2012
 

• Raghavan, K. and Ruskin, H.J., Modeling DNA Methylation Dynamics, in Dr. T. Tatarinova and Dr. O. Kerton, DNA Methylation - From Genomics to Technology, (ISBN-9789535103202, 1st Ed., 3-28), InTech Publications, 2012.


• Vasić, J. and Ruskin, H.J., A CA-based model for city traffic including bicycles. To be published in book Urban Traffic. Rijeka: InTech, (book chapter), 2012.


• Vasić, J. and Ruskin, H.J., Interaction of cars and bicycles on a one-way road intersection - a network CA-based model. Paper presented at Traffic and Granular Flow '11, Moscow, Russia, 28th September - 1st October 2011. Proceedings to be published in book by Springer.


• Vasić, J. and Ruskin, H.J., A discrete simulation model for traffic including bicycles on urban networks, applied to intersection of two one-way streets. Paper presented at the Workshop on Complex Collective Systems, held in conjunction with the 9th International Conference on Parallel Processing and Applied Mathematics, Torun, Poland, 11th - 14th September 2011. Proceedings to be published in the Springer LNCS series.


• Vasić, J. and Ruskin, H.J., Cellular automata simulation of traffic including cars and bicycles. Physica A. doi:10.1016/j.physa.2011.12.018


• Sîrbu, A., Ruskin, H. J., and Crane, M., EGIA - Evolutionary optimisation of Gene regulatory networks, an Integrative Approach, Submitted for publication to IEEE Transactions on Computational Biology and Bioinformatics.



2011
 

• Perrin, D. (2011). Complexity and high-end computing in Biology & Medicine, Software Tools and Algorithms for Biological Systems (Advances in Experimental Medicine and Biology series, volume 696), Springer.


• Perrin, D., and Ohsaki, H. (2011). Impact of randomness on information diffusion in Mobile Ad-Hoc Networks, Technical report RCS2011-97, Institute of Electronics, Information and Communication Engineers.


• Perrin, D., and Ohsaki, H. (2011). Decentralised communication in autonomous agent swarms, Technical report CQ2011-30, Institute of Electronics, Information and Communication Engineers.


• Yamada, Y., Ohsaki, H., Perrin, D., and Imase, M. (2011). Impact of Mobility Constraints on Epidemic Broadcast in DTNs, Proceedings of the eighth International Conference on Complex Systems, ICCS 2011:369-375.


• Perrin, D., and Ohsaki, H. (2011). A Parallel Approach to Social Network Generation and Agent-Based Epidemic Simulation, Proceedings of the ninth Australasian Symposium on Parallel and Distributed Computing, AusPDC 2011, CRPIT, 118:33-34.


• Sîrbu, A., Ruskin, H. J. and Crane, M., Integrating Heterogeneous Gene Expression Data for Gene Regulatory Network Modelling, Theory In Biosciences, Springer-Verlag, 1-8 , DOI 10.1007/s12064-011-0133-0


• Sîrbu, A., Kerr, G., Ruskin, H. J. and Crane, M., NGS vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering, Submitted for publication in PLoS ONE.


• Raghavan K. and Ruskin H.J. Computational Epigenetic Micromodel - Framework for Parallel Implementation and Information Flow. Proceedings of 8th International Conference on Complex Systems 2011 (ICCS) , Boston, USA, June 2011.


• Raghavan K. and Ruskin H.J., Modeling DNA Methylation Dynamics , DNA Methylation, ISBN-9799533074534, InTech Publications, Accepted.


• Raghavan K., Ruskin H.J. and Perrin D. Computational Analysis of Epigenetic Information in Human DNA Sequences. International Proceedings of Chemical, Biological and Environmental Engineering,Vol. (5), May 2011


• Daly, J., Ruskin, H. J. and Crane, M. Can random matrix filters be used for trading in the foreign exchange market? - A comparison of foreign exchange and stock portfolio filtering. Journal of Dynamics of Socio-Economic Systems, 2:2, 2011 (as part of the proceedings of the 1st COST Action MP0801 “Physics of Competition and Conflicts”, Rome, May 2009).


• Bezbradica M., Ruskin H.J. and Crane M. Modelling drug coatings: A parallel cellular automata model of ethylcellulose-coated microspheres, Proceedings of The International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2011, Singapore, 26th-28th February 2011.


• Bezbradica M., Crane M. and Ruskin H. J. Probabilistic modelling of drug dissolution, ERCIM news, 84(42/43), January 2011.


• Sîrbu, A., Ruskin, H. J. and Crane, M., Integrating Heterogeneous Gene Expression Data for Gene Regulatory Network Modelling, Presented in ECCS 2010, Accepted for publication in the Special Issue ECCS10 Theory in Biosciences.


