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"Theoretical Advances in Artificial Immune Systems"

has been in the top 5 of the
"Hottest Articles" in Theoretical Computer Science
since publication in August 2008

journal papers

• Andrea Arcuri, David Robert White, John A. Clark.
  Multi-Objective Improvement of Software using Co-evolution and Smart Seeding.
  IEEE Transactions on Evolutionary Computation (accepted)

• Nikolai W.F. Bode, A. Jamie Wood, Daniel W. Franks.
  The impact of social networks on animal collective motion.
  Animal Behaviour (in press)

• Alastair Droop, Simon J. Hickinbotham
  Properties of Biological Mutation Networks and their Implications for Articial Life.
  Artificial Life, 2011 (accepted)

• Verena Fischer, Simon J. Hickinbotham
  Evolving a Metabolic Subsumption Architecture for Cooperative Control of the E-Puck.
  Journal of Mimetic Computing, 2011 (accepted)

• Julio C. Hernandez-Castro, Juan E. Tapiador, Pedro Peris-Lopez, John A. Clark, El-Ghazali Talbi.
  Metaheuristic traceability attack against SLMAP, an RFID lightweight authentication protocol.
  International Journal of Foundations of Computer Science (in press)

• Simon Poulding, John A. Clark.
  Practical and Effective Statistical Testing by Means of Automated Search.
  IEEE Transactions on Software Engineering (accepted)

• Mark Read, Paul S. Andrews, Jon Timmis, Vipin Kumar.
  Techniques for Grounding Agent-Based Simulations in the Real Domain: a case study in Experimental Autoimmune Encephalomyelisis.
  Journal of Mathematical and Computer Modelling of Dynamical Systems (accepted)

refereed workshop and conference papers

• Edward Clark, Simon Hickinbotham, Susan Stepney, Tim Clarke, Adam Nellis, Mungo Pay, Peter Young.
  Degeneracy enriches Artificial Chemistry binding systems.
  ECAL 2011, Paris, France, August 2011. MIT Press, 2011 (in press)

• Richard Coates, Simon Hickinbotham
  Recovering Hidden Swarm Parameters Using a Simulated "Robofish".
  ECAL 2011, Paris, France, August 2011. MIT Press, 2011 (in press)

• Richard Coates, Simon Hickinbotham
  Estimating Swarm Parameters by Evolutionary Learning.
  GECCO 2011, Dublin, Ireland, July 2011. ACM 2011 (in press)

• Tara Gilliam, Richard C. Wilson, John A. Clark
  Segmentation and Normalisation in Grapheme Codebooks.
  IDCAR 2011, Beijing, China, September 2011. IEEE 2011 (in press)

• Simon Hickinbotham, Susan Stepney, Adam Nellis, Tim Clarke, Ed Clark, Mungo Pay, Peter Young.
  Embodied genomes and metaprogramming.
  ECAL 2011, Paris, France, August 2011. MIT Press, 2011 (in press)

• Tim Hoverd, Susan Stepney.
  Energy as a driver of diversity in open-ended evolution.
  ECAL 2011, Paris, France, August 2011. MIT Press, 2011 (in press)

• Dimitrios S. Kolovos, Richard F. Paige, Fiona Polack.
  On the Evolution of OCL for Capturing Structural Constraints in Modelling Languages.
  Dagstuhl Festschrift in Honour of Egon Boerger: Rigorous Object-Oriented Methods. Springer, 2008
  [invited paper]

• Michael A. Lones, Andy M. Tyrrell, Susan Stepney, Leo S. Caves
  Controlling legged robots with coupled Artificial Biochemical Networks.
  ECAL 2011, Paris, France, August 2011. MIT Press, 2011 (in press)

• Fintan Nagle, Simon Hickinbotham
  Embodied reaction logic in a simulated chemical computer.
  ECAL 2011, Paris, France, August 2011. MIT Press, 2011 (in press)

• Adam Nellis, Susan Stepney.
  Embodied copying for richer evolution.
  ECAL 2011, Paris, France, August 2011. MIT Press, 2011 (in press)

• J. Posso, Adam Sampson, J. Simpson, Jon Timmis
  Process-Oriented Subsumption Architecture for Swarm-Robotic Systems.
  CPA 2011, Limerick, Ireland, June 2011. (in press)

• Susan Stepney, Tim Hoverd.
  Reflecting on Open-Ended Evolution.
  ECAL 2011, Paris, France, August 2011. MIT Press, 2011 (in press)

books / proceedings

• Susan Stepney, Peter Welch, Paul Andrews, Carl Ritson, editors.
  Complex Systems Simulation and Modelling Workshop (CoSMoS 2011), Paris, France, August 2011.
  Luniver Press, 2011

book chapters

• Mark Read, Paul Andrews, Jon Timmis.
  An Introduction to Artificial Immune Systems.
  in Grzegorz Rozenberg, Thomas Bäck, Joost Kok, eds, Handbook of Natural Computing, Springer, 2011

• Sevil Sen, John A.Clark, Juan E. Tapiador.
  An Introduction to Artificial Immune Systems.
  In A. K. Pathan, ed. Security of Self-Organizing Networks: MANET, WSN, WMN, VANET, chapter 6. CRC Press 2011

• Susan Stepney.
  Nonclassical Computation: a dynamical systems perspective.
  in Grzegorz Rozenberg, Thomas Bäck, Joost Kok, eds, Handbook of Natural Computing, volume II, chapter 52, Springer, 2011

journal papers

• Nikolai W.F. Bode, Daniel W. Franks, A. Jamie Wood.
  Limited interactions in flocks: relating model simulations to empirical data.
  Journal of the Royal Society Interface 8(55):301-304, 2011
  doi: 10.1098/rsif.2010.0397

• Nikolai W.F. Bode, A. Jamie Wood, Daniel W. Franks.
  Social networks and models for collective motion in animals.
  Behavioural Ecology and Sociobiology 65(2):117-130, 2011
  doi: 10.1007/s00265-010-1111-0

• Byung-Soo Choi, Samuel L. Braunstein.
  Quantum algorithm for the asymmetric weight decision problem and its generalization to multiple weights.
  Quantum Information Processing. 10:177-188 2011
  doi: 10.1007/s11128-010-0187-9

• Daniel W. Franks, G.S. Oxford.
  The interrelationship between crypsis and colour polymorphism.
  Ecology Letters 14(3):295-300, 2011
  doi: 10.1111/j.1461-0248.2010.01583.x

• Omer Qadir, Jerry Lui, Jon Timmis, Gianluca Tempesti, Andy Tyrrell.
  From Bidirectional Associative Memory to a noise-tolerant, robust Self-Organising Associative Memory.
  Artificial Intelligence 175(2):673-693
  doi: 10.1016/j.artint.2010.10.008

• Colin R. Tosh, Graeme D. Ruxton, Jens Krause, Daniel W. Franks.
  Experiments with humans indicate that decision accuracy drives the evolution of niche width.
  Proceedings of the Royal Society of London B: Biological Sciences 2011 (on line)
  doi: 10.1098/rspb.2011.0478

refereed workshop and conference papers

• Kieran Alden, Paul Andrews, Jon Timmis, H. Veiga-Fernandes, Mark Coles
  Towards Argument-Driven Validation of an in-silico Model of Immune Tissue Organogenesis (extended abstract).
  ICARIS 2011, Cambridge, UK, July 2011. LNCS 6825:66-70, Springer
  doi: 10.1007/978-3-642-22371-6_7

• Paul S. Andrews, Susan Stepney, Tim Hoverd, Fiona A. C. Polack, Adam T. Sampson, Jon Timmis.
  CoSMoS process, models, and metamodels.
  CoSMoS workshop, Paris, France, August 2011, pp.1-13. Luniver Press, 2011

• Mark Blyth, Helen Petrie, John A. Clark
  F for fake: four studies on how we fall for phish.
  CHI 2011, Vancouver, Canada, May 2011, pp.3469-78. ACM, 2011
  doi: 10.1145/1978942.1979459

• Alastair Droop, Philip Garnett, Fiona A. C. Polack, Susan Stepney.
  Multiple model simulation: modelling cell division and differentiation in the prostate.
  CoSMoS workshop, Paris, France, August 2011, pp.79-111. Luniver Press 2011

• James Hilder, Nick Owens, Peter Hickey, Stuart Cairns, David Kilgour, Jon Timmis, Andy Tyrrell
  Parameter Optimisation of the Receptor Density Algorithm.
  ICARIS 2011, Cambridge, UK, July 2011. LNCS 6825:226-239, Springer
  doi: 10.1007/978-3-642-22371-6_21

• Amelia Ritahani Ismail, Jon Timmis
  Modelling Containment Mechanisms in the Immune System for Applications in Engineering (extended abstract).
  ICARIS 2011, Cambridge, UK, July 2011. LNCS 6825:77-80, Springer
  doi: 10.1007/978-3-642-22371-6_9

• Viv Kendon, Angelika Sebald, Susan Stepney, Matthias Bechmann, Peter Hines, Robert C. Wagner
  Heterotic Computing.
  Unconventional Computation 2011, Turku, Finland, June 2011. LNCS 6714:113-124, Springer, 2011
  doi: 10.1007/978-3-642-21341-0_16

• HuiKeng Lau, Jon Timmis, Iain Bate
  Collective Self-detection Scheme for Adaptive Error Detection in a Foraging Swarm of Robots.
  ICARIS 2011, Cambridge, UK, July 2011. LNCS 6825:254-267, Springer
  doi: 10.1007/978-3-642-22371-6_23

• Yang Liu, Gianluca Tempesti, James A. Walker, Jon Timmis, Andrew M. Tyrrell, Paul Bremner
  A Self-scaling Instruction Generator Using Cartesian Genetic Programming .
  EuroGP 2011, Torino, Italy, April 2011. LNCS 6621:298-309, Springer, 2011
  doi: 10.1007/978-3-642-20407-4_26

• Yang Liu, Jon Timmis, Tim Clarke
  A Lymphocyte-Cytokine Network Inspired Algorithm for Data Analysis.
  ICARIS 2011, Cambridge, UK, July 2011. LNCS 6825:187-197, Springer
  doi: 10.1007/978-3-642-22371-6_18

• Fiona A. C. Polack, Alastair Droop, Philip Garnett, Teodor Ghetiu, Susan Stepney.
  Simulation validation: exploring the suitability of a simulation of cell division and differentiation in the prostate.
  CoSMoS workshop, Paris, France, August 2011, pp.113-133. Luniver Press, 2011

• Simon Poulding, John A. Clark, Hélène Waeselynck
  A Principled Evaluation of the Effect of Directed Mutation on Search-Based Statistical Testing.
  Search Based Software Testing 2011, at ICST 2011, Berlin, Germany, March 2011. IEEE, 2011
  [best paper]

• Omer Qadir, Jerry Lui, Gianluca Tempesti, Jon Timmis, Andy Tyrrell
  Hardware architecture for a Bidirectional Hetero-Associative Protein Processing Associative Memory.
  CEC 2011, New Orleans, USA, June 2011. IEEE, 2011

• Sam Ratcliff, David R. White, John A. Clark
  Searching for Invariants using Genetic Programming and Mutation Testing.
  GECCO 2011, Dublin, Ireland, July 2011, pp.1907-14. ACM 2011
  doi: 10.1145/2001576.2001832
  [best paper]

• Jan Staunton, John A Clark
  Finding Short Counterexamples in Promela Models Using Estimation of Distribution Algorithms.
  GECCO 2011, Dublin, Ireland, July 2011, pp.1923-30. ACM 2011
  doi: 10.1145/2001576.2001834

• Richard A. Williams, Mark Read, Jon Timmis, Paul S. Andrews, Mark Coles
  In Silico Investigation into CD8Treg Mediated Recovery in Murine Experimental Autoimmune Encephalomyelitis (extended abstract).
  ICARIS 2011, Cambridge, UK, July 2011. LNCS 6825:51-54, Springer (in press)
  doi: 10.1007/978-3-642-22371-6_5
  [best Computational Immunology paper]

• Antonio G. Zamorano, Jon Timmis, Andy Tyrrell
  A Flexible Decentralised Communication Architecture on a Field Programmable Gate Array for Swarm System Simulations.
  CEC 2011, New Orleans, USA, June 2011. IEEE, 2011

other

• Jon Timmis, Paul Andrews, Andrew Hone.
  Special Issue on Theoretical Aspects of Artificial Immune Systems.
  Theoretical Computer Science 412(6):500-1, 2011
  doi: 10.1016/j.tcs.2010.12.014

books / proceedings

• Cristian S. Calude, Masami Hagiya, Kenichi Morita, Grzegorz Rozenberg, Jon Timmis, eds.
  Proceedings of the 9th International Conference on Unconventional Computation (UC 2010), Tokyo, Japan, June 2010.
  LNCS 6079. Springer, 2010.
  doi: 10.1007/978-3-642-13523-1

• Emma Hart, C. McEwan, Jon Timmis, Andy Hone, eds.
  Proceedings of the 9th International Conference on Artificial Immune Systems (ICARIS 2010), Edinburgh, UK, July 2010.
  LNCS 6209. Springer, 2010.
  doi: 10.1007/978-3-642-14547-6

• Mike Hinchey, Bernd Kleinjohann, Lisa Kleinjohann, Peter Lindsay, Franz J. Rammig, Jon Timmis, Marilyn Wolf, eds.
  Distributed, Parallel and Biologically Inspired Systems (DIPES 2010/BICC 2010), Brisbane, Australia, September 2010.
  IFIP Advances in Information and Communication Technology 329. Springer, 2010.
  doi: 10.1007/978-3-642-15234-4

• Susan Stepney, Peter Welch, Paul Andrews, Adam Sampson, editors.
  Complex Systems Simulation and Modelling Workshop (CoSMoS 2010), Odense, Denmark, August 2010.
  Luniver Press, 2010

book chapters

• Paul S. Andrews, Jon Timmis.
  Tunable Detectors for Artificial Immune Systems: From Model to Algorithm.
  in D. Flower, M. Davies, S. Ranganathan, eds, Bioinformatics for Immunomics, Immunomics Reviews 3, Springer, 2010
  doi: 10.1007/978-1-4419-0540-6_9

• Alastair Droop, Simon Hickinbotham
  Application of Small-World Mutation Topologies to an Artificial Life System.
  ECAL 2011, Paris, France, August 2011. MIT Press, 2011 (in press)

• Dan W. Franks, Graeme D. Ruxton.
  Robustness of Neural Network Models.
  in Sangdun Choi, ed, Systems Biology for Signaling Networks, chapter 13, pp337-352, Springer, 2010

• Dan W. Franks, Graeme D. Ruxton.
  Methodological Issues with Modelling Ecological Learning with Artificial Neural Networks.
  in Colin R. Tosh, Graeme D. Ruxton, eds, Modelling Perception With Artificial Neural Networks, chapter 16, pp318-333, CUP, 2010

• Peter Hines, Samuel L. Braunstein.
  The structure of partial isometries.
  in Simon Gay, Ian Mackie, eds, Semantic Techniques in Quantum Computation, chapter 9, pp361-388, CUP, 2010

• Nick Owens, Susan Stepney.
  The Game of Life Rules on Penrose Tilings: still life and oscillators.
  in Andy Adamatsky, ed, Game of Life Cellular Automata, chapter 18, pp331-378, Springer, 2010
  doi: 10.1007/978-1-84996-217-9_18

• Jon Timmis.
  Artificial Immune Systems.
  In Claude Sammut, Geoffrey I. Webb, (eds.) Encyclopedia of Machine Learning (entry 348), Springer 2010

