Publications by Jon Timmis

Here is my complete list of publications. I provide either a pre-print PDF (marked by the PDF icon), a DOI or a link to the journal. Not all entries have something yet, but I am working on it! If in doubt, just email me and ask for the paper.

Quick links to : Papers, Books, Edited Volumes, Reviews

Papers

2013

Journal Papers
  1. Modular self-assembling and self-reconfiguring e-pucks. L. Murray, J. Timmis and A. Tyrrell. Swarm Intelligence. May (2013)
  2. Functional complexity of the Leishmania granuloma and the potential of in silico modelling. J. Moore, D. Moyo, L. Beattie, P. Andrews, J. Timmis and P. Kaye. Front. Immun. 4:35. doi: 10.3389/fimmu.2013.00035
  3. The Receptor Density Algorithm N. Owens, A. Greensted, J. Timmis and A. Tyrrell. Journal of Theoretical Computer Science 481:51-73 (2013) http://dx.doi.org/10.1016/j.tcs.2012.10.057
  4. Spartan: A Comprehensive Tool for Understanding Uncertainlty in Simulations of Biological Systems. K. Alden, M. Read, J. Timmis, P. Andrews, H. Veiga-Fernades and M. Coles. PLoS Comput Biol 9(2): e1002916. doi:10.1371/journal.pcbi.1002916
  5. SABRE: A bio-inspired fault tolerant electronics architecture. P. Bremner, Y. Liu, M. Samie, G. Dragffy, T. Pipe, G. Tempesti, J. Timmis and A. Tyrrell. . Bioinspiration and Biomemetics 8(1 016003 doi:10.1088/1748-3182/8/1/016003)
  6. In Silico investigtation into dendrtic cell regulation of CD8Treg mediated killing of Th1 cells in murine experimental autoimmune encephalomyelitis. R. Williams, R. Greaves, M. Read, J. Timmis, P. Andrews and V. Kumar. BMC Bioinformatics 14(Suppl 6):S9 (2013)
  7. In Silico investigation of novel biological pathways: the role of CD200 in regulation of T Cell priming in experimental autoimmune encephalomyelitis. R. Greaves, M. Read, J. Timmis, P. Andrews, J. Butler, B. Gercknes and V. Kumar. Biosystems 112(2):107-121 (2013)
  8. Automatic Machine Code Generation for a Transport Triggered Architecture using Cartesian Genetic Programming. Walker, J. A., Liu, J., Tempesti, G., Timmis, J. & Tyrrell, A. Journal of Adaptive, Resilient and Autonomic Systems 3(4) (2013)

2012

Journal Papers
  1. Chemical Agent Detection using the Receptor Density Algorithm. J. Hilder, N. Owens, P. Hickey, S. Cairns, D. Kilgour, M. Neal, J. Timmis and A. Tyrrell. IEEE Transactions SMC Part C. 42(6):1730-1741.
  2. Differential RET signaling responses orchestrate lymphoid and nervous enteric system development. A. Patel et al.. Science Signalling. Vol 5, Issue 235.
  3. Pairing experimentation and computational modelling to understand the role of tissue inducer cells in the development of lymphoid organs. K. Alden, J. Timmis, P. Andrews, H. Veiga-Fernandes and M. Coles. Front. Immun. 3:172
Conference Papers (peer reviewed)
  1. Self-reconfigurable Modular e-pucks. L. Murray, J. Timmis and A. Tyrrell. LNCS 7461, pp:133-144. (ANTS 2012).
  2. Immune-inspired Self Healing in Wireless Sensor Networks. T. H. Lim, H. K. Lau, J. Timmis and I. Baite LNCS 7597. pp:42-56. (ICARIS 2012)
  3. Validation of Performance Data using Experimental Verification Process in Wireless Sensor Networks. T. H. Lim, J. Timmis and I. Baite . 17th IEEE International Conference on Emerging Technologies & Factory Automation (ETFA 2012), Krakow, Poland.
  4. Systematic Experimental Analysis and Evaluation of Routing Protocol in Wireless Sensor Networks. T. H. Lim, I. Baite and J. Timmis The UK Electronics Forum (UKEF'12).
  5. Profiling the Fault Tolerance for the Adaptive Protien Processing Associate Memory. O. Qadir, J. Timmis, G. Tempsti and A. Tyrrell NASA/ESA Conference on Adaptive Hardware and Systems (AHS). pp:246-253
  6. Extending an estabished simulation: exploration of the possible effects using a case study in Experimental Autoimmune Encephalomyelitis. R. Greaves, M. Read, J. Timmis, P. Andrews and V. Kumar. LNCS 7223:150-161. on-line
  7. Simulation as a Scientific Instrument, Paul S. Andrews, Susan Stepney, Jon Timmis, Proceedings of CoSMoS 2012, pp:1-10, Luniver Press, 2012
Other
  1. Embodied Immunity in Collective Adaptive Systems. J. Timmis . Extened abstract for Frontiers in Natural Computing.
  2. Domain Modelling - When UML is not enough: A case study using the IL-1 Stimulated NF-kB Intracellular Signalling Pathway. R. Williams, J. Timmis and E. Quarnstrom ICARIS 2012.(abstract)
  3. Building Confidence in Agent-Based Computational Models of the Immune System. J. Timmis et al. ICARIS 2012. (abstract)
  4. CD200 Regulation can Promote Recovery from Autoimmunity in Experimental Autoimmune Encephalomyelitis. M. Read, J. Butler, B. Gerckens, J. Timmis and V. Kumar . ICARIS 2012. (abstract)

