Publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

2026

  1. Relativized Codes, Finite Decodability, and Bounded Languages
    Oscar H. Ibarra and Ian McQuillan
    Information and Computation, 313, pp. 105507, 2026
    DOI PDF
  2. Inductive Inference of Cellular Automata
    Martin Kutrib, Ian McQuillan, Priscilla Raucci, and Matthias Wendlandt
    In Electronic Proceedings in Theoretical Computer Science, 17th International Conference on Automata and Formal Languages (AFL 2026), 2026
    DOI PDF
  3. Resetting Stores on Machine Models
    Oscar H. Ibarra and Ian McQuillan
    In Lecture Notes in Computer Science, From Possibility to Reality: Essays Dedicated to Kai Salomaa, 16865, 2026
  4. Learning L-system Models of Plants Matching Real Images Using Genetic Algorithm
    Nazifa Khan, William Bushell, Mik Cieslak, and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of the 23rd International Conference on Unconventional Computing and Natural Computing, UCNC 2026, 2026
  5. Decidability of Regularity for Families of Languages
    Oscar H. Ibarra and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of the 30th International Conference on Implementation and Application of Automata, CIAA 2026, 16695, pp. 62–77, 2026
    DOI
  6. State-Limited Inductive Inference of Cellular Automata
    Martin Kutrib, Ian McQuillan, Priscilla Raucci, and Matthias Wendlandt
    In Lecture Notes in Computer Science, 27th International Conference on Descriptional Complexity of Formal Systems (DCFS 2026), 16681, pp. 110–121, 2026
    DOI
  7. Store languages of Turing machines and counter machines
    Noah Friesen, Oscar H. Ibarra, Jozef Jirásek, and Ian McQuillan
    Theoretical Computer Science, 1074, pp. 115931, 2026
    DOI PDF
  8. Simulating viral evolution and immune escape reinfection dynamics using agent-based modelling
    C. Malcolm Todd, Yuan Tian, Nathaniel Osgood, Ian McQuillan, and Lingling Jin
    In Lecture Notes in Computer Science, 2025 International Symposium on Bioinformatics Research and Applications (ISBRA 2025), 15757, pp. 190–202, 2026
    DOI

2025

  1. On the containment problem for deterministic multicounter machine models
    Oscar H. Ibarra and Ian McQuillan
    Information and Computation, 307, pp. 105383, 2025
    DOI PDF
  2. FTIO: Frequent Temporally Integrated Objects
    Mohammad Mohammadzadeh Kalati, Farhad Maleki, and Ian McQuillan
    In Frontiers in Artificial Intelligence and Applications, 28th European Conference on Artificial Intelligence (ECAI-2025), 413, pp. 636–642, 2025
    DOI
  3. Relativized Codes, Finite Decodability, and Bounded Languages
    Oscar H. Ibarra and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of the 29th International Conference on Developments in Language Theory, DLT 2025, 16036, pp. 61–76, 2025
    DOI
  4. Left Quotients of Deterministic Context-Free Languages
    Brennan Lockinger and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of the 29th International Conference on Developments in Language Theory, DLT 2025, 16036, pp. 123–137, 2025
    DOI
  5. On Decidability of Problems Involving Insertion Operations
    Oscar H. Ibarra and Ian McQuillan
    Natural Computing, 24, pp. 679–691, 2025
    DOI PDF
  6. Inductive Inference of Lindenmayer Systems: Algorithms and Computational Complexity
    Christopher Duffy, Sam Hillis, Umer Khan, Ian McQuillan, and Sonja Linghui Shan
    Natural Computing, 24, pp. 591–601, 2025
    DOI PDF
  7. Chondrocyte maturation bridges two cross-inhibitory subnetworks of the skeletal cell GRN
    Patsy Gómez-Picos, Katie Ovens, Amir M. Ashique, Marziyeh Hassanzadeh, Ian McQuillan, and B. Frank Eames
    Development, 152, 2025
    DOI PDF
  8. WheatSAM: A Two-Stage Wheat Head Automatic Segmentation Framework
    Md Jaber Al Nahian, Tapotosh Ghosh, Farnaz Sheikhi, Ian McQuillan, and Farhad Maleki
    In 22nd International Conference on Robots and Vision (2025)), 2025
    DOI PDF
  9. Effectiveness of Training with Procedurally Generated Synthetic Images of Crop Plants
    Nazifa Azam Khan, Ian McQuillan, Mikolaj Cieslak, and Mark Eramian
    In 6th International Workshop on Agriculture-Vision: Challenges & Opportunities for Computer Vision in Agriculture (in junction with IEEE/CVF CVPR 2025), pp. 5451–5461, 2025
    PDF
  10. SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies
    C. Malcolm Todd, Lingling Jin, and Ian McQuillan
    Methods, 234, pp. 305–313, 2025
    DOI PDF
  11. On Decision Problems Concerning Contextual Insertions and Deletions
    Oscar H. Ibarra and Ian McQuillan
    Theoretical Computer Science, 1024, pp. 114905, 2025
    DOI PDF

