Newcastle University

Projects

• Cellular senescence – regulatory signalling networks
  Project Leader(s): Thomas von Zglinicki
• Incorporating dataset relevance into functional networks
  Project Leader(s): Jennifer Hallinan, Anil Wipat
• The CISBAN Interactomes Database (CID)
  Project Leader(s): Cedric Simillion

• Misirli G, Wipat A, Mullen J, James K, Pocock M, Smith W, Allenby N, Hallinan J. BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology. Journal of Integrative Bioinformatics 2013, 10(2), 224.
• Weile J, James K, Hallinan J, Cockell SJ, Lord P, Wipat A, Wilkinson DJ. Bayesian integration of networks without gold standards. Bioinformatics 2012, 28(11), 1495-1500.
• Hallinan JS, Park S, Wipat A. Bridging the Gap Between Design and Reality: A Dual Evolutionary Strategy for the Design of Synthetic Genetic Circuits. In: BioInformatics: International Conference on Bioinformatics Models, Methods and Algorithms. 2012, Algarve, Portugal: ScitePress.
• Hallinan JS. Data mining for microbiologists. In: Harwood, C., Wipat, A, ed. Systems Biology of Bacteria. London: Academic Press, 2012, pp.27-79.
• James K, Wipat A, Hallinan J. Is newer better?-evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae. Integrative Biology 2012, 4(7), 715-727.
• Flanagan K, Nakjang S, Hallinan J, Harwood C, Hirt RP, Pocock MR, Wipat A. Microbase2.0: a generic framework for computationally intensive bioinformatics workflows in the cloud. Journal of Integrative Bioinformatics 2012, 9(2), 12.
• Weatherhead S, Farr P, Swan D, Jamieson D, Hallinan J, Lloyd J, Wipat A, Reynolds N. Apoptosis of keratinocytes is a key mechanism in UVB-induced clearance of psoriasis. In: 41st Annual Meeting of the European Society for Dermatological Research. 2011, Barcelona, Spain: Nature Publishing Group.
• Misirli G, Hallinan JS, Pocock M, Cockell SJ, Weile J, Wipat A. BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2011. School of Computing Science Technical Report Series 1237.
• Weile J, Pocock M, Cockell SJ, Lord P, Dewar JM, Holstein EM, Wilkinson D, Lydall D, Hallinan J, Wipat A. Customizable views on semantically integrated networks for systems biology. Bioinformatics 2011, 27(9), 1299-1306.
• Weatherhead SC, Farr PM, Jamieson D, Hallinan JS, Lloyd JL, Wipat A, Reynolds NJ. Keratinocyte Apoptosis in Epidermal Remodeling and Clearance of Psoriasis Induced by UV Radiation. Journal of Investigative Dermatology 2011, 131(9), 1916-1926.
• Misirli G, Hallinan JS, Yu T, Lawson JR, Wimalaratne SM, Cooling MT, Wipat A. Model annotation for synthetic biology: automating model to nucleotide sequence conversion. Bioinformatics 2011, 27(7), 973-979.
• James K, Lycett SJ, Wipat A, Hallinan JS. Multiple Gold Standards Address Bias in Functional Network Integration. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2011. School of Computing Science Technical Report Series 1302.
• Hallinan JS, James K, Wipat A. Network Approaches to the Functional Analysis of Microbial Proteins. Advances in Microbial Physiology 2011, 59, 101-133.
• Weatherhead SC, Farr PM, Hallinan JS, Wipat A, Reynolds NJ. 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. In: 40th Annual Meeting of the European Society for Dermatological Research. 2010, Helsinki, Finland: Journal of Investigative Dermatology: Nature Publishing Group.
• Hallinan J, Misirli G, Wipat A. Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. In: 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). 2010, Buenos Aires, Argentina: IEEE.
• Passos JF, Nelson G, Wang CF, Richter T, Simillion C, Proctor CJ, Miwa S, Olijslagers S, Hallinan J, Wipat A, Saretzki G, Rudolph KL, Kirkwood TBL, von Zglinicki T. Feedback between p21 and reactive oxygen production is necessary for cell senescence. Molecular Systems Biology 2010, 6(1), 347.
• Cooling MT, Rouilly V, Misirli G, Lawson J, Yu T, Hallinan J, Wipat A. Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics 2010, 26(7), 925-931.
• Passos J, Simillion C, Hallinan J, Wipat A, Von Zglinicki T. Cellular senescence: Unravelling complexity. Age 2009, 31(4), 353-363.
• Hallinan JS, Pocock MR, Addinall S, Lydall D, Wipat A. Clustering incorporating shortest paths identifies relevant modules in functional interaction networks. In: CIBCB '09: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. 2009, Nashville, TN, USA: IEEE.
• Jin Y, Hallinan J. Evolving gene regulatory networks. BioSystems 2009, 98(3), vi-vii.
• James K, Wipat A, Hallinan J. Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes. In: DATA INTEGRATION IN THE LIFE SCIENCES, PROCEEDINGS. 2009, HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY: SPRINGER-VERLAG BERLIN.
• James K, Wipat A, Hallinan J. Integration of full-coverage probabilistic functional networks with relevance to specific biological processes. In: Data Integration in the Life Sciences: 6th International Workshop (DILS). 2009, Manchester, UK: Springer.
• James K, Wipat A, Hallinan J. Integration of full-coverage probabilistic functional networks with relevance to specific biological processes. In: Data Integration in the Life Sciences: 6th International Workshop. 2009, Manchester, UK: Springer.
• Addinall SG, Downey M, Yu M, Zubko MK, Dewar J, Leake A, Hallinan J, Shaw O, James K, Wilkinson DJ, Wipat A, Durocher D, Lydall DA. A Genome-wide Suppressor and Enhancer Analysis of cdc13-1 Reveals Varied Cellular Processes Influencing Telomere Capping in Saccharomyces cerevisiae. Genetics 2008, 180(4), 2251-2266.
