## Jan Holub |

*professor*

Department of Theoretical Computer Science

Faculty of Information Technology

Czech Technical University in Prague

Thákurova 2700/9

160 00 Prague 6

Czech Republic

Faculty of Information Technology

Czech Technical University in Prague

Thákurova 2700/9

160 00 Prague 6

Czech Republic

phone:
(+420) 224 359 814,
(+420) 224 359 876
(secretary)

fax: (+420) 224 353 600

e-mail: Jan.Holub@fit.cvut.cz

schedule on CTU FIT office: A-1235 location in a map

fax: (+420) 224 353 600

e-mail: Jan.Holub@fit.cvut.cz

schedule on CTU FIT office: A-1235 location in a map

online office hours: By appointment only.

## Education

**Professor**in Computer Engineering and Informatics, Brno University of Technology, September 2014**Associate Professor**(Doc.) in Computer Engineering and Informatics, CTU FEE, November 2008- Postdoctoral studies, McMaster University, Ontario, Canada, July 2002 - July 2003, supervisor: prof. W. F. Smyth and prof. F. Franěk
**Ph.D.**in Informatics and Computer Science, DCSE, CTU FEE, September 2000, thesis supervisor: prof. B. Melichar**M.Sc.**(Ing.) in Computer Engineering, DCSE, CTU FEE, February 1996, thesis supervisor: prof. B. Melichar

## Research Interests

- Bioinformatics
- Stringology (design of string and sequence processing algorithms)
- Pattern Matching
- Self-Index

- Data Compression
- Efficient Data Structures for Bioinformatics
- Natural Language Text Compression

- Finite automata theory
- Simulation of nondeterministic finite automata

## Teaching Experience

### Supervision of study program/branch

- master study program Informatics (FIT CTU in Prague) - guarantor since 2017
- System Programming, focused on System Programming - 1801T047 (FIT CTU in Prague) - supervisor of the branch in master study program Informatics, CTU FIT
- bachelor study program Chemical Informatics and Bioinformatics (FIT CTU in Prague and UCT) - study coordinator for computer science
- master study program Chemical Informatics and Bioinformatics (FIT CTU in Prague and UCT) - study coordinator for computer science

### Currently running

- Data Compression (NI-KOD, NIE-KOD (in English), graduate course, CTU FIT)

### All

- Automata and Grammars (BI-AAG, BIE-AAG, undergraduate course, CTU FIT)
- Electronic Documentation Design (BI-TED, BIE-TED (in English), undergraduate course, CTU FIT)
- Introduction to Computers and Programming I (undergraduate course, CTU FEE)
- Introduction to Computers and Programming II (undergraduate course, CTU FEE)
- Languages and Translations (36JPR, E36JPR (in English), undergraduate course, CTU FEE)
- Programming Languages and Compilers (X36PJP, undergraduate course, CTU FEE)
- Programming in the C++ Language (X36PJC, undergraduate course, CTU FEE)
- Programming Techniques (E36PT (in English), undergraduate course, CTU FEE)

- Efficient Pattern Matching (NI-EVY, NIE-EVY, graduate course, CTU FIT)
- Data Compression (NI-KOD, NIE-KOD (in English), graduate course, CTU FIT)
- Data Compression (X36KOD, XE36KOD (in English), XD36KOD, graduate course, CTU FEE)
- Languages and Translations (X36JPR, XD36JPR, graduate course, CTU FEE)
- Compiler Construction (36TPR, graduate course, CTU FEE)
- Programming Languages (36PJ, graduate course, CTU FEE)
- Text Algorithms (36TAL, graduate course, CTU FEE)
- Text Information Systems (36TIS, E36TIS (in English), graduate course, CTU FEE, since year 2005/2006 replaced by Text Algorithms and Data Compression)

## Supervision

Several advices for writing theses (in Czech).### Ph.D. students

- Dominika Draesslerová
- Luboš Krčál,
*Randomized Indexing for Approximate Selection Queries on Multidimensional Arrays*(defended in November 2022) - Shibsankar Das, visiting Ph.D. student (September 2013 - March 2014)
- Petr Procházka,
*Natural Language Compression using Byte Codes*(defended in September 2014, awarded by "Rector's 2nd Grade Prize for Excellent Dissertation Thesis" and "Werner von Siemens Prize for the Best Dissertation Thesis") - Michal Voráček,
*Algorithms on Generalized Strings*(defended in March 2011)