2024

  1. Restrictions on Multicounter and Partially-Blind Multicounter Languages
    Oscar H. Ibarra and Ian McQuillan
    Computer Science Journal of Moldova, 32, pp. 389–411, 2024
    DOI PDF
  2. Language Acceptors with a Pushdown: Characterizations and Complexity
    Oscar H. Ibarra and Ian McQuillan
    International Journal of Foundations of Computer Science, 36, pp. 345–370, 2024
    DOI PDF
  3. SVPS, Pairwise Whole Genome Alignment-Based Structural Variant Identification
    C. Malcolm Todd, Lingling Jin, and Ian McQuillan
    In 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 105–112, 2024
    DOI
  4. Techniques for Showing the Decidability of the Boundedness Problem of Language Acceptors
    Oscar H. Ibarra and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of the 28th International Conference on Developments in Language Theory, DLT 2024, 14791, pp. 156–172, 2024
    DOI

2023

  1. Visit-bounded stack automata
    Jozef Jirásek Jr. and Ian McQuillan
    Theory of Computing Systems, 67, pp. 956–975, 2023
    DOI PDF
  2. On the containment problem for deterministic multicounter machine models
    Oscar H. Ibarra and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of the 21st International Symposium on Automated Technology for Verification and Analysis, ATVA 2023, 14215, pp. 74–94, 2023
    DOI
  3. Deciphering the functions of Stromal Interaction Molecule-1 in Amelogenesis using AmelX-iCre mice
    Raed Samir Said, Helyasadat Mortazavi, David Cooper, Katie Ovens, Ian McQuillan, Silvana Papagerakis, and Petros Papagerakis
    Frontiers in Physiology, 14, 2023
    DOI PDF
  4. On the complexity of decision problems for some classes of machines and applications
    Oscar H. Ibarra and Ian McQuillan
    Information and Computation, 294, pp. 105080, 2023
    DOI PDF
  5. New characterizations of exponential, elementary, and non-elementary time-bounded Turing machines
    Oscar H. Ibarra and Ian McQuillan
    Information and Computation, 292, pp. 105027, 2023
    DOI PDF
  6. Unboundedness problems for machines with reversal-bounded counters
    Pascal Baumann, Flavio D’Alessandro, Moses Ganardi, Oscar H. Ibarra, Ian McQuillan, Lia Schütze, and Georg Zetzsche
    In Lecture Notes in Computer Science, Proceedings of the 26th International Conference on Foundations of Software Science and Computation Structures, FoSSaCS 2023, 13992, pp. 240–264, 2023
    Won the Best Paper Award
    DOI PDF
  7. Stochastic L-system inference from multiple string sequence inputs
    Jason Bernard and Ian McQuillan
    Soft Computing, 27, pp. 6783–6798, 2023
    DOI PDF

