Bag Automata and Stochastic Retrieval of Biomolecules in Solution. - Mark Daley; Mark G. Eramian; Ian McQuillan (CIAA, 2003)

The LD and DLAD Bio-Operations on Formal Languages. - Mark Daley; Oscar H. Ibarra; Lila Kari; Ian McQuillan; Koji Nakano (J. Autom. Lang. Comb., 2003)

Viral Gene Compression: Complexity and Verification. - Mark Daley; Ian McQuillan (CIAA, 2004)

Descriptional Complexity of Block-Synchronization Context-Free Grammars. - Ian McQuillan (J. Autom. Lang. Comb., 2004)

Families of languages defined by ciliate bio-operations. - Mark Daley; Lila Kari; Ian McQuillan (Theor. Comput. Sci., 2004)

On Computational Properties of Template-Guided DNA Recombination. - Mark Daley; Ian McQuillan (DNA, 2005)

Formal modelling of viral gene compression. - Mark Daley; Ian McQuillan (Int. J. Found. Comput. Sci., 2005)

Template-guided DNA recombination. - Mark Daley; Ian McQuillan (Theor. Comput. Sci., 2005)

The generative capacity of block-synchronized context-free grammars. - Ian McQuillan (Theor. Comput. Sci., 2005)

Iterated TGR Languages: Membership Problem and Effective Closure Properties. - Ian McQuillan; Kai Salomaa; Mark Daley (COCOON, 2006)

Useful Templates and Iterated Template-Guided DNA Recombination in Ciliates. - Mark Daley; Ian McQuillan (Theory Comput. Syst., 2006)

An infinite hierarchy induced by depth synchronization. - Franziska Biegler; Ian McQuillan; Kai Salomaa (Theor. Comput. Sci., 2007)

No Going Back: An Interactive Visualization Application for Trailblazing on the Web. - Christopher Power; Ian McQuillan; Helen Petrie; Peter Kennaugh; Mark Daley; Geoff Wozniak (IV, 2008)

The Bag Automaton: A Model of Nondeterministic Storage. - Mark Daley; Mark G. Eramian; Ian McQuillan (J. Autom. Lang. Comb., 2008)

Homomorphisms Preserving Types of Density. - Helmut Jürgensen; Ian McQuillan (Acta Cybern., 2009)

On the Shuffle Automaton Size for Words - Franziska Biegler; Mark Daley; Ian McQuillan (DCFS, 2009)

On the uniqueness of shuffle on words and finite languages. - Franziska Biegler; Mark Daley; Markus Holzer 001; Ian McQuillan (Theor. Comput. Sci., 2009)

Speed improvements of peptide-spectrum matching using SIMD instructions. - Jian Zhang; Ian McQuillan; Fang-Xiang Wu (BIBM Workshops, 2010)

Modelling programmed frameshifting with frameshift machines. - Mark Daley; Ian McQuillan (Nat. Comput., 2010)

Algorithmic properties of ciliate sequence alignment. - J. Mark Keil; Jing Liu; Ian McQuillan (Theor. Comput. Sci., 2010)

Parallelizing Peptide-Spectrum scoring using modern graphics processing units. - Jian Zhang; Ian McQuillan; Fang-Xiang Wu (ICCABS, 2011)

Theoretical and computational properties of transpositions. - Mark Daley; Ian McQuillan; James M. McQuillan; Kalpana Mahalingam (Nat. Comput., 2011)

Generalized Derivations with Synchronized Context-Free Grammars. - Markus Holzer 001; Sebastian Jakobi; Ian McQuillan (Developments in Language Theory, 2012)

Preface. - Ian McQuillan; Giovanni Pighizzini (Int. J. Found. Comput. Sci., 2012)

Algorithmic decomposition of shuffle on words. - Franziska Biegler; Mark Daley; Ian McQuillan (Theor. Comput. Sci., 2012)

Computational Modelling of the Interruptional Activities between Transposable Elements. - Lingling Jin; Ian McQuillan (TPNC, 2013)

On Comparing Deterministic Finite Automata and the Shuffle of Words. - Franziska Biegler; Ian McQuillan (CIAA, 2014)

Simulation of the 2JLP Gene Assembly Process in Ciliates. - Md. Sowgat Ibne Mahmud; Ian McQuillan (UCNC, 2015)

Computational identification of regions that influence activity of transposable elements in the human genome. - Lingling Jin; Ian McQuillan; Longhai Li (BIBM, 2016)

On Bounded Semilinear Languages, Counter Machines, and Finite-Index ET0L. - Oscar H. Ibarra; Ian McQuillan (CIAA, 2016)

