopus, ORCID, DBLP, Microsoft Academics, Google Scholar, CSB, CiteSeer, Erdös Number(Jan Holub)=2

2024

  1. 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

  1. 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

  1. 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

  1. 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 2021), pp. 60-72, SIAM 2021, ISBN 978-1-61197-647-2.

  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

  3. 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

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

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

2019

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

  2. 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

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

  2. 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.

  3. 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.

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

2017

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

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

  3. 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.

  4. 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

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

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

  3. 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.

  4. 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.

  5. 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

  1. 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.

  2. Holub J., Žďárek J. (editors): Proceedings of the Prague Stringology Conference 2015. Czech Technical University in Prague, Prague, August 2015.

  3. 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.

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

2014

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

  2. Holub J., Žďárek J. (editors): Proceedings of the Prague Stringology Conference 2014. Czech Technical University in Prague, Prague, August 2014.

  3. 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

  1. Holub J.: ACM Student Project of the Year 2013 Competition. Information Sciences and Technologies Bulletin of the ACM Slovakia, Vol. 5(4), pp.  55-56, 2013.

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

  3. 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.

  4. 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.

  5. 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

  1. Holub J.: The Finite Automata Approaches for Bioinformatics (invited talk). In F. Mráz (ed.): Proceedings of Theorietag 2012, pp. 1-2, 2012.

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

  3. Holub J. (editor): Special Issue - Prague Stringology Conference, International Journal of Foundations of Computer Science, Vol. 23, No. 2, 2012.

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

2011

  1. 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.

  2. 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.

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

  4. 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.

  5. 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, 2011.

2010

  1. 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.

  2. 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.

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

  4. 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.

2009

  1. Ďurian B., Holub J., 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.

  2. 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.

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

  4. Holub J. (editor): Special Issue - Prague Stringology Conference 2008, International Journal of Foundations of Computer Science, Vol. 20, No. 6, 2009.

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

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

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

  8. Procházka P., Holub J.: New Word-based Adaptive Dense Compressors. Proceedings of the 20th Workshop on Combinatorial Algorithms (IWOCA 2009), Hradec nad Moravici, June 2009, LNCS 5874, Springer-Verlag, pp. 420-431, 2009.

2008

  1. 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.

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

  3. Holub J. (editor): Special Issue: Prague Stringology Conference 2006 (PSC'06), International Journal of Foundations of Computer Science, Vol. 19, No. 1, 2008.

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

2007

  1. 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, pp. 115-133, 2007.

  2. Holub J. (editor): Special Issue, Journal of Automata, Languages and Combinatorics, Vol. 10, No. 5/6, 2005, (printed in 2007).

  3. Holub J.: Finite Automata Implementations Considering CPU Cache. In Acta Polytechnica, Vol. 47, No. 6, pp. 51-55, 2007.

  4. Holub J., Žďárek J. (editors): Pre-proceedings of CIAA 2007. Czech Technical University in Prague, Prague, July 16-18, 2007, 284 pages, ISBN 978-80-01-03764-5, 2007.

  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.

2006

  1. 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 11th International Conference on Implementation and Application of Automata (CIAA2006), National Taiwan University, Taipei, Taiwan, LNCS 4094, Springer-Verlag, pp. 69-77, 2006.

  2. Holub J. (editor): Special Issue: Prague Stringology Conference 2005, International Journal of Foundations of Computer Science, Vol. 17, No. 6, 2006.

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

2005

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

  2. 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 16th Australasian Workshop on Combinatorial Algorithms AWOCA'05, University of Ballarat, Victoria, Australia, pp. 415-428, 2005.

  3. Holub J., Šimánek M. (editors): Proceedings of the Prague Stringology Conference '05. Czech Technical University in Prague, Prague, September 2005.

2004

  1. 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, pp. 89-94, 2004.

  2. Holub J., Šimánek M. (editors): Proceedings of the Prague Stringology Conference '04. Czech Technical University in Prague, Prague, September 2004.

  3. 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, pp. 73-95, 2004.

