- On Finite-index indexed grammars and their restrictions. In Lecture Notes in Computer Science, pages 287-298, 11th International Conference on Language and Automata Theory and Applications, LATA 2017, Umeå, Sweden, Proceedings 10168, 2017,
**Won the Springer Best Paper Award for LATA 2017 out of 31 accepted papers**. - Descrambling Order Analysis in Ciliates. In Lecture Notes in Computer Science, pages 15 pages, 16th International Conference on Unconventional and Natural Computation, UCNC 2017, Fayetteville, USA TBA, 2017.
- CSA-X: Modularized Constrained Multiple Sequence Alignment. In Lecture Notes in Computer Science, pages 1-12, 4th International Conference on Algorithms for Computational Biology, AlCob 2016, Aveiro, Portugal TBA, 2017, Accepted.
- On the Density of Context-Free and Counter Languages. In
*International Journal of Foundations of Computer Science*, TBA: 1-18, 2017, Accepted. - On the Complexity and Decidability of Some Problems Involving Shuffle. In
*Information and Computation*, TBA: 1-14, 2017, Accepted. - Deletion Operations on Deterministic Families of Automata. In
*Information and Computation*, TBA: 1-20, 2017, Accepted.

- Computational Identification of Regions that Influence Activity of Transposable Elements in the Human Genome. In Proceedings of the International Conference on Bioinformatics and Biomedicine, 2016, pages 1-8, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Shenzhen, China , 2016.
- The effect of end-markers on counter machines and commutativity. In
*Theoretical Computer Science*, 627 (C): 71-81, 2016. - On Families of Full Trios Containing Counter Machine Languages. In Lecture Notes in Computer Science, pages 216-228, Developments in Language Theory: 20th International Conference, DLT 2016, Montréal, Canada, July 25-28, 2016, Proceedings 9840, 2016.
- On Bounded Semilinear Languages, Counter Machines, and Finite-Index ET0L. In Lecture Notes in Computer Science, pages 138-149, Implementation and Application of Automata: 21st International Conference, CIAA 2016, Seoul, South Korea, July 19-22, 2016, Proceedings 9705, 2016.

- On Some Decision Problems Concerning Commutation, Reversal, and Palindromes. In Multidiciplinary Creativity --- Homage to Gheorghe Păun on His 65th Birthday, pages 265-277, Spandugino Publishing House, 2015, Refereed.
- Computational Modelling of Interruptional Activities Between Transposable Elements Using Grammars and the Linear Ordering Problem. In
*Soft Computing*, 454: 1-17, 2015. - A Formal Model Based on the 2JLP Model of Gene Assembly in Ciliates. In Lecture Notes in Computer Science, pages 227-238, 14th International Conference on Unconventional and Natural Computation, UCNC 2015, Auckland, New Zealand 9252, 2015.
- On the Complexity and Decidability of Some Problems Involving Shuffle. In Lecture Notes in Computer Science, pages 105-116, 17th International Workshop on Descriptional Complexity of Formal Systems, DCFS 2015, Waterloo, Canada 9118, 2015.
- On the Density of Context-Free and Counter Languages. In Lecture Notes in Computer Science, pages 228-239, 19th International Conference on Developments in Language Theory, DLT 2015, Liverpool, UK 9168, 2015.
- Deletion Operations on Deterministic Families of Automata. In Lecture Notes in Computer Science, pages 388-399, 12th Annual Conference on Theory and Applications of Models of Computation, TAMC 2015, Singapore 9076, 2015.
- Insertion Operations on Deterministic Reversal-Bounded Counter Machines. In Lecture Notes in Computer Science, pages 200-211, 9th International Conference on Language and Automata Theory and Applications, LATA 2015, Nice, France 8977, 2015.

- On comparing deterministic finite automata and the shuffle of words. In Lecture Notes in Computer Science, pages 98-109, 19th International Conference on Implementation and Application of Automata, CIAA 2014, Giessen, Germany 8587, 2014.

- Computational Modelling of the Interruptional Activities Between Transposable Elements. In Lecture Notes in Computer Science, pages 108-120, 2nd International Conference on the Theory and Practice of Natural Computing, TPNC 2014, Granada, Spain 8273, 2013.

- Generalized Derivations with Synchronized Context-Free Grammars. In Lecture Notes in Computer Science, pages 109-120, Developments in Language Theory - 16th International Conference, DLT 2012, Taipei, Taiwan 7410, 2012.
- Algorithmic Decomposition of Shuffle on Words. In
*Theoretical Computer Science*, 454: 38-50, 2012.

- Speed Improvements of peptide-spectrum matching using Single-Instruction Multiple-Data instructions. In
*Proteomics*, 11 (19): 3779-3785, 2011. - Parallelizing Peptide-Spectrum Scoring Using Modern Graphics Processing Units. In 1st IEEE International Conference on Computational Advances in Bio and medical Sciences, pages 208-213, 2011.
- Theoretical and computational properties of transpositions. In
*Natural Computing*, 10 (2): 795-804, 2011, 10.1007/s11047-010-9207-z.

