Advanced Computational Modelling Centre Publications

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Hosseini Cici, S. Z., Adkins, S W and Hanan, J S (2006). 3D modelling of cicer arietinum architecture and phenology: relating phenotype to genotype. In: Handbook & Abstracts 3rd International Conference on Legume Genomics & Genetics. Genes to Crops, Brisbane Convention & Exhibition Centre, (81-81). 9-13 April 2006. 162  
Renton, M., Hanan, J. S. and Burrage, K. (2004). A canonical toolkit for modelling plant function. In: C. Godin and et al., Proceedings of the 4th International Workshop on Functional-Structural Plant Models. 4th International Workshop on Functional-Structural Plant Models, Montpellier, France, (226-230). 7-11 June, 2004. 288  
Burrage, Kevin, Mac, Shev and Tian, Tianhai (2006). Accelerated leap methods for simulating discrete stochastic chemical kinetics. In: Christian Commault and Nicholas Marchand, Lecture Notes in Control and Information Sciences: 2nd Multidisciplinary International Symposium on Positive Sys. 2nd Multidisciplinary International Symposium on Positive Sys, Grenoble, France, (359-366). 30 August -1 September, 2006. doi:10.1007/11757344_46 227   3 Cited 3 times in Scopus3 0
Burrage, K, Hertono, G, Jackiewicz, Z and Welfert, BD (2001) Acceleration of convergence of static and dynamic iterations. Bit, 41 4: 645-655. doi:10.1023/A:1021935700208 117   1 0
Lesmono, D., Tonkes, E. J. and Burrage, K. (2005) A Continuous Time Model for Election Timing. Australian Mathematical Society Gazette, 32 5: 329-339. 108  
Burrage, PM, Herdiana, R and Burrage, K (2004) Adaptive stepsize based on control theory for stochastic differential equations. Journal of Computational And Applied Mathematics, 170 2: 317-336. doi:10.1016/j.cam.2004.01.027 160   17 Cited 20 times in Scopus20 0
Burrage, Kevin, Hood, Lindsay and Ragan, Mark A. (2006) Advanced computing for systems biology. Briefings in Bioinformatics, 7 4: 390-398. doi:10.1093/bib/bbl033 103   21 Cited 21 times in Scopus21 0
Alcock, J and Burrage, K (2004) A genetic estimation algorithm for parameters of stochastic ordinary differential equations. Computational Statistics & Data Analysis, 47 2: 255-275. doi:10.1016/j.csda.2003.11.025 151   8 Cited 10 times in Scopus10 0
Duczmal, Katherine, Robinson, Peter and Hanan, Jim (2005). Agent-based virtual insects. In: Robert Bridle, Simon Thornton and Arun Vishwanath, Proceedings of the Australian Undergraduate Students’ Computing Conference 2005. Proceedings of the Australian Undergraduate Students’ Computing Conference 2005, Canberra, Australia, (1-8). 28-29 November, 2005. 159  
Burrage, K., Burrage, P. M., Jeffrey, S. J., Pickett, T., Sidje, R. B. and Tian, T. (2003). A Grid Implementation of Chemical Kinetic Simulation Methods in Genetic Regulation. In: J. Young and R. Chhabra, Proceedings of the APAC Conference and Exhibition on Advanced Computing, Grid Applications and eResearch. APAC'03, Royal Pines Resort, Gold Coast, (1-8). 29 September - 2 October 2003. 151  
Burrage, K., Hegland, M., Macnamara, F. and Sidje, B. (2006). A Krylov-based Finite State Projection algorithm for solving the chemical master equation arising in the discrete modelling of biological systems. In: A. N. Langville and W. J. Stewart, Mam 2006 : Markov Anniversary Meeting: an international conference to celebrate the 150th anniversary of the birth of A.A. Markov. Markov Anniversary Meeting: an international conference to celebrate the 150th anniversary of the birth of A.A. Markov, Charleston, South Carolina, USA, (21-38). June 12-14, 2006. 272  