• Vasić, J. and Ruskin, H.J., A discrete flow simulation model for urban road networks, with application to combined car and single-file bicycle traffic. IN: Murgante, B., Gervasi, O., Iglesias, A., Taniar, D., Apduhan, B. (eds.) Computational Science and Its Applications - ICCSA 2011. Volume 6782 of Lecture Notes in Computer Science. Berlin/Heidelberg: Springer-Verlag, pp. 602-614, 2011.


• Vasić, J. and Ruskin, HJ, Simulation of urban traffic including bicycles, ERCIM News, April 2011.


• Murphy, J.T., Walshe, R. and Devocelle, M. A Computational Modelling Approach to Explore the Anti-Microbial Pro-Drug Delivery System, Proceedings of the BIOINFORMATICS 2011 Conference, Rome, Italy, 26-29 Jan, 2011


• Sîrbu A., Ruskin H.J. and Crane M. Stages of Gene Regulatory Network Inference: the Evolutionary Algorithm Role, Evolutionary Algorithms, Eisuke Kita (Ed.), ISNB 978-953-307-171-8, InTech, 2011



2010
 

• Bezbradica M., Ruskin H.J. and Crane M. Probabilistic models for dissolution of ethylcellulose coated microspheres, Proceedings of The European Simulation and Modelling conference, ESM' 2010, Hasselt, Belgium, 25th-27th October 2010.


• Barat A., Ruskin H.J. A Manually Curated Novel Knowledge Management System for Genetic and Epigenetic Molecular Determinants of Colon Cancer, The Open Colorectal Cancer Journal, 3, pp36-46, 2010.


• Raghavan K., Ruskin H.J., Perrin D., Goasmat F., Burns J. Computational Micromodel for Epigenetic Mechanisms., PLoS ONE 5(11): e14031, 2010.


• Murphy J.T., Walshe R., Devocelle M. A Theoretical Analysis of the Pro-Drug Delivery System for Treating Antibiotic-Resistant Bacteria IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15 Jul. 2010. IEEE computer Society Digital Library. IEEE Computer Society. 2010


• Murphy J.T., Walshe R. Modeling Antibiotic Resistance in Bacterial Colonies Using Agent-Based Approach, Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology, 131-155, ed. Werner Dubitzky, Springer, (book chapter) ,2010.


• Perrin, D., Ruskin, H. J., and Niwa, T. Cell type-dependent, infection-induced, aberrant DNA methylation in gastric cancer. Journal of Theoretical Biology 264(2):570–577, 2010


• Perrin, D., Ruskin H. J., and Crane, M. Model refinement through high-performance computing: an agent-based HIV example. Immunome Research 6(Suppl 1): S3, 2010


• Kerr, G., Perrin, D., Ruskin, H.J., Crane, M. Edge Weighting of Gene Expression Graphs, Advances in Complex Systems, 13:2, 217-238, World Scientific 2010.


• Shakya, K., Ruskin, H. J., Kerr, G., Crane, M., Becker, J., Comparison of Microarray Pre-Processing Methods, Chapter 2, Advances in Computational Biology, Springer, ISBN: 978-1-4419-5912-6, 2010.


• Sîrbu A., Ruskin H.J. and Crane M. Regulatory network modelling: Correlation for structure and parameter optimisation, Proceedings of The IASTED International Conference on Computational Bioscience, Cambridge, Massachusetts, 1-3 Nov, 2010.


• Sîrbu A., Ruskin H.J. and Crane M. Cross-platform microarray data normalisation for regulatory network inference, PLoS ONE 5(11): e13822. doi:10.1371/journal.pone.0013822, 2010.


• Sîrbu A., Ruskin H.J. and Crane M. Modelling Gene Regulatory Networks - An Integrative Approach, ERCIM News, 81(36-37), Special Issue: Computational Science/Scientific Computing. Simulation & Modelling for Research and Industry , April 2010.


• Daly, J., Crane, M. and Ruskin, H. J. Random matrix theory filters and currency portfolio optimisation. Journal of Physics: Conference Series, 221(1), 2010 (as part of the proceedings of APFA7: Applications of Physics in Financial Analysis 7, Tokyo, March 2009).


• Sîrbu A., Ruskin H.J. and Crane M. Comparison of evolutionary algorithms in gene regulatory network model inference, BMC Bioinformatics, 11:59, 2010.



2009
 

• Conlon, T., Ruskin, H.J., Crane, M. Multiscaled Cross-Correlation Dynamics in Financial Time Series, Advances in Complex Systems, 12(4-5), 439-454, 2009.


