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School of Computing

Publications by Dr Colin Johnson

Publication period   (11/1996 onwards)   -   ordered by publication type and date

Books

• Studying programming. Sally Fincher and the Computing Education Research Group. Palgrave Study Guides. Palgrave Macmillan, January 2006.

Journal Papers

• A hierarchical multi-label classification ant colony algorithm for protein function prediction. F.E.B. Otero, A.A. Freitas, and C.G. Johnson. Memetic Computing, 2(3):165-181, September 2010.
• A hierarchical multi-label classification ant colony algorithm for protein function prediction. F.E.B. Otero, A.A. Freitas, and C.G. Johnson. Memetic Computing, 2(3):165-181, January 2010.
• Semantic analysis of program initialisation in genetic programming. Lawrence Beadle and Colin G Johnson. Genetic Programming and Evolvable Machines, 10(3):307-337, September 2009.
• Message-passing algorithms for the prediction of protein domain interactions from protein–protein interaction data. Mudassar Iqbal, Alex A. Freitas, Colin G. Johnson, and Massimo Vergassola. Bioinformatics, 24(18):2064-2070, September 2008.
• Particle swarm for attribute selection in bayesian classification: an application to protein function prediction. Elon S Correa, Alex A Freitas, and Colin G Johnson. Journal of Artificial Evolution and Applications, 2008:12 pages, May 2008.
• A design framework for metaheuristics. Colin G. Johnson. Artificial Intelliigence Review, 29(2):163-178, April 2008.
• Developing a computer science-specific learning taxonomy. U. Fuller, C.G. Johnson, T. Ahoniemi, D. Cukierman, I. Hernán-Losada, J. Jackova, E. Lahtinen, T.L. Lewis, D. McGee Thompson, C. Riesdel, and E. Thompson. ACM SIGCSE Bulletin, 39(4):152-170, December 2007.
• Journeys in non-classical computation II: Initial journeys and waypoints. S Stepney, SL Braunstein, JA Clark, A Tyrrell, A Adamatzky, RE 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, April 2006.
• Journeys in non-classical computation I: A grand challenge for computing research. S. Stepney, S.L. Braunstein, J.A. Clark, A. Tyrrell, A. Adamatzky, R.E. 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, March 2005.
• Simulating complex intracellular processes using object-oriented computational modelling. Colin G. Johnson, Jacki P. Goldman, and William J. Gullick. Progress in Biophysics and Molecular Biology, 86(3):379-406, November 2004.
• Individual-based simulation of the clustering behaviour of epidermal growth factor receptors. Jacki P. Goldman, William J. Gullick, and Colin G. Johnson. Scientific Programming, 12(1):25-43, January 2004.
• Exploring sound-space with interactive genetic algorithms. Colin G. Johnson. Leonardo, 36(1):51-54, January 2003.
• Evolutionary computing in visual art and music. Colin G. Johnson and Juan Jesus Romero Cardalda. Leonardo, 35(2):175-184, April 2002.
• Understanding complex systems through examples: A framework for qualitative example finding. Colin G. Johnson. Systems Research and Information Systems, 10(3-4):239-267, January 2001.
• Modelling robot manipulators with multivariate B-splines. Colin G. Johnson and Duncan Marsh. Robotica, 17(3):239-247, May 1999.