• Jon Timmis, Andy Tyrrell, M. Mokhtar, A. Ismail, Nick Owens, Ran Bi.
  An Artificial Immune System for Robot Organisms.
  in P. Levi, S. Kernback, eds, Symbiotic Multi-Robot Organisms: Reliability, Adaptability and Evolution, pp.282-305, Springer, 2010
  doi: 10.1007/978-3-642-11692-6_5

journal papers

• Nikolai W.F. Bode, Jolyon S. Faria, Daniel W. Franks, Jens Krause, A. Jamie Wood.
  How perceived threat increases synchronization in collectively moving animal groups.
  Proc. Roy. Soc. London B: Biological Sciences 277(1697):3065-3070, 2010
  doi: 10.1098/rspb.2010.0855

• Nikolai W.F. Bode, Daniel W. Franks, A. Jamie Wood.
  Making noise: emergent stochasticity in collective motion.
  Journal of Theoretical Biology 267(3):292-299, 2010
  doi: 10.1016/j.jtbi.2010.08.034

• Xun Dong, John A. Clark, Jeremy L. Jacob.
  Defending the weakest link: phishing websites detection by analysing user behaviours.
  Telecommunication Systems, 45(2-3):215-226, 2010
  doi: 10.1007/s11235-009-9247-9

• Dan W. Franks, Graeme D. Ruxton, Richard James.
  Sampling Animal Association Networks with the Gambit of the Group.
  Behavioral Ecology and Sociobiology, 64(3):493-503, 2010
  doi: 10.1007/s00265-009-0865-8

• Philip Garnett, Arno Steinacher, Susan Stepney, Richard Clayton, Ottoline Leyser.
  Computer Simulation: the imaginary friend of auxin transport biology.
  BioEssays, 32(9):828-835, 2010
  doi: 10.1002/bies.200900185

• A. MacFarlane, A. Secker, P. May, Jon Timmis.
  An Experimental Comparison of a Genetic Algorithm and a Hill-Climber for Term Selection.
  Journal of Documentation. 66(4):513-531, 2010
  doi: 10.1108/00220411011052939

• Nick Owens, Susan Stepney.
  Investigations of the Game of Life cellular automata rules on Penrose Tilings: lifetime, ash and oscillator statistics.
  Journal of Cellular Automata, 5(3):207-225, 2010
  [special issue, Automata 2008]

• Nick Owens, Jon Timmis, Andrew Greensted, Andy Tyrrell.
  Elucidation of T Cell Signalling Models.
  Journal of Theoretical Biology 262(3):452-470, 2010
  doi: 10.1016/j.jtbi.2009.10.017

• Edward J. Powley, Susan Stepney.
  Counting preimages of homogeneous configurations in 1-dimensional cellular automata.
  Journal of Cellular Automata, 5(4-5):353-381, 2010

• Marta Roselló-Merino, Matthias Bechmann, Angelika Sebald, Susan Stepney.
  Classical Computing in Nuclear Magnetic Resonance.
  Int. J. Unconventional Computing, 6(3-4):163-195, 2010

• Andrew Secker, Matthew N. Davies, Alex A. Freitas, Ed Clark, Jon Timmis, Darren R. Flower.
  Hierarchical Classification of G-Protein-Coupled-Receptors with Data-Driven Selection of Attributes and Classifiers.
  International Journal of Data Mining and Bioinformatics 4(2):191-210, 2010
  doi: 10.1504/IJDMB.2010.032150

• Jon Timmis, Paul Andrews, Emma Hart.
  On Artificial Immune Systems and Swarm Intelligence.
  Swarm Intelligence 4:247-273, 2010
  doi: 10.1007/s11721-010-0045-5

• Thomas A. Walker, Samuel L. Braunstein.
  Five-wave-packet linear optics quantum-error-correcting code.
  Physics Review A 81(6):062305, 2010
  doi: 10.1103/PhysRevA.81.062305

refereed workshop and conference papers

• Luca Albergante, Jon Timmis, Paul Andrews, Lynette Beattie, Paul M. Kaye.
  A Petri Net Model of Granulomatous Inflammation.
  ICARIS 2010, Edinburgh, UK, July 2010, LNCS 6209:1-3, Springer 2010
  doi: 10.1007/978-3-642-14547-6_1

• Matthias Bechmann, Angelika Sebald, Susan Stepney.
  From binary to continuous gates -- and back again
  ICES 2010, York, UK, September 2010. LNCS 6274:335-347, Springer, 2010
  doi: 10.1007/978-3-642-15323-5_29

• Ran Bi, Jon Timmis, Andy Tyrrell.
  The Diagnostic Dendritic Cell Algorithm for Robotic Systems.
  CEC 2010, Barcelona, Spain, July 2010, pp4280-87, IEEE Press, 2010

• Mark Blythe, John A. Clark.
  The Phish in the Pond: Scam emails as Literature.
  Critical Dialogue: Interaction, Experience and Cultural Theory Workshop, at ACM CHI 2010, Atlanta, USA, April 2010, pp1-7, 2010

• Hao Chen, John A. Clark, Siraj A. Shaikh, Howard Chivers, Philip Nobles.
  Optimising IDS Sensor Placement.
  ARES 2010, Krakow, Poland, February 2010, pp315-320, IEEE Press, 2010
  doi: 10.1109/ARES.2010.92

• Adam Faulconbridge, Susan Stepney, Julian Miller, Leo Caves
  RBN-World: The hunt for a rich AChem.
  ALife XII, Odense, Denmark, August 2010, pp261-268. MIT Press, 2010

• Verena Fischer, Simon J. Hickinbotham
  A metabolic subsumption architecture for cooperative control of the e-puck.
  NICSO'10: Grenada, Spain 2010, SCI 284:1-12, Springer, 2010
  doi: 10.1007/978-3-642-12538-6_1

• Philip Garnett, Susan Stepney, Francesca Day, Ottoline Leyser.
  Using the CoSMoS Process to Enhance an Executable Model of Auxin Transport Canalisation.
  CoSMoS workshop, Odense, Denmark, August 2010, pp9-32. Luniver Press 2010

• Tara Gilliam, Richard Wilson, John A. Clark.
  Scribe Identification in Medieval English Manuscripts.
  ICPR 2010, Istanbul, Turkey, August 2010, pp1880-1883, IEEE Press, 2010
  doi: 10.1109/ICPR.2010.463

• Simon Hickinbotham, Edward Clark, Susan Stepney, Tim Clarke, Adam Nellis, Mungo Pay, Peter Young.
  Diversity from a monoculture: effects of mutation-on-copy in a string-based artificial chemistry.
  ALife XII, Odense, Denmark, August 2010, pp24-31. MIT Press, 2010

• Tim Hoverd, Susan Stepney.
  Formalising Harmony Seeking Rules of Morphogenesis.
  ALife XII, Odense, Denmark, August 2010, pp386-393. MIT Press, 2010

• Mic Lones, Andy Tyrrell, Susan Stepney, Leo Caves.
  Controlling Complex Dynamics with Artificial Biochemical Networks.
  EuroGP 2010, Istanbul, Turkey, April 2010, LNCS 6021:159-170, Springer 2010
  doi: 10.1007/978-3-642-12148-7_14

• Yang Liu, Jon Timmis, Omer Qadir, Gianluca Tempesti, Andy Tyrrell.
  A Developmental and Immune-Inspired Dynamic Task Allocation Algorithm for Microprocessor Array Systems.
  ICARIS 2010, Edinburgh, UK, July 2010, LNCS 6209:199-212, Springer 2010
  doi: 10.1007/978-3-642-14547-6_16

• Adam Nellis, Susan Stepney.
  Automatically moving between meta-levels in Artificial Chemistries.
  ALife XII, Odense, Denmark, August 2010, pp269-276. MIT Press, 2010

• Jennifer Owen, Susan Stepney, Jon Timmis, Alan Winfield
  Exploiting Loose Horizontal Coupling in Evolutionary Swarm Robotics.
  ANTS 2010, Brussels, Belgium, September 2010, LNCS 6234:432-439, Springer 2010
  doi: 10.1007/978-3-642-15461-4_41

• Fiona Polack, Paul Andrews, Teodor Ghetiu, Mark Read, Susan Stepney, Jon Timmis, Adam Sampson.
  Reflections on the Simulation of Complex Systems for Science.
  ICECCS 2010, Oxford, UK, March 2010, pp.276-285, IEEE 2010

• Omer Qadir, J. Liu, Jon Timmis, Gianluca Tempesti, Andy Tyrrell.
  Principles of Protein Processing for a Self-Organising Associative Memory.
  CEC 2010, Barcelona, Spain, July 2010, pp3836-43, IEEE Press, 2010

• Jan Staunton, John A. Clark.
  Searching for Safety Violations Using Estimation of Distribution Algorithms.
  ICSTW 2010, Paris, France, April 2010, pp212-221, IEEE Press, 2010
  doi: 10.1109/ICSTW.2010.24
  [best student paper]

• J. E. Tapiador, John A. Clark.
  Learning Autonomic Security Reconfiguration Policies.
  TSP-10, at CIT 2010, Bradford, UK, June 2010, pp902-909, IEEE Press, 2010
  doi: 10.1109/CIT.2010.168

• Jon Timmis, Lachlan Murray, Mark Neal.
  A Neural-Endocrine Architecture for Foraging in Swarm Robotic Systems.
  Studies in Computational Intelligence, NISCO 2010, Granada, Spain, May 2010, pp319-330, Springer 2010
  doi: 10.1007/978-3-642-12538-6_27

• Jon Timmis, Andy Tyrrell.
  On Homeostasis in Collective Robotic Systems.
  ICARIS 2010, Edinburgh, UK, July 2010, LNCS 6209:307-309, Springer 2010
  doi: 10.1007/978-3-642-14547-6_25

• David Robert White, Juan E. Tapiador, Julio César Hernández Castro, John A. Clark.
  Fine-Grained Timing Using Genetic Programming.
  EuroGP 2010, Istanbul, Turkey, April 2010, LNCS 6021:325-336, Springer 2010
  doi: 10.1007/978-3-642-12148-7_28

technical reports

• Paul S. Andrews, Adam T. Sampson, Fiona Polack, Susan Stepney, Jon Timmis
  The CoSMoS Process, version 0.1: A Process for the Modelling and Simulation of Complex Systems,
  Technical report YCS-2010-453, University of York, March 2010

• Simon Hickinbotham, Edward Clark, Susan Stepney, Tim Clarke, Adam Nellis, Mungo Pay, Peter Young
  Specification of the stringmol chemical programming language version 0.1,
  Technical report YCS-2010-457, University of York, 2010

• Susan Stepney
  Visualising the dynamics of Random Boolean Networks: examples of network size, mutation, canalisation,
  Technical report YCS-2010-448, University of York, February 2010

other

• Susan Stepney
  Report on 8th International Conference on Unconventional Computation 2009.
  EATCS Bulletin, 100:173-175, 2010

• Jon Timmis, Paul Andrews, Emma Hart.
  Special Issue on Artificial Immune Systems.
  Swarm Intelligence 4:245-6, 2010
  doi: 10.1007/s11721-010-0047-3

books / proceedings

• Paul Andrews, Jon Timmis, Nick Owens, Uwe Aickelin, Emma Hart, Andrew Hone, Andy Tyrrell, editors.
  Proceedings of the 8th International Conference on Artificial Immune Systems (ICARIS 2009), York, UK, August 2009.
  LNCS 5666. Springer, 2009.
  doi: 10.1007/978-3-642-03246-2

• Susan Stepney, Peter Welch, Paul Andrews, Jon Timmis, editors.
  Complex Systems Simulation and Modelling Workshop (CoSMoS 2009), York, UK, August 2009.
  Luniver Press, 2009

book chapters

• Sevil Sen, John A. Clark.
  Intrusion Detection in Mobile Ad Hoc Networks.
  In Sudip Misra, Isaac Woungang, Subhas C. Misra (eds) Guide to Wireless Ad Hoc Networks, chapter 17. Springer 2009
  doi: 10.1007/978-1-84800-328-6_17

• Jon Timmis.
  ImmuneComputing.
  In Robert A. Meyers (ed) Encyclopaedia of Complexity and System Science, volume LXXX, part 9, pp4776-4788 (entry 282). Springer 2009
  doi: 10.1007/978-0-387-30440-3_282

journal papers

• Takao Aoki, Go Takahashi, Tadashi Kajiya, Jun-ichi Yoshikawa, Samuel L. Braunstein, Peter van Loock, Akira Furusawa.
  Quantum error correction beyond qubits.
  Nature Physics 5:541-546, 2009
  doi: 10.1038/nphys1309

• Howard Chivers, John A. Clark, Pau-Chen Cheng.
  Risk profiles and distributed risk assessment .
  Computers and Security, 28(7):521-535, 2009
  doi: 10.1016/j.cose.2009.04.005

• Dan W. Franks, Richard James, Jason Noble, Graeme D. Ruxton.
  A foundation for developing a methodology for social network sampling.
  Behavioral Ecology and Sociobiology, 63(7):1079-1088, 2009
  doi: 10.1007/s00265-009-0729-2

• Dan W. Franks, Geoff S. Oxford.
  The evolution of exuberant visible polymorphisms.
  Evolution 63(10):2697-2706, 2009
  doi: 10.1111/j.1558-5646.2009.00748.x

• Dan W. Franks, Graeme D. Ruxton, Thomas N. Sherratt.
  Warning signals evolve to disengage Batesian mimics.
  Evolution, 63(1):256-267, 2009
  doi: 10.1111/j.1558-5646.2008.00509.x

• Peter Kaufmann, Sigrid Stagl, Dan W. Franks.
  Simulating the Diffusion of Organic Farming Practices in Two New EU Member States.
  Ecological Economics, 68(10):2580-2593, 2009
  doi: 10.1016/j.ecolecon.2009.04.001

• A. K. Pati, Samuel L. Braunstein.
  Role of entanglement in quantum computation.
  Journal of the Indian Institute of Science 89(3):295-302, 2009

• Stefano Pirandola, Samuel L. Braunstein, Seth Lloyd, Stefano Mancini.
  Confidential Direct Communications: A Quantum Approach Using Continuous Variables.
  IEEE Journal of Selected Topics in Quantum Electronics 15(6):1570-80 2009
  doi: 10.1109/JSTQE.2009.2021147

• Stefano Pirandola, R. García-Patrón, Samuel L. Braunstein, Seth Lloyd.
  Direct and reverse secret-key capacities of a quantum channel.
  Physics Review Letters 102:050503-1/4 2009
  doi: 10.1103/PhysRevLett.102.050503

• Edward J. Powley, Susan Stepney.
  Automorphisms of transition graphs for linear cellular automata.
  Journal of Cellular Automata 4(4):293-310, 2009
  [special issue, Automata 2008]

• Edward J. Powley, Susan Stepney.
  Automorphisms of transition graphs for elementary cellular automata.
  Journal of Cellular Automata 4(2):125-136, 2009
  [special issue, Automata 2007]

• Andrew Secker, Matthew N. Davies, Alex A. Freitas, Jon Timmis, Ed Clark, Darren R. Flower.
  An artificial immune system for clustering amino acids in the context of protein function classification.
  Journal of Mathematical Modelling and Algorithms, 8(2):103-123, 2009
  doi: 10.1007/s10852-009-9107-3

• Susan Stepney.
  Non-Classical Hypercomputation.
  Int. J. Unconventional Computing 5(3-4):267-276, 2009