2011

Journal papers
  1. Techniques for Grouding Agent-Based Simulations in the REal Domain: a case srudy in Experimental Autoimmune Encephalomyelisis. Read, M., Timmis, J. Andrews, P. and Kumar , K. Journal of Mathematical and Compuutational Modelling of Dynamical Systems. 17(4):296-302.
  2. Adaptive data-driven error detection in swarm robotics with statistical classifiers. K. Lau, I. Baite, P. Cairns and J. Timmis Journal of Robotics and Autonmous Systems. 59(12):1021-1035. On-line here
  3. From Bidirectional Associative Memory to a noise-tolerant, robust Protein Processor Associative Memory. O. Qadir, J. Lui, G. Tempesti, J. Timmis and A. Tyrrell. Artificial Intelligence 175(2):673-693. 2011.
Conference papers
  1. Multi-modal routing to tolerate failures. T. H. Lim, I. Bate and J. Timmis The 7th International Conference on Intelligent Sensors, Sensor Networks and Information Processing (ISSNIP 2011), Adelaide, Australia.
  2. The Protein Processor Associative Memory on a Robotic Hand-Eye Corodination Task. O. Qadir, J. Timmis, G. Tempesti and A. Tyrrell.. Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering. Vol:103, pp:29-43.
  3. Analysing the Reliability of a Self-reconfigurable Modular Robotic System. L. Murray, W. Liu, A. Winfield, J. Timmis and A. Tyrrell. Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering. Vol:103, pp:44-58.
  4. Bio-inspired error detection in complex systems. M. Drozda, I. Bate and J. Timmis IEEE Pacific Rim International Symposium on Dependable Computing. pp:154-163. Download paper
  5. CoCoRo: The Self-aware underwater Swarm . T. Schmickl, R. Thenius, C. Moslinger, J. Timmis, A. Tyrrell, M. Read, J. Hilder, J. Halloy, A. Campo, C. Stefani, L. Manfredi, T. Dipper, D. Sutantyo and S. Kernback. Self-Adaptive and Self-Aware Systems. 2011.
  6. CoSMoS Process, Models and Metamodels. P. Andrews, S. Stepney, Tim Hoverd, Fiona Polack, Adam Sampson and Jon Timmis In Proceedings of the 2011 Workshop on Complex Systems MOdelling and Simulation. Part of ECAL 2011. pp: 1-14.
  7. A Lymphocyte-Cytokine Network Inspired Algorithm for Data Analysis. Yang Liu, J. Timmis and T. Clarke. LNCS 6825, pp:187-197.
  8. Parameter Optimisation of the Receptor Density Algorithm. J. Hilder, N. Owens, P. Hickey, S. Cairns, D. Kilgour, J. Timmis and A. Tyrrell. LNCS 6825, pp:226-239.
  9. Collective Monitoring to Achieve Self-Detection of Errors in Swarm Robotics. H.K. Lau, I. Bate and J. Timmis LNCS 6826, pp:254-267.
  10. Process-Oriented Subsumption Architecture for Swarm-Robotic Systems. J. Posso, A. Sampson, J. Simpson and J. Timmis. In Communicating Process Architectures (CPA) 2011, Vol 68 of Concurrent Systems Engineering. pp:303-316.
  11. A Flexible Decentralised Communication Architecture on a Field Programmable Gate Array for Swarm System Simulations. A. G. Zamorano, J. Timmis and A. Tyrrell. IEEE CEC 201, pp:230-237.
  12. Hardware architecture for a Bidirectional Hetero-Associative Protein Processing Associative Memory. O. Qadir, Y Liu, J. Timmis, G. Tempesti and A. Tyrrell. IEEE CEC 2011, pp:208-215.
  13. A Self-Scaling Instruction Generator Using Cartesian Genetic Programming. Y. Liu, G. Tempesti, J. A. Walker, J. Timmis, A. M. Tyrrell, and P. Bremner. LNCS 6621, pp:298-309.
Other
  1. In Silico Investigation into CD8Treg Mediated Recovery in Murine Experimental Autoimmune Encephalomyelitis R. Williams, P. Andrews, J. Timmis and V. Kumar Extended Abstract in LNCS 6825, pp:51-54.
  2. Towards Argument-Driven Validation of an in-silico Model of Immune Tissue Organogenesis. K. Alden P. Andrews, J. Timmis, H. Veiga-Fernandes and M. Coles. Extended Abstract in LNCS 6826, pp:66-70.
  3. Modelling Containment Mechanisms in the Immune System for Applications in Engineering. Amelia Ismail and Jon Timmis Extended Abstract in LNCS 6826, pp:77-80.

2010

Journal papers
  1. Elucidation of T cell signalling models. N. Owens, J. Timmis, A. Greensted and A. Tyrrell. Journal of Theoretical Biology 262:452-470. 2010 on-line pre-print
  2. On Artificial Immune Systems and Swarm Intelligence. J. Timmis, E. Hart and P. Andrews . Swarm Intelligence 4:247-273. On-line here.
  3. An Experimental Comparision of a Genetic Algorithm and a Hill-Climber for Term Selection. A. MacFarlane, A. Secker, P. May and J.Timmis. Journal of Documentation 6(44) 2010
  4. Hierarchical Classification of G-Protein-Coupled-Receptors with Data-Driven Selection of Attributes and Classifiers. A. Secker, M. Davis, A. Fretais, J. Timmis, E. Clark and D. Flower International Journal of Data Mining and Bioinformatics Vol.4, No.2, pp:191-210.
Conference papers
  1. Exploiting Loose Horizontal Coupling in Evolutionary Swarm Robotics. J. Owen, S. Stepney, J. Timmis and A. Winfield LNCS 6234, pp:432-439..
  2. The Diagnostic Dendritic Cell Algorithm for Robotic Systems. R. Bi, J. Timmis and A. Tyrrell . 12th IEEE Congress on Evolutionary Computation (CEC10), Barcelona, pp 4280-4287, July 2010.
  3. Principles of Protein Processing for a Self-Organising Associative Memory. O. Qadir, J. Liu, J. Timmis, G. Tempesti and A. Tyrrell. 12th IEEE Congress on Evolutionary Computation (CEC10), Barcelona, pp 3836-3843, July 2010.
  4. A Petri Net Model of Granulomatous Inflammation. L. Albergante, J. Timmis, P. Andrews, L. Beattie and P. Kaye. LNCS 6209, pp:1-3. Hart et al, (Eds), pp:1-3. Hart et al, (Eds)
  5. On Homeostasis in Collective Robotic Systems. J. Timmis and A. Tyrrell LNCS 6209, pp:307-309. Hart et al. (Eds)
  6. A Developmental and Immune-Inspired Dynamic Task Allocation Algorithm for Microprocessor Array Systems. Y. Liu, J. Timmis, O. Qadir, G. Tempesti and A. Tyrrell LNCS 6209, pp:199-212, Hart el al. (Eds).
  7. Reflections on the Simulation of Complex Systems for Science Fiona A. C. Polack, Paul S. Andrews, Teodor Ghetiu, Mark Read, Susan Stepney, Jon Timmis and Adam T. Sampson In ICECCS 2010: Fifteenth IEEE International Conference on Engineering of Complex Computer Systems pp. 276-285 IEEE Press
  8. A Neural-Endocrine Architecture for Foraging in Swarm Robotic Systems. J. Timmis, L. Murray and M. Neal. Studies in Computational Intelligence Vol. 284, pp:319-330. Springer.
Other
  1. An Artificial Immune System for Robot Organisms. J. Timmis, A. Tyrrell, M. Mokhtar, A. Ismail, N. Owens and R. Bi. Symbiotic Multi-Robot Organisms: Reliability, Adaptability and Evolution. Levi, P and Kernback, S. (Eds). pp: 268-288.
  2. An Introduction to Artificial Immune Systems. M. Read, P. Andrews and J. Timmis. To appear in the Handbook of Natural Computation.
  3. Artificial Immune Systems. Encyclopedia of Machine Learning Entry 348. J. Timmis. Springer.
  4. Tunable Detectors for Artificial Immune Systems: From Model to Algorithm P. Andrews and J. Timmis. The Handbook of Bioinformatics, pp:107-123. Flower, D and Davies, M. (Eds) doi

