Refereed Publications

Journal and refereed conference papers are both listed. For conference papers where an extended journal version exists, the keyword [JOURNAL] is written.

2019

  1. Maleki, F.; Ovens, K.; McQuillan, I. and Kusalik, Anthony. J. Size matters: How sample size affects the reproducibility and specificity of gene set analysis. In BMC Human Genomics, accepted, 2019.
  2. Ibarra, O. H. and McQuillan, I. On Families of Full Trios Containing Counter Machine Languages. In Theoretical Computer Science, accepted, 2019.
  3. D'Alessandro, F.; Ibarra, O. H. and McQuillan, I. On Finite-index indexed grammars and their restrictions. In Information and Computation, accepted, 2019.
  4. Maleki, F.; Ovens, K.; McQuillan, I.; Rezaei, E.; Rosenberg, A. M. and Kusalik, Anthony. J. Gene Set Databases: A Fountain of Knowledge or a Siren Call?. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, pages 269-278, ACM-BCB 2019 , 2019.
  5. Ibarra, O. H. and McQuillan, I. On Store Languages and Applications. In Information and Computation, 267: 28-48, 2019.
  6. Ibarra, O. H. and McQuillan, I. State Grammars with Stores. In Theoretical Computer Science, TBA, 2019.
  7. Ibarra, O. H.; McQuillan, I. and Ravikumar, B. On Counting Functions and Slenderness of Languages. In Theoretical Computer Science, 777: 356-378, 2019. pdf 
  8. Eremondi, J.; Ibarra, O. H. and McQuillan, I. Insertion Operations on Deterministic Reversal-Bounded Counter Machines. In Journal of Computer and System Sciences, 104: 244-257, 2019. pdf 

2018

  1. Maleki, F.; Ovens, K.; McQuillan, I. and Kusalik, Anthony. J. Sample Size and Reproducibility of Gene Set Analysis bf [JOURNAL]. In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pages 122-129, 2018. pdf 
  2. Jin, L. and McQuillan, I. Prediction of transposable elements evolution using tabu search. In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pages 665-670, 2018. pdf 
  3. Bernard, J. and McQuillan, I. Inferring Stochastic L-systems Using a Hybrid Greedy Algorithm. In 2018 IEEE 30th International Conference on Tools with Artificial Intelligence (ICTAI), pages 600-607, 2018. pdf 
  4. Bernard, J. and McQuillan, I. A Fast and Reliable Hybrid Approach for Inferring L-Systems. In Proceedings of the 2018 Conference on Artificial Life (ALIFE 2018), MIT Press, pages 444-451, 2018. pdf 
  5. McQuillan, I.; Bernard, J. and Prusinkiewicz, P. Algorithms for Inferring Context-Sensitive L-Systems. In Lecture Notes in Computer Science, pages 117-130, Proceedings of the 17th International Conference on Unconventional Computation and Natural Computation, UCNC 2018 10867, 2018. pdf 
  6. Bernard, J. and McQuillan, I. New Techniques for Inferring L-systems Using Genetic Algorithm. In Lecture Notes in Computer Science, pages 13-25, Proceedings of the 8th International Conference on Bioinspired Optimization Methods and Their Applications, BIOMA 2018 10835, 2018. pdf 
  7. Ibarra, O. H. and McQuillan, I. Semilinearity of Families of Languages. In Lecture Notes in Computer Science, pages 211-222, Proceedings of the 23rd International Conference on Implementation and Application of Automata, CIAA 2018 10977, 2018.
  8. Ibarra, O. H. and McQuillan, I. Generalizations of Checking Stack Automata: Characterizations and Hierarchies. In Lecture Notes in Computer Science, pages 416-428, Proceedings of the 22nd International Conference on Developments in Language Theory, DLT 2018 11088, 2018.
  9. Ibarra, O. H.; McQuillan, I. and Ravikumar, B. On Counting Functions of Languages [JOURNAL]. In Lecture Notes in Computer Science, pages 429-440, Proceedings of the 22nd International Conference on Developments in Language Theory, DLT 2018 11088, 2018.
  10. Ibarra, O. H. and McQuillan, I. State Grammars with Stores bf [JOURNAL]. In Lecture Notes in Computer Science, pages 163-174, Proceedings of the 20th International Workshop on Descriptional Complexity of Formal Systems, DCFS 2018 10952, 2018.
  11. Zahan, R.; McQuillan, I. and Osgood, N. D. DNA Methylation Data to Predict Suicidal and Non-Suicidal Deaths: A Machine Learning Approach. In Proceedings of the Sixth IEEE International Conference on Healthcare Informatics, ICHI 2018, pages 363-365, 2018.
  12. Ibarra, O. H. and McQuillan, I. On Store Languages of Language Acceptors. In Theoretical Computer Science, 745: 114-132, 2018. pdf 
  13. Ibarra, O. H. and McQuillan, I. Variations of Checking Stack Automata: Obtaining Unexpected Decidability Properties. In Theoretical Computer Science, 738: 1-12, 2018. pdf 
  14. Ibarra, O. H. and McQuillan, I. Reversibility and Universality: Essays Presented to Kenichi Morita on the Occasion of his 70th Birthday. pdf  doi 
  15. Daley, M.; Eramian, M.; Power, C. and McQuillan, I. From Helmut Jürgensen's Former Students: The Game of Informatics Research. In Journal of Automata, Languages and Combinatorics, 23: 127-141, 2018. pdf 
  16. Ibarra, O. H. and McQuillan, I. On the Density of Languages Accepted by Turing Machines and Other Machine Models. In Journal of Automata, Languages and Combinatorics, 23: 189-199, 2018. pdf 
  17. Eremondi, J.; Ibarra, O. H. and McQuillan, I. On the Density of Context-Free and Counter Languages. In International Journal of Foundations of Computer Science, 29 (2): 233-250, 2018. pdf 
  18. Eremondi, J.; Ibarra, O. H. and McQuillan, I. On the Complexity and Decidability of Some Problems Involving Shuffle. In Information and Computation, 259: 214-224, 2018. pdf 

