Jennifer Hallinan's Publications

Jennifer Hallinan's Publications

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  • Hallinan, J. (2013). Computational intelligence for the design of synthetic microbial genetic systems. Methods in Microbiology. C. Harwood and A. Wipat (eds.). 1 - 37.This is not the final version
  • Misirli, G., A. Wipat, J. Mullen, K. James, M. Pocock, W. Smith, N. Allenby and J. S. Hallinan (2013). "BacillOndex: An integrated data resource for systems and synthetic biology." Journal of Integrative Bioinformatics 10(2): 224.


  • Hallinan, J.S. (2012) Chapter 2- Data mining for microbiologists. Methods in Microbiology 39, 27 - 79.
  • Hallinan, J., Park, S. & Wipat, A. (2012). Bridging the gap between design and reality: A dual evolutionary strategy for the design of synthetic genetic circuits. Bioinformatics: The International Conference on Bioinformatics Models, Methods and Algorithms. Algarve, Portugal.
  • Flanagan, K., Nakjang, S., Hallinan, J., Harwood, C. Hirt, R. P., Pocock, M. R. & Wipat, A. (2012). Microbase2.0: A generic framework for computationally intensive bioinformatics workflows in the cloud. 2012 International Symposium on Integrative Bioinformatics (IB2012), Hangzhou, China.


  • Hallinan, J., James, J. & Wipat, A. (2011). Network approaches to the functional analysis of microbial proteins. Advances in Microbial Physiology 59: 101 - 123.
  • Weile, J., Pocock, M. Cockell, S. J., Lord, P., Dewar, J. M., Holstein, E., Wilkinson, D., Lydall, D., Hallinan, J. S. & Wipat, A. (2011). Customisable views on semantically integrated networks for systems biology. Bioinformatics 27(9): 1299 - 1306.
  • Misirli, G., Hallinan, J. S., Yu, T., Lawson, J. R., Wimalaratne, S. M., Cooling, M. T. & Wipat, A. (2011). Model annotation for synthetic biology: Automated model to nucleotide conversion. Bioinformatics 27(7): 973 - 979.


  • Weatherhead S, Hallinan J, Wipat A, Farr P, Reynolds N. (2010). Development of a dynamic mathematical model of epidermis reveals critical importance of increasing the proportion of both cycling stem and transient amplifying cells, in the development of psoriatic plaques. Journal of Investigative Dermatology: 40th Annual Meeting of the European Society for Dermatological Research.Helsinki, Finland:Nature Publishing Group.
  • Cooling, M. T., Rouilly, V., Misirli, G., Lawson, J., Yu, T., Hallinan, J. & Wipat, A. (2010). Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics 26: 925 - 931.
  • Hallinan, J., Misirli, G. & Wipat, A. (2010). Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. Proceedings of the 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2010).
  • Passos, J., Nelson, G., Wang, C., Richter, T., Simillion, C., Proctor, C. J., Miwa, S., Olijslagers, S., Hallinan, J., Wipat, A., Saretski, G., Rudolph, K. L., Kirkwood, T. B. L. & von Zglinicki, T. (2010). Feedback between p21 and reactive oxygen production is necessary for establishment of cell senescence. Molecular Systems Biology 6: 364.


  • Passos, J. F., Simillion, C., Hallinan, J., Wipat, A. & von Zglinicki, T. (2009). Cellular senescence: Unravelling complexity. Age. 31(4):353 - 363.
  • Hallinan, J., Pocock, M., Addinall, S., Lydall, D. A. & Wipat, A. (2009). Clustering incorporating shortest paths identifies relevant modules in functional interaction networks. 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB09).
  • James, K., Wipat, A. & Hallinan, J. (2009). Integration of full-coverage probabilistic functional networks with relevance to specific biological processes. Data Integration in the Life Sciences (DILS 2009) 5647: 31 - 46.
  • Presentation on Systems Biology of Ageing, given at Brunel University on 27 June.
  • Hallinan, J., Pocock, M. & Wipat, A. (2009). Bacillus subtilis as a chassis for synthetic biology. Poster at BioSysBio 2009.