• Conlon T., Ruskin H.J. and Crane M., Seizure characterisation using frequency-dependent multivariate dynamics, Computers in Biology and Medicine, 39(9), 760-767, 2009.


• Conlon, T., Ruskin, H.J., Crane, M., Cross-Correlation Dynamics in Financial Time Series, Physica A, 388, 705-714, 2009


• Burns, J., Ruskin, H.J., Perrin, D. and Walsh, J. Visualization of Complex Biological Systems: An Immune Response Model Using OpenGL, Book – Complex Sciences, Book Series - Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, ISBN - 978-3-642-02465-8 (Print) 978-3-642-02466-5 (Online), Volume 4, Part1, p. 671-679, 2009.


• Murphy J.T., Walshe R. and Devocelle M. Modelling the Population Dynamics of Antibiotic-Resistant Bacteria: An Agent-Based Approach, International Journal of Modern Physics C, 20(3):435-457, 2009.


• Murphy J.T., Walshe R.Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology, ed. Werner Dubitzky. (Springer, book chapter - in press), 2009.


• Perrin, D., Ruskin, H.J., Crane, M.,In Silico Biology: Making the most of parallel computing,Lazakidou, A.A. (Ed), Handbook of Research on Biocomputation and Biomedical Informatics: Case Studies and Applications, IGI Global (was Idea Group Publishing Ltd), 2009



2008
 

• Quinn-Whelton, N., Killen, L., Guinee, T. and Buckley, F.,Dedetction of abnormal recordings in Irish milk recorded data, Irish Journal of Agricultureal and food Research 46: 117-127,2008


• Conlon T., Ruskin H.J. and Crane M.,Multiscaled cross-correlation dynamics in financial time series,5th European Conference on Complex Systems, Jerusalem, Israel, Sept. 10-19 2008


• Murphy J.T., Walshe R. and Devocelle M.,A Computational Model of Antibiotic-Resistance Mechanisms in Methicillin-Resistant /Staphylococcus aureus(MRSA), Journal of Theoretical Biology, 254(2):284-93, 2008


• McGuinness, E., Crane, M., Ruskin, H.J., Crane, L.,Simplification of HIV Pathogenesis Models Using Dimensional Analysis,submitted to Mathematical Biosciences, 2008


• Conlon, T., Crane, M., Ruskin, H.J., Wavelet Multiscale Analysis of Hedge Funds,Statistical and Theoretical Physics, Vol 387/21, pp5197-5204, Elsevier, 2008


• Kumar, B., Delaure, Y.,Crane, M.,High Performance Computing of Multiphase Flow,ERCIM News, Vol. 74, pp 43-44, July 2008


• Kumar, B., Crane, M., Delaure, Y.,On the Development of Object Oriented Parallel Penta-diagonal Preconditioned Krylov Subspace (K- S) Solvers,ESM 2008, Le Havre France, pp 348-353,27-29 Oct, 2008


• Barat A., Crane M., Ruskin H.J.,Quantitative multi-agent models for simulating protein release from PLGA bioerodible nano- and microspheres,Journal of Pharmaceutical and Biomedical Analysis, Vol 48(2), pp361-368, Elsevier, 2008.


• Barat A., Ruskin H.J. and Crane M.,3D Multi-Agent Models for Protein Release from PLGA Spherical Particles with Complex Inner Morphologies,Theory in Biosciences, Vol 127(2), pp95-105, Springer Verlag, 2008.


• Daly, J., Crane, M., Ruskin, H.J.,Random Matrix Theory Filters in Portfolio Optimization: A Stability and Risk Assessment, Physica A., 387, pp4248-4260, 2008.


• Matos, J.-A., Gama, S., Ruskin, H.J., Sharkasi, Crane, M., Time and scale Hurst exponent analysis for financial markets,Vol 387/15, pp3910-3915, Physica A: Statistical and Theoretical Physics, Elsevier, 2008


• Perrin D., Ruskin H.J., Crane M. and Walshe R.,Epigenetic modelling,ERCIM News No. 72, January 2008.