Tian, T. and Burrage, K. (2005). A mathematical model for genetic regulation of the lactose operon. In: Osvaldo Gervasi, Computational Science and Its Applications - Iccsa 2005, Pt 2. International Conference on Computational Science and its Appl, Singapore, (1245-1253). 9-12 May, 2005. 90   0 0
Thornby, D. F. and Hanan, J. S. (2004). A modelling exploration of branch extension, defoliation responses, and carbohydrate physiology in cotton (Gossypium hirsutum L.). In: C. Godin and et al., Proceedings of the 4th International Workshop on Functional-Structural Plant Models. 4th International Workshop on Functional-Structural Plant Models, Montpellier, France, (319-322). 7-11 June, 2004. 75  
Burrage, Kevin, Tian, Tianhai and Burrage, Pamela (2004) A multi-scaled approach for simulating chemical reaction systems. Progress in Biophysics and Molecular Biology, 85 2-3: 217-234. doi:10.1016/j.pbiomolbio.2004.01.004 87   68 Cited 81 times in Scopus81 3
Sidje, R. B., Burrage, K. and Philippe, B. (2003) An augmented Lanczos algorithm for the efficient computation of a dot-product of a function of a large sparse symmetric matrix. Computational Science - ICCS 2003, LNCS 2659 693-704. 124   1 0
Lesmono, D., Tonkes, E. J. and Burrage, K. (2003) An early political election problem. The ANZIAM Journal Electronic Supplement, 45 Part C: 16-33. 43  
Prusinkiewiez, P, Hanan, J and Mech, R (2000) An L-system-based plant modeling language. Applications of Graph Transformations With Industrial Relevance, Proceedings, 1779 395-410. 151   24
Alcock, Jamie and Burrage, Kevin (2006) A note on the Balanced method. Bit Numerical Mathematics, 46 4: 689-710. doi:10.1007/s10543-006-0098-4 128   30 Cited 32 times in Scopus32 0
Loch, B.I., Belward, J.A. and Hanan, J.S. (2005). Application of Surface Fitting Techniques for the Representation of Leaf Surfaces. In: Andre Zerger and Robert M. Argent, International Congress on Modelling and Simulation Advances and Applications for Management and Decision Making. MODSIM05, University of Melbourne, (1272-1278). 12-15 December 2005. 136  
Kumar, S. K., Hanan, J. S. and Adkins, S. W. (2002). Architectural responses of intra- and inter-species plant-plant interactions. In: H. Spafford Jacob, J. Dodd and J.H. Moore, 13th Australian Weeds Conference Paper & Proceedings. 13th Australian Weeds Conference, Perth, W.A./Sheraton Perth Hotel, (261-261). 8-13 September, 2002. 74  
Kaitaniemi, P, Room, PM and Hanan, JS (1999) Architecture and morphogenesis of grain sorghum, Sorghum bicolor (L.) Moench. Field Crops Research, 61 1: 51-60. doi:10.1016/S0378-4290(98)00148-8 158   34 Cited 30 times in Scopus30 0
Thanaraj, TA, Stamm, S, Clark, F, Riethoven, JJ, Le Texier, V and Muilu, J (2004) ASD: the Alternative Splicing Database. Nucleic Acids Research, 32 Database issue: D64-D69. doi:10.1093/nar/gkh030 63   135 0 0
Burrage, PM and Burrage, K (2002) A variable stepsize implementation for stochastic differential equations. Siam Journal On Scientific Computing, 24 3: 848-864. doi:10.1137/S1064827500376922 258   32 Cited 29 times in Scopus29 0
Tian, TH and Burrage, K (2004) Binomial leap methods for simulating stochastic chemical kinetics. Journal of Chemical Physics, 121 21: 10356-10364. doi:10.1063/1.1810475 129   176 Cited 192 times in Scopus192 0
Tian, TH and Burrage, K (2004) Bistability and switching in the lysis/lysogeny genetic regulatory network of bacteriophage lambda. Journal of Theoretical Biology, 227 2: 229-237. doi:10.1016/j.jtbi.2003.11.003 305   49 Cited 55 times in Scopus55 0
Loch, B. I., Belward, J. A. and Hanan, J. S. (2003). Boundary treatment for virtual leaf surfaces. In: S.N. Spencer, Graphite 2003. 1st International Conference on Computer Graphics & Interacting Techniques in Australasia & South East Asia, Melbourne, (261-262). 11-14 February 2003. 50  
