School of Computing

Publications by Dr Dominique Chu

Also view these in the Kent Academic Repository

Article
Chu, D. (2016). Limited by sensing-A minimal stochastic model of the lag-phase during diauxic growth. Journal of Theoretical Biology [Online] 414:137-146. Available at: http://dx.doi.org/10.1016/j.jtbi.2016.10.019.
Chu, D. and Barnes, D. (2016). The lag-phase during diauxic growth is a trade-off between fast adaptation and high growth rate. Scientific Reports [Online] 6:25191. Available at: http://doi.org/10.1038/srep25191.
Chu, D. (2016). Performance limits and trade-offs in entropy-driven chemical computers. n/a.
Chu, D. and Salykin, A. (2015). Evolutionary pressures on the yeast transcriptome. IEEE/ACM Transactions on Computational Biology and Bioinformatics [Online]:1-1. Available at: http://doi.org/10.1109/TCBB.2015.2420554.
Chu, D. (2015). In silico evolution of diauxic growth. BMC evolutionary biology [Online] 15. Available at: http://doi.org/10.1186/s12862-015-0492-0.
Chu, D., Thompson, J. and von der Haar, T. (2014). Charting the dynamics of translation. Bio Systems [Online] 119:1-9. Available at: http://dx.doi.org/10.1016/j.biosystems.2014.02.005.
Chu, D., Barnes, D. and Perkins, S. (2014). Amorphous computing in the presence of stochastic disturbances. Biosystems [Online] 125:32-42. Available at: http://dx.doi.org/10.1016/j.biosystems.2014.09.010.
Chu, D. et al. (2014). Translation elongation can control translation initiation on eukaryotic mRNAs. EMBO Journal [Online] 33:21-34. Available at: http://dx.doi.org/10.1002/embj.201385651.
Wang, F. et al. (2013). Adaptive Neuromorphic Architecture (ANA). Neural Networks [Online] 45:111-116. Available at: http://dx.doi.org/10.1016/j.neunet.2013.02.009.
Chu, D. and von der Haar, T. (2012). The architecture of eukaryotic translation. Nucleic Acids Research [Online] 40:10098-10106. Available at: http://dx.doi.org/10.1093/nar/gks825.
Chu, D., Zabet, N. and von der Haar, T. (2012). A novel and versatile computational tool to model translation. Bioinformatics [Online] 28:292-293. Available at: http://dx.doi.org/10.1093/bioinformatics/btr650.
Chu, D., Zabet, N. and Hone, A. (2011). Optimal Parameter Settings for Information Processing in Gene Regulatory Networks. BioSystems [Online]:182-196. Available at: http://www.cs.kent.ac.uk/pubs/2011/3081.
Chu, D., Barnes, D. and von der Haar, T. (2011). The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae. Nucleic Acids Research [Online] 39:6705-6714. Available at: http://dx.doi.org/10.1093/nar/gkr300.
Chu, D. (2011). Complexity: Against Systems. Theory in Biosciences [Online]:182-196. Available at: http://www.cs.kent.ac.uk/pubs/2011/3099.
Zabet, N. and Chu, D. (2010). Computational limits to binary genes. Journal of the Royal Society, Interface [Online] 7:182-196. Available at: http://dx.doi.org/10.1098/rsif.2009.0474.
Chu, D. and Barnes, D. (2010). Modeling fimbriae mediated parasite-host interactions. Journal of Theoretical Biology [Online] 264:1169-1176. Available at: http://dx.doi.org/10.1016/j.jtbi.2010.03.037.
Chu, D., Zabet, N. and Mitavskiy, B. (2009). Models of transcription factor binding: Sensitivity of activation functions to model assumptions. Journal of Theoretical Biology [Online] 257:419-429. Available at: http://dx.doi.org/10.1016/j.jtbi.2008.11.026.
Chu, D., Shih-Chi, C. and Barigou, M. (2009). Qualitative models of particle de-agglomeration. Powder Technology [Online] 195. Available at: http://dx.doi.org/10.1016/j.powtec.2009.05.011.