• Kerr, G., Ruskin, H.J., Crane, M.,Techniques for Clustering Gene Expression data,Computers in Biology and Medicine, Vol 38/3, pp 283-293, Elsevier 2008


• Hecquet D., Ruskin, H.J., Crane, M.,Bernaschi et al.,Optimisation and parallelisation strategies for Monte Carlo simulation of HIV infection,, 38(2), p282, Computers in Biology and Medicine, 2008


• Gunning, P, Horgan, J.M, and Keogh G.,An Implementation Strategy for Efficient Convergence of the Lavallée and Hidiroglou Stratification,Journal of Official Statistics,pp 213-228,2008


• Editors Wang R. and Ruskin H.J., Special Issue on Modelling Complex Systems, International Journal of Modelling, Identification and Control, Vol 1, No 3, 2008


• Conlon, T., Ruskin, H.J., Crane, M. Multiscaled Cross-Correlation Dynamics in Financial Time Series,European Conference on Complex Systems (ECCS08), Jerusalem, Israel, September 14-19, 2008


• Perrin, D., Ruskin, H.J., Crane, M.,Towards Epigenetic Modelling: An Initial Map,IET Conference on Synthetic Biology, Systems Biology and Bioinformatics (BioSysBio 2008), London, April 20-22, 2008


• Hecquet D., Ruskin H.J., Crane M., Response to the comments by Bernaschi et al. on “Optimisation and parallelisation strategies for Monte Carlo simulation of HIV infection, Computers in Biology and Medicine, Vol 38/2, p282, 2008


• Matos J.-A., Gama S., Ruskin H.J., Sharkasi A., Crane M., Time and scale Hurst exponent analysis for financial markets, Vol 387/15, pp3910-3915, Physica A: Statistical and Theoretical Physics, Elsevier, 2008


• Murphy J.T., Walshe R. and Devocelle M., An Agent Based Approach to Modelling Microbial Ecosystems, ERCIM News No. 73:39-40, April 2008.


• Murphy J.T., Walshe R. and Devocelle M., A Novel Cellular Model of Methicillin-Resistant S. aureus (MRSA) for Predicting Antibiotic Susceptibility, Genomes 2008 - Functional Genomics of Microorganisms conference, Institut Pasteur, Paris, France, April 8-11 2008.


• Kerr G., Ruskin H.J. and Crane M., Pattern Discovery in Gene Expression Data, in Wang, H.F. (Ed), Intelligent Data Analysis: Developing New Methodologies Through Pattern Discovery and Recovery, Idea Group Publishing Ltd, 2008, ISBN 978-1599049823.



2007
 

• Quinn N., Killen L., Buckley F.,Modelling fat and protein concentration curves for Irish dairy cows,Irish Journal of Agricultureal and food Research 45: 13-23, 2007


• Murphy J.T., Walshe R. and Devocelle M. (2007), Agent-Based Model of Methicillin-Resistant Staphylococcus aureus and Antibiotics in Batch Culture, Proceeedings of the 21st Annual European Simulation and Modelling Conference, Eurosis-ETI, pp. 409-414, 2007.


• Conlon T., Ruskin H.J. and Crane M. (2007), Random matrix theory and hedge fund portfolio optimisation, Physica A 382(2):565-576, 2007.


• Daly C. and Horgan J.M. (2007), Profiling The Plagiarists: An Examination of the Factors that Lead Students to Cheat, Journal Of Educational Research 36:39-50, 2007.


• Deo P. and Ruskin, H.J. (2007), Performance evaluation of heterogeneous motorized traffic at urban single-lane junctions and roundabouts, ERCIM News No. 68, January 2007, pp.28-29.


• Feng Y., Liu Y., Deo P. and Ruskin H.J. (2007), Heterogeneous traffic flow model for a two lane roundabout and controlled intersection, International journal of modern physics C (IJMPC) 18(1):107-118, January 2007. (link)


• Gunning P. and Horgan J.M. (2007), Choosing the Strata when Auditing: An Example Using Excel, Irish Accounting Review 12(1):53-65, 2007.


• Gunning P. and Horgan J.M. (2007), Improving the Lavallée and Hidiroglou Algorithm for Stratification of Skewed Populations, Journal of Statistical Computation and Simulation 4(77):277–291.


• Hecquet D., Ruskin H.J. and Crane, M. (2007). Optimisation and parallelisation strategies for Monte-Carlo simulation of HIV Infection, Computers in Biology and Medicine, 37(2007):691-699, May 2007.


• McMahon N., Crane M., Ruskin H.J. and Crane L. (2007), The Importance of Boundary Conditions in the Simulation of Dissolution in the USP Apparatus., Simulation Modelling Practice and Theory, 15(3):247-255, March 2007.


• Perrin D., McMahon N., Crane M., Ruskin H.J., Crane L. and Hurley B. (2007), The Effect of a Meteorological Tower on its Top-Mounted Anemometer. Applied Energy, 84(4):413-424, April 2007.


• Yu D., Ghita O., Sutherland A. and Whelan P.F., A New Manifold Representation for Visual Speech Recognition, LNCS 4673:374-382, 2007.