2022

  1. On the complexity of decision problems for counter machines with applications to coding theory
    Oscar H. Ibarra and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of the 26th International Conference on Developments in Language Theory, DLT 2022, 13257, pp. 177–188, 2022
    DOI
  2. Visit-Bounded Stack Automata
    Jozef Jirásek Jr. and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of the 26th International Conference on Developments in Language Theory, DLT 2022, 13257, pp. 189–200, 2022
    Won the Best Paper Award
    DOI
  3. Exploiting high-throughput indoor phenotyping to characterize the founders of a structured B. napus breeding population
    Jana Ebersbach, Nazifa Azam Khan, Ian McQuillan, Erin E Higgins, Kyla Horner, Venkat Bandi, Carl Gutwin, Sally Lynne Vail, Steve J Robinson, and Isobel AP Parkin
    Frontiers in Plant Science, 12, 2022
    DOI PDF

2021

  1. L-system models for image-based phenomics: case studies of maize and canola
    Mikolaj Cieslak, Nazifa Azam Khan, Pascal Ferraro, Raju Soolanayakanahally, Stephen J. Robinson, Isobel Parkin, Ian McQuillan, and Przemyslaw Prusinkiewicz
    in silico Plants, 4, 2021
    DOI PDF
  2. Silver: forging almost gold standard datasets
    Farhad Maleki, Katie Ovens, Ian McQuillan, and Anthony J. Kusalik
    Genes, 12, pp. 1523, 2021
    DOI PDF
  3. Space complexity of stack automata models
    Oscar H. Ibarra, Jozef Jirásek Jr., Ian McQuillan, and Luca Prigionero
    International Journal of Foundations of Computer Science, 32, pp. 801–823, 2021
    DOI PDF
  4. Comparative analyses of gene co-expression networks: Implementations and applications in the study of evolution
    Katie Ovens, B. Frank Eames, and Ian McQuillan
    Frontiers in Genetics, 12, 2021
    DOI PDF
  5. Techniques for inferring context-free Lindenmayer systems with genetic algorithm
    Jason Bernard and Ian McQuillan
    Swarm and Evolutionary Computation, 64, pp. 100893, 2021
    DOI PDF
  6. Juxtapose: a gene-embedding approach for comparing co-expression networks
    Katie Ovens, Farhad Maleki, B. Frank Eames, and Ian McQuillan
    BMC Bioinformatics, 22, pp. 26, 2021
    DOI PDF
  7. Generalizations of checking stack automata: characterizations and hierarchies
    Oscar H. Ibarra and Ian McQuillan
    International Journal of Foundations of Computer Science, 32, pp. 481–508, 2021
    DOI PDF
  8. Relationships between bounded languages, counter machines, finite-index grammars, ambiguity, and commutative regularity
    Arturo Carpi, Flavio D’Alessandro, Oscar H. Ibarra, and Ian McQuillan
    Theoretical Computer Science, 862, pp. 97–118, 2021
    DOI PDF
  9. On Finite-index indexed grammars and their restrictions
    Flavio D’Alessandro, Oscar H. Ibarra, and Ian McQuillan
    Information and Computation, 279, pp. 104613, 2021
    DOI PDF