2009

Journal papers
  1. An artificial immune system for clustering amino acids in the context of protein function classification. A. Secker, M.N. Davies, A.A. Freitas, J. Timmis, E. Clark and D.R. Flower. Journal of Mathematical Modeling and Algorithms (2009), 8: 103-123.
Conference papers
  1. Profile Adaptation in Adaptive Information Filtering: A Immune-Inspired Approach. N. Azmi, J. Timmis and F. Polack. IEEE International Conference on Soft Computing and Pattern Recognition, Malaysia.pp:414-419
  2. Towards Energy Homeostasis in an Autonomous Self-Reconfigurable Modular Robotic Organism. R. Humza, O. Scholz, M. Mokhtar, J. Timmis and A. Tyrrell. Comptation World'09. pp:21-26. IEEE Press. doi
  3. On Adaptive Self-Organisation in Artificial Robot Organisms. S. Kernbach et al. Computation World'09. pp:33-43 IEEE Press.
  4. A Domain Model of Experimental Autoimmune Encephalomyelitis. M. Read, J. Timmis, P. Andrews and V. Kumar. 2nd Workshop on Complex Systems Modelling and Simulation.pp:9-44 (2009)
  5. An Immuno-engineering Approach for Anomaly Detection in Swarm Robotics Hui Keng Lau, I. Bate and J. Timmis Proceedings of 8th International Conference on AIS. LNCS 5666. pp:136-150 (2009)
  6. Using UML to Model EAE and its Regulatory Network. M. Read, J. Timmis, P. Andrews and V. Kumar Proceedings of 8th International Conference on AIS. LNCS 566. pp:4-6 (2009)
  7. T cell Receptor Signalling Inspired Kernal Density Estimation and Anomaly Detection. N. Owens, A. Greensted, J. Timmis and A. Tyrrell. Proceedings of 8th International Conference on AIS.LNCS 5666. pp:122-135. (2009)
  8. Nominal-Yield-Area Trade off in Automatic Synthesis of Analogue Circuits: A Genetic Programming Approach using Immune-Inspired Operators. P. Conca, G. Nicosia, G. Stracquadanio and J. Timmis NASA/ESA Conference on Adaptive Hardware and Systems (AHS-2009), co-located with the 46th Design Automation Conference (DAC 2009), July 29 - August 1, 2009, San Francisco, CA, USA; pp. 399-406, IEEE Computer Society Press.
  9. Modelling and Simulation of Granuloma Formation in Visceral Leishmaniasis A. Flugge, J. Timmis, P. ANdrews, J. Moore and P. Kaye Congress on Evolutionary Computation (CEC). pp.3052-3059. IEEE Press.
  10. Anomaly Detection Inspired by Immune Network Theory: A Proposal. HuiKeng Lau, J. Timmis and I. Baite Congress on Evolutionary Computation (CEC). pp.3045-3041 IEEE press.
  11. A Modified Dendritic Cell Algorithm for On-Line Error Detection in Robotic System. M. Mokhtar, J. Timmis, A. Tyrrell and R. Bi Congress on Evolutionary Computation (CEC) pp.2055-2062 IEEE press
  12. An Adaptive Neuro-Endocrine System for Robotic Systems J. Timmis, M. Neal and J. Thorniley IEEE Workshop on Robotic Intelligence in Informationally Structured Space. Part of IEEE Workshops on Computational Intelligence. pp: 129-136. Nashville, 2009. Digital Object Identifier 10.1109/RIISS.2009.4937917
Other
  1. Aggregation of Swarms for Fault Tolerance in Swarm Robotics using an Immuno-engineering Approach. A. R. Ismail and J. Timmis. UKCI 2009
  2. ImmuneComputing. J. Timmis Encyclopedia of Complexity and Systems Science Editor-in-chief: Meyers, Robert, A. Entry number: 283