Computational modelling of interruptional activities between transposable elements using grammars and the linear ordering problem. - Lingling Jin; Ian McQuillan (Soft Comput., 2016)

The effect of end-markers on counter machines and commutativity. - Oscar H. Ibarra; Ian McQuillan (Theor. Comput. Sci., 2016)

CSA-X: Modularized Constrained Multiple Sequence Alignment. - T. M. Rezwanul Islam; Ian McQuillan (AlCoB, 2017)

Descrambling Order Analysis in Ciliates. - Nazifa Azam Khan; Ian McQuillan (UCNC, 2017)

Deletion operations on deterministic families of automata. - Joey Eremondi; Oscar H. Ibarra; Ian McQuillan (Inf. Comput., 2017)

Prediction of transposable elements evolution using tabu search. - Lingling Jin; Ian McQuillan (BIBM, 2018)

Sample Size and Reproducibility of Gene Set Analysis. - Farhad Maleki; Katie L. Ovens; Ian McQuillan; Anthony J. Kusalik (BIBM, 2018)

New Techniques for Inferring L-systems Using Genetic Algorithm. - Jason Bernard; Ian McQuillan (BIOMA, 2018)

Input-Position-Restricted Models of Language Acceptors. - Oscar H. Ibarra; Ian McQuillan (Reversibility and Universality, 2018)

On Counting Functions of Languages. - Oscar H. Ibarra; Ian McQuillan; Bala Ravikumar (DLT, 2018)

DNA Methylation Data to Predict Suicidal and Non-Suicidal Deaths: A Machine Learning Approach. - Rifat Zahan; Ian McQuillan; Nathaniel Osgood (ICHI, 2018)

Inferring Stochastic L-Systems Using a Hybrid Greedy Algorithm. - Jason Bernard; Ian McQuillan (ICTAI, 2018)

A Fast and Reliable Hybrid Approach for Inferring L-systems . - Jason Bernard; Ian McQuillan (ALIFE, 2018)

Algorithms for Inferring Context-Sensitive L-Systems. - Ian McQuillan; Jason Bernard; Przemyslaw Prusinkiewicz (UCNC, 2018)

On the complexity and decidability of some problems involving shuffle. - Joey Eremondi; Oscar H. Ibarra; Ian McQuillan (Inf. Comput., 2018)

On the Density of Context-Free and Counter Languages. - Joey Eremondi; Oscar H. Ibarra; Ian McQuillan (Int. J. Found. Comput. Sci., 2018)

From Helmut Jürgensen's Former Students: The Game of Informatics Research. - Mark Daley; Mark G. Eramian; Christopher Power; Ian McQuillan (J. Autom. Lang. Comb., 2018)

On the Density of Languages Accepted by Turing Machines and Other Machine Models. - Oscar H. Ibarra; Ian McQuillan (J. Autom. Lang. Comb., 2018)

Variations of checking stack automata: Obtaining unexpected decidability properties. - Oscar H. Ibarra; Ian McQuillan (Theor. Comput. Sci., 2018)

On store languages of language acceptors. - Oscar H. Ibarra; Ian McQuillan (Theor. Comput. Sci., 2018)

Gene Set Databases: A Fountain of Knowledge or a Siren Call? - Farhad Maleki; Katie L. Ovens; Ian McQuillan; Elham Rezaei; Alan M. Rosenberg; Anthony J. Kusalik (BCB, 2019)

On store languages and applications. - Oscar H. Ibarra; Ian McQuillan (Inf. Comput., 2019)

Insertion operations on deterministic reversal-bounded counter machines. - Joey Eremondi; Oscar H. Ibarra; Ian McQuillan (J. Comput. Syst. Sci., 2019)

State grammars with stores. - Oscar H. Ibarra; Ian McQuillan (Theor. Comput. Sci., 2019)

On families of full trios containing counter machine languages. - Oscar H. Ibarra; Ian McQuillan (Theor. Comput. Sci., 2019)

On counting functions and slenderness of languages. - Oscar H. Ibarra; Ian McQuillan; Bala Ravikumar (Theor. Comput. Sci., 2019)

The impact of sample size and tissue type on the reproducibility of gene co-expression networks. - Katie L. Ovens; B. Frank Eames; Ian McQuillan (BCB, 2020)

A Novel Technique Combining Image Processing, Plant Development Properties, and the Hungarian Algorithm, to Improve Leaf Detection in Maize. - Nazifa Azam Khan; Oliver A. S. Lyon; Mark G. Eramian; Ian McQuillan (CVPR Workshops, 2020)

Inferring Temporal Parametric L-systems Using Cartesian Genetic Programming. - Jason Bernard; Ian McQuillan (ICTAI, 2020)

