个人简介

I am an Associate Professor in the Department of Computer Science at the University of Saskatchewan. I am a member of the Bioinformatics Lab, teach as part of the Bioinformatics Program, and am an associate member of the Division of Biomedical Engineering. My main areas of research include natural computing, biological modelling and bioinformatics, formal language and automata theory, and theoretical computer science. I am a project co-lead research scientist as part of the Plant Phenotyping and Imaging Research Centre (P2IRC) for the Model-Driven Genomic-Phenomic Linkages Sub-Theme. I completed my Ph.D. in Computer Science at the University of Western Ontario. I also completed my undergraduate degree at Western in Mathematics and Computer Science. My research is currently supported by the Natural Sciences and Engineering Research Council of Canada, and the Plant Phenotyping and Imaging Research Centre (funded by CFREF). I am currently looking for a postdoctural fellow to work on plant modeling and simulation for the P2IRC project.

研究领域

Natural Computing Computational and Mathematical Modelling of Biological Systems Bioinformatics Formal Language and Automata Theory Theoretical Computer Science Data Analytics

Most of my research falls into the areas of Natural Computing, Biological Modelling, and Theoretical Computer Science. I am currently working on several interesting biological models that often involve the use of modelling, bioinformatics, and mathematical analysis. Some examples include the analysis and simulation of transposable elements, the modelling and simulation of plant growth, and the gene assembly process in ciliates. I have also worked extensively in the area of theoretical computer science. Particular interests include various string operations such as the shuffle operation, various grammatical models, and operations on automata, with applications to several areas such as verification.

近期论文

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D'Alessandro, F.; Ibarra, O. H. and McQuillan, I. 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. Khan, N. and McQuillan, I. 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. Islam, T.M. R. and McQuillan, I. 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. 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, TBA: 1-18, 2017, Accepted. Eremondi, J.; Ibarra, O. H. and McQuillan, I. On the Complexity and Decidability of Some Problems Involving Shuffle. In Information and Computation, TBA: 1-14, 2017, Accepted. Eremondi, J.; Ibarra, O. H. and McQuillan, I. Deletion Operations on Deterministic Families of Automata. In Information and Computation, TBA: 1-20, 2017, Accepted. Jin, L. and McQuillan, I. 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. 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. Ibarra, O. H. and McQuillan, I. 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. 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. 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, Refereed. Jin, L. and McQuillan, I. Computational Modelling of Interruptional Activities Between Transposable Elements Using Grammars and the Linear Ordering Problem. In Soft Computing, 454: 1-17, 2015. Mahmud, Md. S. I. and McQuillan, I. 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. Eremondi, J.; Ibarra, O. H. and McQuillan, I. 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. Eremondi, J.; Ibarra, O. H. and McQuillan, I. 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. Eremondi, J.; Ibarra, O. H. and McQuillan, I. 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. Eremondi, J.; Ibarra, O. H. and McQuillan, I. 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. 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. Jin, L. and McQuillan, I. 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. 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. Daley, M.; Biegler, F. and McQuillan, I. Algorithmic Decomposition of Shuffle on Words. In Theoretical Computer Science, 454: 38-50, 2012.