• Juan E. Tapiador, J. C. Hernandez-Castro, John A. Clark, Susan Stepney.
  Highly entangled multi-qubit states with simple algebraic structure.
  J. Phys. A, 42:415301, 2009
  doi: 10.1088/1751-8113/42/41/415301

refereed workshop and conference papers

• Nurulhuda Firdaus Mohd Azmi, Jon Timmis, Fiona Polack.
  Profile Adaptation in Adaptive Inforamtion Filtering: A Immune-Inspired Approach.
  International Conference on Soft Computing and Pattern Recognition, Malacca, Malaysia, 4-7 December 2009, pp.414-441, IEEE Press, 2009
  doi: 10.1109/SoCPaR.2009.87

• Darren Beaumont, Susan Stepney.
  Grammatical Evolution of L-Systems.
  CEC 2009, Trondheim, Norway, May 2009, pp.2446-2453. IEEE Press, 2009

doi: 10.1109/CEC.2009.4983247

• Hao Chen, John A. Clark, Juan E. Tapiador, Siraj A. Shaikh, Howard Chivers and Philip Nobles.
  A Multi-objective Optimisation Approach to IDS Sensor Placement.
  CISIS 2009, Burgos, Spain, September 2009, AISC 63:101-108, Springer, 2009
  doi: 10.1007/978-3-642-04091-7_13

• Piero Conca, Giuseppe Nicosia, Giovanni Stracquadanio, Jon Timmis.
  Nominal-Yield-Area Trade off in Automatic Synthesis of Analog Circuits: A Genetic Programming Approach using Immune-Inspired Operators.
  NASA/ESA Conference on Adaptive Hardware and Systems, San Fransisco, USA, July 2009. pp399-406, IEEE Press

• Gemma Danks, Susan Stepney, Leo Caves.
  Co-translational protein folding with L-Systems.
  ECAL 2009, Budapest, Hungary, September 2009. LNCS 5777:289-296. Springer, 2011
  doi: 10.1007/978-3-642-21283-3_36

• Adam Faulconbridge, Susan Stepney, Julian Miller, Leo Caves
  RBNWorld: Sub-symbolic Artificial Chemistry.
  ECAL 2009, Budapest, Hungary, September 2009. LNCS 5777:377-384. Springer, 2011
  doi: 10.1007/978-3-642-21283-3_47

• Anton Flugge, Jon Timmis, Paul Andrews, J. Moore, Paul Kaye.
  Modelling and Simulation of Granuloma Formation in Visceral Leishmaniasis.
  CEC 2009, Trondheim, Norway, May 2009, pp.3052-3059. IEEE Press, 2009

doi: 10.1109/CEC.2009.4983329

• Kamran Ghani, John A. Clark
  Automatic Test Data Generation for Multiple Condition and MCDC Coverage.
  ICSEA 2009, Porto, Portugal, September 2009, pp.152-157. IEEE Press, 2009

doi: 10.1109/ICSEA.2009.31
[top paper prize]

• Kamran Ghani, John A. Clark
  Widening the Goal Posts: Program Stretching to Aid Search Based Software Testing.
  SSBSE 2009, Windsor, UK, May 2009, pp.122-131. IEEE, 2009

doi: 10.1109/SSBSE.2009.26

• Kamran Ghani, John A. Clark, Yuan Zhan
  Comparing Algorithms for Search-Based Test Data Generation of Matlab Simulink Models.
  CEC 2009, Trondheim, Norway, May 2009, pp.2940-2947. IEEE Press, 2009

doi: 10.1109/CEC.2009.4983313

• Teodor Ghetiu, Robert D. Alexander, Paul Andrews, Fiona Polack, James Bown.
  Equivalence Arguments for Complex Systems Simulations -- A Case-Study.
  CoSMoS 2009, York, UK, August 2009. pp101-140. Luniver Press, 2009

• Julio C. Hernandez-Castro, Juan E. Tapiador, Pedro Peris-Lopez, John A. Clark, El-Ghazali Talbi.
  Metaheuristic traceability attack against SLMAP, an RFID lightweight authentication protocol.
  IPDPS 2009, Rome, Italy, May 2009, pp.1-5, IEEE Press, 2009
  doi: 10.1109/IPDPS.2009.5161121

• Simon Hickinbotham, Ed Clark, Susan Stepney, Tim Clarke, Adam Nellis, Mungo Pay, Peter Young
  Molecular microprograms.
  ECAL 2009, Budapest, Hungary, September 2009. LNCS 5777:297-304. Springer, 2011
  doi: 10.1007/978-3-642-21283-3_37

• Simon Hickinbotham, Ed Clark, Susan Stepney, Tim Clarke, Peter Young
  Gene Regulation in a Particle Metabolome.
  CEC 2009, Trondheim, Norway, May 2009, pp.3024-3031. IEEE Press, 2009

doi: 10.1109/CEC.2009.4983325

• Tim Hoverd, Susan Stepney.
  Environment orientation: an architecture for simulating complex system.
  CoSMoS 2009, York, UK, August 2009. pp67-82. Luniver Press, 2009

• Raja Humza, Oliver Scholz, Maizura Mokhtar, Jon Timmis, Andy Tyrrell.
  Towards Energy Homeostasis in an Autonomous Self-Reconfigurable Modular Robotic Organism.
  ComputationWorld 2009, Athens, Greece, 15-20 November 2009 pp.21-26, IEEE Press, 2009

doi: 10.1109/ComputationWorld.2009.83

• Amelia Rita Ismail, Jon Timmis.
  Aggregation of Swarms for Fault Tolerance in Swarm Robotics using an Immuno-engineering Approach.
  UKCI 2009, Nottingham, UK, 7-9 September 2009

• Serge Kernbach, Heiko Hamann, Jürgen Stradner, Ronald Thenius, Thomas Schmickl, Karl Crailsheim, A.C. van Rossum, Michele Sebag, Nicolas Bredeche, Yao Yao, Guy Baele, Yves Van de Peer, Jon Timmis, Maizura Mokhtar, Andy Tyrrell, A.E. Eiben, S.P. McKibbin, Wenguo Liu, Alan F.T. Winfield.
  On adaptive self-organization in artificial robot organisms.
  ComputationWorld 2009, Athens, Greece, 15-20 November 2009 pp.33-43, IEEE Press, 2009
  doi: 10.1109/ComputationWorld.2009.9

• Dimitrios S. Kolovos, Louis Rose, Richard Paige, Fiona Polack.
  Raising the Level of Abstraction in the Development of GMF-based Graphical Model Editors.
  Proc. 3rd Workshop on Modeling in Software Engineering (MISE), Vancouver, Canada, May 2009, pp.13-19, IEEE Press, 2009
  doi: 10.1109/MISE.2009.5069891

• HuiKeng Lau, Iain Bate, Jon Timmis.
  An Immuno-engineering Approach for Anomaly Detection in Swarm Robotics.
  ICARIS 2009, York, UK, August 2009. LNCS 5666:136-150, Springer, 2009
  doi: 10.1007/978-3-642-03246-2_16

• Yow Tzu Lim, Pau-Chen Cheng, Pankhaj Rohatgi, John A. Clark.
  Continuous Security Policy Learning.
  WISG'09, at CCS 2009, Chicago, USA, November 2009, pp39-48. ACM, 2009
  doi: 10.1145/1655168.1655177

• HuiKeng Lau, Jon Timmis, Ian Bate.
  Anomaly Detection Inspired by Immune Network Theory: A Proposal.
  CEC 2009, Trondheim, Norway, May 2009, pp.3045-3041. IEEE Press, 2009
  doi: 10.1109/CEC.2009.4983328

• M. Mokhtar, Ran Bi, Jon Timmis, Andy Tyrrell.
  A Modified Dendritic Cell Algorithm for On-Line Error Detection in Robotic System.
  CEC 2009, Trondheim, Norway, May 2009, pp.2055-2062. IEEE Press, 2009
  doi: 10.1109/CEC.2009.4983194

• Nick Owens, Andy Greensted, Jon Timmis, Andy Tyrrell.
  T-cell Recpetor Signalling Inspired Kernal Density Estimation and Anomaly Detection.
  ICARIS 2009, York, UK, August 2009. LNCS 5666:122-135, Springer, 2009
  doi: 10.1007/978-3-642-03246-2_15

• Richard Paige, Dimitrios S. Kolovos, Louis Rose, Nicholas Drivalos, Fiona Polack.
  The Design of a Conceptual Framework and Technical Infrastructure for Model Management Language Engineering.
  ICECCS'09, Potsdam, Germany, 2009, pp.162-171, IEEE Press, 2009
  doi: 10.1109/ICECCS.2009.14

• Andrew J. Payne, Susan Stepney.
  Representation and Structural biases in CGP.
  CEC 2009, Trondheim, Norway, May 2009, pp.1064-1071. IEEE Press, 2009
  doi: 10.1109/CEC.2009.4983064

• Stefano Pirandola, Samuel L. Braunstein and Seth Lloyd.
  On the Security and Degradability of Gaussian Channels.
  TQC 2009, Waterloo, Canada, May 2009. LNCS 5906:47-55, Springer, 2009
  doi: 10.1007/978-3-642-10698-9_5

• Fiona Polack, Paul Andrews, Adam Sampson
  The engineering of concurrent simulations of complex systems.
  CEC 2009, Trondheim, Norway, May 2009, pp.217-224. IEEE Press, 2009
  doi: 10.1109/CEC.2009.4982951

• Mark Read, Jon Timmis, Paul Andrews, Vipin Kumar.
  Using UML to Model EAE and its Regulatory Network.
  ICARIS 2009, York, UK, August 2009. LNCS 5666:4-6, Springer, 2009
  doi: 10.1007/978-3-642-03246-2_2

• Mark Read, Jon Timmis, Paul Andrews, Vipin Kumar.
  A Domain Model of Experimental Autoimmune Encephalomyelitis.
  CoSMoS 2009, York, UK, August 2009. pp9-44. Luniver Press, 2009

• Sion Ll. Rhys, Simon M. Poulding, John A. Clark.
  Using automated search to generate test data for Matlab.
  GECCO 2009, Montreal, Canada, July 2009. pp1697-1704. ACM Press, 2009
  doi: 10.1145/1569901.1570128

• Sevil Sen, John A. Clark.
  A grammatical evolution approach to intrusion detection on mobile ad hoc networks.
  WISEC 2009, Zurich, Switzerland, March 2009, pp95-102. ACM Press 2009.
  doi: 10.1145/1514274.1514289

• Sevil Sen, John A. Clark, Juan E. Tapiador.
  Power-Aware Intrusion Detection in Mobile Ad Hoc Networks .
  ADHOCNETS 2009, Niagra Falls, Ontario, Canada, September 2009, LNICS 28:224-239. Springer 2009.
  doi: 10.1007/978-3-642-11723-7_15

• Siraj A. Shaikh, Howard Chivers, Philip Nobles, John A. Clark, Hao Chen.
  A Deployment Value Model for Intrusion Detection Sensors.
  ISA 2009, Seoul, Korea, June 2009. LNCS 5576:250-259, Springer, 2009
  doi: 10.1007/978-3-642-02617-1_26

[best paper]

• Susan Stepney.
  Visualising Random Boolean Network Dynamics: mutation and canalisation.
  ECAL 2009, Budapest, Hungary, September 2009. LNCS 5777:369-376. Springer, 2011
  doi: 10.1007/978-3-642-21283-3_46

• Susan Stepney.
  Visualising Random Boolean Network Dynamics.
  GECCO 2009, Montreal, Canada, July 2009. pp1781-82. ACM Press, 2009
  doi: 10.1007/10.1145/1569901.1570157

• Jon Timmis, Mark Neal, James Thorniley.
  An adaptive neuro-endocrine system for robotic systems.
  RIISS 2009, Nashville, TN, USA, March 2009, pp.128-136. IEEE Press, 2009

doi: 10.1109/RIISS.2009.4937917

• David R. White, Simon Poulding.
  A Rigorous Evaluation of Crossover and Mutation in Genetic Programming .
  EuroGP 2009, Tubingen, Germany, April 2009. LNCS 5481:220-231. Springer, 2009
  doi: 10.1007/978-3-642-01181-8_19

technical reports

• Yow Tzu Lim, Pau Chen Cheng, Pankaj Rohatgi, John A. Clark
  Dynamic Security Policy Learning,
  Technical report RC24865, IBM, 2009

books / proceedings

• Susan Stepney, Fiona Polack, Peter Welch, editors.
  Complex Systems Simulation and Modelling Workshop (CoSMoS 2008), York, UK, September 2008.
  Luniver Press, 2008

• Peter H. Welch, Susan Stepney, Fiona Polack, Fred Barnes, Alistair McEwan, G. S. Stiles, J. F. Broenink, Adam Sampson, editors.
  Communicating Process Architectures (CPA 2008), York, UK, September 2008.
  IOS Press, 2008.

book chapters

• Arun K. Pati, Samuel L. Braunstein.
  Can Arbitrary Quantum Systems Undergo Self-Replication?
  In Derek Abbott, Paul C. W. Davies, Arun K. Pati, eds. Quantum Aspects of Life. Chapter 11. Imperial College Press, 2008

journal papers

• Matthew N. Davies, Andrew Secker, Alex A. Freitas, Ed Clark, Jon Timmis, Darren R. Flower.
  Optimising amino acid groupings for GPCR classification
  Bioinformatics 24(18):1980-1986, 2008
  doi: 10.1093/bioinformatics/btn382

• Matthew N. Davies, Andrew Secker, Alex A. Freitas, Jon Timmis, Ed Clark, Darren R. Flower.
  Alignment-Independent Techniques for Protein Classification
  Current Proteomics 5(4):217-223, 2008
  doi: 10.2174/157016408786733770

• Matthew N. Davies, Andrew Secker, Mark Halling-Brown, David S. Moss, Alex A. Freitas, Jon Timmis, Edward Clark, Darren R. Flower.
  GPCRTree: online hierarchical classification of GPCR function
  BMC Research Notes 1:67, 2008
  doi: 10.1186/1756-0500-1-67

• Dan W. Franks, Jason Noble, Peter Kaufmann, Sigrid Stagl.
  Extremism Propagation in Social Networks with Hubs.
  Adaptive Behaviour 16(4):264-274, 2008

• Dan W. Franks, Graeme D. Ruxton.
  How Robust are Neural Network Models of Stimulus Generalisation?
  Biosystems, 92(2):175-81 2008
  doi: 10.1016/j.biosystems.2008.02.003

• Emma Hart, Jon Timmis.
  Application Areas of AIS: The Past, Present and the Future.
  Journal of Applied Soft Computing 8(1):191-201 January 2008
  doi: 10.1016/j.asoc.2006.12.004

• Peter Hines.
  Machine semantics.
  Theoretical Computer Science 409(1):1-23 2008
  doi: 10.1016/j.tcs.2008.07.015

• Peter Hines.
  Machine Semantics---From Causality to Computational Models.
  Int. J. Unconventional Computing 4(3):249-272, 2008
  [special issue, UC 2006]

• Regine Laleau, Fiona Polack.
  Using formal metamodels to check consistency of functional views in information systems specification.
  Information and Software Technology Journal 50(7-8):797-814 June 2008
  doi: 10.1016/j.infsof.2007.10.007

• M. Owari, Samuel L. Braunstein, K. Nemoto, M. Murao.
  epsilon-convertibility of entangled states and extension of Schmidt rank in infinite-dimensional systems.
  Quantum Information and Computation 8(1,2):30-52 2008