  • Addinall, S. G., Downey, M., Yu, M., Zubko, M. K., Dewar, J., Leake, A., Hallinan, J., Shaw, O., James, K., Wilkinson, D. J., Wipat, A., Durocher, D. & Lydall, D. (2008). A genome-wide suppressor and enhancer analysis of cdc13-1 reveals varied cellular processes influencing telomere capping in Saccharomyces cerevisiae. Genetics 180: 2251 - 2266.
  • Craddock, T., Harwood, C. R., Hallinan, J. & Wipat, A. (2008). e-Science: Relieving bottlenecks in large-scale genomic analyses. Nature Reviews Microbiology 6: 948 - 954.
  • Hallinan, J. & Wipat, A. (2008). Network motifs in context: An exploration of the evolution of oscillatory dynamics in transcriptional networks. Proceedings of the 2008 IEEE Conference on Computational Intelligennce in Bioinformatics and Computational Biology (CIBCB08).
  • Hallinan, J. (2008). Gene Networks and Evolutionary Computation. In Computational Intelligence in Bioinformatics, ed. by G. B. Fogel, D. W. Corne & Y. Pan. IEEE CS Press/Wiley. 67 - 96.
  • Hallinan, J. (2008). Synthetic Biology: Life, Jim, But Not as We Know It.. In Design by Evolution ed. P. Hingston, L. C. Barone & Z. Michalewicz. Springer. 53 - 68.
  • Hallinan, J., Pocock, M. & Wipat, A.(2008). Evolving genetic circuit designs for synthetic biology. Poster at Synthetic Biology 4.0, Hong Kong. 10 - 12 October.
  • Cooling, M., Lawson, J., Hallinan, J., Canton, B., Rouilly, V. & Wipat, A. (2008). Standard virtual biological parts - physiome standards in synthetic biology. Poster at IET BioSysBio 2008.
  • Hallinan, J., Pocock, M., Taschuk, M. & Wipat, A. (2008). Data Integration to Constrain Computational Modelling in Synthetic Biology Poster at BioSysBio 2008.


  • Hallinan, J. & Wipat, A. (2007). Motifs and modules in a fractured yeast functional network. 2007 Symposium on Computational Intelligence in Bioinformatics and Computational Biology.


  • Hallinan, J. & Wipat, A. (2006). Clustering and crosstalk in a yeast functional interaction network. 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.
  • Hallinan, J., Bradley, D., Mattick, J. & Wiles, J. (2006). Effects of an RNA control layer on the state space of Boolean models of genetic regulatory networks. IEEE World Congress on Computational Intelligence, Vancouver, BC Canada, July 16 - 21, 2006.
  • Hallinan, J. Bradley, D. & Wiles, J. (2006). Effects of constitutive gene activation on the dynamics of genetic regulatory networks. IEEE World Congress on Computational Intelligence, Vancouver, BC Canada, July 16 - 21, 2006.


  • Hallinan, J. & Jackway, P. (2005). Network motifs, feedback loops and the dynamics of genetic regulatory networks. Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. IEEE Press. 90 - 96.
  • Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M., Nishida, H., Yap, C. C., Suzuki, M., Caminci, P., Hayashizaki, Y., Wells, C., Frith, M., Ravasi, T., Pang, C., Hallinan, J., Mattick, J., Hume, D. A., Lipovitch, L., Batalov, S., Engstrom, P. G., Mizuno, Y., Faghihi, M. A., Sandelin, A., Chalk, A. M., Mottagui-Tabar, S., Liang, Z., Lenhard, B. & Wahlstedt, C. (2005). Antisense transcription in the mammalian transcriptome. Science 309: 1564 - 1566.
  • Wiles, J., Geard, N., Watson, J., Willadsen, K., Mattick, J., Bradley, D. & Hallinan, J. (2005). There's more to a model than code: Using Complex Systems Patterns to formalize in silico modeling experience. In Beyer, H. G., O'Reilly, U.-M., Arnold, D. V., Banzhaf, W., Blum, C., Bonaneau, E. W., Cantu Paz, E., Dasgupta, D., Deb, K., Foster, J. A., de Jong, E. D., Lipson, H., Llora, X., Mancoridis, S., Pelikan, M., Raidl, G. R., Soule, T., Tyrrell, A., Watson, J.-P. & Zitzler, E. Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2005. ACM Press: New York.
  • Hallinan, J. (2005). Evolving neural networks for the identification of Malignancy Associated Changes. In Gallagher, M., Hogan, J. & Maire, F. (Eds.) Intelligent Data Engineering and Automated Learning - IDEAL 2005. Lecture Notes in Computer Science 3578:382 - 389.
  • Hallinan, J. (2005). Game Theory. In Encyclopedia of Nonlinear Science ed. by A. Scott. Fitzroy Dearborn: London. 355 - 356.
  • Hallinan, J. (2005). Game of Life. In Encyclopedia of Nonlinear Science ed. by A. Scott. Fitzroy Dearborn: London. 352 - 354.