2008

Journal papers
  1. Application Areas of AIS: The Past, Present and the Future. E. Hart and J. Timmis Journal of Applied Soft Computing 8(1). pp.191-201. Jan.2008
    doi: 10.1016/j/asoc.2006.12.004
  2. Theoretical Advances in Artificial Immune Systems. J.Timmis, A. Hone, T. Stibor and E. Clark. Theoretical Computer Science 403(1):11-32 (2008).
    doi: 10.1016/j.tcs.2008.02.011
  3. An Immune Network Inspired Evolutionary Algorithm for the Diagnosis of Parkinsons Disease. S. Smith and J. Timmis Biosystems 94(1-2) pp: 34-46. doi:10.1016/j.biosystems.2008.05.024
  4. Alignment-Independent Techniques for Protein Classification. M. Davies, A. Secker, A. Freitas, J. Timmis, E. Clark and D. Flower. Current Proteomics. 5(4), pp.217-223. 2008.
  5. GPCRTree: Online Hierarchical Classification of GPCR Function . M. Davies, A. Secker, M. Halling-Brown, D. Moss, A. Freitas, J. Timmis, E. Clark and D. Flower BMC Research Notes 1(67) 2008. on-line
  6. Optimising amino acid groupings for GPCR classification. M. Davies, A. Secker, A. Freatis, J. Timmis, E. Clark and D. Flower. (2008) Bioinformatics
    doi:10.1093/bioinformatics/btn382
  7. An Interdisciplinary Perspective on Artificial Immune Systems. J. Timmis, P. Andrews, N. Owens and E. Clark. Evolutionary Intelligence 1(1):5-26. (2008).
    doi:10.1007/s12065-007-0004-2
  8. AISSID: An Artificial Immune System for Interesting Information Discovery. A. Secker, A. Freitas and J. Timmis. Journal of Applied Soft Computing 8(2): 885-905. (2008). doi: 10.1016/j.asoc.2007.07.007
Conference papers
  1. Artificial Immune Systems for Data Fusion: A Novel Biologically Inspired Approach. Knowles, A.; Timmis, J.; de Lemos, R.; Forrest, S.; McCracken, H. Information Fusion, 2008 11th International Conference on, June 30 2008-July 3 2008 Page(s):1 - 7
  2. A New Paradigm for SpeckNEts: Inspiration from Fungal Colonies. R. Falconer, J. Bown. E. Hart and J. Timmis To appear in Workshop on Pervasive Adaptive Systems, part of SASO 2008.
  3. An Artificial Lymph Node Architecture for Homeostasis in Collective Robotic Systems. M. Mokhtar, J. Timmis, A. Tyrrell and R. Bi .To appear in Workshop on Pervasive Adaptive Systems, part of SOSA 2008.
  4. Simulating biology: towards understanding what the simulation shows. P. Andrews, F. Polack, A. Sampson, J. Timmis, L. Scott and M. Coles CoSMoS workshop on Modelling and Simulating of Complex Systems. 2008.
  5. Grand Challenge 7 : Journeys in Non-Classical Computation. S. Stepney, S. Abramsky, A. Adamatsky, C. Johnson and J. Timmis . Grand Challenge in Non-Classical Computation. Visions of Computer Science, London, UK, September 2008. pp407-421. BCS 2008
  6. Immune Systems and Computation: An Interdisciplinary Adventure. J. Timmis, P. Andrews, N. Owens and E. Clark. Proceedings of Unconvential Computing. LNCS 5204. pp. 8-18. Calude et al (Eds) (2008)
  7. Hardware Acceleration of an Immune Network Inspired Evolutionary Algorithm for Medical Diagnosis. S. Smith, A. Greensted and J. Timmis . International Conference on Evolvable Systems. LNCS 5216. pp. 34-46. 2008.
  8. Immuno-Engineering. J.Timmis, E. Hart, A. Hone, M. Neal, A. Robins, S. Stepney and A. Tyrrell. . 2nd IFIP International Conference on Biologically Inspired Collaborative Computing, 20th IFIP World Computer Congress, Milan, Italy, September 2008. IEEE Press Vol: 268/2008 pp. 3-17. 2008.
    Link to Springer
  9. Complex Systems Models: Engineering Simulations. F. Polack, S. Stepney, A. Sampson, J. Timmis and T. Hoverd. pp. 482-489. ALife XI 2008.
  10. Investigating Patterns for the Process-Oriented Modelling and Simulation of Space in Complex Systems. P. Andrews, A. Sampson, J.M. Bjorndalen, S. Stepney, J. Timmis, D. Warren and P. Welch.
  11. An Artificial Immune System for Evolving Amino Acid Clusters Tailored to Protein Function Prediction. A.Secker, M.Davies, A. Freitas, J.Timmis, E. Clark and D. Flower LNCS 5132. pp. 242-253. Bentley et al (Eds). 2008. DOI link to LNCS
  12. A Neuro-Immune Inspired Robust Real Time Visual Tracking System. Yang Liu, J. Timmis and T. Clarke. LNCS 5132. pp. 188-199. Bentley et al (Eds). 2008
    doi: 10.1007/978-3-540-85072-4_22
  13. The Pathways of Complement. J. Aitken, T. Clarke and J. Timmis. LNCS 5132. pp. 364-375. Bentley et al (Eds). 2008
    doi: 10.1007/978-3-540-85072-4_32
  14. Empirical Investigation of an Artificial Cytokine Network. M. Read, J. Timmis and P. Andrews. LNCS 5132. pp. 340-351. Bentley et al (Eds). 2008
    doi: 10.1007/978-3-540-85072-4_30
  15. Adaptable Lymphocytes for Artificial Immune Systems. P. Andrews and J. Timmis. LNCS 5132. pp. 376-386. Bentley et al (Eds). 2008
    doi: 10.1007/978-3-540-85072-4_33
  16. Modelling the Tunability of Early T Cell Signalling Events. N. Owens, J. Timmis, A.Tyrrell and A. Greensted. LNCS 5132. pp. 12-23. Bentley et al (Eds) 2008
    doi: 10.1007/978-3-540-85072-4_2