• Stefano Pirandola, Samuel L. Braunstein, Seth Lloyd.
  Characterization of collective Gaussian attacks and security of coherent-state quantum cryptography.
  Physics Review Letters 101:200504-1/4 2008
  doi: 10.1103/PhysRevLett.101.200504

• Stefano Pirandola, Samuel L. Braunstein, Stefano Mancini, Seth Lloyd.
  Quantum direct communication with continuous variables.
  Euro Physics Letters 84:20013-1/6 2008
  doi: 10.1209/0295-5075/84/20013

• Stefano Pirandola, Stefano Mancini, Samuel L. Braunstein, David Vitali.
  Minimal qudit code for a qubit in the phase damping channel.
  Physical Review A 77:032309-1/9 2008
  doi: 10.1103/PhysRevA.77.032309

• Stefano Pirandola, Stefano Mancini, Seth Lloyd, Samuel L. Braunstein.
  Continuous-variable quantum cryptography using two-way quantum communication.
  Nature Physics 4:726-730 2008
  doi: 10.1038/nphys1018

• S. M. Roy, Samuel L. Braunstein.
  Exponentially enhanced quantum metrology.
  Physical Review Letters. 100:2220501-1/4 2008
  doi: 10.1103/PhysRevLett.100.220501

• Graeme D. Ruxton, Dan W. Franks, Alexandra C. V. Balogh, Olof Leimar.
  Evolutionary implications of the form of predator generalization for aposematic signals and mimicry in prey.
  Evolution 62(11):2913-2921, 2008
  doi: 10.1111/j.1558-5646.2008.00485.x

• Andrew Secker, Alex A. Freitas, Jon Timmis.
  AISIID: An artificial immune system for interesting information discovery on the web.
  Journal of Applied Soft Computing 8(2):885-905, March 2008
  doi: 10.1016/j.asoc.2007.07.007

• Stephen L. Smith, Jon Timmis.
  An Immune Network Inspired Evolutionary Algorithm for the Diagnosis of Parkinson's Disease.
  Biosystems 94(1-2):34-46, October-November 2008
  doi: 10.1016/j.biosystems.2008.05.024

• Susan Stepney.
  The Neglected Pillar of Material Computation.
  Physica D: Nonlinear Phenomena 237(9):1157-1164, July 2008
  doi: 10.1016/j.physd.2008.01.028

• Susan Stepney, John A. Clark.
  Searching for Quantum Programs and Quantum Protocols: a review.
  Journal of Computational and Theoretical Nanoscience 5(5):942-969, 2008

• Jon Timmis, Paul Andrews, Nick Owens, Ed Clark.
  An Interdisciplinary Perspective on Artificial Immune Systems.
  Evolutionary Intelligence 1(1):5-26, March 2008
  doi: 10.1007/s12065-007-0004-2

• Jon Timmis, Andy Hone, Thomas Stibor, Ed Clark.
  Theoretical Advances in Artificial Immune Systems.
  Theoretical Computer Science 403(1):11-32
  doi: 10.1016/j.tcs.2008.02.011

• P. van Loock, W. J. Munro, Kae Nemoto, T. P. Spiller, T. D. Ladd, Samuel L. Braunstein, G. J. Milburn.
  Hybrid quantum computation in quantum optics
  Physical Review A. 78:022303-1/5, 2008
  doi: 10.1103/PhysRevA.78.022303

• T. A. Walker, Fiona Polack, Samuel L. Braunstein.
  Error correcting Bell inequalities.
  Physical Review Letters. 101:080501-1/4 2008
  doi: 10.1103/PhysRevLett.101.080501

• Jim Woodcock, Susan Stepney, David Cooper, John A. Clark, Jeremy L. Jacob.
  The certification of the Mondex electronic purse to ITSEC Level E6.
  Formal Aspects of Computing 20(1):5-19, 2008
  doi: 10.1007/s00165-007-0060-5

• Yuan Zhan, John A. Clark.
  A Search-Based Framework for Automatic Testing of MATLAB/Simulink Models.
  Journal of Systems and Software, 81(2):262-285, 2008
  doi: 10.1016/j.jss.2007.05.039
  [special issue on Model-Based Software Testing]

refereed workshop and conference papers

• Andrea Arcuri, David R. White, John A. Clark, Xin Yao.
  Multi-objective Improvement of Software Using Co-evolution and Smart Seeding.
  SEAL 2008, Melbourne, Australia, December 2008, LNCS 5361:61-70, Springer 2008
  doi: 10.1007/978-3-540-89694-4_7

• Jonathan M. Aitken, Tim Clarke, Jon Timmis.
  The Pathways of Complement.
  ICARIS 2008, Phuket, Thailand, August 2008. LNCS 5132:364-375. Springer 2008.
  doi: 10.1007/978-3-540-85072-4_32

• Nuno Amalio, Fiona Polack, Jing Zhang.
  Autonomous objects and bottom-up composition in ZOO applied to a case study of biological reactivity.
  ABZ 2008, London, UK, September 2008. LNCS 5238:323-336, Springer 2008.
  doi: 10.1007/978-3-540-87603-8_25

• Paul S. Andrews, Fiona Polack, Adam Sampson, Jon Timmis, Lisa Soctt, Mark Coles.
  Simulating biology: towards understanding what the simulation shows.
  CoSMoS workshop, York, UK, September 2008, pp93-123. Luniver Press 2008

• Paul S. Andrews, Adam T. Sampson, John Markus Bjørndalen, Susan Stepney, Jon Timmis, Douglas N. Warren, Peter H. Welch
  Investigating Patterns for the Process-Oriented Modelling and Simulation of Space in Complex Systems.
  ALife XI, Winchester, UK, August 2008, pp17-24. MIT Press, 2008

• Paul S. Andrews, Jon Timmis.
  Adaptable Lymphocytes for Artificial Immune Systems.
  ICARIS 2008, Phuket, Thailand, August 2008. LNCS 5132:376-386. Springer 2008.
  doi: 10.1007/978-3-540-85072-4_33

• Kester Clegg, Susan Stepney.
  Adaptive Circuit Control through Gene Expression.
  EvoHot, EuroWorkshops, Naples, Italy, March 2008, LNCS 4974:154-163, Springer 2008
  doi: 10.1007/978-3-540-78761-7_16

• Gemma Danks, Susan Stepney, Leo Caves.
  Protein folding with stochastic L-Systems.
  ALife XI, Winchester, UK, August 2008, pp150-157. MIT Press, 2008

• Xun Dong, John A. Clark, Jeremy L. Jacob.
  Modelling user-phishing interaction.
  HSI 2008, Krakow, Poland, May 2008, pp.627-632, IEEE 2008
  doi: 10.1109/HSI.2008.4581513

• Xun Dong, John A. Clark, Jeremy L. Jacob.
  Threat Modelling in User Performed Authentication.
  ICICS 2008, Birmingham, UK, October 2008, LNCS 5308:49-64, Springer 2008
  doi: 10.1007/978-3-540-88625-9_4

• Xun Dong, John A. Clark, Jeremy L. Jacob.
  User behaviour based phishing websites detection.
  IMCSIT 2008, Wisla, Poland, October 2008, pp.783-790, IEEE 2008
  doi: 10.1109/IMCSIT.2008.4747332

• Ruth Falconer, Jim Bown, Emma Hart, Jon Timmis.
  A New Paradigm for SpeckNets: Inspiration from Fungal Colonies.
  Workshop on Pervasive Adaptive Systems, SASO 2008, Venice, Italy, October 2008. pp90-95, IEEE
  doi: 10.1109/SASOW.2008.55

• Philip Garnett, Susan Stepney, Ottoline Leyser.
  Towards an executable model of auxin transport canalisation.
  CoSMoS workshop, York, UK, September 2008, pp63-91. Luniver Press 2008

• Kamran Ghani, John A. Clark.
  Strengthening Inferred Specification using Search Based Testing.
  SBST workshop, ICST 2008, Lillehammer, Norway, April 2008. IEEE 2008
  doi: 110.1109/ICSTW.2008.39

• Dimitrios S. Kolovos, Richard Paige, Fiona Polack.
  Detecting and repairing inconsistencies across heterogeneous models.
  ICST 2008, Lillehammer, Norway, April 2008, pp 356-364. IEEE Press, 2008
  doi: 10.1109/ICST.2008.23

• Dimitrios S. Kolovos, Richard Paige, Fiona Polack.
  A Framework for Composing Modular and Interoperable Model Management Tasks.
  MDTPI workshop, EC-MDA 2008, Berlin, Germany, June 2008

• Dimitrios S. Kolovos, Richard Paige, Fiona Polack.
  The Epsilon Transformation Language.
  ICMT 2008, Zurich, Switzerland, July 2008, LNCS 5063:46-60. Springer 2008
  doi: 10.1007/978-3-540-69927-9_4

• Dimitrios S. Kolovos, Richard Paige, Louis Rose, Fiona Polack.
  Unit Testing Model Management Operations.
  MoDeVVA workshop, ICST 2008, Lillehammer, Norway, April 2008. IEEE 2008
  doi: 10.1109/ICSTW.2008.50

• Dimitrios S. Kolovos, Richard Paige, Fiona Polack.
  Novel Features in Model Management Languages of the Epsilon Platform.
  MISE 2008 Workshop, ICSE 2008, Leipzig, Germany, May 2008

• Yow Tzu Lim, Pau Chen Cheng, John A. Clark, Pankaj Rohatgi.
  Policy Evolution with Grammatical Evolution .
  SEAL 2008, Melbourne, Australia, December 2008, LNCS 5361:71-80, Springer 2008
  doi: 10.1007/978-3-540-89694-4_8

• Yow Tzu Lim, Pau Chen Cheng, John A. Clark, Pankaj Rohatgi.
  Policy Evolution with Grammatical Evolution .
  ACITA 2008, London, UK, September 2008, pp.253-260, 2008
  [extended version of SEAL 2008 paper]

• Yow Tzu Lim, Pau Chen Cheng, John A. Clark, Pankaj Rohatgi.
  Policy Evolution with Genetic Programming: a Comparison of Three Approaches.
  CEC 2008, Hong Kong, June 2008. pp.1792-1800, IEEE Press, 2008
  doi: 10.1109/CEC.2008.4631032

• Yow Tzu Lim, Pau Chen Cheng, Pankaj Rohatgi, John A. Clark.
  MLS security policy evolution with genetic programming.
  GECCO 2008, Atlanta, GA, USA, July 2008, pp1571-1578. ACM Press, 2008
  doi: 10.1145/1389095.1389395

• Yang Liu, Jon Timmis, Tim Clarke.
  A Neuro-Immune Inspired Robust Real Time Visual Tracking System.
  ICARIS 2008, Phuket, Thailand, August 2008. LNCS 5132:188-199. Springer, 2008
  doi: 10.1007/978-3-540-85072-4_17

• Maizura Mokhtar, Jon Timmis, Andy Tyrrell, Ran Bi.
  An Artificial Lymph Node Architecture for Homeostasis in Collective Robotic Systems.
  Workshop on Pervasive Adaptive Systems, SASO 2008, Venice, Italy, October 2008. pp 126-131, IEEE
  doi: 10.1109/SASOW.2008.12

• Nick Owens, Susan Stepney.
  Investigations of the Game of Life Cellular Automata rules on Penrose Tilings: lifetime and ash statistics.
  Automata 2008, Bristol, UK, June 2008, pp 1-35. Luniver Press, 2008

• Nick D. L. Owens, Jon Timmis, Andrew Greensted, Andy Tyrrell.
  Modelling the Tunability of Early T Cell Signalling Events.
  ICARIS 2008, Phuket, Thailand, August 2008. LNCS 5132:12-23. Springer, 2008
  doi: 10.1007/978-3-540-85072-4_2

• Fiona Polack, Susan Stepney, Adam T. Sampson, Jon Timmis, Tim Hoverd.
  Complex Systems Models: Engineering Simulations.
  ALife XI, Winchester, UK, August 2008, pp482-489. MIT Press, 2008

• Edward J. Powley, Susan Stepney.
  Automorphisms of transition graphs for a linear cellular automaton.
  Automata 2008, Bristol, UK, June 2008, pp 55-66. Luniver Press, 2008

• Mark Read, Jon Timmis, Paul Andrews.
  Empirical Investigation of an Artificial Cytokine Network.
  ICARIS 2008, Phuket, Thailand, August 2008. LNCS 5132:340-351. Springer 2008.
  doi: 10.1007/978-3-540-85072-4_30

• Louis M. Rose, Richard Paige, Dimitrios S. Kolovos, Fiona Polack.
  The Epsilon Generation Language.
  EC-MDA 2008, Berlin, Germany, June 2008, LNCS 5095:1-16. Springer 2008
  doi: 10.1007/978-3-540-69100-6_1

• Louis M. Rose, Richard Paige, Dimitrios S. Kolovos, Fiona Polack.
  Constructing Models with the Human-Usable Textual Notation.
  MoDELS/UML 2008, Toulouse, France, October 2008, LNCS 5301:249-263. Springer 2008
  doi: 10.1007/978-3-540-87875-9_18

• Andrew Secker, Matthew N. Davies, Alex A. Freitas, Jon Timmis, Ed Clark, Darren R. Flower.
  An Artificial Immune System for Evolving Amino Acid Clusters Tailored to Protein Function Prediction.
  ICARIS 2008, Phuket, Thailand, August 2008. LNCS 5132:242-253. Springer 2008.
  doi: 10.1007/978-3-540-85072-4_22

• Sevil Sen, John A. Clark.
  Evolving Intrusion Detection Rules on Mobile Ad Hoc Networks.
  PRICAI-08, Hanoi, Vietnam, December 2008. LNCS 5351:1053-1058. Springer 2008.
  doi: 10.1007/978-3-540-89197-0_106

• Stephen L. Smith, Andy Greensted, Jon Timmis.
  Hardware Acceleration of an Immune Network Inspired Evolutionary Algorithm for Medical Diagnosis.
  International Conference on Evolvable Systems, Prague, Czech Republic, September 2008. LNCS 5216:34-46. Springer 2008
  doi: 10.1007/978-3-540-85857-7_4

• Susan Stepney, Samson Abramsky, Andy Adamatzky, Colin Johnson, Jon Timmis.
  Grand Challenge in Non-Classical Computation.
  Visions of Computer Science, London, UK, September 2008. pp407-421. BCS 2008

• Andrew Weeks, Fiona Polack, Susan Stepney.
  Investigating emergence by coarse graining Elementary Cellular Automata.
  ALife XI, Winchester, UK, August 2008, pp686-693. MIT Press, 2008

• David R. White, John A. Clark, Jeremy Jacob, Simon Poulding.
  Searching for Resource-Efficient Programs: Low-Power Pseudorandom Number Generators.
  GECCO 2008, Atlanta, GA, USA, July 2008, pp1775-1782. ACM Press, 2008
  doi: 10.1145/1389095.1389437

other

• Jon Timmis, Paul Andrews, Nick Owens, Ed Clark.
  Immune Systems and Computation: An Interdisciplinary Adventure.
  Unconventional Computing 2008, Vienna, Austria, August 2008. LNCS 5204:8-18. Springer 2008
  doi: 10.1007/978-3-540-85194-3_4
  [invited talk]

• Jon Timmis, Emma Hart, Andy Hone, Mark Neal, Adrian Robins, Susan Stepney, Andy Tyrrell.
  Immuno-Engineering.
  2nd IFIP International Conference on Biologically Inspired Collaborative Computing, 20th IFIP World Computer Congress, Milan, Italy, September 2008, pp3-17. Springer 2008.
  doi: 10.1007/978-0-387-09655-1_2
  [invited talk]

books / proceedings

• Andy Adamatzky, Larry Bull, Ben De Lacy Costello, Susan Stepney, Christof Teuscher, editors.
  Unconventional Computing 2007, Bristol, UK, July 2007.
  Luniver Press, 2007.