Hosseini Cici, S. Z., Adkins, S. W., Sindel, M. and Hanan, J. S. (2006). Canopy interference of chickpea with sowthistle - model development. In: C. Preston, J. H. Wats and N. D. Crossman, 15th Australian Weeds Conference: Papers and Proceedings. Managing Weeds in a Changing Climate, Adelaide Convention Centre, SA, (426-427). 24-28 September, 2006. 120  
Clark, F and Thanaraj, TA (2002) Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human. Human Molecular Genetics, 11 4: 451-464. doi:10.1093/hmg/11.4.451 51   141 0 0
Burrage, K., Burrage,P. M., Hamilton, N. and Tian, T (2006). Computer-intensive simulations for cellular models. In Albert Y Zomaya (Ed.), Parallel Computing in Bioinformatics and Computational Biology 1 ed. (pp. 79-119) New Jersey, USA: John Wiley & Sons. 96  
Gates, K. E., Hanson, G. R. and Burrage, K. (2001). Computer simulation of magnetic resonance spectra employing homotopy. GB2320579. 76  
Nicolau Jr., Dan V., Burrage, Kevin and Nicolau, Dan V. (2007). Computing with motile bio-agents. In: Biomedical Applications of Micro- and Nanoengineering III. Biomedical Applications of Micro- and Nanoengineering III, Adelaide, Australia, (). 11-13 December 2006. doi:10.1117/12.707691 17   0 0 0
Banks, Jasmine, Eriksson, Geoffery, Burrage, Kevin, Yellowlees, Peter, Ivermee, Sean and Tichon, Jennifer (2004) Constructing the hallucinations of psychosis in Virtual Reality. Journal of Network And Computer Applications, 27 1: 1-11. doi:10.1016/S1084-8045(03)00031-6 215   7 Cited 14 times in Scopus14 0
Yuan, DJ and Burrage, K (2003) Convergence of the parallel chaotic waveform relaxation method for stiff systems. Journal of Computational And Applied Mathematics, 151 1: 201-213. doi:10.1016/S0377-0427(02)00749-5 78   2 Cited 1 times in Scopus1 0
Runqiang, B., Chen, Y., Burrage, K., Hanan, J. S., Room, P. M. and Belward, J. A. (2002). Derivation of L-system models from measurements of biological branching structures using genetic algorithms. In: T. Hendtlass and M. Ali, Developments in Applied Artificial Intelligence, Proceedings. 15th International Conference on Industrial & Engineering Applications of Artificial Intelligence & Expert Systems, IEA/AIE 2002, Cairns, Australia, (514-524). 17-20 June, 2002. 93   1
Wei, LY, Wei, RY and Tang, TB (2004) Design and implementation of a windows-based parallel computing environment for large scale optimization. Advances In Engineering Software, 35 8 - 9: 577-584. doi:10.1016/j.advengsoft.2004.06.002 74   2 Cited 2 times in Scopus2 0
Burrage, K. and Tian, T. (2004). Effective simulation techniques for biological systems. In: D. Abbott, S.M. Bezrukov, A. Der and A. Sanchez, Fluctuations and noise in biological, biophysical, and biomedical systems II (Proceedings of SPIE). Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems II, Maspalomas, Gran Canaria, Spain, (311-325). 26-28 May 2004. doi:10.1117/12.548672 81   0 0 0
Leier, Andre, Kuo, P. Dwight, Banzhaf, Wolfgang and Burrage, Kevin (2006). Evolving noisy oscillatory dynamics in genetic regulatory networks. In: P. Collet, M. Tomassini, M. Ebner, S. Gustafson and A. Ekart, Lecture Notes in Computer Science: Genetic Programming. 9th European Conference on Genetic Programming EuroGP2006, Budapest, Hungary, (290-299). 10-12 April, 2004. doi:10.1007/11729976_26 76   13 Cited 11 times in Scopus11 0
Song, JN, Wang, ML and Burrage, K (2006) Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E-coli genome. Journal of Theoretical Biology, 241 2: 390-401. doi:10.1016/j.jtbi.2005.12.004 117   2 Cited 2 times in Scopus2 0