2007

  1. On the hierarchical classification of G Protein-Coupled Receptors. M. N. Davies; A. Secker; A. A. Freitas; M. Mendao; J. Timmis; D. R. Flower Bioinformatics 23: 3113-3118. 2007.
    doi:10.1093/bioinformatics/btm506
  2. Proteomic applications of automated GPCR classification. M. Davies, D. Gloriam, A. Secker, A. Freitas, M. Mendao, J. Timmis and D. Flower. Proteomics Vol. 7 (6). pp. 2800-2814.(2007)
    doi:10.1002/pmic.200700093
  3. Immune-Inspired Adaptable Error Detection for Automated Teller Machines. R. de Lemos, J. Timmis, S. Forrest and M. Ayara. IEEE SMC Part C: Applications and Reviews. 37(5).pp. 873-886. (2007)
    doi: 10.1109/TSMCC.2007.900662
  4. Revisiting the Foundations of Artificial Immune Systems for Data Mining. A. Freitas and J. Timmis IEEE Transactions on Evolutionary Computation 11(4) pp. 521-540 (2007)
    doi: 10.1109/TEVC.2006.884042
  5. Power Distribution Outage Cause Identification With Imbalanced Data Using Artificial Immune Recognition System (AIRS) Algorithm. L. Xu, M.Y. Chow, J. Timmis and L. Taylor IEEE Transactions on Power Systems 22(1) pp. 198-204. (2007)
    doi: 10.1016DOI: 10.1109/TPWRS.2006.889040
  6. Artificial Immune Systems - Today and Tomorrow. J. Timmis. Natural Computing 6(1) pp. 1-18. (2007)
    doi: 10.1007/s11047-006-9029-1
  7. An Immune Algorithm for Protein Structure Prediction on Lattice Models. V. Cutello, G. Nicosia, M. Pavone and J. Timmis IEEE Transactions in Evolutionary Computation. Vol. 11, No. 1. pp. 101-117. (2007)
    doi: 10.1109/TEVC.2006.880328
  8. A Beginners Guide to Artificial Immune Systems. J. Timmis and P. Andrews. Chapter 3, pp:47-64 of In Silico Immunology Flower, Timmis (Eds)
  9. Alternative Inspiration for the Next Generation of Artificial Immune Systems. P. Andrews and J. Timmis. Chapter 7, pp:119-138 of In Silico Immunology Flower, Timmis (Eds)
  10. Comments on Real-Valued Negative Selection vs Real-Valued Positive Selection and One-class Support Vector Machines. T. Stibor and J. Timmis. Congress on Evolutionary Computation (CEC). Singapore. 2007
  11. Comparison of a Multi-layered Artificial Immune System and Kohonen Networks. T. Knight and J. Timmis. Congress on Evolutionary Computation (CEC). Singapore. 2007
  12. Natural Computation Inspired by Protein Binding. S. Smith, S. Murant and J. Timmis. IPCAT 2007.
  13. On Immune Inspired Homeostasis for Electronic Systems. N. Owens, J. Timmis, A. Greensted and A. Tyrrell. LNCS 4628. 6th International Conference on Artificial Immune Systems. Brazil pp. 216-227. (2007)
    doi: 10.1007/978-3-540-73922-7_19
  14. Immune and Evolutionary Aproaches to Software Mutation Testing. P. May, J. Timmis and K. Mander. LNCS 4628. 6th International Conference on Artificial Immune Systems. Brazil. pp. 336-347. (2007) DOI link to LNCS
  15. An Experimental Comparison of Classification Algorithms for the Hierarchical Prediction of Protein Function. A. Secker, M. Davies, A. Freitas, J. Timmis, M. Mendao and D. Flower. 3rd UK Data Mining and Knowledge Discovery Symposium. pp. 13-18. (2007)
  16. An Investigation into the Compression Quality of aiNET. T. Stibor and J. Timmis. Foundations of Computational Intelligence. IEEE Symposium on Computational Intelligence, HI. USA. (2007) pp. 495-502.
  17. Evolvable Hardware, the Fundamental Technology for Homeostasis. A. Tyrrell, J. Timmis, A. Greensted and N. Owens. IEEE Workshop on Adaptive and Evolvable Hardware. IEEE Symposium on Computational Intelligence, HI. USA. (2007) pp. 40-45.
  18. The Immune System in Pieces: Computational Lessions from Degeneracy in the Immune System. M. Mendoa, J. Timmis, P. Andrews and M. Davies.Foundations of Computational Intelligence. IEEE Symposium on Computational Intelligence, HI. USA. (2007) 394-400.

2006

  1. "Going back to our Roots": Second Generation Biocomputing. J. Timmis, M. Amos, W. Banzhaf and A. Tyrrell International Journal on Unconventional Computing. 2(4):349-382, 2006.
    arxiv link (with PDF)
  2. Artificial Immune Systems for IT-Security. T. Stibor, J. Timmis and C. Eckert. Information Technology 48:168-173. 2006.
    doi: 10.1524/itit.2006.48.2.168
  3. Journeys in Non-Classical Computation II: Initial Journeys and Waypoints S. Stepney, S. Braunstein, J. Clark, A. Tyrrell, A. Adamatzky, R. Smith, T. Addis, C. Johnson, J. Timmis, P. Welch, R. Milner and D. Partridge. International Journal of Parallel, Emergent and Distributed Systems 21(2):97-125. 2006.
    doi:10.1080/17445760500355454
  4. A Computational Model of Degeneracy in a Lymph Node. P. Andrews and J. Timmis. LNCS 4163. Proc. 5th International Conference on Artifical Immune Systems (ICARIS). pp. 164-177. Bersini and Carneiro (Eds). 2006.
    doi: 10.1007/11823940_13
  5. On the Use of Hyperspheres in Artificial Immune Systems as Antibody Recognition Regions. T. Stibor, J. Timmis and C. Eckert. LNCS 4163. Proc. 5th International Conference on Artifical Immune Systems (ICARIS). pp. 215-228. Bersini and Carneiro (Eds). 2006.
    doi: 10.1007/11823940_17
  6. On Permutation Masks in Hamming Negative Selection. T. Stibor, J. Timmis and C. Eckert. LNCS 4163. Proc. 5th International Conference on Artifical Immune Systems (ICARIS). pp. 122-135. Bersini and Carneiro (Eds). 2006.
    doi: 10.1007/11823940_10
  7. Recognising regular human activity through a learning context memory. P. Mohr, N. Ryan and J. Timmis Proceedings of the 3rd International Workshop of Modelling and Retrieval of Context (MRC 2006), in conjunction with AAAI-06. Boston, USA. 2006.
  8. On the Investigation of Artificial Immune Systems on Imbalanced Data Classification for Power Distribution System Fault Cause Identification. Le Xu, Mo-Yuen Chow, Jon Timmis, Leroy Taylor and Andrew WatkinsPart of the World Congress On Computational Intelligence. CEC pp. 522-527. Canada. 2006.
  9. The Link between r-contiguous Detectors and k-CNF Satisfiability. T. Stibor, J. Timmis and C. Eckert CEC, Part of the World Congress On Computational Intelligence. pp. 491-498. Canada. 2006.
  10. Generalization Regions in Hamming Negative Selection. T. Stibor, J. Timmis and C. Eckert New Trends in Intelligent Information Processing and Web Mining. Intelligent Information Processing and Web Mining. Advances in Soft Computing Vol. 35, pp. 447-456. Springer-Verlag. 2006.
    doi: 10.1007/3-540-33521-8_49
  11. On Diversity and Artificial Immune Systems: Incorporating a Diversity Operator into aiNET. P. Andrews and J. Timmis. Proceedings of WIRN/NAIS June 2005. LNCS 3931. pp. 293-306. 2006
    doi: 10.1007/11731177_37
  12. Challenges for Artificial Immune Systems. J. Timmis. Proceedings of WIRN/NAIS June 2005. LNCS 3931. pp.355-367. 2006
    doi: 10.1007/11731177_42