2003

  1. Franěk F., Holub J., Smyth W. F., Xiao X.: Computing Quasi Suffix Arrays. Journal of Automata, Languages and Combinatorics, Vol. 8, No. 4, Otto-von-Guericke University, Magdeburg, pp. 593-606, 2003.

  2. Holub J.: Dynamic Programming - NFA Simulation. Proceedings of the 7th Conference on Implementation and Application of Automata, University of Tours, Tours, France, July 2002, LNCS 2608, Springer-Verlag, pp. 295-300, 2003.

  3. Holub J. (editor): Special Issue: Selected Papers of the Prague Stringology Coference (PSC'02), Nordic Journal of Computing, Vol. 10, No. 1, 2003.

  4. Holub J., Crochemore M.: On the Implementation of Compact DAWG's. Proceedings of the 7th Conference on Implementation and Application of Automata, University of Tours, Tours, France, July 2002, LNCS 2608, Springer-Verlag, pp. 289-294, 2003.

  5. 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, 2003.

2002

  1. Holub J.: Bit Parallelism - NFA Simulation. Proceedings of the 6th Conference on Implementation and Application of Automata, University of Pretoria, Pretoria, South Africa, July 2001, LNCS 2494, Springer-Verlag, pp. 149-160, 2002.

  2. Holub J.: Dynamic Programming for Reduced NFAs for Approximate String and Sequence Matching. Kybernetika, Vol. 38 (1), pp. 81-90, 2002.

2001

  1. Holub J., Iliopoulos 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, pp. 191-204, 2001.

2000

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

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

1999

  1. 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, Perth, Australia, pp. 114-128, 1999.

  2. 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.

  3. Holub J., Šimánek M. (editors): Proceedings of the Prague Stringology Club Workshop '99. Czech Technical University in Prague, Prague, July 1999.

  4. Melichar B., Holub J.: Algorithms for Pattern Matching. In Sborník z Letní školy Informační systémy a jejich aplikace 1999, Ruprechtov, Czech Republic, pp. 69-78, September 1999.

1998

  1. Holub J.: Simulation of Nondeterministic Finite Automata in Approximate String and Sequence Matching. Research Report DC-98-04, Czech Technical University in Prague, Prague, 28 pages, April 1998.

  2. Holub J.: Dynamic Programming for Reduced NFAs for Approximate String and Sequence Matching. Proceedings of the Prague Stringology Club Workshop '98, Czech Technical University in Prague, Prague, pp. 73-82, September 1998.

  3. 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, Perth, West Australia, pp. 28-39, July 1998.

  4. Holub J., Šimánek M. (editors): Proceedings of the Prague Stringology Club Workshop '98. Czech Technical University in Prague, Prague, September 1998.

  5. Melichar B., Holub J.: Pattern Matching and Finite Automata. In Sborník z Letní školy Informační systémy a jejich aplikace 1998, Ruprechtov, Czech Republic, pp. 154-183, September 1998.

1997

  1. Holub J. (editor): Proceedings of the Prague Stringology Club Workshop '97. Czech Technical University in Prague, Prague, 68 pages, July 1997.

  2. Holub J.: Simulation of NFA in Approximate String and Sequence Matching. Proceedings of the Prague Stringology Club Workshop '97, Czech Technical University in Prague, Prague, pp. 39-46, July 1997.

  3. Melichar B., Holub J.: 6D Classification of Pattern Matching Problems. Proceedings of the Prague Stringology Club Workshop '97, Czech Technical University in Prague, Prague, pp. 24-32, July 1997.

  4. Melichar B., Holub J., Mužátko P.: Languages and Translations. Czech Technical University in Prague, Prague, 143 pages, textbook, November 1997.

1996

  1. Holub J. (editor): Proceedings of the Prague Stringology Club Workshop '96. Czech Technical University in Prague, Prague, 83 pages, August 1996.

  2. Holub J.: Reduced Nondeterministic Finite Automata for Approximate String Matching. Proceedings of the Prague Stringology Club Workshop '96, Czech Technical University in Prague, Prague, pp. 19-27, August 1996.