Book Chapters

• A hybrid rule-induction/likelihood-ratio based approach for predicting protein-protein interactions. M. Iqbal, A.A. Freitas, and C.G. Johnson. In Christine L. Mumford and Lakhmi C. Jain, editors, Computational Intelligence: Collaboration, Fusion and Emergence, Intelligent Systems Reference Library, pages 623-637. Springer, July 2009.
• An empirical evaluation of the effectiveness of different types of predictor attributes in protein function prediction.. F. Otero, M. Segond, A.A. Freitas, C.G. Johnson, D. Robilliard, and C. Fonlupt, volume Foundations of Computational Intelligence Vol. 5 of Studies in Computational Intelligence 205, pages 339-357. Springer, June 2009.
• The non-classical mind: Cognitive science and non-classical computing. Colin G. Johnson. In Alfons Schuster, editor, Intelligent Computing Everywhere, pages 45-59. Springer, October 2007.
• Does a functioning mind need a functioning body?. Colin G Johnson. In Darryl N Davis, editor, Visions of Mind, pages 307-321. Idea Group Publishing, January 2005.
• What kinds of natural processes can be regarded as computations?. Colin G Johnson. In Ray Paton, editor, Computation in Cells and Tissues: Perspectives and Tools of Thought. Springer, January 2004.