2020

  1. Inferring temporal parametric L-systems using cartesian genetic programming
    Jason Bernard and Ian McQuillan
    In 2020 IEEE 32nd International Conference on Tools with Artificial Intelligence (ICTAI), pp. 580–588, 2020
    Won the C.V. Ramamoorthy Best Paper Award
    DOI
  2. The impact of sample size and tissue type on the reproducibility of gene co-expression networks
    Katie Ovens, B. Frank Eames, and Ian McQuillan
    In Proceedings of the 11th International Conference on Bioinformatics, Computational Biology and Health Informatics, ACM-BCB 2020, ACM-BCB 2020, pp. 1–10, 2020
    DOI
  3. A novel technique combining image processing, plant development properties, and the Hungarian algorithm, to improve leaf detection in Maize
    Nazifa Azam Khan, Oliver Lyon, Mark Eramian, and Ian McQuillan
    In 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW 2020), pp. 330–339, 2020
    DOI PDF
  4. Semilinearity of families of languages
    Oscar H. Ibarra and Ian McQuillan
    International Journal of Foundations of Computer Science, 31, pp. 1179–1198, 2020
    DOI PDF
  5. Space complexity of stack automata models
    Oscar H. Ibarra, Jozef Jirásek Jr., Ian McQuillan, and Luca Prigioniero
    In Lecture Notes in Computer Science, Proceedings of the 24th International Conference on Developments in Language Theory, DLT 2020, 12086, pp. 137–149, 2020

2019

  1. Pineplot: an R package for visualizing symmetric relationships
    Katie Ovens, Daniel Hogan, Farhad Maleki, Ian McQuillan, and Anthony J. Kusalik
    In Proceedings of the 10th International Conference on Computational Systems-Biology and Bioinformatics, CSBio 2019, CSBio 2019, pp. 1–8, 2019
    DOI
  2. Size matters: How sample size affects the reproducibility and specificity of gene set analysis
    Farhad Maleki, Katie Ovens, Ian McQuillan, and Anthony. J. Kusalik
    BMC Human Genomics, 13, pp. 42, 2019
    DOI PDF
  3. On Families of Full Trios Containing Counter Machine Languages
    Oscar H. Ibarra and Ian McQuillan
    Theoretical Computer Science, 799, pp. 71–93, 2019
    DOI PDF
  4. Gene Set Databases: A Fountain of Knowledge or a Siren Call?
    Farhad Maleki, Katie Ovens, Ian McQuillan, Elham Rezaei, Alan M. Rosenberg, and Anthony. J. Kusalik
    In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, ACM-BCB 2019, pp. 269–278, 2019
    DOI
  5. On Store Languages and Applications
    Oscar H. Ibarra and Ian McQuillan
    Information and Computation, 267, pp. 28–48, 2019
    DOI PDF
  6. State Grammars with Stores
    Oscar H. Ibarra and Ian McQuillan
    Theoretical Computer Science, 798, pp. 23–39, 2019
    DOI PDF
  7. On Counting Functions and Slenderness of Languages
    Oscar H. Ibarra, Ian McQuillan, and Bala Ravikumar
    Theoretical Computer Science, 777, pp. 356–378, 2019
    DOI PDF
  8. Insertion Operations on Deterministic Reversal-Bounded Counter Machines
    Joey Eremondi, Oscar H. Ibarra, and Ian McQuillan
    Journal of Computer and System Sciences, 104, pp. 244–257, 2019
    DOI PDF