Semilinearity of Families of Languages. - Oscar H. Ibarra; Ian McQuillan (Int. J. Found. Comput. Sci., 2020)

Juxtapose: a gene-embedding approach for comparing co-expression networks. - Katie L. Ovens; Farhad Maleki; B. Frank Eames; Ian McQuillan (BMC Bioinform., 2021)

On finite-index indexed grammars and their restrictions. - Flavio D'Alessandro; Oscar H. Ibarra; Ian McQuillan (Inf. Comput., 2021)

Space Complexity of Stack Automata Models. - Oscar H. Ibarra; Jozef Jirásek 002; Ian McQuillan; Luca Prigioniero (Int. J. Found. Comput. Sci., 2021)

Generalizations of Checking Stack Automata: Characterizations and Hierarchies. - Oscar H. Ibarra; Ian McQuillan (Int. J. Found. Comput. Sci., 2021)

Preface. - Ian McQuillan; Shinnosuke Seki 001 (Nat. Comput., 2021)

Techniques for inferring context-free Lindenmayer systems with genetic algorithm. - Jason Bernard; Ian McQuillan (Swarm Evol. Comput., 2021)

Relationships between bounded languages, counter machines, finite-index grammars, ambiguity, and commutative regularity. - Arturo Carpi; Flavio D'Alessandro; Oscar H. Ibarra; Ian McQuillan (Theor. Comput. Sci., 2021)

On the Complexity of Decision Problems for Counter Machines with Applications to Coding Theory. - Oscar H. Ibarra; Ian McQuillan (DLT, 2022)

On the Containment Problem for Deterministic Multicounter Machine Models. - Oscar H. Ibarra; Ian McQuillan (ATVA (1), 2023)

Unboundedness Problems for Machines with Reversal-Bounded Counters. - Pascal Baumann 001; Flavio D'Alessandro; Moses Ganardi; Oscar H. Ibarra; Ian McQuillan; Lia Schütze; Georg Zetzsche (FoSSaCS, 2023)

Stochastic L-system inference from multiple string sequence inputs. - Jason Bernard; Ian McQuillan (Soft Comput., 2023)

New characterizations of exponential, elementary, and non-elementary time-bounded Turing machines. - Oscar H. Ibarra; Ian McQuillan (Inf. Comput., 2023)

On the complexity of decision problems for some classes of machines and applications. - Oscar H. Ibarra; Ian McQuillan (Inf. Comput., 2023)

Visit-Bounded Stack Automata. - Jozef Jirásek 002; Ian McQuillan (Theory Comput. Syst., 2023)

SVPS, pairwise whole genome alignment-based structural variant identification. - C. Malcolm Todd; Lingling Jin; Ian McQuillan (BIBM, 2024)

Techniques for Showing the Decidability of the Boundedness Problem of Language Acceptors. - Oscar H. Ibarra; Ian McQuillan (DLT, 2024)

Discovering Knowledge Embedded in Gene Set Databases: A Mathematical Modelling Approach. - Katie L. Ovens; Ebunoluwa Makinde; Samuel Horovatin; Elham Rezaei; Alan M. Rosenberg; Lingling Jin; Ian McQuillan; Anthony J. Kusalik; Farhad Maleki (ICCBB, 2024)

Improving Deep Learning Predictions with Simulated Images, and Vice Versa. - Nazifa Azam Khan; Mikolaj Cieslak; Ian McQuillan (CoRR, 2024)

Optimal L-Systems for Stochastic L-system Inference Problems. - Ali Lotfi; Ian McQuillan (CoRR, 2024)

Classical and Quantum Algorithms for the Deterministic L-system Inductive Inference Problem. - Ali Lotfi; Ian McQuillan; Steven Rayan (CoRR, 2024)

Restrictions on Multicounter and Partially-Blind Multicounter Languages. - Oscar H. Ibarra; Ian McQuillan (Comput. Sci. J. Moldova, 2024)

Effectiveness of Training with Procedurally Generated Synthetic Images of Crop Plants. - Nazifa Azam Khan; Mikolaj Cieslak; Mark G. Eramian; Ian McQuillan (CVPR Workshops, 2025)

Simulating Viral Evolution and Immune Escape Reinfection Dynamics Using Agent-Based Modelling. - C. Malcolm Todd; Yuan Tian 023; Nathaniel Osgood; Ian McQuillan; Lingling Jin (ISBRA (2), 2025)

Language Acceptors with a Pushdown: Characterizations and Complexity. - Oscar H. Ibarra; Ian McQuillan (Int. J. Found. Comput. Sci., 2025)

On decision problems concerning contextual insertions and deletions. - Oscar H. Ibarra; Ian McQuillan (Theor. Comput. Sci., 2025)