Conference Papers

• Evolving high-level imperative program trees with strongly formed genetic programming. Tom Castle and Colin G. Johnson. In Alberto Moraglio, Sara Silva, Krzysztof Krawiec, Penousal Machado, and Carlos Cotta, editors, Proceedings of the 15th European Conference on Genetic Programming, EuroGP 2012, volume 7244 of LNCS, pages 1-12, Malaga, April 2012. Springer.
• The aco encoding. A. Moraglio, F.E.B. Otero, and C.G. Johnson. In M. Dorigo et al., editor, Swarm Intelligence - 7th International Conference (ANTS 2010), Lecture Notes in Computer Science 6234, pages 528-535, September 2010.
• ME-CGP: Multi expression Cartesian genetic programming.. Phil T. Cattani and Colin G. Johnson. In Proceedings of the 2010 IEEE World Congress on Computational Intelligence, July 2010.
• The Effect of Level of Rationality on Macro-Activities of the Lucas-Island Model. Ahmed Okasha and Colin G. Johnson. In 2010 IEEE Congress on Evolutionary Computation. IEEE Press, July 2010.
• Positional effect of crossover and mutation in Grammatical Evolution. Tom Castle and C. G. Johnson. In Anna I. Esparcia-Alcazar, Aniko Ekart, Sara Silva, Stephen Dignum, and Sima Uyar, editors, Proceedings of the 13th European Conference on Genetic Programming, EuroGP 2010, volume 6021 of LNCS, Istanbul, April 2010. EvoStar, Springer.
• Typed cartesian genetic programming for image classification. Phil T. Cattani and Colin G. Johnson. In Proceedings of the 2009 UK Workshop on Computational Intelligence, pages 106-111, University of Nottingham, September 2009.
• Semantically driven mutation in genetic programming. Lawrence Beadle and Colin G. Johnson. In Proceedings of the 2009 IEEE Congress on Evolutionary Computation, pages 1336-1342. IEEE Press, May 2009.
• Handling continuous attributes in ant colony classification algorithms. F.E.B. Otero, A.A. Freitas, and C.G. Johnson. In Proc. of the 2009 IEEE Symposium on Computational Intelligence in Data Mining (CIDM 2009), pages 225-231. IEEE Press, March 2009.
• A hierarchical classification ant colony algorithm for predicting gene ontology terms. F.E.B. Otero, A.A. Freitas, and C.G. Johnson. In C. Pizzuti, M.D. Ritchie, and M. Giacobini, editors, Proc. 7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBio-2009), volume Lecture Notes in Computer Science 5483, pages 68-79. Springer, March 2009.
• cAnt-Miner: an ant colony classification algorithm to cope with continuous attributes. F.E.B. Otero, A.A. Freitas, and C.G. Johnson. In M. Dorigo et al., editor, Ant Colony Optimization and Swarm Intelligence (Proc. ANTS 2008), LNCS 5217, pages 48-59. Springer, September 2008.
• Multi-level neutrality in optimization. Colin G. Johnson. In Proceedings of the 2008 IEEE World Congress on Computational Intelligence, pages 2604-2609. IEEE Press, June 2008.
• Protein interaction inference using particle swarm optimization algorithm.. M. Iqbal, A.A. Freitas, and C.G. Johnson. In E. Marchiori and J.H. Moore, editors, Proc. Sixth European Conf. on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBio-2008), Lecture Notes in Computer Science 4973, pages 61-70. Springer, March 2008.
• Semantically driven crossover in genetic programming. Lawrence Beadle and Colin G Johnson. In IEEE World Congress on Computational Intelligence, pages 111-116. IEEE, January 2008.
• Particle swarm and bayesian networks applied to attribute selection for protein functional classification.. E.S. Correa, A.A. Freitas, and C.G. Johnson. In T. Yu, editor, Proc. of the GECCO-2007 Workshop on Particle Swarms: The Second Decade, pages 2651-2658. ACM, July 2007.
• A genetic algorithm for coverage problems. Colin G. Johnson. In Dirk Thierens et al., editor, Proceedings of the 2007 Genetic and Evolutionary Computation Conference, volume II, page 1521. ACM Press, July 2007.
• Genetic programming with fitness based on model checking. Colin G. Johnson. In Marc Ebner and et al., editors, Genetic Programming, volume 4445 of Lecture Notes in Computer Science, pages 114-124. Springer-Verlag, April 2007.
• Is Bloom's taxonomy appropriate for computer science?. Colin G. Johnson and Ursula Fuller. In Anders Berglund and Mattias Wiggberg, editors, Proceedings of the Sixth Baltic Sea Conference on Computing Education Research, volume 2007-006 of Uppsala University Department of Information Technology Technical Reports, pages 120-123. Uppsala University, February 2007.
• A new discrete particle swarm algorithm applied to attribute selection in a bioinformatics data set.. E.S. Correa, A.A. Freitas, and C.G. Johnson. In M. Keijzer and et. al., editors, Proc. Genetic and Evolutionary Computation Conference (GECCO-2006), pages 35-42. ACM Press, July 2006.