2018

  1. Sample Size and Reproducibility of Gene Set Analysis
    Farhad Maleki, Katie Ovens, Ian McQuillan, and Anthony. J. Kusalik
    In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 122–129, 2018
    DOI PDF
  2. Prediction of transposable elements evolution using tabu search
    Lingling Jin and Ian McQuillan
    In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 665–670, 2018
    DOI PDF
  3. Inferring Stochastic L-systems Using a Hybrid Greedy Algorithm
    Jason Bernard and Ian McQuillan
    In 2018 IEEE 30th International Conference on Tools with Artificial Intelligence (ICTAI), pp. 600–607, 2018
    DOI PDF
  4. A Fast and Reliable Hybrid Approach for Inferring L-Systems
    Jason Bernard and Ian McQuillan
    In Proceedings of the 2018 Conference on Artificial Life (ALIFE 2018), MIT Press, pp. 444–451, 2018
    DOI
  5. Algorithms for Inferring Context-Sensitive L-Systems
    Ian McQuillan, Jason Bernard, and Przemyslaw Prusinkiewicz
    In Lecture Notes in Computer Science, Proceedings of the 17th International Conference on Unconventional Computation and Natural Computation, UCNC 2018, 10867, pp. 117–130, 2018
    DOI PDF
  6. New Techniques for Inferring L-systems Using Genetic Algorithm
    Jason Bernard and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of the 8th International Conference on Bioinspired Optimization Methods and Their Applications, BIOMA 2018, 10835, pp. 13–25, 2018
  7. Semilinearity of Families of Languages
    Oscar H. Ibarra and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of the 23rd International Conference on Implementation and Application of Automata, CIAA 2018, 10977, pp. 211–222, 2018
  8. Generalizations of Checking Stack Automata: Characterizations and Hierarchies
    Oscar H. Ibarra and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of the 22nd International Conference on Developments in Language Theory, DLT 2018, 11088, pp. 416–428, 2018
  9. On Counting Functions of Languages
    Oscar H. Ibarra, Ian McQuillan, and Bala Ravikumar
    In Lecture Notes in Computer Science, Proceedings of the 22nd International Conference on Developments in Language Theory, DLT 2018, 11088, pp. 429–440, 2018
  10. State Grammars with Stores
    Oscar H. Ibarra and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of the 20th International Workshop on Descriptional Complexity of Formal Systems, DCFS 2018, 10952, pp. 163–174, 2018
  11. DNA Methylation Data to Predict Suicidal and Non-Suicidal Deaths: A Machine Learning Approach
    Rifat Zahan, Ian McQuillan, and Nathaniel D. Osgood
    In Proceedings of the Sixth IEEE International Conference on Healthcare Informatics, ICHI 2018, 10952, pp. 363–365, 2018
    Short paper
    DOI
  12. On Store Languages of Language Acceptors
    Oscar H. Ibarra and Ian McQuillan
    Theoretical Computer Science, 745, pp. 114–132, 2018
    DOI PDF
  13. Variations of Checking Stack Automata: Obtaining Unexpected Decidability Properties
    Oscar H. Ibarra and Ian McQuillan
    Theoretical Computer Science, 738, pp. 1–12, 2018
    DOI PDF
  14. Input-Position-Restricted Models of Language Acceptors
    Oscar H. Ibarra and Ian McQuillan
    In Reversibility and Universality: Essays Presented to Kenichi Morita on the Occasion of his 70th Birthday, pp. 357–372, 2018
    DOI PDF
  15. From Helmut Jürgensen’s Former Students: The Game of Informatics Research
    Mark Daley, Mark Eramian, Christopher Power, and Ian McQuillan
    Journal of Automata, Languages and Combinatorics, 23, pp. 127–141, 2018
    DOI PDF
  16. On the Density of Languages Accepted by Turing Machines and Other Machine Models
    Oscar H. Ibarra and Ian McQuillan
    Journal of Automata, Languages and Combinatorics, 23, pp. 189–199, 2018
    DOI PDF
  17. On the Density of Context-Free and Counter Languages
    Joey Eremondi, Oscar H. Ibarra, and Ian McQuillan
    International Journal of Foundations of Computer Science, 29, pp. 233–250, 2018
    DOI PDF
  18. On the Complexity and Decidability of Some Problems Involving Shuffle
    Joey Eremondi, Oscar H. Ibarra, and Ian McQuillan
    Information and Computation, 259, pp. 214–224, 2018
    DOI PDF

