How to Compute with DNA. - Lila Kari; Mark Daley; Greg Gloor; Rani Siromoney; Laura F. Landweber (FSTTCS, 1999)

Circular Contextual Insertions/Deletions with Applications to Biomolecular Computation. - Mark Daley; Lila Kari; Greg Gloor; Rani Siromoney (SPIRE/CRIWG, 1999)

Some Properties of Ciliate Bio-operations. - Mark Daley; Lila Kari (Developments in Language Theory, 2002)

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)

Closure and decidability properties of some language classes with respect to ciliate bio-operations. - Mark Daley; Oscar H. Ibarra; Lila Kari (Theor. Comput. Sci., 2003)

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

Voronoi diagrams, vectors and the visually impaired. - Christopher Power; Dawn Gill; Mark Daley (CHI Extended Abstracts, 2006)

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)

Dynamic ADTs: a "don't ask, don't tell" policy for data abstraction. - Geoff Wozniak; Mark Daley; Stephen M. Watt (ILC, 2007)

Intra-Molecular Template-Guided Recombination. - Mark Daley; Michael Domaratzki; Alexis Morris (Int. J. Found. Comput. Sci., 2007)

Regulated RNA rewriting: Modelling RNA editing with guided insertion. - Franziska Biegler; Michael J. Burrell; Mark Daley (Theor. Comput. Sci., 2007)

On codes defined by bio-operations. - Mark Daley; Michael Domaratzki (Theor. Comput. Sci., 2007)

On the Processing Power of Protozoa. - Mark Daley (CiE, 2008)

State Complexity of Orthogonal Catenation. - Mark Daley; Michael Domaratzki; Kai Salomaa (DCFS, 2008)

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)

A Useful Bounded Resource Functional Language. - Michael J. Burrell; James H. Andrews; Mark Daley (SOFSEM, 2008)

Computation by Annotation: Modelling Epigenetic Regulation. - Franziska Biegler; Mark Daley; Marjorie Elizabeth Osborne Locke (Int. J. Found. Comput. Sci., 2008)

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

Template-Guided Recombination: From Theory to Laboratory. - Mark Daley; Michael Domaratzki (Algorithmic Bioprocesses, 2009)

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

Constructures: supporting human ingenuity in software. - Jeff Smith; David Mould; Mark Daley (Digit. Creativity, 2009)

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

Orthogonal Concatenation: Language Equations and State Complexity. - Mark Daley; Michael Domaratzki; Kai Salomaa (J. Univers. Comput. Sci., 2010)

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

A relation by palindromic subwords. - Mark Daley; Kalpana Mahalingam (Nat. Comput., 2010)

Orthogonal Shuffle on Trajectories. - Mark Daley; Lila Kari; Shinnosuke Seki 001; Petr Sosík (Int. J. Found. Comput. Sci., 2011)

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

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

One-reversal counter machines and multihead automata: Revisited. - Ehsan Chiniforooshan; Mark Daley; Oscar H. Ibarra; Lila Kari; Shinnosuke Seki 001 (Theor. Comput. Sci., 2012)

Relativized codes. - Mark Daley; Helmut Jürgensen; Lila Kari; Kalpana Mahalingam (Theor. Comput. Sci., 2012)

Computational Nature of Gene Assembly in Ciliates. - Robert Brijder; Mark Daley; Tero Harju; Natasa Jonoska; Ion Petre; Grzegorz Rozenberg (Handbook of Natural Computing, 2012)

HD-CNV: hotspot detector for copy number variants. - Jenna L. Butler; Marjorie Elizabeth Osborne Locke; Kathleen A. Hill; Mark Daley (Bioinform., 2013)

Simulating Cancer Growth Using Cellular Automata to Detect Combination Drug Targets. - Jenna L. Butler; Frances Mackay; Colin Denniston; Mark Daley (UCNC, 2014)

Gene co-citation networks associated with worker sterility in honey bees. - Emma Kate Mullen; Mark Daley; Alanna Gabrielle Backx; Graham James Thompson (BMC Syst. Biol., 2014)

An Invitation to the Study of Brain Networks, with Some Statistical Analysis of Thresholding Techniques. - Mark Daley (Discrete and Topological Models in Molecular Biology, 2014)

Finding Nonlinear Relationships in fMRI Time Series with Symbolic Regression. - James Alexander Hughes; Mark Daley (GECCO (Companion), 2016)

Halting the hallmarks: a cellular automaton model of early cancer growth inhibition. - Jenna L. Butler; Frances Mackay; Colin Denniston; Mark Daley (Nat. Comput., 2016)

Modelling intracranial pressure with noninvasive physiological measures. - James Alexander Hughes; Ethan C. Jackson; Mark Daley (CIBCB, 2017)

An algebraic generalization for graph and tensor-based neural networks. - Ethan C. Jackson; James Alexander Hughes; Mark Daley; Michael Winter 001 (CIBCB, 2017)

Searching for nonlinear relationships in fMRI data with symbolic regression. - James Alexander Hughes; Mark Daley (GECCO, 2017)

Analysis of symbolic models of biometrie data and their use for action and user identification. - James Alexander Hughes; Joseph Alexander Brown; Adil Mehmood Khan; Asad Masood Khattak; Mark Daley (CIBCB, 2018)

On the generalizability of linear and non-linear region of interest-based multivariate regression models for fMRI data. - Ethan C. Jackson; James Alexander Hughes; Mark Daley (CIBCB, 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)

User and Task Identification of Smartwatch Data with an Ensemble of Nonlinear Symbolic Models. - James Alexander Hughes; Joseph Alexander Brown; Adil Mehmood Khan; Asad Masood Khattak; Mark Daley (CEC, 2019)

Generating Nonlinear Models of Functional Connectivity from Functional Magnetic Resonance Imaging Data with Genetic Programming. - James Alexander Hughes; Mark Daley (CEC, 2019)

Novelty search for deep reinforcement learning policy network weights by action sequence edit metric distance. - Ethan C. Jackson; Mark Daley (GECCO (Companion), 2019)

A Fully-Connected Neural Network Derived from an Electron Microscopy Map of Olfactory Neurons in Drosophila Melanogaster for Odor Classification. - Jacob Morra; Mark Daley (SMC, 2020)

Is Human Walking a Network Medicine Problem? An Analysis Using Symbolic Regression Models with Genetic Programming. - Pritika Dasgupta; James Alexander Hughes; Mark Daley; Ervin Sejdic (Comput. Methods Programs Biomed., 2021)

Imposing Connectome-Derived Topology on an Echo State Network. - Jacob Morra; Mark Daley (IJCNN, 2022)

Using Connectome Features to Constrain Echo State Networks. - Jacob Morra; Mark Daley (IJCNN, 2023)

Multifunctionality in a Connectome-Based Reservoir Computer. - Jacob Morra; Andrew Flynn; Andreas Amann; Mark Daley (SMC, 2023)