 
 

2006
 

• Quinn N., Killen L., Buckley F.,Empirical algebraic modelling of Irish dairy cows,Livestock Science103: 141-147,2006


• Awad G., Han J. and Sutherland A. (2006). A Unified System for Segmentation and Tracking of Face and Hands in Sign Language Recognition, to appear in Proceedings International Conference on Pattern Recognition, ICPR, 2006.


• Barat A., Ruskin H.J. and Crane, M., Probabilistic Models for Drug Dissolution Part 1: A Review of Monte-Carlo & Cellular Automata Approaches, Simulation Modelling Practice and Theory (SIMPAT), 14(7):843-856, 2006.


• Barat A., Ruskin H.J. and Crane M., Probabilistic Models for Drug Dissolution Part 2: Modelling a Soluble Binary Drug Delivery System Dissolving in vitro, Simulation Modelling Practice and Theory (SIMPAT), vol 14(7):857-873, 2006.


• Callaghan A. (2006). Emergent Properties of the Human Immune Response to HIV Infection: Results from Multi-Agent Computer Simulations, ERCIM News No. 64, January 2006.


• Coogan T. and Sutherland A. (2006). Transformation Invariance in Hand Shape Recognition, to appear in Proceedings of International Conference on Pattern Recognition, ICPR, 2006.


• Coogan T., Awad G., Han J. and Sutherland A. (2006). Real Time Hand Gesture Recognition Including Hand Segmentation and Tracking, LNCS 4291:495-504, 2006.


• Coyle M. and Tuohey W.G. (2006). Software development projects - Portfolio selection & staffing with tool support, Projects & Profits – The ICFAI University Press, Rs. 60, 75-86.


• Deo P. and Ruskin H.J. (2006). Comparison of Homogeneous and Heterogeneous Motorised Traffic at Signalised and Two-way Stop control Single lane Intersection, M. Gavrilova et al. (Eds.): ICCSA 2006, LNCS 3980, pp. 622-632, 2006.


• Deo P. and Ruskin H.J. (2006). Simulation of Heterogeneous Motorised Traffic at a Signalised Intersection, S. El Yacoubi et al (Eds.) ACRI 2006, LNCS 4173, pp. 522-531, 2006.


• Han J., Awad G. and Sutherland A. (2006). Automatic Skin Segmentation for Gesture Recognition Combining Region and Support Vector Machine Active Learning, In proceedings 7th International Conference on Automatic Face and Gesture Recognition, FG2006, pp 243-248, 2006.


• Matos J.A.O., Gama S.M.A., Ruskin H.J., Sharkasi A. and Crane, M. (2006). Correlation of worldwide markets' entropies: time-scale approach, Proceedings of the Workshop Perspectives on Econophysics, pp9-22, University of Evora Press, ISBN 989-95091-0-8, 2006.


• Meagher D.P., Hashmi M.S. and Tuohey W.G. (2006). Regulatory Considerations and Business Implications for Automated System Suppliers, Pharmaceutical Engineering, pp24-36, November/December 2006.


• O'Leary C., Humphrys M. and Walshe R. (2006). Collaborative Online Development of Modular Intelligent Agents, ERCIM News No. 64, January 2006.


• Perrin D. (2006). Agent-Based Modelling of Viral Infection, ERCIM News No. 64, January 2006.


• Perrin D., Ruskin H.J., Burns J. and Crane M. (2006). An agent-based approach to immune modelling, 2006 International Conference on Computational Science and its Applications (ICCSA 2006), M. Gavrilova et al. (Eds.): ICCSA 2006, LNCS 3980, pp. 612-621, 2006.


• Perrin D., Ruskin H.J. and Crane M., An agent-based approach to immune modelling: Priming individual response, selected proceedings of Third International Conference on Modeling and Simulation (ICMS06), pp 81-86, ISBN 975-00803-7-8, 2006.


• Perrin D., Ruskin H.J. and Crane M., HIV Modelling - A Parallel Implementation of a Lymph Network, selected proceedings of The Third International Conference on Cluster and Grid Computing Systems (CGCS 2006), pp84-89, ISBN 975-00803-6-X, 2006.


• Ruskin H. and Burns J. (2006). Network Emergence in Immune System Shape, ERCIM News No. 64, January 2006.


• Ruskin H. and Burns, J. (2006). Weighted networks in immune system shape space, Physica A, The Journal of Statistical Mechanics and its Applications, 365(2):549-555, 2006.


• Ruskin H. and Walshe R. (2006). Introduction to the Special Theme, ERCIM News No. 64, January 2006.


• Sharkasi A., Crane M., Ruskin H. and Matos J.A.O. (2006). The Reaction of Stock Markets to Crashes and Events: A Comparison Study between Emerging and Mature Markets using Wavelet Transforms, Physica A: Statistical and Theoretical Physics, Elsevier, Vol. 368, No. 2, pp 511-521.