2017

  1. Computational Identification of Harmful Mutation Regions to the Activity of Transposable Elements
    Lingling Jin and Ian McQuillan
    BMC Genomics, 18, pp. 862, 2017
    DOI PDF
  2. Variations of Checking Stack Automata: Obtaining Unexpected Decidability Properties
    Oscar H. Ibarra and Ian McQuillan
    In Lecture Notes in Computer Science, 21st International Conference on Developments in Language Theory, DLT 2017, Liège, Belgium, 10396, pp. 235–246, 2017
  3. On Finite-index indexed grammars and their restrictions
    Flavio D’Alessandro, Oscar H. Ibarra, and Ian McQuillan
    In Lecture Notes in Computer Science, 11th International Conference on Language and Automata Theory and Applications, LATA 2017, Umeå, Sweden, Proceedings, 10168, pp. 287–298, 2017
    Won the Springer Best Paper Award for LATA 2017
  4. Descrambling Order Analysis in Ciliates
    Nazifa Azam Khan and Ian McQuillan
    In Lecture Notes in Computer Science, 16th International Conference on Unconventional and Natural Computation, UCNC 2017, Fayetteville, USA, 10240, pp. 206–219, 2017
    DOI PDF
  5. CSA-X: Modularized Constrained Multiple Sequence Alignment
    T.M. Rezwanul Islam and Ian McQuillan
    In Lecture Notes in Computer Science, 4th International Conference on Algorithms for Computational Biology, AlCob 2016, Aveiro, Portugal, 10252, pp. 143–154, 2017
    DOI PDF
  6. Deletion Operations on Deterministic Families of Automata
    Joey Eremondi, Oscar H. Ibarra, and Ian McQuillan
    Information and Computation, 256, pp. 237–252, 2017
    DOI PDF

2016

  1. Computational Identification of Regions that Influence Activity of Transposable Elements in the Human Genome
    Lingling Jin and Ian McQuillan
    In Proceedings of the International Conference on Bioinformatics and Biomedicine, 2016, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Shenzhen, China, pp. 592–599, 2016
  2. The effect of end-markers on counter machines and commutativity
    Oscar H. Ibarra and Ian McQuillan
    Theoretical Computer Science, 627, pp. 71–81, 2016
    DOI PDF
  3. Run for Third! A defense of Aggressive Base Running
    Peter Macdonald, Dan McQuillan, and Ian McQuillan
    Math Horizons, 23, pp. 14–15, 2016
    DOI
  4. On Families of Full Trios Containing Counter Machine Languages
    Oscar H. Ibarra and Ian McQuillan
    In Lecture Notes in Computer Science, Developments in Language Theory: 20th International Conference, DLT 2016, Montréal, Canada, July 25-28, 2016, Proceedings, 9840, pp. 216–228, 2016
  5. On Bounded Semilinear Languages, Counter Machines, and Finite-Index ET0L
    Oscar H. Ibarra and Ian McQuillan
    In Lecture Notes in Computer Science, Implementation and Application of Automata: 21st International Conference, CIAA 2016, Seoul, South Korea, July 19-22, 2016, Proceedings, 9705, pp. 138–149, 2016
  6. Computational Modelling of Interruptional Activities Between Transposable Elements Using Grammars and the Linear Ordering Problem
    Lingling Jin and Ian McQuillan
    Soft Computing, 20, pp. 19–35, 2016
    DOI PDF

2015

  1. On Some Decision Problems Concerning Commutation, Reversal, and Palindromes
    Oscar H. Ibarra and Ian McQuillan
    In Multidiciplinary Creativity — Homage to Gheorghe Păun on His 65th Birthday, pp. 265–277, 2015
  2. Simulation of the 2JLP Gene Assembly Process in Ciliates
    Md. Sowgat Ibne Mahmud and Ian McQuillan
    In Lecture Notes in Computer Science, 14th International Conference on Unconventional and Natural Computation, UCNC 2015, Auckland, New Zealand, 9252, pp. 227–238, 2015
    DOI PDF
  3. On the Complexity and Decidability of Some Problems Involving Shuffle
    Joey Eremondi, Oscar H. Ibarra, and Ian McQuillan
    In Lecture Notes in Computer Science, 17th International Workshop on Descriptional Complexity of Formal Systems, DCFS 2015, Waterloo, Canada, 9118, pp. 105–116, 2015
  4. On the Density of Context-Free and Counter Languages
    Joey Eremondi, Oscar H. Ibarra, and Ian McQuillan
    In Lecture Notes in Computer Science, 19th International Conference on Developments in Language Theory, DLT 2015, Liverpool, UK, 9168, pp. 228–239, 2015
  5. Deletion Operations on Deterministic Families of Automata
    Joey Eremondi, Oscar H. Ibarra, and Ian McQuillan
    In Lecture Notes in Computer Science, 12th Annual Conference on Theory and Applications of Models of Computation, TAMC 2015, Singapore, 9076, pp. 388–399, 2015
  6. Insertion Operations on Deterministic Reversal-Bounded Counter Machines
    Joey Eremondi, Oscar H. Ibarra, and Ian McQuillan
    In Lecture Notes in Computer Science, 9th International Conference on Language and Automata Theory and Applications, LATA 2015, Nice, France, 8977, pp. 200–211, 2015

