Publications

Papers in Refereed Journals and Conferences

  1. J. Zhang, I. McQuillan, and FangXiang Wu. Speed improvements of peptide-spectrum matching using single-instruction multiple-data instructions. Proteomics, 11(19):3779–3785, 2011.
  2. J. Zhang, I. McQuillan, and FangXiang Wu. Parallelizing peptide-spectrum scoring using modern graphics processing units. In 1st IEEE International Conference on Computational Advances in Bio and medical Sciences, 2011. Accepted.
  3. M. Daley, F. Biegler, and I. McQuillan. On the shuffle automaton size for words. Journal of Automata, Languages and Combinatorics, 15:53–70, 2010.
  4. J. Zhang, I. McQuillan, and FangXiang Wu. Speed improvements of peptide-spectrum matching using SIMD instructions. In IEEE BIBM2010 International Workshop on Computational Proteomics, 2010. Accepted.
  5. M. Keil, J. Liu, and I. McQuillan. Algorithmic properties of ciliate sequence alignment. Theoretical Computer Science, 411:919–925, 2010.
  6. M. Daley, I. McQuillan, J. McQuillan, and K. Mahalingam. Theoretical and computational properties of transpositions. Natural Computing, pages 1–10, 2010. 
  7. M. Daley and I. McQuillan. Modelling programmed frameshifting with frameshift machines. Natural Computing, 9(1):239–261, 2009.
  8. H. Jürgensen and I. McQuillan. Homomorphisms preserving types of density. Acta Cybernetica, 19:499–516, 2009.
  9. F. Biegler, M. Daley, and I. McQuillan. On the shuffle automaton size for words. In Jürgen Dassow, Giovanni Pighizzini, and Bianca Truthe, editors, Proceedings of the 11th International Workshop on Descriptional Complexity of Formal Systems, pages 115–126, Magdeburg, Germany, 2009.
  10. F. Biegler, M. Daley, M. Holzer, and I. McQuillan. On the uniqueness of shuffle on words and finite languages. Theoretical Computer Science, 410:3711–3724, 2009.
  11. M. Daley, M. Eramian, and I. McQuillan. The bag automaton: A model of nondeterministic storage. Journal of Automata, Languages and Combinatorics, 13(3/4): 185–206, 2008.
  12. H. Jürgensen and I. McQuillan. Homomorphisms preserving types of density. In Erzsébet Csuhaj-Varjú and Zoltán Ésik, editors, Proceedings of the 12th International Conference on Automata and Formal Languages, pages 183–194, Balatonfüred, Hungary, 2008. Computer and Automation Research Institute, Hungarian Academy of Sciences.
  13. C. Power, I. McQuillan, H. Petrie, P. Kennaugh, M. Daley, and G. Wozniak. No going back: an interactive visualization application for trailblazing on the web. InProceedings of the 12th International Conference on Information Visualisation (IV08), pages 133–142, London, UK, 2008. Los Alamitos, CA: IEEE Computer Society/CPS Publishing.
  14. M. Daley, I. McQuillan, and J. McQuillan. 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.
  15. F. Biegler, I. McQuillan, and K. Salomaa. An infinite hierarchy induced by depth synchronization. Theoretical Computer Science, 387(2):113–124, 2007.
  16. M. Daley and I. McQuillan. Useful templates and iterated template-guided DNA recombination in ciliates. Theory of Computing Systems, 39(5):619–633, 2006.
  17. F. Biegler, I. McQuillan, and K. Salomaa. An infinite hierarchy induced by depth synchronization. In H. Leung and G. Pighizzini, editors, the Eighth International Workshop on Descriptional Complexity of Formal Systems, Las Cruces, New Mexico, Proceedings, pages 82–93. Computer Science, New Mexico State University, 2006.
  18. I. McQuillan, K. Salomaa, and M. Daley. Iterated TGR languages: Membership problem and effective closure properties. In Lecture Notes in Computer Science, volume 4112 of the Twelfth Annual International Computing and Combinatorics Conference (COCOON 2006), pages 94–103, 2006.
  19. M. Daley and I. McQuillan. On computational properties of template-guided DNA recombination. In A. Carbone and N. Pierce, editors, Lecture Notes in Computer Science, volume 3892 of Proceedings of DNA computing, pages 27–37. Springer-Verlag, 2006.
  20. M. Daley and I. McQuillan. Frameshift machines: Translation as transduction. In Proceedings of IEEE International Conference on Computational Intelligence, Robotics and Autonomous Systems (CIRAS), Special session on Biomolecular Computers and Other Bio-Inspired Systems, ISBN: 0219–6131. Research Studies Press U.K., 2005.
  21. M. Daley and I. McQuillan. Formal modelling of viral gene compression. International Journal of Foundations of Computer Science, 16(3):453–469, 2005. Listed as third most accessed article for this journal for that year.
  22. I. McQuillan. The generative capacity of block-synchronized context-free grammars. Theoretical Computer Science, 337:119–133, 2005.
  23. M. Daley and I. McQuillan. Template-guided DNA recombination. Theoretical Computer Science, 330(2):237–250, 2005. Listed in top 25 most downloaded articles for 6 months.
  24. M. Daley and I. McQuillan. Viral gene compression: complexity and verification. In M. Domaratzki, A. Okhotin, K. Salomaa, and S. Yu, editors, Lecture Notes in Computer Science, volume 3317 of Conference on Implementation and Application of Automata (CIAA 2004), pages 102–112. Springer-Verlag, 2005.
  25. M. Daley, L. Kari, and I. McQuillan. Families of languages defined by ciliate bio-operations. Theoretical Computer Science, 320:51–69, 2004.
  26. I. McQuillan. Descriptional complexity of block-synchronization context-free grammars. 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.
  27. M. Daley and I. McQuillan. Template-guided DNA recombination. In E. Csuhaj-Varjú, C. Kintala, D. Wotschke, and Gy. Vaszil, editors, 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.
  28. M. Daley, M. Eramian, and I. McQuillan. Bag automata and stochastic retrieval of biomolecules from solution. In Lecture Notes in Computer Science, volume 2759 ofConference on Implementation and Application of Automata (CIAA 2003), pages 239–250. Springer-Verlag, 2003.
  29. M. Daley, O. Ibarra, L. Kari, I. McQuillan, and K. Nakano. Closure and decision properties of some language classes under ld and dlad bio-operations. Journal of Automata, Languages and Combinatorics, 8:477–498, 2003.
  30. I. McQuillan. Descriptional complexity of block-synchronization context-free grammars. In J. Dassow, M. Hoeberechts, J. Jürgensen, and D. Wotschke, editors,Descriptional Complexity of Formal Systems (DCFS) Pre-Proceedings of a Workshop, pages 188–203, London, Canada, 2002. Department of Computer Science, University of Western Ontario. Report No. 586.