2005

  1. Conceptual Frameworks for Artificial Immune Systems. S. Stepney, R. Smith, J. Timmis, A. Tyrrell, M. Neal and A. Hone International Journal of Unconventional Computing. 1(3) 2005.
  2. Journeys in Non-Classical Computation I: A Grand Challange for Computing Research. S. Stepney, S. Braunstein, J. Clark, A. Tyrrell, A. Adamatzky, R. Smith, T. Addis, C. Johnson, J. Timmis, P. Welch, R. Milner and D. Partridge. International Journal of Parallel, Emergent and Distributed Systems 20(1):5-19. 2005.
    doi:10.1080/17445760500033291 Once More Unto the Breach: Towards Artificial Homeostasis?. M Neal and J Timmis. In L N De Castro and F J Von Zuben, editor, Recent Developments in Biologically Inspired Computing, pages 340-365. Idea Group, January 2005.
  3. Towards a danger theory inspired artificial immune system for web mining. Andrew Secker, Alex Freitas, and Jon Timmis. In A Scime, editor, Web Mining: applications and techniques, pages 145-168. Idea Group, January 2005.
  4. Artificial Homeostasis: A Novel Approach. P. Vargas, R. Moioli, L.N. De Castro, J. Timmis, M. Neal and F. Von Zuben. Proceedings of ECAL 2005. LNAI 3630. pp. 754-763. Capcarrere et. al. (Eds) 2005.
    doi: 10.1007/11553090_76
  5. Immunising Automated Teller Machines A. Ayara, J. Timmis, R. De Lemos and S. Forrest. International Conference on Artificial Immune Systems (ICARIS), Banf, Canada. LNCS 3627. pp. 404-417. C.Jacob Et. al. (Eds) 2005
  6. Inspiration for the Next Generation of Artificial Immune Systems . P. Andrews and J.Timmis. International Conference on Artificial Immune Systems (ICARIS), Banf, Canada. LNCS 3627. pp.126-138 . C.Jacob Et. al. (Eds) 2005
  7. Application Areas of AIS: Past, Present and Future E. Hart and J.Timmis. International Conference on Artificial Immune Systems (ICARIS), Banf, Canada. LNCS 3627. pp. 483-497. C.Jacob Et. al. (Eds) 2005.
  8. A Markov Chain Model of the B-cell Algorithm E. Clarke, A.N.W.Hone and J. Timmis. International Conference on Artificial Immune Systems (ICARIS), Banf, Canada. LNCS 3627. pp. 318-330 C.Jacob Et. al. (Eds) 2005.
  9. A Comparative Study of Real-Valued Negative Selection to Statistical Anomaly Detection Techniques T. Stibor, J. Timmis, and C. Eckert. International Conference on Artificial Immune Systems (ICARIS), Banf, Canada. LNCS 3627. pp. 262-275 C.Jacob Et. al. (Eds) 2005. (BEST PAPER)
  10. Biomolecular Immune-Computer: Theoretical Basis and Experimental Simulator L. B. Goncharova, Y. Jacques, C. Martin-Vide, A. O. Tarakanov, and J. Timmis. International Conference on Artificial Immune Systems (ICARIS), Banf, Canada. LNCS 3627. pp. 72-85 C.Jacob Et. al. (Eds) 2005
  11. Immune Inspired Context Memory P. Mohr, J. Timmis and N. Ryan International Workshop on Exploiting Context Histories in Smart Environments. Munich, Germany.(2005)
  12. Is Negative Selection Appropriate for Anomaly Detection? T. Stibor, P. Mohr, J. Timmis and C. Eckert. Proceedings of Genetic and Evolutionary Computation Conference (GECCO)Washington DC. USA. ACM Press. pp.321-328. 2005.
  13. On the Appropriateness of Negative Selection defined over Hamming Shape Space As a Network Intrustion Detection System. T. Stibor, J. Timmis and C. Eckert. Proceedings of the Congress on Evolutionary Computation (CEC). Edinburgh, UK. 2005.
  14. International Workshop on Natural and Artificial Immune Systems. Italy.
  15. On Diversity and Artificial Immune Systems: Incorporating a Diversity Operator into aiNET (2005). Paul Andrews and Jon Timmis.International Workshop on Natural and Artificial Immune Systems . Italy.

2004

  1. Artificial Immune Recognition System (AIRS): An Immune Inspired Supervised Machine Learning Algorithm. Andrew Watkins, Jon Timmis, and Lois Boggess. Genetic Programming and Evolvable Machines, 5(3),pp.291-317 2004.
    doi: 10.1023/B:GENP.0000030197.83685.94 An overview of artificial immune systems. J Timmis, T Knight, L N De Castro, and E Hart. In R Paton, H Bolouri, M Holcombe, J H Parish, and R Tateson, editors, "Computation in Cells and Tissues: Perspectives and Tools for Thought", Natural Computation Series, pages 51-86. Springer, November 2004.
  2. A Fractal Immune Network. P Bentley and J Timmis. In G Nicosia et al, editor, Third International Conference on Artificial Immune Systems, number 3239 in LNCS, pages 133-145. Springer, September 2004.
  3. Exploiting Immunological Properties for Ubiqitous Computing Systems. P Mohr, N Ryan, and J Timmis. In G Nicosia et al, editor, Third International Conference on Artificial Immune Systems, number 3239 in LNCS, pages 277-289. Springer, September 2004.
  4. Towards a Conceptual Framework for Artificial Immune Systems. S Stepney, R Smith, J Timmis, and A Tyrrell. In G Nicosia et al, editor, Third International Conference on Artificial Immune Systems, number 3239 in LNCS, pages 53-64. Springer, September 2004.
  5. Exploiting Parallelism Inherent in AIRS, an Artificial Immune Classifier. A Watkins and J Timmis. In G Nicosia et al, editor, Third International Conference on Artificial Immune Systems, number 3239 in LNCS, pages 427-438. Springer, September 2004.
  6. Assessing the Performance of Two Immune Inspired Algorithms and a Hybrid Genetic Algorithm for Function Optimisation. J Timmis, C Edmonds, and J Kelsey. In Proceedings of the Congress on Evolutionary Computation, volume 1, pages 1044-1051, Potland, Oregon. USA., July 2004. IEEE.
  7. A Comment on opt-AINet: An Immune Network Algorithm for Optimisation. J Timmis and C Edmonds. In D Kalyanmoy et al, editor, Genetic and Evolutionary Computation, volume 3102 of Lecture Notes in Computer Science, pages 308-317. Springer, July 2004.