### MSc. students

- Dominika Draesslerová,
*Bioinformatics Index Tool for Elastic Degenerate String Matching*(graduated in February 2023) - Jakub Kulík,
*PPM Data Compression Method using de Bruijn Graphs*(graduated in February 2019) - Jan Navara,
*Compression of Natural Czech Text*(graduated in February 2017) - Ondřej Cvacho,
*Searching for CRISPR Segments using Self-index*(graduated in June 2016) - Ondřej Fiedler,
*Parallel Lossless Data Compression*(graduated in June 2016, Dean's Prize for Excellent Diploma Thesis awarded) - Lukáš Hrbek,
*Approximate String Matching for Self-Indexes*(graduated in June 2015, Dean's Prize for Excellent Diploma Thesis awarded) - Ondřej Perutka,
*Compressing and Indexing Highly Similar Strings using LZW*(graduated in June 2015, Dean's Prize for Excellent Diploma Thesis awarded) - Luboš Krčál,
*Incremental Clustering-Based Compression*(graduated in June 2014, Dean's Prize for Excellent Diploma Thesis awarded, 2. place award in ICT Master Thesis 2014 in section "Business Information Systems and Other IT Thesis", finals in ACM SPY 2014) - Jiří Krotil,
*PPM Data Compresssion Methods*(graduated in June 2012, Dean's Prize for Excellent Diploma Thesis awarded) - Jan Baier,
*Music Sheet Compression*(graduated in February 2012) - Michal Valach,
*Effient Implementation of ACB Compression Algorithm for ExCom Library*(graduated in June 2011) - Martin Kopta,
*Efficient DNA Indexing*(graduated in June 2011) - Jan Skalický,
*On Applications of DCA*(graduated in June 2010) - Jakub Řezníček,
*Corpus for Comparing Compression Methods and an Extension of ExCom Library*(graduated in June 2010, Dean's Prize for Excellent Diploma Thesis awarded) - Filip Šimek,
*C++ Library of Data Compression Algorithms*(graduated in June 2009, Dean's Prize for Excellent Diploma Thesis awarded) - Jakub Jaroš,
*Word-based Dictionary Data Compression Methods*(graduated in June 2008) - Martin Kočica,
*Comparison of Losless Data Compression Algorithms*(graduated in June 2008) - Petr Procházka,
*Word-based Statistical Data Compression Methods*(graduated in June 2008, Dean's Prize for Excellent Diploma Thesis awarded) - Tomáš Lakatos,
*FM-Index Implementation*(graduated in February 2008) - Stanislav Štekr,
*Simulation of Finite Automata on Parallel Computers*(graduated in February 2008) - Petr Abraham,
*Library for Indexing Structures*(graduated in June 2007) - Martin Fiala,
*Implementation of DCA Compression Method*(graduated in June 2007, Dean's Prize for Excellent Diploma Thesis awarded, 4.-5. place in IT Master Thesis of the Year competition) - Pavel Vedra,
*Finite Automata Manipulation Tool*(graduated in June 2007) - Tomáš Kadlec,
*Deterministic State Cache*(graduated in February 2007) - Tomáš Mlčoch,
*Evolutive Pattern Retrieval using Suffix Automaton*(graduated in February 2007) - Milan Kynzl,
*NFA Simulation with Fail Function*(graduated in June 2006) - Zuzana Škodová,
*Evolutive Pattern Matching*(graduated in February 2006, Dean's Prize for Excellent Diploma Thesis awarded) - Petr Špiller,
*Selection of Optimum Simulation Method*(graduated in February 2004)

### Bc. students

- Jan Opravil,
*Editor of Phraseology Dictionary*(graduated in September 2008)

## Activities

**PSC 2024, IT SPY 2024 (local info in Czech)**

**PSC 2023, CPM 2023, IT SPY 2023**

**CPM 2022, CIAA 2022, IT SPY 2022**

- The Prague Stringology Club (research group)
- Research Center for Informatics (OP VVV MEYS funded project)