• Darren Flower, Jon Timmis, eds.
  In Silico Immunology.
  Springer, 2007
  doi: 10.1007/978-0-387-39241-7

book chapters

• Paul Andrews, Jon Timmis.
  Alternative Inspiration For Artificial Immune Systems: Exploiting Cohen’s Cognitive Immune Model.
  In Darren Flower, Jon Timmis, eds. In Silico Immunology, pp.119-137, Springer, 2007
  doi: 10.1007/978-0-387-39241-7_8

• Susan Stepney.
  Embodiment.
  In Darren Flower, Jon Timmis, eds. In Silico Immunology, pp.265-288, Springer, 2007
  doi: 10.1007/978-0-387-39241-7_13

• Jon Timmis, Paul Andrews.
  Artificial Immune Systems: A Beginners Guide.
  In Darren Flower, Jon Timmis, eds. In Silico Immunology, pp.47-62, Springer, 2007
  doi: 10.1007/978-0-387-39241-7_4

journal papers

• Richard Banach, Michael Poppleton, Czeslaw Jeske, Susan Stepney.
  Engineering and Theoretical Underpinnings of Retrenchment.
  Science of Computer Programming, 67(2-3):301-329, July 2007
  doi: 10.1016/j.scico.2007.04.002

• Richard Banach, Michael Poppleton, Czeslaw Jeske, Susan Stepney.
  Retrenching the Purse: the balance enquiry quandary, and generalised and (1,1) forward refinements.
  Fundamenta Informaticae 77(1-2):29-69, 2007

• Samuel L. Braunstein, Byung-Soo Choi, Subhroshekhar Ghosh, Subhamoy Maitra.
  Exact quantum algorithm to distinguish Boolean functions of different weights.
  Journal of Physics A. 40:8441-8454 2007
  doi: 10.1088/1751-8113/40/29/017

• Samuel L. Braunstein, Sibasish Ghosh, Simone Severini.
  Estimation of pure qubits on circles.
  Journal of Physics A. 40:1809-1834 2007
  doi: 10.1088/1751-8113/40/8/009
  [Included in IoP Select, February 2007]

• Samuel L. Braunstein, Arun K. Pati.
  Quantum information cannot be completely hidden in correlations: Implications for the black-hole information paradox.
  Physical Review Letters. 98:080502-1/4 2007
  doi: 10.1103/PhysRevLett.98.080502
  [Selected by Physical Review Letters as a 'Suggestions' paper for this issue]
  [Included in the Virtual Journal of Quantum Information, March 2007]
  [Included in the Virtual Journal of Nanoscale Science & Technology, March 2007]

• Byung-Soo Choi, Thomas A. Walker, Samuel L. Braunstein.
  Sure success partial search.
  Quantum Information Processing. 6:1-8 2007
  doi: 10.1007/s11128-006-0037-y

• Vincenzo Cutello, Giuseppe Nicosia, Mario Pavone, Jon Timmis.
  An Immune Algorithm for Protein Structure Prediction on Lattice Models.
  IEEE Transactions on Evolutionary Computation. 11(1):101-117 2007
  doi: 10.1109/TEVC.2006.880328

• Matthew N. Davies, David Gloriam, Andrew Secker, Alex A. Freitas, Miguel Mendao, Jon Timmis, Darren R. Flower.
  Proteomic applications of automated GPCR classification.
  Proteomics 7(6):2800-2814 2007
  doi: 10.1002/pmic.200700093

• Matthew N. Davies, Andrew Secker, Alex A. Freitas, Miguel Mendao, Jon Timmis, Darren R. Flower.
  On the hierarchical classification of G Protein-Coupled Receptors.
  Bioinformatics 23(23):3113-3118 2007
  doi: 10.1093/bioinformatics/btm506

• Rogerio de Lemos, Jon Timmis, Modupe Ayara, Simon Forrest.
  Immune-Inspired Adaptable Error Detection for Automated Teller Machines.
  IEEE Transactions on Systems, Man and Cybernetics Part C: Applications and Reviews 37(5) 2007
  doi: 10.1109/TSMCC.2007.900662

• Dan W. Franks, Thomas N. Sherratt.
  The evolution of multicomponent mimicry .
  Journal of Theoretical Biology, 244(4):631-639 2007
  doi: 10.1016/j.jtbi.2006.09.019

• Alex A. Freitas, Jon Timmis.
  Revisiting the Foundations of Artificial Immune Systems for Data Mining.
  IEEE Transactions on Evolutionary Computation 11(4):521-540 2007
  doi: 10.1109/TEVC.2006.884042

• Dimitrios S. Kolovos, Richard F. Paige, Fiona Polack.
  Aligning OCL with Domain-Specific Languages to Support Instance-Level Model Queries.
  Proc. OCLApps 2006: OCL for (Meta-)Models in Multiple Application Domains, Genova, Italy, October 2006.
  Journal of the Electronic Communications of the EASST. 5 2007

• Dimitrios S. Kolovos, Richard F. Paige, Fiona Polack, Louis M. Rose.
  Update Transformations in the Small with the Epsilon Wizard Language.
  Journal of Object Technology 6(9):53-69 2007
  [Special Issue of Proc. TOOLS Europe 2007, Zurich, Switzerland, June 2007]

• Jon Timmis.
  Artificial Immune Systems -- Today and Tomorrow.
  Natural Computation. 6:1-18 2007
  doi: 10.1007/s11047-006-9029-1
  [special issue on Natural and Artificial Immune Systems]

• Heather Turner, Susan Stepney, Fiona Polack.
  Rule Migration: Exploring a design framework for emergence.
  Int. J. Unconventional Computing. 3(1):49-66 2007

• Thomas A. Walker, Samuel L. Braunstein.
  Classical broadcasting is possible with arbitrarily high fidelity and resolution.
  Physical Review Letters. 98:080501-1/4 2007
  doi: 10.1103/PhysRevLett.98.080501
  [Included in the Virtual Journal of Quantum Information, March 2007]

• Le Xu, Mo-Yuen Chow, Jon Timmis, Leroy Taylor.
  Power Distribution Outage Cause Identification With Imbalanced Data Using Artificial Immune Recognition System (AIRS) Algorithm.
  IEEE Transactions on Power Systems 22(1):198-204 2007
  doi: 10.1109/TPWRS.2006.889040

• Hidehiro Yonezawa, Samuel L. Braunstein, Akira Furusawa.
  Experimental Demonstration of Quantum Teleportation of Broadband Squeezing.
  Physical Review Letters. 99:110503 2007
  doi: 10.1103/PhysRevLett.99.110503

refereed workshop and conference papers

• Nuno Amálio, Fiona Polack, Susan Stepney.
  Frameworks based on templates for rigorous model-driven development.
  Proc. Doctoral Symposium affiliated with IFM 2005. ENTCS 191:3-23. Elsevier, 2007

• Richard Banach, Czeslaw Jeske, A. Hall, Susan Stepney.
  Retrenchment and the Atomicity Pattern.
  SEFM 07, London, UK, September 2007. IEEE Press, 2007

• Matthias Bechmann, John A. Clark, Angelika Sebald, Susan Stepney.
  Unentangling nuclear magnetic resonance computing.
  Unconventional Computing 2007, Bristol, UK, July 2007. Luniver Press, 2007.

• John A. Clark, John Murdoch, John A. McDermid, Sevil Sen, Howard R. Chivers, Olwen Worthington.
  Threat Modeling for Ad Hoc Networks.
  ACITA 2007, Maryland, USA. 2007 2007

• Kester Clegg, Susan Stepney, Tim Clarke.
  Evolutionary search applied to reconfigurable analogue control.
  FPL 2007, Amsterdam, Netherlands, August 2007. IEEE 2007

• Kester Clegg, Susan Stepney, Tim Clarke.
  Using Feedback to Regulate Gene Expression in a Developmental Control Architecture.
  GECCO'07, London, UK, July 2007, pp.966-973. ACM Press 2007
  doi: 10.1145/1276958.1277154

• Gemma Danks, Susan Stepney, Leo Caves.
  Folding Protein-Like Structures with Open L-systems.
  ECAL 2007, Lisbon, Portugal, September 2007. LNAI 4648:1100-1109, Springer 2007
  doi: 10.1007/978-3-540-74913-4_110

• George Despotou, Dimitrios S. Kolovos, Richard F. Paige, Tim P. Kelly, Fiona Polack.
  Towards a Metamodel for Dependability Cases.
  Proc. OMG Software Assurance Workshop 2007, March 2007.

• Xiaocheng Ge, Richard F. Paige, Fiona Polack, Phillip J. Brooke.
  Extreme programming security practices.
  Proc. Extreme Programming 2007, Lake Como, Italy, June 2007. LNCS 4536:226-230. Springer 2007
  doi: 10.1007/978-3-540-73101-6_42

• T. Knight, Jon Timmis.
  Comparison of a Multi-layered Artificial Immune System and Kohonen Networks.
  CEC 2007, Singapore, September 2007. pp.3735-3742, IEEE Press, 2007
  doi: 10.1109/CEC.2007.4424957

• Dimitrios S. Kolovos, Richard F. Paige, Fiona Polack.
  Agile Model Editing in the Eclipse Modeling Framework using Executable Metamodel Annotations.
  Proc. Towers of Models Workshop, co-located with TOOLS Europe 2007, Zurich, Switzerland, June 2007.

• Dimitrios S. Kolovos, Richard F. Paige, Louis M. Rose, Fiona Polack.
  Bridging the Epsilon Wizard Language and the Eclipse Graphical Modelling Framework.
  Modelling Symposium, Eclipse Summit Europe 2007, Ludwigsburg, Germany, October 2007.

• Dimitrios S. Kolovos, Richard F. Paige, Louis M. Rose, Fiona Polack.
  Implementing the Interactive Television Applications Case Study using Epsilon.
  Proc. MDD Tool Implementers Forum, co-located with TOOLS Europe 2007, Zurich, Switzerland, June 2007.

• Peter May, Jon Timmis, Keith Mander.
  Immune and Evolutionary Aproaches to Software Mutation Testing.
  ICARIS 2007, Santos/SP, Brazil, August 2007. LNCS 4628:336-347, Springer, 2007
  doi: 10.1007/978-3-540-73922-7_29

• Miguel Mendao, Jon Timmis, Paul Andrews, M. Davies.
  The Immune System in Pieces: Computational Lessions from Degeneracy in the Immune System.
  FOCI'07, Hawaii, USA, April 2007, pp.394-400. IEEE Press, 2007
  doi: 10.1109/FOCI.2007.371502

• John Murdoch, John A. Clark, John A. McDermid, Howard R. Chivers and Olwen Worthington.
  Aggregation of Information Leaked by a MANET.
  ACITA 2007, Maryland, USA. 2007

• Nick D. Owens, Jon Timmis, Andrew J. Greensted, Andy M. Tyrrell.
  On Immune Inspired Homeostasis for Electronic Systems.
  ICARIS 2007, Santos/SP, Brazil, August 2007. LNCS 4628:216-227, Springer, 2007
  doi: 10.1007/978-3-540-73922-7_19

• Simon Poulding, Paul Emberson, Iain Bate, John A. Clark.
  An Efficient Experimental Methodology for Configuring Search-Based Design Algorithms.
  10th IEEE High Assurance Systems Engineering Symposium. pp53-62. IEEE Press, 2007
  doi: 10.1109/HASE.2007.27

• Andrew Secker, M. Davies, Alex A. Freitas, Jon Timmis, Miguel Mendao, Darren Flower.
  An Experimental Comparison of Classification Algorithms for the Hierarchical Prediction of Protein Function.
  UK KDD Symposium 2007, Canterbury, UK, April 2007.

• Susan Stepney, Tim Clarke, Peter Young.
  PLAZZMID: an agent-based architecture inspired by bee and bacterial genomes.
  ECAL 2007, Lisbon, Portugal, September 2007. LNAI 4648:1151-1160, Springer 2007
  doi: 10.1007/978-3-540-74913-4_115

• Steve L. Smith, S. J. Murant, Jon Timmis.
  Natural Computation Inspired by Protein Binding.
  IPCAT 2007, Oxford, UK, August 2007.

• Thomas Stibor, Jon Timmis.
  An Investigation into the Compression Quality of aiNET.
  FOCI'07, Hawaii, USA, April 2007, pp.495-502. IEEE Press, 2007
  doi: 10.1109/FOCI.2007.371518

• Thomas Stibor, Jon Timmis.
  Comments on Real-Valued Negative Selection vs Real-Valued Positive Selection and One-class Support Vector Machines.
  CEC 2007, Singapore, September 2007. pp.3727-3734, IEEE Press, 2007
  doi: 10.1109/CEC.2007.4424956

• Juan M. E. Tapiador, Julio C. Hernandez-Castro, John A. Clark.
  Heuristic Search for Non-Linear Cryptanalytic Approximations.
  CEC 2007, Singapore, September 2007. pp3561-3568. IEEE Press, 2007
  doi: 10.1109/CEC.2007.4424934

• Juan M. E. Tapiador, John A. Clark, Julio C. Hernandez-Castro.
  Non-linear Cryptanalysis Revisited: Heuristic Search for Approximations to S-Boxes.
  Cryptography and Coding 2007, Cirencester, UK, December 2007. LNCS 4887:99-117, Springer 2007
  doi: 10.1007/978-3-540-77272-9_7

• Andy M. Tyrrell, Jon Timmis, Andy Greensted, Nick Owens.
  Evolvable Hardware, the Fundamental Technology for Homeostasis.
  IEEE Workshop on Adaptive and Evolvable Hardware (WEAH2007), part of FOCI'07, Hawaii, USA, April 2007, pp.40-45. IEEE Press, 2007

• Andrew Weeks, Susan Stepney, Fiona Polack.
  Neutral Emergence and Coarse Graining.
  ECAL 2007, Lisbon, Portugal, September 2007. LNAI 4648:1131-1140, Springer 2007
  doi: 10.1007/978-3-540-74913-4_113

other

• Philip Garnett, Susan Stepney, Ottoline Leyser.
  Integrative Hybrid Modelling of Plant Shoot Branching.
  5th International Workshop on Functional Structural Plant Models: FSPM07, New Zealand, November 2007

• T. Nguyen, Fiona Polack, Susan Stepney, Ian Toyn.
  Practical use of real numbers in Z.
  Z User Meeting 2007, in conjunction with ICECCS 2007, Waikato, New Zealand, 11-14 July 2007

• Andrew Weeks, Susan Stepney, Fiona Polack.
  Neutral Emergence: a proposal.
  Symposium on Complex Systems Engineering, RAND Corporation, Santa Monica, CA, USA, 11-12 January 2007

• Hidehiro Yonezawa, Samuel L. Braunstein, Akira Furusawa.
  Teleporting below the vacuum-noise level: Non-local transfer of squeezing and entanglement.
  Quantum Electronics and Laser Science Conference 2007, Optical Society of America, 2007

books / proceedings

• Cristian S. Calude, Michael J. Dinneen, Gheorghe Paun, Grzegorz Rozenberg, Susan Stepney, eds.
  Proceedings of the 5th International Conference on Unconventional Computation (UC 2006), York, UK, September 2006.
  LNCS 4135. Springer, 2006.
  doi: 10.1007/11839132