2003

  1. Artificial Immune Systems as a Novel Soft Computing Paradigm . L.N de Castro and J. Timmis. Soft Computing, 7(8):526-544, 2003. A Multi-layered Immune Inspired Machine Learning Algorithm. T. Knight and J. Timmis. In A. Lotfi and M. Garibaldi, editors, Applications and Science in Soft Computing, pages 195-202. Springer, December 2003.
  2. Timidity: A Useful Mechanism for Robot Control?. Mark Neal and Jon Timmis. Informatica, 27(2):197-204, 2003.
  3. Chasings Chaos. J. Kelsy, J. Timmis, and A. Hone. In R. Sarker, R. Reynolds, H. Abbass, T. Kay-Chen, R. McKay, D Essam, and T. Gedeon, editors, Proceedings of the Congress on Evolutionary Computation, pages 413-419, Canberra. Australia, December 2003. IEEE.
  4. AISEC: An Artificial Immune System for E-mail Classification. A. Secker, A Freitas, and J. Timmis. In R. Sarker, R. Reynolds, H. Abbass, T. Kay-Chen, R. McKay, D Essam, and T. Gedeon, editors, Proceedings of the Congress on Evolutionary Computation, pages 131-139, Canberra. Australia, December 2003. IEEE.
  5. Revisiting the Foundations of Artificial Immune Systems: A Problem Oriented Perspective. A Freitas and J Timmis. In J. Timmis, P. Bentley, and E. Hart, editors, Proceedings of the 2nd International Conference on Artificial Immune Systems, volume 2787 of Lecture Notes in Computer Science, pages 229-241. Springer, September 2003.
  6. Mutation Testing: An Artificial Immune System Approach. P. May, K Mander, and J. Timmis. In UK-Softest. UK Software Testing Workshop, University of York. UK., September 2003.
  7. Software Vaccination: An Artificial Immune Systems Approach. P. May, K. Mander, and J. Timmis. In J. Timmis, P. Bentley, and E. Hart, editors, Proceedings of the 2nd International Conference on Artificial Immune Systems, volume 2787 of Lecture Notes in Computer Science, pages 81-92. Springer, September 2003.
  8. A Danger Theory Approach to Web Mining. A. Secker, A Freitas, and J. Timmis. In J. Timmis, P. Bentley, and E. Hart, editors, Proceedings of the 2nd International Conference on Artificial Immune Systems, volume 2787 of Lecture Notes in Computer Science, pages 156-167. Springer, September 2003.
  9. Immune Inspired Somatic Contiguous Hypermutation for Function Optimisation. J. Kelsey and J. Timmis. In E. Cant\u033c-Paz et al, editor, Genetic and Evolutionary Computation Conference - GECCO 2003, volume 2723 of Lecture Notes in Computer Science, Chicago. USA., July 2003. Springer-Verlag. Journeys in non-classical computation: A grand challenge for computing research. S. Stepney, J.A. Clark, A. Tyrrell, C.G. Johnson, J. Timmis, D. Partridge, A. Adamatsky, and R.E. Smith. Grand Challenge Report 7, National E-Science Centre, University of Edinburgh, May 2003.
  10. Artificial Homeostasis: Integrating Biologically Inspired Computing. J Timmis and M Neal. Technical Report UWA-DCS-03-043, University of Wales, Aberystwyth, February 2003.

2002

  1. Artificial Immune Systems: A Novel Approach to Pattern Recognition. L.N de Castro and J Timmis. In L Alonso J Corchado and C Fyfe, editors, Artificial Neural Networks in Pattern Recognition, pages 67-84. University of Paisley, January 2002.
  2. A Multi-Layered Immune Inspired Approach to Data Mining. T Knight and J Timmis. In A Lotfi, J Garibaldi, and R John, editors, Proceedings of the 4th International Conference on Recent Advances in Soft Computing, pages 266-271, Nottingham, UK., December 2002.
  3. Towards immune inspired fault tolerance in embedded systems. J Timmis, R de Lemos, M Ayara, and R Duncan. In L Wang, J Rajapakse, K Fukushima, S Lee, and X Yao, editors, Proceedings of 9th International Conference on Neural Information Processing, pages 1459-1463. IEEE, November 2002.
  4. Negative selection: How to generate detectors. M. Ayara, J. Timmis, L.N. de Lemos, R. de Castro, and R. Duncan. In J. Timmis and P.J. Bentley, editors, 1st International Conference on Artificial Immune Systems, pages 89-98, University of Kent at Canterbury, September 2002. Unversity of Kent at Canterbury Printing Unit.
  5. Hierarchy and convergance of immune networks: Basic ideas and premilinary results. L.N de Castro and J Timmis. In J. Timmis and P.J. Bentley, editors, 1st International Conference on Artificial Immune Systems, pages 231-240, University of Kent at Canterbury, September 2002. Unversity of Kent at Canterbury Printing Unit.
  6. Artificial Immune Recognition System (AIRS): Revisions and Refinements. A. Watkins and J. Timmis. In J. Timmis and P.J. Bentley, editors, 1st International Conference on Artificial Immune Systems, pages 173-181, University of Kent at Canterbury, September 2002. Unversity of Kent at Canterbury Printing Unit.
  7. An artificial immune network for multimodal optimisation. L.N de Castro and J Timmis. In 2002 Congress on Evolutionary Computation. Part of the 2002 IEEE World Congress on Computational Intelligence., pages 699-704, Honolulu, Hawaii, USA, May 2002. IEEE.