• A design framework for metaheuristics: Problem types and avoiding bottlenecking. Colin G. Johnson. In Konstantinos Sirlantzis, editor, Proceedings of the Sixth International Conference on Recent Advances in Soft Computing. University of Kent, July 2006.
• Timbre interfaces using adjectives and adverbs. Colin G. Johnson and Alex Gounaropoulos. In Norbert Schnell and et al, editors, New Interfaces for Musical Expression, pages 101-102, Paris, June 2006. IRCAM.
• Abstract interpretation of student programs as a strategy for courseware development. Colin G. Johnson. In Methods, Materials and Tools for Programming Education, volume 5 of Tampere Polytechnic Series A. Research Reports, pages 14-19, Tampere, Finland, May 2006. Tampere Polytechnic University of Applied Sciences.
• Synthesising timbres and timbre-changes from adjectives/adverbs. Alex Gounaropoulos and Colin Johnson. In F. Rothlauf and et al, editors, Applications of Evolutionary Computing, volume 3907 of Lecture Notes in Computer Science, pages 664-675. Springer-Verlag, April 2006.
• Roles of variables and program analysis. Craig Bishop and Colin G. Johnson. In Tapio Salakoski, editor, Proceedings of the 5th Finnish/Baltic Conference on Computer Science Education. University of Turku, November 2005.
• Varying the topology and probability of re-initialization in particle swarm optimization. Mudassar Iqbal, Alex A. Freitas, and Colin G. Johnson. In E.-G. Talbi, editor, Evolution Artificielle 2005. University of Lille, October 2005.
• Advances in artificial life - proc. 8th european conf. (ecal-2005). MS Capcarrere, AA Freitas, PJ Bentley, CG Johnson, and J Timmis, editors, volume Lecture Notes in Artificial Intelligence 3630. Springer Verlag, September 2005.
• Search and notions of creativity. Colin G. Johnson. In Tony Veale, Alison Pease, and Geraint Wiggins, editors, Proceedings of the IJCAI-2005 Workshop on Computational Creativity. IJCAI, July 2005.
• What can post-classical computation do for post-cognitivist psychology?. Colin G. Johnson. In Proceedings of the 2005 Post-Cognitivist Psychology Conference. University of Strathclyde, July 2005.
• Non-classical computation and the computationalist stance towards the natural and cognitive sciences. Colin G. Johnson. In Susan Stepney, editor, The Grand Challenge in Non-Classical Computation. University of York, April 2005.
• Varieties of openness in evolutionary computation. Colin G. Johnson. In Robert Zimmer, editor, Proceedings of the Workshop on Creative Evolutionary Computation. Goldsmiths College, February 2005.
• Using tabu search and genetic algorithms in mathematics research. Colin G. Johnson. In Ahmed Lotfi, editor, Proceedings of the Fifth International Conference on Recent Advances in Soft Computing, pages 243-248. Nottingham Trent University, December 2004.
• Automatic programming with ant colony optimization. Jennifer Green, Jacqueline L. Whalley, and Colin G. Johnson. In Mark Withall and Chris Hinde, editors, Proceedings of the 2004 UK Workshop on Computational Intelligence, pages 70-77. Loughborough University, September 2004.
• Post-industrial-revolution HCI. Colin G. Johnson. In Anne Bruseberg, Peter Johnson, and Peter J. Wild, editors, Coping with Complexity: Sharing New Approaches for the Design of Human-Computer Systems in Complex Settings, pages 7-8. University of Bath, September 2004.
• Do somatic markers need to be somatic? Analogies from evolution and from hardware interlocks. Colin G. Johnson. In Proceedings of the AISB 2004 Convention, pages 33-35. Sociaty for the Study of Artificial Intelligence and Simulation of Behaviour, April 2004.
• Artificial immune systems and the grand challenge for non-classical computation. Susan Stepney, John A. Clark, Colin G. Johnson, Derek Partridge, and Robert E. Smith. In Jon Timmis, Peter Bentley, and Emma Hart, editors, Proceedings of the 2003 International Conference on Artificial Immune Systems, LNCS 2787, pages 204-216. Springer, September 2003.
• Colour merging for the visualization of biomolecular sequence data. Mark Alston, Gary Robinson, and Colin G. Johnson. In E. Banissi, K. Borner, C. Chen, G. Clapworthy, C. Maple, A. Lobben, C. Moore, J. Roberts, A. Ursyn, and J. Zhang, editors, Proceedings of the Seventh International Conference on Information Visualization, pages 169-175. IEEE Computer Society, July 2003.
• Artificial immune systems programming for symbolic regression. Colin G. Johnson. In C. Ryan, T. Soule, M. Keijzer, E. Tsang, R. Poli, and E. Costa, editors, Genetic Programming: 6th European Conference, LNCS 2610, pages 345-353. Springer, April 2003.