2014

  1. On comparing deterministic finite automata and the shuffle of words
    Franziska Biegler and Ian McQuillan
    In Lecture Notes in Computer Science, 19th International Conference on Implementation and Application of Automata, CIAA 2014, Giessen, Germany, 8587, pp. 98–109, 2014
    DOI PDF

2013

  1. Computational Modelling of the Interruptional Activities Between Transposable Elements
    Lingling Jin and Ian McQuillan
    In Lecture Notes in Computer Science, 2nd International Conference on the Theory and Practice of Natural Computing, TPNC 2014, Granada, Spain, 8273, pp. 108–120, 2013

2012

  1. Generalized Derivations with Synchronized Context-Free Grammars
    Markus Holzer, Sebastian Jakobi, and Ian McQuillan
    In Lecture Notes in Computer Science, Developments in Language Theory - 16th International Conference, DLT 2012, Taipei, Taiwan, 7410, pp. 109–120, 2012
    DOI PDF
  2. Algorithmic Decomposition of Shuffle on Words
    Mark Daley, Franziska Biegler, and Ian McQuillan
    Theoretical Computer Science, 454, pp. 38–50, 2012
    DOI PDF

2011

  1. Speed Improvements of peptide-spectrum matching using Single-Instruction Multiple-Data instructions
    Jian Zhang, Ian McQuillan, and FangXiang Wu
    Proteomics, 11, pp. 3779–3785, 2011
    DOI
  2. Parallelizing Peptide-Spectrum Scoring Using Modern Graphics Processing Units
    Jian Zhang, Ian McQuillan, and FangXiang Wu
    In 1st IEEE International Conference on Computational Advances in Bio and medical Sciences, pp. 208–213, 2011
    DOI
  3. Theoretical and computational properties of transpositions
    Mark Daley, Ian McQuillan, James McQuillan, and Kalpana Mahalingam
    Natural Computing, 10, pp. 795–804, 2011
    DOI PDF

2010

  1. On the shuffle automaton size for words
    Mark Daley, Franziska Biegler, and Ian McQuillan
    Journal of Automata, Languages and Combinatorics, 15, pp. 53–70, 2010
    DOI PDF
  2. Speed Improvements of Peptide-Spectrum matching Using SIMD Instructions
    Jian Zhang, Ian McQuillan, and FangXiang Wu
    In IEEE BIBM 2010 International Workshop on Computational Proteomics, pp. 1–6, 2010
  3. Algorithmic properties of ciliate sequence alignment
    Mark Keil, Jing Liu, and Ian McQuillan
    Theoretical Computer Science, 411, pp. 919–925, 2010
    DOI PDF
  4. Modelling programmed frameshifting with frameshift machines
    Mark Daley and Ian McQuillan
    Natural Computing, 9, pp. 239–261, 2010
    DOI PDF

2009

  1. Homomorphisms Preserving Types of Density
    Helmut Jürgensen and Ian McQuillan
    Acta Cybernetica, 19, pp. 499–516, 2009
    PDF
  2. On the shuffle automaton size for words
    Franziska Biegler, Mark Daley, and Ian McQuillan
    In Proceedings of the 11th International Workshop on Descriptional Complexity of Formal Systems, pp. 115–126, 2009
  3. On the uniqueness of shuffle on words and finite languages
    Franziska Biegler, Mark Daley, Markus Holzer, and Ian McQuillan
    Theoretical Computer Science, 410, pp. 3711–3724, 2009
    DOI PDF