• Sharkasi A., Crane M. and Ruskin H. (2006). Apples and Oranges: the Difference Between the Reaction of Emerging and Mature Markets to Crashes, Proceedings of the Third Nikkei Econophysics Symposium - Practical Fruits of Econophysics, Tokyo, Japan, 2006. Hideki Takayasu(Ed.), Springer-Verlag, ISBN: 104-431-28914-3. (attendance funded by Nikkei)


• Sharkasi A., Ruskin H.J and Crane, M. (2006). Long-term memory in the Irish market (ISEQ): evidence from wavelet analysis, arXiv:physics/0607182 v1 20 Jul 2006.


• Walshe R. (2006). Modelling Bacterial Growth Patterns in the presence of Antibiotic, In Proceedings of 11th IEEE International Conference on Engineering of Complex Computer Systems (ICECCS 2006), IEEE Computer Society, pp 177-186.


• Wang R. and Ruskin H.J. (2006). Modelling Traffic Flow at Multi-Lane Urban Roundabouts, International Journal of Modern Physics C [Computational Physics and Physical Computation], Vol. 17, No. 5 (2006) 693-710.




 
 

2005
 

• Barat A., Ruskin H.J. and Crane M., Modelling the in vitro Dissolution of Soluble Binary Drug Delivery Systems using Direct Monte Carlo techniques, In: Hill, D.R.C., Barra, V., Traore, M.K., (Eds): Open International Conference on Modeling and Simulation - OICMS 2005, 12-15.6.2005, Clermont-Ferrand, France, pp377-385, 2005.


• Callaghan A. (2005). Agent-Based Modelling applied to HIV/AIDS, ERCIM News No. 60, January 2005.


• Daly, C. and Horgan, J. (2005) A technique for detecting plagiarism in computer code, The Computer Journal (to appear).


• Deo, P. and Ruskin, H. J., (2005). Space-requirement Implications for Heterogeneous Traffic Manoeuvres, Proceedings of the International Conference on Computational Science and Its Applications - ICCSA 2005, Gervasi,O., Gavrilova,M., Kumar, V., Lagana, A., Lee, H.P., Mun, Y., Taniar, D., Tan, C.J. (Eds), Lecture Notes in Computer Science, Springer, Vol 3482, Pg 196, ISBN 3540258620


• Gunning, P., Horgan, J.M. and Keogh, G. (2005) Efficient Pareto Stratification , The Mathematical Proceedings of the Royal Irish Academy (to appear)


• Gunning, P. and Horgan, J.M. (2005) Improving the Lavallee Hidiroglou Algorithm for Stratification of Skewed Population, Journal of Statistical Computation and Simulation (to appear)


• Kerr G. (2005). BAIT: Bacteria - Antibiotic Interaction Tool, ERCIM News No. 60, January 2005.


• Mathuna, D. and Horgan, J.M. (2005). Seasonal Allergic Study Results of Questionable Relevance to Homeopathy, The Annals of Pharmocotherapy, Vol. 39, 736-738.


• O'Mongain, E. and Tuohey, L. (April 2005). Extracting Maximum Information from Airborne Remote Sensing, ERCIM News No. 61


• Quinn N., Killen L. and Buckley F., (Feb 2005) Modelling Lactation Curves for Irish Dairy Cows, Performance recording of animals: State of the art, 2004. Wageningen Academic Publishers, The Netherlands Pg 247-252


• Quinn N., Killen L. and Buckley F., (March 2005) Modelling Liveweight for Irish Dairy Cows, Proceedings of Agricultural Research Forum 2005, Tullamore, Co.Offaly. Pg 43.


• Quinn N., Killen L. and Buckley F., (May 2005) Modelling Liveweight change over a Lactation in Irish Dairy Cows., Book of Abstracts of the 56th Annual Meeting of the European Association of Animal Production, Uppsala Sweden. Pg. 119.


• Quinn N., Killen L. and Buckley F., 2005. Empirical Algebraic Modelling of Lactation Curves using Irish Data, submitted to the Irish Journal of Agricultural and Food Research.


• Quinn N., Killen L. and Buckley F. (July 2005). Statistical Modelling of Fat and Protein Content Curves for Irish Dairy Cows, In Proceedings of the 25th European Meeting of Statisticians 24th – 28th July 2005 Pg 437.


• Ruskin, H., Burns, J., Weighted networks in immune system shape space To appear in: Physica A, The Journal of Statistical Mechanics and Its Applications.