  • Hallinan, J. & Wiles, J. (2004). Asynchronous dynamics of an artificial genetic regulatory network. Ninth International Conference on the Simulation and Synthesis of Living Systems (ALife9) Boston, September 12 - 15, 2004.
  • Hallinan, J. (2004). Cluster analysis of the p53 genetic regulatory network: Topology and biology. 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. San Diego 7-8 October, 2004.
  • Hallinan, J. (2004). Gene duplication and hierarchical modularity in intracellular interaction networks. BioSystems 74(1-3):51 - 62.
  • Hallinan, J. & Wiles, J. (2004). Evolving genetic regulatory networks using an artificial genome. In Chen, Y.-P. (ed.) 2nd Asia-Pacific Bioinformatics Conference (APBC2004), Dunedin, New Zealand. Conferences in Research and Practice in Information Technology, Australian Computer Society, Inc. Vol. 29:291 - 296.


  • Hallinan, J. (2003). Self-organization leads to hierarchical modularity in an internet community. Proceedings of 7th International Conference on Knowledge-Based Intelligent Information and Engineering Systems(KES2003) 3, 4 & 5 September 2003 University of Oxford, United Kingdom. Lecture Notes in AI 2773 ed. by V. Palade, R. J. Howlett & L. C. Jain. Springer-Verlag: Berlin.
  • Wiles, J. & Hallinan, J. (2003). Evolutionary computation and cognitive science. In Fogel, D. B. & Robinson, C. J. (eds.) Computational Intelligence: The Experts Speak. San Diego: IEEE Press: 179 - 189.


  • Geard, N., Wiles, J., Hallinan, J., Tonkes, B. & Skellett, B. (2002). A comparison of neutral landscapes - NK, NKp and NKq. Proceedings of the 2002 Congress on Evolutionary Computation CEC2002, pp. 205-210, IEEE Press.
  • Hallinan, J. & Wiles, J. (2002). Evolutionary Algorithms. In The Encyclopedia of Cognitive Sciences. Macmillan: New York.40 - 47.
  • Wiles, J. & Hallinan, J. (2002). Evolutionary Computation and Cognitive Science. Encyclopedia of Cognitive Science. Macmillan: London.


  • Wiles, J., Schulz, R., Hallinan, J., Bolland, S. & Tonkes, B. (2001). Probing the persistent question marks. Proceedings of the Genetic and Evolutionary Computation Conference 2001 (GECCO 2001).
  • Wiles, J., Schulz, R., Bolland, S., Tonkes, B. & Hallinan, J. (2001). Selection procedures for module discovery: Exploring evolutionary algorithms for cognitive science. Proceedings of the Twenty-Third Annual Conference of the Cognitive Science Society , 1 - 4 August, 2001, Edinburgh, Scotland. Moore, J. & Stenning, K. (eds). Lawrence Erlbaum Associates: Mahwah, N. J. pp. 1124 - 1129.
  • Wiles, J. & Hallinan, J. (2001). Guest editorial - Evolutionary Computation and cognitive science:Modeling evolution and evolving models. IEEE Transactions on Evolutionary Computation 5(2):89.