• John A. Clark, Richard F. Paige, Fiona Polack, Phillip J. Brooke, eds.
  Security in Pervasive Computing (SPC) 2006, York, UK, April 2006.
  LNCS 3934. Springer, 2006.
  doi: 10.1007/11734666

book chapters

• Nuno Amálio, Fiona Polack, Susan Stepney.
  UML + Z: UML augmented with Z.
  In M. Frappier, H. Habrias, eds. Software Specification Methods: an Overview Using a Case Study, new edn, chapter 5. Hermes Science Publishing, 2006

• Fiona Polack.
  SAZ: SSADM Version 4 and Z.
  In M. Frappier, H. Habrias, eds. Software Specification Methods: an Overview Using a Case Study, new edn, chapter 2. Hermes Science Publishing, 2006

• Susan Stepney, John A. Clark.
  Evolving Quantum Programs and Protocols.
  In M. Rieth, W. Schommers, eds. Handbook of Theoretical and Computational Nanotechnology, chapter 90. American Scientific Publishers, 2006

journal papers

• Michael Batty, Samuel L. Braunstein, Andrew J. Duncan.
  Extending the promise of the Deutsch-Jozsa-Hoyer algorithm for finite groups
  LMS Journal of Computation and Mathematics. 9:40-63, January 2006

• Samuel L. Braunstein.
  Quantum metrology: Size isn't everything
  Nature. 440:617-618, March 2006.
  doi: 10.1038/440617a
  [News and Views]

• Samuel L. Braunstein, Sibasish Ghosh, Toufik Mansour, Simone Severini, Richard C. Wilson.
  Some families of density matrices for which separability is easily tested
  Physical Review A. 73:012320-1/10, January 2006
  doi: 10.1103/PhysRevA.73.012320

• Samuel L. Braunstein, Sibasish Ghosh, Simone Severini.
  The Laplacian of a graph as a density matrix: A basic combinatorial approach to separability of mixed states.
  Annals of Combinatorics 10(3):291-317, 2006
  doi: 10.1007/s00026-006-0289-3

• Netta Cohen, J. W. Handley, R. D. Boyle, Samuel L. Braunstein, Elizabeth Berry.
  Experimental signature of registration noise in pulsed terahertz systems
  Fluctuation and Noise Letters. 6(1):L77-L84, March 2006
  doi: 10.1142/S0219477506003161

• Satoshi Koike, Hiroki Takahashi, Hidehiro Yonezawa, Nobuyuki Takei, Samuel L. Braunstein, Takao Aoki, Akira Furusawa.
  Demonstration of quantum telecloning of optical coherent states
  Physical Review Letters. 96:060504-1/4, June 2006
  doi: 10.1103/PhysRevLett.96.060504

• Pieter Kok, Samuel L. Braunstein.
  Relativistic quantum information processing with bosonic and fermionic interferometers
  International Journal of Quantum Information. 4(1):119-130, February 2006
  doi: 10.1142/S0219749906001736
  [Asher Peres Memorial Issue]

• Paul Massey, John A. Clark, Susan Stepney.
  Human-Competitive Evolution of Quantum Computing Artefacts by Genetic Programming.
  Evolutionary Computation Journal 14(1):22-40, 2006.
  doi: 10.1162/evco.2006.14.1.21
  [Special Issue on the Best of GECCO 2004]

• T. P. Spiller, Kae Nemoto, Samuel L. Braunstein, W. J. Munro, P. van Loock, G. J. Milburn.
  Quantum computation by communication
  New Journal of Physics. 8:30-1/2, February 2006
  doi: 10.1088/1367-2630/8/2/030

• Susan Stepney, Samuel L. Braunstein, John A. Clark, Andy M. Tyrrell, Andy Adamatzky, Robert E. Smith, Tom Addis, Colin G. Johnson, Jon Timmis, Peter Welch, Robin Milner, Derek Partridge.
  Journeys in Non-Classical Computation II: Initial journeys and waypoints.
  Int. J. Parallel, Emergent and Distributed Systems. 21(2):97-125, April 2006
  doi: 10.1080/17445760500355454

• Thomas Stibor, Claudia Eckert, Jon Timmis.
  Artificial Immune Systems for IT-Security.
  it - Information Technology, 48:168-173, 2006
  doi: 10.1524/itit.2006.48.3.168

• Jon Timmis, Martyn Amos, Wolfgang Banzhaf, Andy M. Tyrrell.
  "Going back to our Roots": Second Generation Biocomputing.
  Int. J. Unconventional Computing. 2(4):349-382, 2006

• Jing Zhang, Samuel L. Braunstein
  Continuous-variable Gaussian analog of cluster states.
  Physical Review A. 73:032318-1/5, March 2006
  doi: 10.1103/PhysRevA.73.032318

refereed workshop and conference papers

• Nuno Amálio, Susan Stepney, Fiona Polack.
  A Formal Template Language enabling Metaproof.
  FM'06, Hamilton, Canada, August 2006. LNCS 4085:252-267, Springer, 2006
  doi: 10.1007/11813040_18

• Paul Andrews, Jon Timmis.
  On Diversity and Artificial Immune Systems: Incorporating a Diversity Operator into aiNET
  Proc. WIRN/NAIS, June 2005. LNCS 3931:293-306. Springer, 2006
  doi: 10.1007/11731177_37

• Paul Andrews, Jon Timmis.
  A Computational Model of Degeneracy in a Lymph Node
  ICARIS 2006, Oeiras, Portugal, September 2006. LNCS 4163:164-177. Springer, 2006
  doi: 10.1007/11823940_13

• Richard Banach, Michael Poppleton, Czeslaw Jeske, Susan Stepney.
  Retrenching the Purse: hashing injective CLEAR codes, and security properties
  ISoLA 2006, Cyprus, November 2006

• Richard Banach, Michael Poppleton, Czeslaw Jeske, Susan Stepney.
  Retrenching the Purse: finite exception logs, and validating the small
  30th Annual IEEE/NASA Software Engineering Workshop, Columbia, MD, USA, April 2006, pp.234-248. IEEE Press, 2006
  doi: 10.1109/SEW.2006.28

• Hao Chen, John A. Clark, Jeremy L. Jacob.
  Human Competitive Security Protocols Synthesis (poster paper)
  GECCO 2006, Seattle, WA, USA, July 2006, pp.1855-1856. ACM Press, 2006
  doi: 10.1145/1143997.1144297

• John A. Clark, Susan Stepney.
  Fusing Natural Computational Paradigms for Cryptography
  CEC-2006, Vancouver, Canada, July 2006, pp.200-206. IEEE Press, 2006

• Xiaocheng Ge, Richard F. Paige, Fiona Polack, Howard Chivers, Phillip J. Brooke.
  Agile Development of Secure Web Applications
  ICWE 2006, Menlo Park, CA, USA, July 2006, pp.305-312. ACM Press, 2006
  doi: 10.1145/1145581.1145641

• Peter Hines.
  Physical Systems as Constructive Logics
  UC 2006, York, UK, September 2006, LNCS 4135:101-112. Springer, 2006.
  doi: 10.1007/11839132_9

• Dimitrios S. Kolovos, Richard F. Paige, Tim Kelly, Fiona Polack.
  Requirements for Domain-Specific Languages
  1st ECOOP Workshop on Domain-Specific Program Development (DSPD), Nantes, France, July 2006

• Dimitrios S. Kolovos, Richard F. Paige, Fiona Polack.
  Epsilon Development Tools for Eclipse
  Proc. Eclipse Summit 2006, Esslingen, Germany, October 2006

• Dimitrios S. Kolovos, Richard F. Paige, Fiona Polack.
  Merging Models with the Epsilon Merging Language (EML).
  Proc. ACM/IEEE 9th Intl. Conf. Model Driven Engineering Languages and Systems, Genova, Italy, October 2006. LNCS 4199:215-229. Springer, 2006
  doi: 10.1007/11880240_16

• Dimitrios S. Kolovos, Richard F. Paige, Fiona Polack.
  Towards using OCL for Instance-Level Queries in Domain-Specific Languages.
  OCLApps 2006, Genova, Italy, October 2006.

• Dimitrios S. Kolovos, Richard F. Paige, Fiona Polack.
  On-Demand Merging of Traceability Links with Models.
  2nd ECMDA Traceability Workshop, Bilbao, Spain, July 2006.

• Dimitrios S. Kolovos, Richard F. Paige, Fiona Polack.
  The Epsilon Object Language (EOL).
  EC-MDA 2006, Bilbao, Spain, July 2006. LNCS 4066:128-142. Springer, 2006
  doi: 10.1007/11787044_11

• Dimitrios S. Kolovos, Richard F. Paige, Fiona Polack.
  Model Comparison: A Foundation for Model Composition and Model Transformation Testings.
  GaMMa 2006, 1st International Workshop on Global Integrated Model Management, Shanghai, May 2006, pp.13-20, ACM Press, 2006
  doi: 10.1145/1138304.1138308

• P. Mohr, N. Ryan, Jon Timmis.
  Recognising regular human activity through a learning context memory
  Proc. 3rd International Workshop of Modelling and Retrieval of Context (MRC 2006). Boston, USA, July 2006

• Richard F. Paige, Dimitrios S. Kolovos, Fiona Polack.
  Adding an Action Semantics to MOF 2.0 (short paper)
  21st ACM Symposium on Applied Computing, Dijon, France, April 2006

• Fiona Polack, Thitima Srivatanakul, Tim Kelly, John A. Clark.
  Deviational analyses for validating regulations on real systems.
  REMO2V workshop, CAiSE'06, Luxembourg, June 2006

• Susan Stepney, Fiona Polack, Heather Turner.
  Engineering Emergence.
  ICECCS'06, Stanford, CA, USA, August 2006, pp.89-97. IEEE Press, 2006
  doi: 10.1109/ICECCS.2006.1690358
  [invited paper]

• Thomas Stibor, Jon Timmis, Claudia Eckert.
  On the Use of Hyperspheres in Artificial Immune Systems as Antibody Recognition Regions
  ICARIS 2006, Oeiras, Portugal, September 2006. LNCS 4163:215-228. Springer, 2006

• Thomas Stibor, Jon Timmis, Claudia Eckert.
  On Permutation Masks in Hamming Negative Selection
  ICARIS 2006, Oeiras, Portugal, September 2006. LNCS 4163:122-135. Springer, 2006

• Thomas Stibor, Jon Timmis, Claudia Eckert.
  The Link between r-contiguous Detectors and k-CNF Satisfiability.
  CEC-2006, Vancouver, Canada, July 2006

• Thomas Stibor, Jon Timmis, C. Eckert.
  Generalization Regions in Hamming Negative Selection.
  New Trends in Intelligent Information Processing and Web Mining, Poland, June 2006

• Jon Timmis.
  Challenges for Artificial Immune Systems
  Proc. WIRN/NAIS, June 2005. LNCS 3931:355-367. Springer, 2006

• Peter Welch, Fred Barnes, Fiona Polack.
  Communicating Complex Systems.
  ICECCS'06, Stanford, CA, USA, pp.107-117, August 2006

• Le Xu, Mo-Yuen Chow, Jon Timmis, Leroy Taylor, Andrew Watkins.
  On the Investigation of Artificial Immune Systems on Imbalanced Data Classification for Power Distribution System Fault Cause Identification.
  CEC-2006, Vancouver, Canada, July 2006

• Yuan Zhan, John A. Clark.
  The State Problem for Test Generation in Simulink.
  GECCO 2006, Seattle, WA, USA, July 2006

other

• Kester Clegg, Susan Stepney.
  Binding Analogue Feedback to Digital Genomes: Bio-inspired Regulatory Control for Analogue Devices (abstract).
  ECSIS Symposium on Intelligent Systems for Defense and Security (ISDS), Iasi, Romania, September 2006

• Susan Stepney.
  Hypercomputation and the Grand Challenge in Non-Classical Computation.
  International Interdisciplinary Workshop on Future Trends in Hypercomputation, Sheffield, UK, September 2006

books / proceedings

• Mathieu S. Capcarrere, Alex A. Freitas, Peter J. Bentley, Colin G. Johnson, Jon Timmis, editors.
  Proceedings of the 8th European Conference on Artificial Life (ECAL 2005), Canterbury, UK, September 2005.
  LNAI 3630. Springer, 2005
  doi: 10.1007/11553090

• Christian Jacob, Marcin L. Pilat, Peter J. Bentley, Jon Timmis, editors.
  Proceedings of the 4th International Conference on Artificial Immune Systems (ICARIS 2005), Banff, Canada, August 2005.
  LNCS 3627. Springer, 2004.
  doi: 10.1007/11536444

book chapters

• Samuel L. Braunstein, P. Kok.
  Quantum teleportation in Europe
  In T. Van der Pyl, A. Karlson, M. Belina-Podgaetsky, eds, Quantum Information Processing and Communications in Europe, pp.57-61. European Commission, March 2005

• Mark Neal, Jon Timmis.
  Once More Unto the Breach: Towards Artificial Homeostasis?
  In Leandro N. de Castro, F. J. Von Zuben, eds, Recent Developments in Biologically Inspired Computing, pp.340-365. Idea Group, 2005

journal papers

• Samuel L. Braunstein.
  Squeezing as an irreducible resource.
  Physical Review A 71:055801-1/4, 2005
  [Included in the Virtual Journal of Quantum Information - June 2005]

• Samuel L. Braunstein.
  A quantum optical shutter.
  Journal of Optics B 7:S28-S31, 2005

• Samuel L. Braunstein, P. van Loock.
  Quantum information with continuous variables.
  Reviews of Modern Physics 77:513-577, 2005
  [Included in the Virtual Journal of Quantum Information - July 2005]

• Iain Brown, Susan Stepney, Anthony Sudbery, Samuel L. Braunstein.
  Searching for highly entangled multi-qubit states.
  J. Phys. A, 38:1119-1131, 2005
  doi: 10.1088/0305-4470/38/5/013

• John A. Clark, Jeremy L. Jacob, Susan Stepney.
  The design of S-boxes by simulated annealing.
  New Generation Computing, 23(3):219-231, May 2005

• Thomas N. Sherratt, Dan W. Franks.
  Do unprofitable prey evolve traits that profitable prey find difficult to exploit?
  Proc. Roy. Soc. London B: Biological Sciences, 272:2441-2447, 2005.