2017

  1. Jin, L. and McQuillan, I. Computational Identification of Harmful Mutation Regions to the Activity of Transposable Elements. In BMC Genomics, 18: 862, 2017. pdf 
  2. Ibarra, O. H. and McQuillan, I. Variations of Checking Stack Automata: Obtaining Unexpected Decidability Properties [JOURNAL]. In Lecture Notes in Computer Science, pages 235-246, 21st International Conference on Developments in Language Theory, DLT 2017, Li`ege, Belgium 10396, 2017.
  3. D'Alessandro, F.; Ibarra, O. H. and McQuillan, I. On Finite-index indexed grammars and their restrictions bf [JOURNAL]. 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.
  4. Khan, N. and McQuillan, I. Descrambling Order Analysis in Ciliates. In Lecture Notes in Computer Science, pages 206-219, 16th International Conference on Unconventional and Natural Computation, UCNC 2017, Fayetteville, USA 10240, 2017. pdf 
  5. Islam, T.M. R. and McQuillan, I. CSA-X: Modularized Constrained Multiple Sequence Alignment. In Lecture Notes in Computer Science, pages 143-154, 4th International Conference on Algorithms for Computational Biology, AlCob 2016, Aveiro, Portugal 10252, 2017. pdf 
  6. Eremondi, J.; Ibarra, O. H. and McQuillan, I. Deletion Operations on Deterministic Families of Automata. In Information and Computation, 256: 237-252, 2017. pdf 