• Ruskin, H., Burns, J., 2005. Network Emergence in Immune System Shape Space, Gervasi O., et al. (eds.): Lecture Notes in Computer Science, Vol. 3481. Springer-Verlag, Berlin Heidelberg New York (2005) 1254-1263.


• Shamaie A. and Sutherland A. (2005). Hand tracking in bimanual movements, Image and Vision Computing, Vol. 23(13), 1131-1149.


• Sharkasi, A., Ruskin, H. and Crane, M. (2005). Interrelationships among International Stock Market Indices: Europe, Asia and the Americas. International Journal of Theoretical and Applied Finance (IJTAF). Vol 8(5),Pg 1-18.


• Sharkasi A., Crane M. and Ruskin H.J., Apples and Oranges: the Difference Between the Reaction of Emerging and Mature Markets to Crashes, in Takayasu, Hideki (Ed.), Proceedings of 3rd Nikkei Econophysics Symposium - Practical Fruits of Econophysics, Lecture Notes in Computer Science, Springer 2005, pp38-42, ISBN: 4-431-28914-3, 2005.


• Tuohey, W.G. (2005) Picard style iteration for anisotropic H-functions, Journal of Quantitative Spectroscopy and Radiative Transfer, Vol 96 Pg 85-101


• Wang, R. and Ruskin, H.J. (2005). Modelling traffic flow at multilane urban roundabouts , International Journal of Modern Physics C, (in press)



 
 

2004
 

• Burns, J. and Ruskin, H. (2004) Network Topology in Immune System Shape Space, In: Bubak, M.; Albada, G.D.v.; Sloot, P.M.A.; Dongarra, J. (Eds.): Lecture Notes in Computer Science, Vol. 3038. Springer-Verlag Pg. 1094-1101


• Burns, J. and Ruskin, H. (2004)  Diversity Emergence and Dynamics During Primary Immune Response: A Shape Space, Physical Space Model. Theory in Biosciences, Vol 123/2 Pg 183-194, Elsevier


• Burns, J., Ruskin, H., (2004), A Stochastic Model of the Effector T Cell Lifecycle, In: Sloot P.M.A., Chopard, B. and Hoekstra A.G., (eds.): Cellular Automata, Lecture Notes in Computer Science, Vol. 3305. Springer-Verlag, Berlin Heidelberg (2004) 454-463


• Crane, M., Crane, L., Healy, A.M., Corrigan, O.I., Gallagher, K.M. and McCarthy, L.G., (2004) A Pohlhausen Solution for the Mass Flux From a Multi-layered Compact in the USP Drug Dissolution Apparatus, Simulation Modelling Practice and Theory (SIMP&T), Vol. 12/6 Pg 397-411, Elsevier, 2004


• Crane M., Hurley N., Crane L., Healy A.M., Corrigan, O.I., Gallagher, K.M. and McCarthy, L.G. (2004) Simulation of the USP drug delivery problem using CFD: experimental, numerical and mathematical aspects. to appear in Simulation Modelling Practice and Theory (SIMP&T), Vol. 12/2 Pg 147-158, Elsevier


• Daly, C. and Horgan, J., (2004), A Technique for Measuring Plagiarism in Automated Learning Environments, International Journal of Applied Mathematics and Computer Science, University of Zielona Gora Press. (in press)


• Daly, C. and Horgan, J., (2004) A Statistical Analysis of an Automated Learning Environment, IEEE Transactions on Education, Vol 47(1) Pg 10-17, IEEE


• Feng Y., Ruskin H.J. and Liu Y.,  (2004) Multiple Parameterisation of Human Immune Response in HIV: Many-Cell Models., Proceedings of the International Conference on Computational Science and Its Applications - ICCSA 2004, Laganà, A.; Gavrilova, M.L.; Kumar, V.; Mun, Y.; Tan, C.J.K.; Gervasi, O. (Eds.), Lecture Notes in Computer Science,  Springer, May 2004, Vol. 3045, Pg 498-507, ISBN: 3-540-22057-7


• Gunning, P. and Horgan, J. M. (2004). A Simple Algorithm for Stratifying Skewed Populations, Survey Methodology. 30, 2, 159-166.


• Gunning, P., Horgan, J.M., and Keogh, G. (2004) Obtaining Stratum Boundaries in Skewed Populations, Proceedings Joint Statistical Meeting, Toronto, Canada


• Gunning, P. and Horgan J.M. Un Nouvel Algorithme pour la construction de bornes de stratification dans les populations asymetriques, Techniques d'Enquete, 30, 2, 177-185.


• Gunning, P., Horgan, J. M., and Yancey, W. (2004) A Simple Method for Setting Stratum Boundaries for Statistical Auditing, Proc. Of Amer, Acc, Association Southern Region Meeting, Austin Texas.