2001

  1. Aine: An immunological approach to data mining. T Knight and J Timmis. In N Cercone, T Lin, and Xindon Wu, editors, IEEE International Conference on Data Mining, pages 297-304, San Jose, CA. USA, December 2001. IEEE.
  2. aivis - artificial immune network visualisation. Jon Timmis. In EuroGraphics UK 2001 Conference Proceedings, pages 61-69, Univerisity College London., April 2001. Eurographics.
  3. Artificial immune systems: Using the immune system as inspiration for data mining. Jon Timmis and Thomas Knight. In Hussein A. Abbass, Ruhul A. Sarker, and Charles S. Newton, editors, Data Mining: A Heuristic Approach, chapter XI, pages 209-230. Group Idea Publishing, September 2001.
  4. A resource limited artificial immune system for data analysis. Jon Timmis and Mark Neal. Knowledge Based Systems, 14(3-4):121-130, June 2001.
  5. Assessing the performance of the resource limited artificial immune system AINE. Thomas Knight and Jon Timmis. Technical Report 3-01, Canterbury, Kent. CT2 7NF, May 2001.

2000

  1. An artificial immune system for data analysis. J Timmis, M Neal, and J Hunt. Biosystems, 55(1/3):143-150, 2000.
  2. A Resource Limited Artificial Immune System for Data Analysis. J. Timmis and M. J. Neal. Research and Development in Intelligent Systems XVII, pages 19-32, December 2000. Proceedings of ES2000, Cambridge, UK.
  3. Investigating the evolution and stability of a resource limited artificial immune system. Jon Timmis and Mark Neal. In A.S.Wu, editor, Special Workshop on Artificial Immune Systems, Gentic and Evolutionay Computtion Conference (GECCO) 2000, Workshop Program, pages 40-41, Las Vegas, Nevada, U.S.A., July 2000. AAAI, AAAI Press. Visualising artificial immune networks. J Timmis. Technical Report UWA-DCS-00-034, University of Wales and Aberystwyth, 2000.
  4. On parameter adjustment of the immune inspired machine learning algorithm AINE. Jon Timmis. Technical Report 12-00, Computing Laboratory, Univeristy of Kent at Canterbury, Canterbury, Kent. CT2 7NF., November 2000.

1999

  1. Data analysis with artificial immune systems and cluster analysis and kohonen networks : Some comparisons. J Timmis, M Neal, and J Hunt. In Proc. of Int. Conf. Systems and Man and Cybernetics, pages 922-927, Tokyo, Japan., 1999. IEEE.

1998

  1. Jisys: Development of an artificial immune system for real world applications. J Hunt, J Timmis, D Cooke, M Neal, and C King. In Artificial Immune Systems and their Applications, pages 157-186. Springer-Verlag, 1998.
  2. Augmenting an artificial immune network. M Neal, J Hunt, and J Timmis. In Proc. of Int. Conf. Systems and Man and Cybernetics, pages 3821-3826, San Diego, California, U.S.A., 1998. IEEE.

1996

  1. Generating fault trees from fmea. Wilson M.S. Timmis J. Price, C.J. and C Cain. In 7th International Workshop on Principles of Diagnosis, 1996.
Books
  1. In Silico Immunology. (2007) Edited by D. R. Flower and J. Timmis. Springer, New York.
    doi: 10.1007/978-0-387-39241-7
  2. Artificial Immune Systems: A New Computational Approach. L.N. de Castro and J. Timmis. Springer-Verlag, London. UK., September 2002.
  3. Artificial immune systems: A novel data analysis technique inspired by the immune network theory. Jon Timmis. PhD thesis, Department of Computer Science, University of Wales, Aberystwyth. Ceredigion. Wales., August 2000.
Edited Volumes
  1. Special Issue on Unconventional Computation. J. Timmis and K. Morita. Natural Computing 11(1). 2012.
  2. Proceedings of the 9th International Conference on Artificial Immune Systems (ICARIS). Hart, E., McEwan, C., Timmis, J. and Hone, A. (2010)
  3. Special Issue on Theory and Applications of Artificial Immune Systems in Neural Computing and Applications. Gao, Z., Chow, M., Pelata, ">Proceedings of the 9th International Conference on Artificial Immune Systems (ICARIS). Hart, E., McEwan, C., Timmis, J. and Hone, A. (2010)D. and Timmis, J. (2010)
  4. Proceeding of the 9th International Conference on Unconventional Computing. Calude, C., Hagiya, M., Morita, K., Rozenburg, G. and Timmis, J. LNCS 6079. Springer. (2010).
  5. Proceedings of the 2nd Workshop on Complex Systems on Complex Systems Modelling and Simulation Stepney, S., Welch, P., Andrews, P. and Timmis, J. Luniver Press. ISBN-10:1-905986-22-X
  6. Proceedings of the 8th International Conference on Artifical Immune Systems. P. Andrews, J. Timmis, N. Owens, U. Aickelin, E. Hart, A. Hone and A. Tyrrell. LNCS 5666. 2009.
  7. Proceedings of 4th international conference on artificial immune systems. C.Jacob, M. Pilat, P. Bentley and J. Timmis. Number 3627 in LNCS. Springer. August 2005.
  8. Advances in Artificial Life. Proceedings of the 8th European Conference on Artificial Life (ECAL) LNAI 3630 (2005) M. Capcarrere, A. Freitas, P. Bentley, C. Johson and J. Timmis. Springer, ISBN 35402884181
  9. Special Issue on Artificial Immune Systems (2005). The International Journal of Unconventional Computing. J. Timmis, S. Stepney, P. Bentley, G. Nicosia and V. Cutello.
  10. Proceedings of 3rd international conference on artificial immune systems. G Nicosia, V Cutello, P Bentley, and J Timmis. Number 3239 in LNCS. Springer, September 2004.
  11. Special Issue on Artificial Immune Systems. P Bentley and J Timmis. In Genetic Programming and Evolvable Machines, volume 4(4), pages 307-403. Kluwer, December 2003.
  12. Guest Editorial on Artificial Immune Systems. P Bentley and J Timmis. Genetic Programming and Evolvable Machines, 4(4):307-309, December 2003.
  13. Proceedings of the 2nd international conference on artificial immune systems. J. Timmis, P. Bentley, and E. Hart. Number 2787 in Lecture Notes in Computer Science. Springer-Verlag, Berlin., September 2003.
  14. 1st international conference on artificial immune systems. J. Timmis and P.J. Bentley, editors, University of Kent at Canterbury, September 2002. Unversity of Kent at Canterbury Printing Unit.
Reviews
  1. Membrane Computing: An Introduction (Book Review). Jon Timmis. The Computer Journal, 46(5), September 2003.