2016

  1. Jin, L. and McQuillan, I. Computational Identification of Regions that Influence Activity of Transposable Elements in the Human Genome [JOURNAL]. In Proceedings of the International Conference on Bioinformatics and Biomedicine, 2016, pages 592-599, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Shenzhen, China , 2016.
  2. Ibarra, O. H. and McQuillan, I. The effect of end-markers on counter machines and commutativity. In Theoretical Computer Science, 627 (C): 71-81, 2016. pdf 
  3. Macdonald, P.; McQuillan, D. and McQuillan, I. Run for Third! A defense of Aggressive Base Running. In Math Horizons, 23 (4): 14-15, 2016.
  4. Ibarra, O. H. and McQuillan, I. On Families of Full Trios Containing Counter Machine Languages bf [JOURNAL]. 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.
  5. Ibarra, O. H. and McQuillan, I. 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.
  6. Jin, L. and McQuillan, I. Computational Modelling of Interruptional Activities Between Transposable Elements Using Grammars and the Linear Ordering Problem. In Soft Computing, 20: 19-35, 2016. pdf 

2015

  1. Ibarra, O. H. and McQuillan, I. 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.
  2. Mahmud, Md. S. I. and McQuillan, I. Simulation of the 2JLP Gene Assembly Process 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. pdf 
  3. Eremondi, J.; Ibarra, O. H. and McQuillan, I. On the Complexity and Decidability of Some Problems Involving Shuffle [JOURNAL]. In Lecture Notes in Computer Science, pages 105-116, 17th International Workshop on Descriptional Complexity of Formal Systems, DCFS 2015, Waterloo, Canada 9118, 2015.
  4. Eremondi, J.; Ibarra, O. H. and McQuillan, I. On the Density of Context-Free and Counter Languages [JOURNAL]. In Lecture Notes in Computer Science, pages 228-239, 19th International Conference on Developments in Language Theory, DLT 2015, Liverpool, UK 9168, 2015.
  5. Eremondi, J.; Ibarra, O. H. and McQuillan, I. Deletion Operations on Deterministic Families of Automata [JOURNAL]. 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.
  6. Eremondi, J.; Ibarra, O. H. and McQuillan, I. Insertion Operations on Deterministic Reversal-Bounded Counter Machines [JOURNAL]. 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.

2014

  1. Biegler, F. and McQuillan, I. 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. pdf 

2013

  1. Jin, L. and McQuillan, I. Computational Modelling of the Interruptional Activities Between Transposable Elements [JOURNAL]. 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.

2012

  1. Holzer, M.; Jakobi, S. and McQuillan, I. 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. pdf 
  2. Daley, M.; Biegler, F. and McQuillan, I. Algorithmic Decomposition of Shuffle on Words. In Theoretical Computer Science, 454: 38-50, 2012. pdf 

2011

  1. Zhang, J.; McQuillan, I. and Wu, F. Speed Improvements of peptide-spectrum matching using Single-Instruction Multiple-Data instructions. In Proteomics, 11 (19): 3779-3785, 2011.
  2. Zhang, J.; McQuillan, I. and Wu, F. 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.
  3. Daley, M.; McQuillan, I.; McQuillan, J. and Mahalingam, K. Theoretical and computational properties of transpositions. In Natural Computing, 10 (2): 795-804, 2011. pdf 

2010

  1. Daley, M.; Biegler, F. and McQuillan, I. On the shuffle automaton size for words. In Journal of Automata, Languages and Combinatorics, 15: 53-70, 2010. pdf 
  2. Zhang, J.; McQuillan, I. and Wu, F. Speed Improvements of Peptide-Spectrum matching Using SIMD Instructions [JOURNAL]. In IEEE BIBM 2010 International Workshop on Computational Proteomics, pages 1-6, 2010.
  3. Keil, M.; Liu, J. and McQuillan, I. Algorithmic properties of ciliate sequence alignment. In Theoretical Computer Science, 411: 919-925, 2010. pdf 
  4. Daley, M. and McQuillan, I. Modelling programmed frameshifting with frameshift machines. In Natural Computing, 9 (1): 239-261, 2010. pdf 

2009

  1. Jürgensen, H. and McQuillan, I. Homomorphisms Preserving Types of Density. In Acta Cybernetica, 19: 499-516, 2009.
  2. Biegler, F.; Daley, M. and McQuillan, I. On the shuffle automaton size for words [JOURNAL]. In Proceedings of the 11th International Workshop on Descriptional Complexity of Formal Systems, pages 115-126, Magdeburg, Germany, 2009.
  3. Biegler, F.; Daley, M.; Holzer, M. and McQuillan, I. On the uniqueness of shuffle on words and finite languages. In Theoretical Computer Science, 410: 3711-3724, 2009. pdf 