Chu, D. (2008). Modes of evolution in a parasitehost interaction: Dis-entangling factors determining the evolution of regulated fimbriation in E. coli. Biosystems [Online] 95:67-74. Available at: http://dx.doi.org/10.1016/j.biosystems.2008.07.001.
Chu, D. (2008). Criteria For Conceptual And Operational Notions of Complexity. Artificial Life 14:313-323.
Haggett, S., Chu, D. and Marshall, I. (2008). Evolving a Dynamic Predictive Coding Mechanism for Novelty Detection. Knowledge-Based Systems 21:217-224.
Chu, D., Roobol, J. and Blomfield, I. (2008). A theoretical interpretation of the transient sialic acid toxicity of a nanR mutant of Escherichia coli. Journal of Molecular Biology [Online] 375:875-889. Available at: http://dx.doi.org/10.1016/j.jmb.2007.10.073.
Chu, D. (2008). The evolution of group-level pathogenic traits. Journal of Theoretical Biology [Online] 253:355-362. Available at: http://dx.doi.org/10.1016/j.jtbi.2008.03.017.
Chu, D. and Ho, W. (2007). The Localization Hypothesis and Machines. Artificial Life 13:299-302.
Chu, D. and Ho, W. (2007). Computational Realizations of Living Systems. Artificial Life [Online] 13:369-381. Available at: http://dx.doi.org/10.1162/artl.2007.13.4.369.
Chu, D. and Ho, W. (2006). A Category Theoretical Argument Against the Possibility of Artificial Life. Artificial Life [Online] 12:117-135. Available at: 10.1162/106454606775186392.
Chu, D. and Blomfield, I. (2006). Orientational Control is an Efficient Control Mechanism for Phase Switching in the E coli fim System. Journal of Theoretical Biology [Online] 244:541-551. Available at: http://dx.doi.org/10.1016/j.jtbi.2006.08.016.
Chu, D., Rowe, J. and Lee, H. (2006). Evaluation of the current models for the evolution of bacterial DNA uptake signal sequences. Journal of Theoretical Biology [Online] 238:157-166. Available at: http://dx.doi.org/10.1016/j.jtbi.2005.05.024 .
Chu, D., Lee, H. and Lenaerts, T. (2005). Emergence of Uptake Signals in Bacterial DNA. Artificial Life 11:317-338.
Lenaerts, T., Chu, D. and Watson, R. (2005). Dynamical Hierarchies. Artificial Life 11:403-405.
Chu, D., Lee, H. and Lanaerts, T. (2005). Evolution of DNA Uptake Signal Sequences. Artificial Life 11:317-338.
Chu, D., Strand, R. and Fjelland, R. (2003). Theories of Complexity. Complexity [Online] 8:19-30. Available at: http://dx.doi.org/10.1002/cplx.10059.
Book section
Chu, D. and Rowe, J. (2005). A Fitness-Landscape for the Evolution of Uptake Signal Sequences on Bacterial DNA. in: Capcarrere, M. S. et al. eds. Advances in Artificial Life. Berlin: Springer, pp. 845-853.
Conference or workshop item
Chu, D. and Barnes, D. (2015). An Ansatz for a Theory of Living Systems. in: IEEE Symposium Series on Computational Intelligence 2015. IEEE, pp. 1087-1093. Available at: http://doi.org/10.1109/SSCI.2015.156.
Chu, D. and Barnes, D. (2015). Evolving strategies for single-celled organisms in multi-nutrient environments. in: European Conference on Artificial Life 2015. MIT Press, pp. 226-233. Available at: http://dx.doi.org/10.7551/978-0-262-33027-5-ch046.
Barnes, D. and Chu, D. (2014). Evolving Parameters for a Noisy Biological System The Impact of Alternative Approaches. in: 13th International Conference, ICAISC 2014. Springer International Publishing, pp. 95-106. Available at: http://dx.doi.org/10.1007/978-3-319-07176-3_9.