• Susan Stepney, Samuel L. Braunstein, John A. Clark, Andy M. Tyrrell, Andy Adamatzky, Robert E. Smith, Tom Addis, Colin G. Johnson, Jonathan Timmis, Peter Welch, Robin Milner, Derek Partridge.
  Journeys in Non-Classical Computation I: A Grand Challenge for computing research.
  Int. J. Parallel, Emergent and Distributed Systems 20(1):5-19, March 2005
  doi: 10.1080/17445760500033291

• Susan Stepney, Robert E. Smith, Jon Timmis, Andy M. Tyrrell, Mark J. Neal, Andrew N. W. Hone.
  Conceptual Frameworks for Artificial Immune Systems.
  Int. J. Unconventional Computing. 1(3):315-338, July 2005

refereed workshop and conference papers

• Nuno Amálio, Fiona Polack, Susan Stepney.
  An Object-Oriented structuring for Z based on Views.
  ZB2005, Guildford, UK, April 2005. LNCS 3455:262-278, Springer, 2005
  doi: 10.1007/11415787_16

• Paul Andrews, Jon Timmis.
  Inspiration for the Next Generation of Artificial Immune Systems.
  ICARIS 2005, Banff, Canada, August 2005. LNCS 3627:126-138. Springer, 2005

• Paul Andrews, Jon Timmis.
  On Diversity and Artificial Immune Systems: Incorporating a Diversity Operator into aiNET.
  International Workshop on Natural and Artificial Immune Systems, Italy, 2005

• M. Ayara, Jon Timmis, Rogerio De Lemos, S. Forrest.
  Immunising Automated Teller Machines
  ICARIS 2005, Banff, Canada, August 2005. LNCS 3627:404-417. Springer, 2005

• Richard Banach, Michael Poppleton, Czeslaw Jeske, Susan Stepney.
  Retrenching the Purse : finite sequence numbers and the Tower Pattern.
  FM 2005, Newcastle, UK, July 2005. LNCS 3582:382-398, Springer 2005
  doi: 10.1007/11526841_26

• Richard Banach, Michael Poppleton, Czeslaw Jeske, Susan Stepney.
  Retrenchment and the Mondex Electronic Purse (extended abstract).
  Proc. ASM'05, Paris, France, March 2005

• Samuel L. Braunstein.
  Quantum weight decision algorithm of a Boolean function.
  Proc. NATO Advanced Research Workshop on Decoherence, Entanglement and Information Protection in Complex Quantum Systems, Les Houches, France, April 2004. pp.17-26. Kluwer, 2005

• Samuel L. Braunstein, Byung-Soo Choi, S. Maitra, D. Chakrabarti, S. Ghosh, P. Mukhopadhyay.
  Entanglement in quantum information processing.
  Proc. ERATO conference on Quantum Information Science (EQIS 2005), Japan. pp.127-128. 2005

• John A. Clark, Susan Stepney, Howard Chivers.
  Breaking the Model: finalisation and a taxonomy of security attacks.
  REFINE 2005, Surrey, UK, April 2005. ENTCS 137:225-242. Elsevier 2005
  [best paper]

• Ed Clark, Andrew N. W. Hone, Jon Timmis.
  A Markov Chain Model of the B-cell Algorithm
  ICARIS 2005, Banff, Canada, August 2005. LNCS 3627:318-330 Springer, 2005

• Xiaocheng Ge, Howard Chivers, Fiona Polack, Richard F. Paige.
  Adapting security risk analysis to the design of data-base-centric Web-based information systems
  ICSSEA 2005, CNAM, Paris, November 2005.

• L. B. Goncharova, Y. Jacques, C. Martin-Vide, A. O. Tarakanov, Jon Timmis.
  Biomolecular Immune-Computer: Theoretical Basis and Experimental Simulator
  ICARIS 2005, Banff, Canada, August 2005. LNCS 3627:72-85 Springer, 2005

• Emma Hart, Jon Timmis.
  Application Areas of AIS: Past, Present and Future
  ICARIS 2005, Banff, Canada, August 2005. LNCS 3627:483-497. Springer, 2005

• Chen Hao, John A. Clark and Jeremy L. Jacob.
  Synthesising Efficient and Effective Security Protocols.
  Proc. Workshop on Automated Reasoning for Security Protocol Analysis 2004. ENTCS 125(1):25-41. March 2005.

• Margaret Hill, Susan Stepney, Francis Wan.
  Penrose Life: ash and oscillators.
  ECAL 2005, Canterbury, UK, September 2005. LNAI 3630:471-480. Springer, 2005
  doi: 10.1007/11553090_48

• Dimitrios S. Kolovos, Richard F. Paige, Fiona Polack
  An Agile and Extensible Code Generation Framework.
  XP2005, Sheffield, June 2005, LNCS 3556:226-229. Springer 2005
  doi: 10.1007/11499053_33

• Yang Liu, John A. Clark, Susan Stepney.
  "Devices are People Too": using process patterns to elicit security requirements in novel domains.
  In Security of Pervasive Computing, SPC'05, Boppard, Germany, April 2005. LNCS 3450. Springer, 2005
  doi: 10.1007/b135497

• Paul Massey, John A. Clark, Susan Stepney.
  Evolution of a Human-Competitive Quantum Fourier Transform algorithm using genetic programming.
  GECCO'05, Washington DC, June 2005, pp.1657-1664. ACM Press, 2005
  [Silver Medallist in the "Human Competitive GP" competition]

• John Newborough, Susan Stepney.
  A generic framework for population-based algorithms, implemented on multiple FPGAs.
  ICARIS 2005, Banff, Canada, August 2005. LNCS 3627:43-55. Springer, 2005
  doi: 10.1007/11536444_4

• Richard F. Paige, Dimitrios S. Kolovos, Fiona Polack
  Refinement via Consistency Checking in MDA.
  REFINE 2005, Surrey, UK, April 2005. ENTCS 137:151-161. Elsevier 2005

• Fiona Polack, Susan Stepney.
  Emergent Properties do not Refine.
  REFINE 2005, Surrey, UK, April 2005. ENTCS 137:163-181. Elsevier 2005

• Fiona Polack, Susan Stepney, Heather Turner, Peter Welch, Fred Barnes.
  An architecture for modelling emergence in CA-like systems.
  ECAL 2005, Canterbury, UK, September 2005. LNAI 3630:433-442. Springer, 2005
  doi: 10.1007/11553090_44

• Jemima Rossmorris, Susan Stepney.
  Requirements as Conjectures: intuitive DVD menu navigation.
  ZB2005, Guildford, UK, April 2005. LNCS 3455:172-186, Springer, 2005
  doi: 10.1007/11415787_11

• Andrew Secker, Alex A. Freitas, Jon Timmis.
  Towards a danger theory inspired artificial immune system for web mining.
  In A Scime, ed, Web Mining: applications and techniques, pp.145-168. Idea Group, 2005.

• Thitima Srivatanakul, John A. Clark, Fiona Polack.
  Stressing Security Requirements: Exploiting the Flaw Hypothesis Method with Deviational Techniques.
  SREIS 2005, Paris, France, August 2005.

• Thomas Stibor, P. Mohr, Jon Timmis, Claudia Eckert.
  Is Negative Selection Appropriate for Anomaly Detection?
  GECCO'05, Washington DC, June 2005, pp.321-328. ACM Press, 2005

• Thomas Stibor, Jon Timmis, Claudia Eckert.
  A Comparative Study of Real-Valued Negative Selection to Statistical Anomaly Detection Techniques.
  ICARIS 2005, Banff, Canada, August 2005. LNCS 3627:262-275 Springer, 2005
  [best paper]

• Thomas Stibor, Jon Timmis, Claudia Eckert.
  On the Appropriateness of Negative Selection defined over Hamming Shape Space As a Network Intrustion Detection System.
  CEC 2005, Edinburgh, UK, 2005. IEEE Press, 2005

• Jon Timmis
  Challenges for Artificial Immune Systems.
  International Workshop on Natural and Artificial Immune Systems, Italy, 2005

• Heather Turner, Susan Stepney.
  Rule Migration: Exploring a design framework for modelling emergence in CA-like systems.
  ECAL Workshop on Unconventional Computing, 2005

• Heather Turner, Susan Stepney, Fiona Polack.
  A simulation environment for emergent properties (extended abstract).
  ECCS'05, Paris, France, November 2005

• Andrew Weeks, Susan Stepney.
  Artificial catalysed reaction networks for search.
  ECAL Workshop on Artificial Chemistry, 2005

• Peter Worth, Susan Stepney.
  Growing Music: musical interpretations of L-Systems.
  EvoMUSART, EuroGP, Lausanne, Switzerland, March 2005. LNCS 3449:545-550. Springer, 2005
  doi: 10.1007/b106856

• Yuan Zhan, John A Clark.
  Search-Based Mutation Testing
  GECCO'05, Washington DC, June 2005. ACM Press, 2005

technical reports

• Susan Stepney, Fiona Polack, Ian Toyn.
  Diagram Patterns and Meta-patterns to support formal modelling.
  Technical Report YCS-2005-394, University of York. October 2005

• Joss Wright, Susan Stepney, John A. Clark, Jeremy L. Jacob.
  Formalizing Anonymity: a review.
  Technical Report YCS-2005-389, University of York. 2005

other

• Susan Stepney.
  Desert Island Column.
  Automated Software Engineering, 12(1):139-141, 2005
  doi: 10.1023/B:AUSE.0000049211.24331.cf

books / proceedings

• G. Nicosia, V. Cutello, Peter J. Bentley, Jon Timmis, editors.
  Proceedings of the 3rd International Conference on Artificial Immune Systems (ICARIS 2004), Sicily, September 2004.
  LNCS 3239. Springer, 2004.

book chapters

• Jon Timmis, T. Knight, Leandro N. de Castro, Emma Hart.
  An overview of artificial immune systems.
  In R. Paton, H. Bolouri, M. Holcombe, J. H. Parish, R. Tateson, eds, Computation in Cells and Tissues: Perspectives and Tools for Thought, pp.51-86. Springer 2004.

journal papers

• K. M. R. Audenaert, Samuel L. Braunstein.
  On strong superadditivity of the entanglement of formation.
  Communications in Mathematical Physics 246:443-452, 2004

• Michael Batty, Samuel L. Braunstein, Andrew J. Duncan, S. Rees.
  Quantum algorithms in group theory.
  Contemporary Mathematics 349:1-62, 2004

• Samuel L. Braunstein, K. Nemoto.
  Quantum coherence: myth or fact.
  Physics Letters A 333:378-381, 2004

• Phillip J. Brooke, Richard F. Paige, John A. Clark, Susan Stepney.
  Playing the Game: cheating, loopholes, and virtual identity.
  ACM Computers and Society, 34(3), September 2004

• Hao Chen, John A. Clark, Jeremy L. Jacob.
  Automatic Design of Security Protocols.
  Computational Intelligence 20(3):503-516. August 2004

• Howard Chivers, John A. Clark.
  Smart Dust – Friend or Foe? Replacing Identity with Configuration Trust.
  Computer Networks 46:723-740. 2004

• John A. Clark, Jeremy L. Jacob, S. Maitra, P. Stanica.
  Almost Boolean Functions: the Design of Boolean Functions by Spectral Inversion.
  Computational Intelligence 20(3):450-462. August 2004

• Dan W. Franks, J. Noble.
  Warning Signals and Predator-Prey Coevolution.
  Proc. Roy. Soc. London B: Biological Sciences, 271:1859-1866, 2004.

• A. Gilchrist, K. Nemoto, W. J. Munro, T. C. Ralph, S. Glancy, Samuel L. Braunstein, G. J. Milburn.
  Schrödinger cats and their power for quantum information processing.
  Journal of Optics B 6:S828-S833, 2004

• P. Kok, Samuel L. Braunstein, J. P. Dowling.
  Quantum lithography, entanglement and Heisenberg-limited parameter estimation.
  Journal of Optics B 6:S811-S815, 2004

• H. Lee, U. Yurtsever, P. Kok, G. M. Hockney, C. Adami, Samuel L. Braunstein, J. P. Dowling.
  Towards photostatistics from photon-number discriminating detectors.
  Journal of Modern Optics 51:1517-1528, 2004

• J. Noble, Dan W. Franks.
  Social Learning in a Multi-Agent System.
  Computing and Informatics, 22:101-114, 2004.

• Andrew Watkins, Jon Timmis, Lois Boggess.
  Artificial Immune Recognition System (AIRS): An Immune Inspired Supervised Machine Learning Algorithm.
  Genetic Programming and Evolvable Machines, 5(3):291-317, 2004
  doi: 10.1023/B:GENP.0000030197.83685.94

refereed workshop and conference papers

• Nuno Amálio, Susan Stepney, and Fiona Polack
  Formal Proof from UML Models.
  ICFEM 2004, Seattle, USA. LNCS 3308:418-433, Springer, 2004
  doi: 10.1007/b102837

• Richard Banach, Czeslaw Jeske, Simon Fraser, Richard Cross, Mike Poppleton, Susan Stepney, Steve King.
  Approaching the Formal Design and Development of Complex Systems: the Retrenchment Position.
  Workshop on Software and Complex Systems, 9th IEEE Intl. Conf. on Engineering of Complex Computer Systems, Florence, Italy, April 2004

• Peter J. Bentley, Jon Timmis.
  A Fractal Immune Network.
  ICARIS 2004, Sicily, September 2004. LNCS 3239:133-145. Springer, 2004.

• Leo Caves, John A. Clark, Susan Stepney.
  Acquiring a Debt Worth Repaying.
  BioGEC workshop, GECCO'04, Seattle, June 2004

• Hao Chen, John A. Clark, Jeremy L. Jacob.
  The Synthesis of Effective and Efficient Security Protocols.
  2nd International Joint Conference on Automated Reasoning, Cork, Ireland. July 2004.

• John A. Clark, Jeremy L. Jacob, Susan Stepney.
  The design of S-boxes by simulated annealing.
  CEC-2004, Portland OR, USA, June 2004, pp.1533-1537. IEEE, 2004

• John A. Clark, Jeremy L. Jacob, Susan Stepney.
  Searching for cost functions.
  CEC-2004, Portland OR, USA, June 2004, pp.1517-1524. IEEE 2004

• Dan W. Franks, J. Noble.
  Effects of the topology of social networks on information transmission.
  From Animals to Animats 8, pp.395-404, 2004.

• Xiaocheng Ge, Fiona Polack, Regine Laleau
  Secure Databases: an Analysis of Clark-Wilson Model in a Database Environment
  CAiSE 2004, Riga, Latvia, June 2004. LNCS 3084:234-247. Springer 2004
  doi: 10.1007/b98058

• M. Harman, John A. Clark.
  Metrics are Fitness Functions too.
  10th IEEE International Metrics Symposium, Chicago, USA. September 2004

• Paul Massey, John A. Clark, Susan Stepney.
  Evolving quantum circuits and programs through genetic programming.
  GECCO'04, Seattle, June 2004. LNCS 3103:569-580. Springer, 2004
  [best in GP stream]

• P. Mohr, N. Ryan, Jon Timmis.
  Exploiting Immunological Properties for Ubiqitous Computing Systems.
  ICARIS 2004, Sicily, September 2004. LNCS 3239:277-289. Springer, 2004
  doi: 10.1007/b100486

• Thitima Srivatanakul, John A. Clark, Fiona Polack
  Effective security requirements analysis: HAZOP and use cases
  ISC 2004, Palo Alto, CA, USA, September 2004, LNCS 3225:416-427, Springer 2004
  doi: 10.1007/b100936

• Pante Stanica, Subhamoy Maitra, John A. Clark.
  Results on Rotation Symmetric Bent and Correlation Immune Boolean Functions.
  FSE 2004, Delhi, India, February 2004, Revised Papers. LNCS 3017:161-177. Spinger 2004

• Susan Stepney.
  Teaching Post-Classical Computation.
  ITiCSE, Leeds, UK, June 2004. ACM Press, 2004
  [keynote paper]

• Susan Stepney, Robert E. Smith, Jon Timmis, Andy M. Tyrrell.
  Towards a Conceptual Framework for Artificial Immune Systems.
  ICARIS 2004, Sicily, September 2004. LNCS 3239:53-64. Springer, 2004
  doi: 10.1007/b100486

• Jon Timmis, Camilla Edmonds.
  A Comment on opt-AINet: An Immune Network Algorithm for Optimisation.
  GECCO'04, Seattle, June 2004. LNCS 3102:308-317. Springer, 2004.

• Jon Timmis, C. Edmonds, J. Kelsey.
  Assessing the Performance of Two Immune Inspired Algorithms and a Hybrid Genetic Algorithm for Function Optimisation.
  CEC-2004, Portland OR, USA, June 2004, pp.1044-1051. IEEE, 2004

• Andrew Watkins, Jon Timmis.
  Exploiting Parallelism Inherent in AIRS, an Artificial Immune Classifier.
  ICARIS 2004, Sicily, September 2004. LNCS 3239:427-438. Springer, 2004.