  • Hallinan, J. & Wiles, J. (2000). Modelling the spread of antibiotic resistance. Congress on Evolutionary Computation 2000, 16 - 19 July, 2000, San Digeo, CA.
  • Wiles, J., Chenery, H. J., Hallinan, J., Blair, A. & Naumann, D. (2000). Stroop performance in Alzheimer's disease: A preliminary test of theories of damage using a connectionist simulation. Brain and Language 74(3): 341 - 344.
  • Wiles, J., Chenery, H., Hallinan, J., Blair, A. & Naumann, D. (2000). Effects of damage to the CDM Stroop model. Cognitive Science in Australia 2000: Proceedings of the Fifth Biennial Conference of the Australasian Cognitive Science Society. Adelaide: Causal.
  • Hallinan, J. (2000). Feature selection and classification in the diagnosis of cervical cancer. In Chambers, L. (ed). Practical Handbook of Genetic Algorithms, 2nd Edition. CRC Press.

    Ancient History

  • Hallinan, J. (2004). Tunable asynchrony in an artifical genome. International Conference on Complex Systems (ICCS 2004). Boston, May 16 - 22, 2004.
  • Hallinan, J. & Smith, G. (2002). Iterative vector diffusion for the detection of modularity in large networks. InterJournal Complex Systems Barticle 584.
  • Hallinan, J. (2001). Thinking beyond the fringe. Meeting Report, 23rd Annual Conference of the Cognitive Science Society. Trends in Cognitive Sciences 5(12): 506 - 507.
  • Hallinan, J. & Jackway, P. (1999). Simultaneous evolution of feature subset and neural classifier on high-dimensional data. 1999 Conference on Digital Image Computing and Applications (DICTA'99) 7 - 8 December 1999, Perth, WA pp.237 - 240.
  • Hallinan, J. (1999). Detection of Malignancy Associated Changes in Visually Normal Cells: A Review, CSSIP Technical Report TR 18/99.
  • Sawbridge, T. I., Drenth, J., Hallinan, J., Anderson, M., Norris, B. & Teasdale, R. D. (1999). EST sequencing in Eucalyptus. PAG VII, Plant and Animal Genome VII Conference, 17-21 January, San Diego, CA.
  • Sawbridge, T. I., Drenth, J., Anderson, M., Hallinan, J., Norris, B. & Teasdale, R. D. (1999). Applications of EST sequencing in a forestry biotech company. PAG-VII, Plant and Animal Genome VII Conference, 17 - 21 January, San Diego, CA.
  • Hallinan, J.S. & Jackway, P.T. (1998). Co-operative Evolution of a Neural Classifier and Feature Subset. In: B. McKay, X. Yao, C.S. Newton, J.-H. Kim, T. Furuhashi (Eds.): Simulated Evolution and Learning: Second Asia-Pacific Conference on Simulated Evolution and Learning, SEAL'98, Canberra, Australia, November 1998. Selected Papers. Lecture Notes in Artificial Intelligence, 1585, pp. 397-404.
  • Hallinan, J. S. & Jackway, P. T. (1995). Detection of malignancy associated changes in thionin stained cervical cells. DICTA-95 Digital Image Computing: Techniques and Applications, 6-8 Dec 1995, pp.426-431, Brisbane, Australia.
  • James, M. & Hallinan, J. (1995). Homicides in Australia 1992-93. Trends and Issues in Crime and Criminal Justice No.51. Australian Institute of Criminology: Canberra. ISBN 0 642 24007 8
  • Hallinan, J. (1993). Human factors in computer security: A review. Journal of Law and Information Systems 4(1):94-115.
  • Walker, J., Hallinan, J. & Dagger, D. (1992). Australian Prisoners 1991: Results of the 1991 National Prison Census. Australian Institute of Criminology: Canberra. ISSN 0813-2364


  • Hallinan, J. (1999). Detection of Malignancy Associated Changes in Cervical Cells using Statistical and Evolutionary Computation Techniques. Unpublished PhD Thesis, University of Queensland.
  • Hallinan, J. (1992). Human Factors in the Implementation of Computer Security and Risk Assessment Policies in Mid-Sized Businesses. Unpublished M.Inf.Sc. thesis, Australian Defence Force Academy, University College, University of New South Wales.
  • Lonie, J. (1982). Genetic Variability in Eucalyptus pulverulenta. Unpublished Honours thesis, Australian National University.
    Last edited: 28 July 2013 by Jennifer Hallinan