### Conferences:

- The Prague Stringology Conference (annual conference since 1996) - member of Program Committee and Organizing Committee, chair since 2006
- Annual Symposium on Combinatorial Pattern Matching: CPM 2013, CPM 2017 - member of Program Committee
- Annual Symposium on Combinatorial Pattern Matching: CPM 2022 - chair of Program Committee
- Finite-State Methods and Natural Language Processing: FSMNLP 2011, FSMNLP 2012 - member of Program Committee
- String Processing and Information Retrieval Symposium: SPIRE 2008, SPIRE 2011, SPIRE 2012, SPIRE 2017 - member of Program Committee
- International Conference on Implementation and Application of Automata: CIAA 2006, CIAA 2008, CIAA 2009, CIAA 2011, CIAA 2013, CIAA 2021 - member of Program Committee
- International Conference on Implementation and Application of Automata: CIAA 2007 - chair of Program Committee
- International Symposium on Mathematical Foundation of Computer Science: MFCS 2015 - member of Program Committee
- International Workshop on Combinatorial Algorithms: IWOCA 2009, IWOCA 2010, IWOCA 2011, IWOCA 2012, IWOCA 2013, IWOCA 2014, IWOCA 2019 - member of Program Committee
- Lab Surfing workshop: Lab Surfing workshop 2015 - member of Program Committee
- Workshop on Algorithms in Molecular Biology: ALBIO 2008 - member of Program Committee

### Other:

- chair (since 2019) and member (2015-2018) of WG 1.10 – String Algorithmics & Applications in TC 1 - Foundations of Computer Science of International Federation for Information Processing (IFIP)
- guest editor in Discrete Applied Mathematics, Theoretical Computer Science, International Journal of Foundations of Computer Science, Nordic Journal of Computing, and Journal of Automata, Languages and Combinatorics
- IT Student Project of the Year (IT SPY 2017-2021) - member of evaluation committee
- Czech ACM Chapter & Slovakia ACM Chapter Student Project of the Year (ACM SPY 2013, 2014) - chair of evaluation committee
- Czech ACM Chapter & Slovakia ACM Chapter Student Project of the Year (ACM SPY 2010-2012, 2015) - member of evaluation committee
- Student research competition SVOČ 2010 - chair of evaluation committee in section S8 Applied Informatics
- courses Data Compression within ATHENS programme (Advanced Technology Higher Education Network, Socrates) - author and responsible professor (since 2006)
- courses Text Searching Algorithms within ATHENS programme (Advanced Technology Higher Education Network, Socrates) - participating professor
- chair of Study Program Council, Master study program Informatics, Faculty of Information Technology, Czech Technical University in Prague, 2017-2021
- member of Evaluation Board, Czech Science Foundation (GA ČR), 2009-2011, 2011-2013
- member of Scientific Council, Faculty of Information Technology, Czech Technical University in Prague, 2009-2021
- member of Scientific Council, Faculty of Electrical Engineering, Czech Technical University in Prague, 2015-2019
- member of Scientific Council, It4Innovations, 2017-2021
- member of Board of Doctoral Study Program Informatics, Faculty of Mathematics and Physics, Charles University, since 2015
- member of Board of Doctoral Study Program, Branch 4I2 Software Systems, Faculty of Mathematics and Physics, Charles University, since 2012
- member of Doctoral Thesis Defence Board, Faculty of Mathematics and Physics, Charles University, since 2011

## Visits

- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, Pennsylvania, USA: September 5, 2016 - February 5, 2017; Fulbright Scholar

- Department of Computer Science, Aalto University, Espoo, Finland: April 10 - July 10, 2016

- AMIB, INRIA, and Laboratoire d'Informatique, École Polytechnique, Paris, France: September 8 - October 8, 2014
- Department of Computing and Software, McMaster University, Hamilton, Ontario, Canada: February 10 - March 12, 2007
- Department of Computing and Software, McMaster University, Hamilton, Ontario, Canada: July 8, 2002 - July 8, 2003
- School of Computing, Curtin University, Perth, Western Australia: August 13 - August 31, 1999
- Gaspard Monge Institute, Université Paris-Est Marne-la-Vallée, Paris, France: May 3 - June 17, 1999
- Gaspard Monge Institute, Université Paris-Est Marne-la-Vallée, Paris, France: November 1 - December 15, 1998

## Selected Publications

Scopus, ORCID, DBLP, Microsoft Academics, Google Scholar, CSB, CiteSeer, Erdös Number(Jan Holub)=2### 2023

- Procházka P., Cvacho O., Krčál L., Holub J.:
**Backward Pattern Matching on Elastic‐Degenerate Strings**.*SN Computer Science*Vol. 4(5), Article 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 2021), 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 S., 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.