Chu, D. and Barnes, D. (2014). Evolving Biological Systems: Evolutionary Pressure to Inefficiency. in: ALIFE 14: The 14th International Conference on the Synthesis and Simulation of Living Systems. MIT Press, pp. 89-96. Available at: http://dx.doi.org/10.7551/978-0-262-32621-6-ch016.
Chu, D. (2013). Replaying the tape of evolution: Evolving parameters for a simple bacterial metabolism. in: IEEE CEC 2013 : IEEE Congress on Evolutionary Computation.. Available at: http://www.cec2013.org/.
Chu, D. (2013). Evolving Parameters for a Noisy Bio-System. in: 2013 IEEE Symposium Series on Computational Intelligence.
Barnes, D. and Chu, D. (2011). Walking, hopping and jumping: a model of transcription factor dynamics on DNA. in: Advances in Artificial Life, ECAL 2011. Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems.
Barnes, D. and Chu, D. (2010). An efficient model for investigating specific site binding of transcription factors. in: Proceedings of the 4th International Conference on Bioinformatics and Biomedical Engineering, June 18-20, Chengdu, China, 2010. pp. 182-196. Available at: http://www.cs.kent.ac.uk/pubs/2010/3021.
Zabet, N. and Chu, D. (2010). Stochasticity and robustness in bi-stable systems. in: Bioinformatics and Biomedical Engineering (iCBBE), 2010 4th International Conference on . IEEE Xplore, pp. 182-196. Available at: http://www.cs.kent.ac.uk/pubs/2010/2981.
Zabet, N., Hone, A. and Chu, D. (2010). Design Principles of Transcriptional Logic Circuits. in: Artificial Life XII Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems. MIT Press, pp. 182-196. Available at: http://www.cs.kent.ac.uk/pubs/2010/3036.
Chu, D. and Barnes, D. (2009). Group Selection vs Multi-Level Selection: Some Example Models Using Evolutionary Games. in: Proceedings of the IEEE Congress on Evolutionary Computation (IEEE CEC'09).
Chu, D. (2008). Crossover operators to control size growth in linear GP and variable length GAs. in: IEEE Congress on Evolutionary Computation (IEEE CEC 2008). USA: IEEE, pp. 336-343. Available at: http://dx.doi.org/10.1109/CEC.2008.4630819.
Chu, D. (2007). Evolving Genetic Regulatory Networks for Systems Biology. in: IEEE Congress on Evolutionary Computation 2007. pp. 875-882. Available at: http://dx.doi.org/10.1109/CEC.2007.4424562 .
Haggett, S., Chu, D. and Marshall, I. (2007). Evolving a Dynamic Predictive Coding Mechanism for Novelty Detection. in: Research and Development in Intelligent Systems XXIV - Proceedings of AI-2007, the Twenty-seventh SGAI International Conference on Artificial Intelligence. Springer, pp. 167-180.
Chu, D. and Rowe, J. (2005). Approaching Perfect Mixing in a Simple Model of the Spread of an Infectious Disease. in: Abbass, H. A., Bossomaier, T. and Wiles, J. eds. Recent Advances in Artificial Life: Proceedings of the Second Australian Conference on Artificial Life (ACAL 2005). World Scientific, pp. 21-32.
Chu, D. and Rowe, J. (2004). Spread of Vector Borne Diseases in a Population with Spatial Structure. in: In Proceedings of PPSN VIII - Eighth International Conference on Parallel Problem Solving from Nature. Springer-Verlag, pp. 222-232.
Book
Barnes, D. and Chu, D. (2015). Guide to Simulation and Modeling for Biosciences. [Online]. Springer. Available at: http://dx.doi.org/10.1007/978-1-4471-6762-4.
Barnes, D. and Chu, D. (2010). Introduction to Modeling for Biosciences. [Online]. Springer. Available at: http://www.cs.kent.ac.uk/pubs/2010/3045.
Total publications in KAR: 51 [See all in KAR]

School of Computing, University of Kent, Canterbury, Kent, CT2 7NF

Enquiries: +44 (0)1227 824180 or contact us.

Last Updated: 17/11/2017