- On the shuffle automaton size for words. In
*Journal of Automata, Languages and Combinatorics*, 15: 53-70, 2010. - Speed Improvements of Peptide-Spectrum matching Using SIMD Instructions. In IEEE BIBM 2010 International Workshop on Computational Proteomics, pages 1-6, 2010.
- Algorithmic properties of ciliate sequence alignment. In
*Theoretical Computer Science*, 411: 919-925, 2010. - Modelling programmed frameshifting with frameshift machines. In
*Natural Computing*, 9 (1): 239-261, 2010.

- Homomorphisms Preserving Types of Density. In
*Acta Cybernetica*, 19: 499-516, 2009. - On the shuffle automaton size for words. In Proceedings of the 11th International Workshop on Descriptional Complexity of Formal Systems, pages 115-126, Magdeburg, Germany, 2009.
- On the uniqueness of shuffle on words and finite languages. In
*Theoretical Computer Science*, 410: 3711-3724, 2009.

- The Bag Automaton: A Model of Nondeterministic Storage. In
*Journal of Automata, Languages and Combinatorics*, 13 (3/4): 185-206, 2008. - Homomorphisms Preserving Types of Density. In Proceedings of the 12th International Conference on Automata and Formal Languages, pages 183-194, Computer and Automation Research Institute, Hungarian Academy of Sciences, Balatonfüred, Hungary, 2008.
- No going back: an interactive visualization application for trailblazing on the web. In Proceedings of the 12th International Conference on Information Visualisation (IV08), pages 133-142, Los Alamitos, CA: IEEE Computer Society/CPS Publishing, London, UK, 2008.

- Theoretical and computational properties of transpositions. In Proceedings of the Language Theory in Biocomputing Workshop, in the Conference on Unconventional Computation, pages 28-38, Kingston, Canada, 2007.
- An Infinite Hierarchy Induced by Depth Synchronization. In
*Theoretical Computer Science*, 387 (2): 113-124, 2007.

- Useful Templates and Iterated Template-Guided DNA Recombination in Ciliates. In
*Theory of Computing Systems*, 39 (5): 619-633, 2006. - An Infinite Hierarchy Induced by Depth Synchronization. In the Eighth International Workshop on Descriptional Complexity of Formal Systems, Las Cruces, New Mexico, Proceedings, pages 82-93, 2006.
- Iterated TGR languages: Membership problem and effective closure properties. In Lecture Notes in Computer Science, pages 94-103, the Twelfth Annual International Computing and Combinatorics Conference (COCOON 2006) 4112, 2006.
- On Computational Properties of Template-Guided DNA Recombination. In Lecture Notes in Computer Science, pages 27-37, Springer-Verlag, Proceedings of DNA computing 3892, 2006.

- Frameshift Machines: Translation as Transduction. In Proceedings of IEEE International Conference on Computational Intelligence, Robotics and Autonomous Systems (CIRAS), Research Studies Press U.K., Special session on Biomolecular Computers and Other Bio-Inspired Systems, ISBN: 0219--6131 , 2005.
- On Computational Properties of Template-Guided DNA Recombination. In The 11th International Meeting on DNA Computing (Pre-Proceedings DNA 11), pages 211-220, London, Canada, 2005.
- Formal Modelling of Viral Gene Compression. In
*International Journal of Foundations of Computer Science*, 16 (3): 453-469, 2005, it Listed as third most accessed article for this journal for that year. - The Generative Capacity of Block-Synchronized Context-Free Grammars. In
*Theoretical Computer Science*, 337: 119-133, 2005. - Template-Guided DNA Recombination. In
*Theoretical Computer Science*, 330 (2): 237-250, 2005, it Listed in top 25 most downloaded articles for 6 months. - Viral gene compression: complexity and verification. In Lecture Notes in Computer Science, pages 102-112, Springer-Verlag, Conference on Implementation and Application of Automata (CIAA 2004) 3317, 2005.

- Viral gene compression: complexity and verification. In Pre-proceedings of CIAA 2004, Ninth International Conference on Implementation and Application of Automata, pages 71-79, Queen's University, 2004.
- Families of Languages Defined by Ciliate Bio-operations. In
*Theoretical Computer Science*, 320: 51-69, 2004. - Descriptional Complexity of Block-Synchronization Context-Free Grammars. In
*Journal of Automata, Languages and Combinatorics*, 9 (2/3): 317-332, 2004, A previous version of this manuscript appeared in the workshop for Descriptional Complexity of Formal Systems 2002..

- Template-Guided DNA Recombination. In Fifth International Workshop, Descriptional Complexity of Formal Systems, Budapest, Hungary, July 12-14, 2003, Proceedings, pages 235-244, MTA SZTAKI, the Computer and Automation Research Institute of the Hungarian Academy of Sciences, 1111 Budapest, Kendeutca 13-17, 2003.
- Bag Automata and Stochastic Retrieval of Biomolecules From Solution. In Lecture Notes in Computer Science, pages 239-250, Springer-Verlag, Conference on Implementation and Application of Automata (CIAA 2003) 2759, 2003.
- Closure and Decision Properties of Some Language Classes Under ld and dlad Bio-operations. In
*Journal of Automata, Languages and Combinatorics*, 8: 477-498, 2003.

- Descriptional Complexity of Block-Synchronization Context-Free Grammars. In Descriptional Complexity of Formal Systems (DCFS) Pre-Proceedings of a Workshop, pages 188-203, London, Canada, 2002, Report No. 586.

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