### 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. - 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

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

### 2014

- Holub J. (editor):
**Special Issue: Stringology Algorithms**.*Discrete Applied Mathematics*, Vol. 163, Part 3, 2014. ISSN 0166-218X. - Holub J., Žďárek J. (editors):
**Proceedings of the Prague Stringology Conference 2014**. Czech Technical University in Prague, Prague, August 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

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

- Holub J.:
**The Finite Automata Approaches for Bioinformatics**(invited talk). In F. Mráz (ed.): Proceedings of Theorietag 2012, pp. 1-2, 2012. - Holub J.:
**The Finite Automata Approaches in Stringology**.*Kybernetika*, Vol. 48 (3), pp. 386-401, 2012. - Holub J. (editor):
**Special Issue - Prague Stringology Conference**,*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.

### 2011

- 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. - 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, 2011.

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

- 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. - 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: Implementation and Application of Automata (CIAA 2007)**,*Theoretical Computer Science*, Elsevier, Vol. 410, No. 37, 2009. - Holub J. (editor):
**Special Issue - Prague Stringology Conference 2008**,*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. - 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

- 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. - 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. - Holub J. (editor):
**Special Issue: Prague Stringology Conference 2006 (PSC'06)**,*International Journal of Foundations of Computer Science*, Vol. 19, No. 1, 2008. - Holub J., Žďárek J. (editors):
**Proceedings of the Prague Stringology Conference 2008**. Czech Technical University in Prague, Prague, August 2008.

### 2007

- 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. - Holub J. (editor):
**Special Issue**,*Journal of Automata, Languages and Combinatorics*, Vol. 10, No. 5/6, 2005, (printed in 2007). - Holub J.:
**Finite Automata Implementations Considering CPU Cache**. In*Acta Polytechnica*, Vol. 47, No. 6, pp. 51-55, 2007. - 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. - 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

- 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, LNCS 4094, Springer-Verlag, pp. 69-77, 2006. - Holub J. (editor):
**Special Issue: Prague Stringology Conference 2005**,*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.

### 2005

- Holub J. (editor):
**Special Issue: Prague Stringology Conference**,*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, pp. 415-428, 2005. - Holub J., Šimánek M. (editors):
**Proceedings of the Prague Stringology Conference '05**. Czech Technical University in Prague, Prague, September 2005.

### 2004

- 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. - 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, pp. 73-95, 2004.

### 2003

- 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. - 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, 2003. - Holub J. (editor):
**Special Issue: Selected Papers of the Prague Stringology Coference (PSC'02)**,*Nordic Journal of Computing*, Vol. 10, No. 1, 2003. - 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, 2003. - Holub J., Smyth W. F.:
**Algorithms on Indeterminate Strings**. In Miller M., Park K. (eds.): Proceedings of the 14^{th}Australasian Workshop on Combinatorial Algorithms AWOCA'03, Seoul National University, Seoul, Korea, pp. 36-45, 2003.

### 2002

- Holub J.:
**Bit Parallelism - NFA Simulation**. Proceedings of the 6^{th}Conference on Implementation and Application of Automata, University of Pretoria, Pretoria, South Africa, July 2001, LNCS 2494, Springer-Verlag, pp. 149-160, 2002. - Holub J.:
**Dynamic Programming for Reduced NFAs for Approximate String and Sequence Matching**.*Kybernetika*, Vol. 38 (1), pp. 81-90, 2002.

### 2001

- 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

- Holub J.:
**Simulation of Nondeterministic Finite Automata in Pattern Matching**. Ph.D. thesis, Czech Technical University in Prague, Prague, p. 118, February 2000. - Holub J., Melichar B.:
**Approximate String Matching using Factor Automata**.*Theoretical Computer Science*, Vol. 249 (2), Elsevier Science, pp. 305-311, 2000.

### 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, Perth, Australia, pp. 114-128, 1999. - 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**. Czech Technical University in Prague, Prague, July 1999. - Melichar B., Holub J.:
**Algorithms for Pattern Matching**. In Proceedings of Summer School of Information Systems and Their Applications 1999, Ruprechtov, Czech Republic, pp. 69-78, September 1999.

### 1998

- 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. - 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. - 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. - Holub J., Šimánek M. (editors):
**Proceedings of the Prague Stringology Club Workshop '98**. Czech Technical University in Prague, 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, pp. 154-183, September 1998.

### 1997

- Holub J. (editor):
**Proceedings of the Prague Stringology Club Workshop '97**. Czech Technical University in Prague, Prague, 68 pages, July 1997. - 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. - 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. - Melichar B., Holub J., Mužátko P.:
**Languages and Translations**. Czech Technical University in Prague, Prague, 143 pages, textbook, November 1997.

### 1996

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