2008

  1. Daley, M.; Eramian, M. and McQuillan, I. The Bag Automaton: A Model of Nondeterministic Storage. In Journal of Automata, Languages and Combinatorics, 13 (3/4): 185-206, 2008.
  2. Jürgensen, H. and McQuillan, I. Homomorphisms Preserving Types of Density [JOURNAL]. 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.
  3. Power, C.; McQuillan, I.; Petrie, H.; Kennaugh, P.; Daley, M. and Wozniak, G. 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.

2007

  1. Daley, M.; McQuillan, I. and McQuillan, J. Theoretical and computational properties of transpositions [JOURNAL]. In Proceedings of the Language Theory in Biocomputing Workshop, in the Conference on Unconventional Computation, pages 28-38, Kingston, Canada, 2007.
  2. Biegler, F.; McQuillan, I. and Salomaa, K. An Infinite Hierarchy Induced by Depth Synchronization. In Theoretical Computer Science, 387 (2): 113-124, 2007. pdf 

2006

  1. Daley, M. and McQuillan, I. Useful Templates and Iterated Template-Guided DNA Recombination in Ciliates. In Theory of Computing Systems, 39 (5): 619-633, 2006. pdf 
  2. Biegler, F.; McQuillan, I. and Salomaa, K. An Infinite Hierarchy Induced by Depth Synchronization [JOURNAL]. In the Eighth International Workshop on Descriptional Complexity of Formal Systems, Las Cruces, New Mexico, Proceedings, pages 82-93, 2006.
  3. Daley, M. and McQuillan, I. 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.

2005

  1. Daley, M. and McQuillan, I. Frameshift Machines: Translation as Transduction [JOURNAL]. 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.
  2. Daley, M. and McQuillan, I. 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.
  3. Daley, M. and McQuillan, I. Formal Modelling of Viral Gene Compression. In International Journal of Foundations of Computer Science, 16 (3): 453-469, 2005.
  4. McQuillan, I. The Generative Capacity of Block-Synchronized Context-Free Grammars. In Theoretical Computer Science, 337: 119-133, 2005. pdf 
  5. Daley, M. and McQuillan, I. Template-Guided DNA Recombination. In Theoretical Computer Science, 330 (2): 237-250, 2005. pdf 
  6. Daley, M. and McQuillan, I. Viral gene compression: complexity and verification [JOURNAL]. In Lecture Notes in Computer Science, pages 102-112, Springer-Verlag, Conference on Implementation and Application of Automata (CIAA 2004) 3317, 2005.

2004

  1. Daley, M.; Kari, L. and McQuillan, I. Families of Languages Defined by Ciliate Bio-operations. In Theoretical Computer Science, 320: 51-69, 2004. pdf 
  2. McQuillan, I. Descriptional Complexity of Block-Synchronization Context-Free Grammars. In Journal of Automata, Languages and Combinatorics, 9 (2/3): 317-332, 2004.

2003

  1. Daley, M. and McQuillan, I. Template-Guided DNA Recombination [JOURNAL]. 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.
  2. Daley, M.; Eramian, M. and McQuillan, I. Bag Automata and Stochastic Retrieval of Biomolecules From Solution [JOURNAL]. In Lecture Notes in Computer Science, pages 239-250, Springer-Verlag, Conference on Implementation and Application of Automata (CIAA 2003) 2759, 2003.
  3. Daley, M.; Ibarra, O. H.; Kari, L.; McQuillan, I. and Nakano, K. 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.

2002

  1. McQuillan, I. Descriptional Complexity of Block-Synchronization Context-Free Grammars [JOURNAL]. In Descriptional Complexity of Formal Systems (DCFS) Pre-Proceedings of a Workshop, pages 188-203, London, Canada, 2002.