2008

  1. The Bag Automaton: A Model of Nondeterministic Storage
    Mark Daley, Mark Eramian, and Ian McQuillan
    Journal of Automata, Languages and Combinatorics, 13, pp. 185–206, 2008
    DOI
  2. Homomorphisms Preserving Types of Density
    H. Jürgensen and Ian McQuillan
    In Proceedings of the 12th International Conference on Automata and Formal Languages, pp. 183–194, 2008
  3. No going back: an interactive visualization application for trailblazing on the web
    C. Power, Ian McQuillan, H. Petrie, P. Kennaugh, Mark Daley, and G. Wozniak
    In Proceedings of the 12th International Conference on Information Visualisation (IV08), pp. 133–142, 2008

2007

  1. Theoretical and computational properties of transpositions
    Mark Daley, Ian McQuillan, and J. McQuillan
    In Proceedings of the Language Theory in Biocomputing Workshop, in the Conference on Unconventional Computation, pp. 28–38, 2007
  2. An Infinite Hierarchy Induced by Depth Synchronization
    Franziska Biegler, Ian McQuillan, and Kai Salomaa
    Theoretical Computer Science, 387, pp. 113–124, 2007
    DOI PDF

2006

  1. Useful Templates and Iterated Template-Guided DNA Recombination in Ciliates
    Mark Daley and Ian McQuillan
    Theory of Computing Systems, 39, pp. 619–633, 2006
    DOI PDF
  2. An Infinite Hierarchy Induced by Depth Synchronization
    Franziska Biegler, Ian McQuillan, and Kai Salomaa
    In the Eighth International Workshop on Descriptional Complexity of Formal Systems, Las Cruces, New Mexico, Proceedings, pp. 82–93, 2006
  3. On Computational Properties of Template-Guided DNA Recombination
    Mark Daley and Ian McQuillan
    In Lecture Notes in Computer Science, Proceedings of DNA computing, 3892, pp. 27–37, 2006
    DOI

2005

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

2004

  1. Families of Languages Defined by Ciliate Bio-operations
    Mark Daley, L. Kari, and Ian McQuillan
    Theoretical Computer Science, 320, pp. 51–69, 2004
    DOI PDF
  2. Descriptional Complexity of Block-Synchronization Context-Free Grammars
    Ian McQuillan
    Journal of Automata, Languages and Combinatorics, 9, pp. 317–332, 2004
    A previous version of this manuscript appeared in the workshop for Descriptional Complexity of Formal Systems 2002.
    DOI

2003

  1. Template-Guided DNA Recombination
    Mark Daley and Ian McQuillan
    In Fifth International Workshop, Descriptional Complexity of Formal Systems, Budapest, Hungary, July 12-14, 2003, Proceedings, pp. 235–244, 2003
  2. Bag Automata and Stochastic Retrieval of Biomolecules From Solution
    Mark Daley, Mark Eramian, and Ian McQuillan
    In Lecture Notes in Computer Science, Conference on Implementation and Application of Automata (CIAA 2003), 2759, pp. 239-250, 2003
  3. Closure and Decision Properties of Some Language Classes Under ld and dlad Bio-operations
    Mark Daley, Oscar H. Ibarra, Lila Kari, Ian McQuillan, and Koji Nakano
    Journal of Automata, Languages and Combinatorics, 8, pp. 477–498, 2003
    DOI

2002

  1. Descriptional Complexity of Block-Synchronization Context-Free Grammars
    Ian McQuillan
    In Descriptional Complexity of Formal Systems (DCFS) Pre-Proceedings of a Workshop, pp. 188–203, 2002
    Report No. 586