Hanan, J. S. and Wang, Y. (2004). Floradig: a configurable program for capturing plant architecture. In: C. Godin et al., Proceedings of the 4th International Workshop on Functional-Structural Plant Models. 4th International Workshop on Functional-Structural Plant Models, Montpellier, France, (407-411). 7-11 June, 2004. 348 33
Hoang, Nguyen S. and Sidje, Roger B. (2009) Functionally fitted explicit pseudo two-step Runge-Kutta methods. Applied Numerical Mathematics, 59 1: 39-55. doi:10.1016/j.apnum.2007.11.023 53   2 Cited 2 times in Scopus2 0
Renton, M, Kaitaniemi, P and Hanan, J (2005) Functional-structural plant modelling using a combination of architectural analysis, L-systems and a canonical model of function. Ecological Modelling, 184 2-4: 277-298. doi:10.1016/j.ecolmodel.2004.10.008 149   17 Cited 27 times in Scopus27 0
Nicolau, Dan V. (Jnr), Burrage, Kevin, Parton, Robert G. and Hancock, John F. (2006) Identifying optimal lipid raft characteristics required to promote nanoscale protein-protein interactions on the plasma membrane. Molecular and Cellular Biology, 26 1: 313-323. doi:10.1128/MCB.26.1.313-323.2006 116   111 Cited 115 times in Scopus115 1
Burrage, K. and Tian, T. (2004) Implicit stochastic Runge-Kutta methods for stochastic differential equations. Bit Numerical Mathematics, 44 1: 21-39. doi:10.1023/B:BITN.0000025089.50729.0f 449   19 Cited 20 times in Scopus20 0
Tian, Tianhai and Burrage, Kevin (2001) Implicit Taylor methods for stiff stochastic differential equations. Applied Numerical Mathematics, 38 1-2: 167-185. doi:10.1016/S0168-9274(01)00034-4 181   42 Cited 45 times in Scopus45 0
Beveridge, C. A., Hanan, J. S. and Burrage, K. (2001). Integrative plant physiology: Dealing with plant development as the outcome of an integrated, coordinated and dynamic regulatory network. In: Molecular Genetics of Model Legumes Conference Proceedings. Molecular Genetics of Model Legumes - Impact for Legume Biolo, Golm, Germany, (68-68). 15th - 19th of September, 2001. 91  
Chelle, M., Hanan, J. S. and Autret, H. (2004). Lighting virtual crops: the CARIBU solution for open L-Systems. In: C. Godin et al., Proceedings of the 4th International Workshop on Functional-Structural Plant Models. 4th International Workshop on Functional-Structural Plant Models, Montpellier, France, (194-194). 7-11 June, 2004. 105  
Prusinkiewicz, P, Karwowski, R, Mech, R and Hanan, J (2000) L-studio/cpfg: A software system for modeling plants. Applications of Graph Transformations With Industrial Relevance, Proceedings, 1779 457-464. 236   38
Hanan, J. S. (2004). Modelling cotton (Gossypium hirsutum L.) with L-systems: A template model for incorporating physiology. In: C. Godin et al., Proceedings of the 4th International Workshop on Functional-Structural Plant Models. 4th International Workshop on Functional-Structural Plant Models, Montpellier, France, (268-272). 7-11 June, 2004. 66  
Hanan, J., Thornby, D. and Adkins, S. (2005). Modelling cotton plant development with L-systems: A template model for incorporating physiology. In: Andre Zerger and Robert M. Argent, MODSIM 2005 International Congress on Modelling and Simulation. MODSIM05 International Congress on Modelling and Simulation, Melbourne, Australia, (1243-1250). 12-15 December 2005. 156  
Hanan, J. S., Birch, C. J. and Voss, J. (2003). Modelling the architecture of plants - some concepts and potential applications. In: C. J. Birch and S. R. Wilson, Versatile Maize - Golden Opportunities. Versatile Maize, Golden Opportunities - 5th Aust. Maize Conf., Toowoomba, Australia, (100-111). 18-20 February, 2003. 51  

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