• Yuan Zhan, John A. Clark.
  Search Based Automatic Test Data Generation at the Architectural Level.
  GECCO'04, Seattle, June 2004. LNCS 3103:1413-1424. Springer, 2004.

technical reports

• Hao Chen, John A. Clark, Jeremy L. Jacob.
  A Search-based Approach to the Automated Design of Security Protocols
  Technical Report YCS-2004-376, University of York, May 2004.

• Thitima Srivatanakul, John A. Clark, Fiona Polack
  Writing Effective Security Abuse Cases
  Technical Report YCS-2004-375, University of York, May 2004.

• Thitima Srivatanakul, John A. Clark, Fiona Polack
  Security Zonal Analysis
  Technical Report YCS-2004-374, University of York, May 2004.

• Samuel H. Valentine, Susan Stepney, Ian Toyn.
  A Z Patterns Catalogue II: definitions and laws, v0.1.
  Technical Report YCS-2004-383, University of York. October 2004

other

• Samuel L. Braunstein.
  Quantum computation: a tutorial [Arabic translation, 3 parts].
  Tronix Magazine. 8:6-8, 9:36-37, 10, 2004

• Susan Stepney.
  Book Review: Evolutionary Electronics: Automatic Design of Electronic Circuits and Systems by Genetic Algorithms.
  Genetic Programming and Evolvable Machines, 5(4):395-396, 2004
  doi: 10.1023/B:GENP.0000036058.08897.cd

books / proceedings

• Jon Timmis, Peter J. Bentley, Emma Hart, editors.
  Proceedings of the 2nd International Conference on Artificial Immune Systems (ICARIS 2003), Edinburgh, UK, September 2003.
  LNCS 2787. Springer, 2003.

journal papers

• John A. Clark, Jose Javier Dolado, Mark Harman, Rob Hierons, Bryan Jones, Mary Lumkin, Brian Mitchell, Spiros Mancoridis, Kearton Rees, Marc Roper, Martin Shepperd.
  Reformulating Software Engineering as a Search Problem.
  IEE Proceedings – Software 150(3):161-175, 2003.

• Leandro N. de Castro, Jon Timmis.
  Artificial Immune Systems as a Novel Soft Computing Paradigm.
  Soft Computing, 7(8):526-544, 2003.

• Dan W. Franks, J. Noble.
  Batesian Mimics Influence Mimicry Ring Evolution.
  Proc. Roy. Soc. London B: Biological Sciences, 271:191-196, 2003.

• K. Nemoto, Samuel L. Braunstein
  Quantum coherence in the presence of unobservable quantities.
  Physical Review A 68:042326-1/4, 2003
  [Included in the Virtual Journal of Quantum Information - November 2003]

• Mark J. Neal, Jon Timmis.
  Timidity: A Useful Mechanism for Robot Control?
  Informatica, 27(2):197-204, 2003.

• A.K. Pati, Samuel L. Braunstein
  Quantum deleting and signalling.
  Physics Letters A 315:208-212, 2003

• J. Zhang, K. Peng, Samuel L. Braunstein
  Backaction-induced spin-squeezed states in detuned quantum-nondemolition measurement.
  Physical Review A 68:035802-1/4, 2003

• J. Zhang, K. Peng, Samuel L. Braunstein
  Quantum-state transfer from light to macroscopic oscillators.
  Physical Review A 68:013808-1/5, 2003
  [Included in the Virtual Journal of Quantum Information - July 2003]

refereed workshop and conference papers

• Nuno Amálio, Fiona Polack
  Comparison of formalisation approaches of UML class constructs in Z and Object-Z
  ZB2003, Turku, Finland, June 2003. LNCS 2651. Springer, 2003.

• Nuno Amálio, Susan Stepney, Fiona Polack.
  Modular UML Semantics: Interpretations in Z based on Templates and Generics.
  FACS'03 Workshop on Formal Aspects of Component Software, Pisa. UNU/IIST Technical Report 284. 2003

• Samuel L. Braunstein, A. N. Boto, P. Kok, D. S. Abrams, C. P. Williams, J. P. Dowling.
  Quantum lithography.
  Fluctuations and Noise in Photonics and Quantum Optics, Santa Fe, USA, June 2003. Proc. SPIE, 5111:268-272, 2003.

• Hao Chen, John A. Clark, Jeremy L. Jacob.
  Automatic Design of Security Protocols.
  CEC-2003, Canberra, Australia, December 2003. IEEE, 2003.

• Howard Chivers, John A. Clark, Susan Stepney.
  Smart Devices and Software Agents: the basics of good behaviour.
  In Security of Pervasive Computing, SPC'03, Boppard, Germany. LNCS 2804. Springer, 2003

• John A. Clark.
  Nature-inspired Cryptography: Past, Present and Future.
  CEC-2003, Canberra, Australia, December 2003. IEEE, 2003.
  [invited paper]

• John A. Clark, Jeremy L. Jacob, Subhamoy Maitra, Pantelimon Stanica
  Almost Boolean Functions: the Design of Boolean Functions by Spectral Inversion.
  CEC-2003, Canberra, Australia, December 2003, 3:2173-2180, IEEE, 2003.

• John A. Clark, Jeremy L. Jacob, Susan Stepney.
  Secret Agents Leave Big Footprints: how to plant a trapdoor in a cryptographic function and why you might not get away with it..
  GECCO'03, Chicago, July 2003. LNCS 2724:2022-2033. Springer, 2003

• Alex A. Freitas, Jon Timmis.
  Revisiting the Foundations of Artificial Immune Systems: A Problem Oriented Perspective.
  ICARIS 2003, Edinburgh, September 2003. LNCS 2787:229-241. Springer, 2003.

• J. Kelsey, Jon Timmis.
  Immune Inspired Somatic Contiguous Hypermutation for Function Optimisation.
  GECCO'03, Chicago, July 2003. LNCS 2723. Springer, 2003
  [best AIS paper]

• J. Kelsey, Jon Timmis, Andrew N. W. Hone.
  Chasing Chaos.
  CEC-2003, Canberra, Australia, December 2003, pp.413-419. IEEE, 2003

• T. Knight, Jon Timmis.
  A Multi-layered Immune Inspired Machine Learning Algorithm.
  In A. Lotfi and M. Garibaldi, ed, Applications and Science in Soft Computing, pp.195-202. Springer 2003.

• Peter May, Keith Mander, Jon Timmis.
  Mutation Testing: An Artificial Immune System Approach.
  UK-Softest. UK Software Testing Workshop, York, UK, September 2003.

• Peter May, Keith Mander, Jon Timmis.
  Software Vaccination: An Artificial Immune Systems Approach.
  ICARIS 2003, Edinburgh, September 2003. LNCS 2787:81-92. Springer, 2003
  doi: 10.1007/b12020

• K. Nemoto, A. Gilchrist, W. J. Munro, T. C. Ralph, Samuel L. Braunstein, G. J. Milburn.
  Quantum information processing with Schrödinger cats.
  Fluctuations and Noise in Photonics and Quantum Optics, Santa Fe, USA, June 2003. Proc. SPIE, 5111:434-443, 2003.

• K. Nemoto, W. J. Munro, G. J. Milburn, Samuel L. Braunstein.
  Quantum metrology: detection of weak forces using Schrödinger cat resources.
  QCMC'02, Cambridge MA, USA, July 2002. pp.333-336. Rinton Press, 2003.

• Matthew D. Russell, John A. Clark, Susan Stepney.
  Making the Most of Two Heuristics: Breaking Transposition Ciphers with Ants.
  CEC-2003, Canberra, Australia, December 2003, 4:2653-2658. IEEE, 2003

• Matthew D. Russell, John A. Clark, Susan Stepney.
  Using Ants to Attack a Classical Cipher. (poster paper)
  GECCO'03, Chicago, July 2003. LNCS 2723:146-147. Springer, 2003

• Andrew Secker, Alex A. Freitas, Jon Timmis.
  AISEC: An Artificial Immune System for E-mail Classification.
  CEC-2003, Canberra, Australia, December 2003, pp.131-139. IEEE, 2003

• Andrew Secker, Alex A. Freitas, Jon Timmis.
  A Danger Theory Approach to Web Mining.
  ICARIS 2003, Edinburgh, September 2003. LNCS 2787:156-167. Springer, 2003.

• Thitima Srivatanakul, John A. Clark, Susan Stepney, Fiona Polack.
  Challenging formal specifications by mutation: a CSP security example.
  APSEC-2003: 10th Asia-Pacific Software Engineering Conference, Chiangmai, Thailand, December 2003, pp.340-350. IEEE, 2003.

• Susan Stepney.
  Critical Critical Systems.
  FASeC'02, London, December 2002. LNCS 2629:62-70. Springer, 2003
  doi: 10.1007/b94774
  [invited paper]

• Susan Stepney, John A. Clark, Colin Johnson, Derek Partridge, Robert E. Smith.
  Artificial Immune Systems and the Grand Challenge for Non-Classical Computation.
  ICARIS 2003, Edinburgh, September 2003. LNCS 2787:204-216. Springer, 2003
  doi: 10.1007/b12020

• Susan Stepney, Fiona Polack, Ian Toyn.
  An Outline Pattern Language for Z.
  ZB2003, Turku, Finland, June 2003. LNCS 2651:2-19, Springer, 2003.

• Susan Stepney, Fiona Polack, Ian Toyn.
  Patterns to Guide Practical Refactoring.
  ZB2003, Turku, Finland, June 2003. LNCS 2651:20-39. Springer, 2003.

technical reports

• Fiona Polack
  Exploring the informal translation of OMT object models in B
  Technical Report YCS-2003-351, University of York. 2003

• Susan Stepney.
  CSP/FDR2 to Handel-C translation.
  Technical Report YCS-2003-357, University of York. June 2003.

• Susan Stepney, Ian T. Nabney.
  The DeCCo Project Papers.
  Technical Report YCS-2003-358--363, University of York. June 2003.

• Susan Stepney, Fiona Polack, Ian Toyn.
  A Z Patterns Catalogue I: specification and refactorings, v0.1.
  Technical Report YCS-2003-349, University of York. January 2003.

other

• Robin Milner, Susan Stepney.
  Nanotechnology: Computer Science opportunities and challenges.
  Submission by the UK Computing Research Committee to the Nanotechnology Working Group of the Royal Society and the Royal Academy of Engineering. August, 2003

books / proceedings

• Leandro N. de Castro, Jon Timmis.
  Artificial Immune Systems: A New Computational Approach.
  Springer 2002.

• Jon Timmis, Peter J. Bentley, editors.
  ICARIS 2002, Kent, UK, September 2002.
  University of Kent, 2002.

journal papers

• S. D. Bartlett, B. C. Sanders, Samuel L. Braunstein, K. Nemoto.
  Efficient classical simulation of continuous variable quantum information processes.
  Physical Review Letters 88:097904/1-4, 2002
  [Included in the Virtual Journal of Quantum Information - March 2002]

• Samuel L. Braunstein
  Quantum teleportation.
  Fortschritte der Physik 50:608-613, 2002

• W. J. Munro, K. Nemoto, G. J. Milburn, Samuel L. Braunstein
  Weak force detection with superposed coherent states.
  Physical Review A 66:023819-1/6, 2002
  [Included in the Virtual Journal of Quantum Information - September 2002]

• K. Nemoto, Samuel L. Braunstein
  A simulated photon-number detector in quantum information processing.
  Quantum Information and Computation 2:556-559, 2002. (special issue)

• K. Nemoto, Samuel L. Braunstein
  Equivalent efficiency of a simulated photon-number detector.
  Physical Review A 66:032306-1/4, 2002
  [Included in the Virtual Journal of Quantum Information - October 2002]

• A. K. Pati, Samuel L. Braunstein
  Speed-up and entanglement in quantum searching.
  Quantum Information and Computation 2:399-409, 2002

refereed workshop and conference papers

• M. Ayara, Jon Timmis, Rogerio de Lemos, Leandro N. de Castro, R. Duncan.
  Negative selection: How to generate detectors.
  ICARIS 2003, Canterbury, UK, pp.89-98, September 2002.

• J. Bowen, K. Bogdanov, John A. Clark, R. Hierons, M. Harman, P. Krause.
  FORTEST: Formal Methods and Testing.
  COMPSAC 2002. pp. 91-104, 2002

• John A. Clark, Jeremy L. Jacob.
  Fault Injection and a Timing Channel on an Analysis Technique.
  EUROCRYPT 2002, Amsterdam, The Netherlands, April 2002. LNCS 2332:181-196. Springer 2002

• John A. Clark, Jeremy L. Jacob, Susan Stepney, S. Maitra, William Millan.
  Evolving Boolean Functions Satisfying Multiple Criteria.
  INDOCRYPT 2002, Hyderabad, December 2002. LNCS 2551:246-259. Springer, 2002

• Leandro N. de Castro, Jon Timmis.
  Hierarchy and convergance of immune networks: Basic ideas and premilinary results.
  ICARIS 2003, Canterbury, UK, pp.231-240, September 2002.

• Leandro N. de Castro, Jon Timmis.
  An artificial immune network for multimodal optimisation.
  CEC 2002, Honolulu, Hawaii, USA, May 2002, pp.699-704. IEEE Press, 2002.

• Leandro N. de Castro, Jon Timmis.
  Artificial Immune Systems: A Novel Approach to Pattern Recognition.
  In L Alonso J Corchado and C Fyfe, eds, Artificial Neural Networks in Pattern Recognition, pp.67-84. University of Paisley 2002.

• Dan W. Franks, J. Noble.
  Conditions for the Evolution of Mimicry.
  From Animals to Animats 7, pp.353-354, 2002.

• Dan W. Franks, J. Noble.
  The Origins of Mimicry Rings.
  Proc. 8th International Conference on Artificial Life, pp.186-191, 2002.

• T. Knight, Jon Timmis.
  A Multi-Layered Immune Inspired Approach to Data Mining.
  Proc. 4th International Conference on Recent Advances in Soft Computing, Nottingham, UK, pp.266-271, December 2002.

• Regine Laleau, Fiona Polack
  Coming and Going from UML to B: a proposal to support traceability in rigorous IS development
  ZB2002, Grenoble, France, January 2002. LNCS 2272, Springer, 2002.
  

• J. Noble, Dan W. Franks.
  Social Learning Mechanisms Compared in a Simple Environment.
  Proc. 8th International Conference on Artificial Life, pp.379-385, 2002.

• Susan Stepney, Fiona Polack, I. Toyn.
  Refactoring in Maintenance and Development of Z Specifications and Proofs.
  REFINE 2002, Copenhagen, July 2002. ENTCS 70(3). Elsevier, 2002

• Jon Timmis, Rogerio De Lemos, M. Ayara, R. Duncan.
  Towards immune inspired fault tolerance in embedded systems.
  Proc. 9th International Conference on Neural Information Processing, pp.1459-1463. IEEE, November 2002.

• Ian Toyn, Susan Stepney.
  Characters + Mark-up = Z Lexis.
  ZB2002, Grenoble, France, January 2002. LNCS 2272:100-119, Springer, 2002.

• A. Watkins, Jon Timmis.
  Artificial Immune Recognition System (AIRS): Revisions and Refinements.
  ICARIS 2003, Canterbury, UK, pp.173-181, September 2002.

technical reports

• David Cooper, Susan Stepney, Jim Woodcock.
  Derivation of Z Refinement Proof Rules.
  Technical Report YCS-2002-347, University of York. December 2002.