• Towards a prehistory of evolutionary and adaptive computation in music. Colin G. Johnson. In G. Raidl, D. Corne, E. Marchiori, J. Gottlieb, S. Cagnoni, J. Romero, C. Johnson, E. Hart, M. Middendorf, A. Guillot, and J.-A. Meyer, editors, Applications of Evolutionary Computing, LNCS 2611, pages 502-509. Springer, April 2003.
• An ant colony algorithm for multiple sequence alignment in bioinformatics. Jonathan D. Moss and Colin G. Johnson. In David W. Pearson, Nigel C. Steele, and Rudolf F. Albrecht, editors, Artificial Neural Networks and Genetic Algorithms, pages 182-186. Springer, April 2003.
• Applications of evolutionary computing. G. Raidl, D. Corne, E. Marchiori, J. Gottlieb, S. Cagnoni, J. Romero, C. Johnson, E. Hart, M. Middendorf, A. Guillot, and J.-A. Meyer, editors, LNCS 2611. Springer, April 2003.
• Genetic programming with guaranteed constraints. Colin G. Johnson. In Ahmad Lofti, Bob John, and Jon Garibaldi, editors, Recent Advances in Soft Computing. Physica/Springer-Verlag, December 2002.
• What can automatic programming learn from theoretical computer science?. Colin G. Johnson. In Xin Yao, editor, Proceedings of the 2002 UK Workshop on Computational Intelligence. University of Birmingham, September 2002.
• A virtual lab for exploring the [PSI]+ yeast prion. Jacqueline L. Whalley, Mick F. Tuite, and Colin G. Johnson. In Faramarz Valafar, editor, Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, volume II, pages 583-589. CSERA Press, June 2002.
• Deriving genetic programming fitness properties by static analysis. Colin G. Johnson. In Evelyne Lutton, James A. Foster, Julian Miller, Conor Ryan, and Andrea G. B. Tettamanzi, editors, Proceedings of the 4th European Conference on Genetic Programming, EuroGP 2002, volume 2278 of Lecture Notes in Computer Science, pages 299-308, Berlin, April 2002. Springer-Verlag.
• Individual-based simulation of the clustering behaviour of epidermal growth factor receptors. Jacki P. Goldman, William J. Gullick, Dennis Bray, and Colin G. Johnson. In Gary Lamont, editor, Proceedings of the 2002 ACM Symposium on Applied Computing, pages 127-131. ACM Press, March 2002.
• Finding diverse examples with genetic algorithms. Colin G. Johnson. In Robert John and Ralph Birkenhead, editors, Developments in Soft Computing, Advances in Soft Computing, pages 92-99. Physica/Springer-Verlag, July 2001.
• Phase transitions in multi-robot interactions. Colin G. Johnson and Steven J. Brodie. In U. Nehmzow and C. Melhuish, editors, Towards Intelligent Mobile Robots - Proceedings of the 3rd British Conference on Autonomous Mobile Robotics and Autonomous Systems, University of Manchester Technical Reports volume UMCS-01-4-1, page 7. University of Manchester, April 2001.
• Proceedings of the AISB'01 symposium on emotion, cognition and affective computing. Colin G. Johnson, editor. Society for the Study of Artificial Intelligence and the Simulation of Behaviour, AISB Press, March 2001.
• Effective affective communication in virtual environments. C.G. Johnson and Gareth J.F. Jones. In Daniel Ballin, editor, Proceedings of the Second Workshop on Intelligent Virtual Agents, pages 135-138. University of Salford, September 1999.
• Exploring the sound-space of synthesis algorithms using interactive genetic algorithms. Colin G. Johnson. In A. Patrizio, G.A. Wiggins, and H. Pain, editors, Proceedings of the AISB'99 Symposium on Musical Creativity, pages 20-27, Brighton, April 1999. Society for the Study of Artificial Intelligence and Simulation of Behaviour.
• Modelling robot manipulators in a CAD environment using B-splines. Colin G. Johnson. In Nikolaos G. Bourbakis, editor, IEEE International Joint Symposia on Intelligence and Systems, pages 194-201. Institute of Electrical and Electronic Engineers, IEEE Press, November 1996.

Miscellaneous

• A Design Framework for Evolutionary Algorithms. Colin Johnson. PhD thesis, Computing Laboratory, University of Kent, Canterbury, Kent, UK, July 2003.
• 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.
• Detecting collisions in sets of moving particles: a survey and some experiments. Colin G. Johnson and Jacqueline Whalley. Technical Report 8-02, University of Kent, Computing Laboratory, June 2002.
• Portrait of 2000/01 Part I Assessments, Part 1: Statistical Analysis. Janet Carter, Jill Tardivel, Sally Fincher, Ursula Fuller, Colin Johnson, Janet Linington, and Ian Utting. Technical Report 10-01, University of Kent, Computing Laboratory, University of Kent at Canterbury, August 2001.