• Craddock T, Harwood CR, Hallinan J, Wipat A. e-Science: relieving bottlenecks in large-scale genome analyses. Nature Reviews in Microbiology 2008, 6(12), 948-954.
• Hallinan JS, Wipat A. Network Motifs in Context: An Exploration of the Evolution of Oscillatory Dynamics in Transcriptional Networks. In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. 2008, Idaho, USA: IEEE.
• Hallinan JS, Wipat A. Motifs and modules in fractured functional yeast networks. In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 07). 2007, Honolulu, Hawaii: IEEE.
• Hallinan J, Wipat A. Clustering and cross-talk in a yeast functional interaction network. In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). 2006, Toronto, Ontario, Canada: IEEE.
• Hallinan J, Bradley D, Wiles J. Effects of an RNA control layer on the state space of Boolean models of genetic regulatory networks. In: IEEE Congress on Evolutionary Computation (CEC). 2006, Vancouver, BC: IEEE.
• Hallinan J, Bradley D, Wiles J. Effects of constitutive gene expression on the dynamics of random Boolean netorks. In: IEEE Congress on Evolutionary Computation (CEC). 2006, Vancouver, BC: IEEE.
• Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Caminci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang C, Hallinan J, Mattick J, Hume DA, Lipovitch L, Batalov S, Engstrom PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlstedt C. Antisense Transcription in the Mammalian Transcriptome. Science 2005, 309(5740), 1564-1566.
• Hallinan J. Evolving neural networks for the classification of Malignancy Associated Changes. In: 6th International Conference Intelligent Data Engineering and Automated Learning (IDEAL). 2005, Brisbane, Australia: Springer.
• Hallinan J. Game of Life. In: Scott, A, ed. Encyclopedia of Nonlinear Science. New York; London: Routledge, 2005, pp.352-354.
• Hallinan J. Game Theory. In: Scott, A, ed. Encyclopedia of Nonlinear Science. New York; London: Routledge, 2005, pp.355-356.
• Hallinan JS, Jackway PT. Network motifs, feedback loops and the dynamics of genetic regulatory networks. In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). 2005, San Diego, California, USA: IEEE.
• Hallinan J, Wiles J. Asynchronous dynamics of an artificial genetic regulatory network. In: Artificial Life IX: Proceedings of the Ninth International Conference on the Simulation and Synthesis of Living Systems. 2004, Boston, Massachusetts, USA: MIT Press.
• Hallinan JS. Cluster analysis of the p53 genetic regulatory network: Topology and biology. In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). 2004, La Jolla, California, USA: IEEE.
• Hallinan J, Wiles J. Evolving genetic regulatory networks using an artificial genome. In: Bioinformatics: Second Asia-Pacific Bioinformatics Conference (APBC). 2004, Dunedin, New Zealand: Australian Computer Society Inc.
• Hallinan J. Gene duplication and hierarchical modularity in intracellular interaction networks. BioSystems 2004, 74(1-3), 51-62.
• Wiles J, Hallinan J. Evolutionary computation and cognitive science. In: Fogel, D. B., Robinson, C. J, ed. Computational Intelligence: The Experts Speak. Hoboken, United States: Wiley-Blackwell, 2003, pp.179-189.
• Hallinan J. Self-organization leads to hierarchical modularity in an internet community. In: 7th International Conference on Knowledge-Based Intelligent Information and Engineering Systems (KES). 2003, Oxford, UK: Springer.
• Geard N, Wiles J, Hallinan J, Tonkes B, Skellett B. A comparison of neutral landscapes - NK, NKp and NKq. In: Proceedings of the Congress on Evolutionary Computation (CEC). 2002, Honolulu, Hawaii: IEEE.
• Hallinan JS, Wiles J. Evolutionary Algorithms. In: Nadel, L, ed. Encyclopedia of Cognitive Science. Chichester, UK: Palgrave Macmillan, 2002, pp.40-47.
• Wiles J, Schulz R, Hallinan J et al. Probing the persistent question marks. In: Proceedings of the Genetic and Evolutionary Computation Conference (GECCO). 2001, San Francisco, California, USA: Morgan Kaufmann.
• Wiles J, Schulz R, Bolland S, Tonkes B, Hallinan J. Selection procedures for module discovery: Exploring evolutionary algorithms for cognitive science. In: Proceedings of the Twenty-Third Annual Conference of the Cognitive Science Society. 2001, University of Edinburgh, Edinburgh, UK: Lawrence Erlbaum Associates.
• Wiles J, Chenery H, Hallinan J, Blair A, Naumann D. Effects of damage to the CDM Stroop model. In: Cognitive Science in Australia: Proceedings of the Fifth Biennial Conference of the Australasian Cognitive Science Society. 2000, Melbourne, Australia: Causal Productions.
• Hallinan J. Feature selection and classification in the diagnosis of cervical cancer. In: Chambers, L, ed. The Practical Handbook of Genetic Algorithms: Applications. Boca Raton, Florida, USA: CRC Press, 2000, pp.167-202.
• Hallinan JS, Wiles J. Modelling the spread of antibiotic resistance. In: Proceedings of the 2000 Congress on Evolutionary Computation (CEC). 2000, La Jolla, California, USA: IEEE.
• Wiles J, Chenery HJ, Hallinan J, Blair A, Naumann D. Stroop performance in Alzheimer's disease: A preliminary test of theories of damage using a connectionist simulation. Brain and Language 2000, 74(3), 341-344.