• Gunning P. and Horgan J.M., (2004) An Algorithm for Obtaining Strata with Equal Coefficients of Variation in COMPSTAT 2004 - Proceedings in Computational Statistics 16th Symposium Prague, Czech Republic, Antoch, Jaromir (Ed.), Pg 1123-1130, Physica-Verlag, Springer, ISBN: 3-7908-1554-3.


• Gunning, P., Horgan, J.M. and Yancey, W , (2004) Geometric Stratification of Accounting Data, de Contaduria y Administracion Pg11-21


• Harte, R. and Keogh, G. (2004) Touche Rouche in Bulletin of Korean Mathematical Society, 40(2), Pg215-221, Korean Mathematical Society.


• Keogh G., Sharifi S., Ruskin H. and Crane M. (2003) Epochs in Market Sector Index Data - Empirical or Optimistic? Proceedings of the 2nd Nikkei Econophysics Symposium - Application of Econophysics, H. Takayasu (Ed.) Lecture Notes in Computer Science, Springer, November 2003, Pg 83-89, ISBN 4-431-14028-X


• Matos J. A. O., Gama S. M.A., Ruskin H. J., and Duarte J.A.M. S. (2004) An Econophysics Approach to the Portuguese Stock Index - PSI-20., 342, Pg665-676, Physica A, Elsevier.


• O'Leary, C., Humphrys, M. and Walshe, R., (2004) Constructing an animat mind using 505 sub-minds from 234 different authors,Proceedings of the Eighth International Conference on the Simulation of Adaptive Behavior, From Animals to Animats 8 (SAB 2004), S. Schaal, A.J. Ijspeert, A. Billard, S. Vijayakumar, J. Hallam, and J.-A. Meyer (Eds.), Pg 39-49, MIT Press, Cambridge, ISBN 0-262-69341-0, 2004


• Podesta, K., Crane, M. and Ruskin, H., (2004) Running EMBOSS on a cluster of workstations, Proceedings of the International Conference on Computational Science and Its Applications - ICCSA 2004, Laganà, A.; Gavrilova, M.L.; Kumar, V.; Mun, Y.; Tan, C.J.K.; Gervasi, O. (Eds.), Lecture Notes in Computer Science,  Springer, May 2004, Vol. 3045, Pg 473-480, ISBN: 3-540-22057-7


• Quinn N., Killen L. and Buckley F., (2004) Statistical Modelling of Lactation Curve Data , in COMPSTAT 2004 - Proceedings in Computational Statistics 16th Symposium Prague, Czech Republic, Antoch, Jaromir (Ed.), Pg1677-1684, Physica-Verlag, Springer, ISBN: 3-7908-1554-3.


• Shamaie, A. and Sutherland, A. (2004) A Dynamic Model for Real-time Tracking of Hands in Bimanual Movements, Gesture-Based Communication in Human-Computer Interaction, Springer-Verlag Heidelberg, 2004 .


• Shamaie, A. and Sutherland, A. (2004) Bayesian Fusion of Hidden Markov Models for Understanding Bimanual Movements, The 6th Int'l Conference on Automatic Face and Gesture Recognition, Seoul, Korea, May 17-19, 2004


• Sharifi S., Crane M., Shamaie A. and Ruskin H.J. (2004) Random Matrix Theory for Portfolio Optimization: A Stability Approach, Physica A, Vol. 335(3-4) Pg629-643, Elsevier


• Sharkasi, A., Ruskin, H. and Crane, M. (2004) Interdependence between Emerging and Major Markets, in COMPSTAT 2004 - Proceedings in Computational Statistics 16th Symposium Prague, Czech Republic, Antoch, Jaromir (Ed.), Physica-Verlag, Springer, ISBN: 3-7908-1554-3.


• Walshe, R., Humphrys, M. and O'Leary, C. (2004) Constructing Complex Brains: Building minds using sub-minds from biotechnology authors in Proceeding of The Symposium on Professional Practice in AI, E. Mercier-Laurent, J. Debenham (Eds.), ISBN:2-907801-05-8, IFIP Press 2004



 
 

2003
 

• Burns J., Ruskin H.J. (2003) A Model of Immune Suppression and Repertoire Evolution. Proceedings of the International Conference on Computational Science 2003, (ICCS03), St. Petersburg, Russia, June 1-4.


• Burns J., Ruskin H.J. (2003) Viral Strain Diversity and Immune Response - a Computational Model. Proceedings of the IASTED International Conference on Biomedical Engineering, Salzburg, Austria, June 25-27, 2003


• Feng Y., Ruskin H. J. and Zhu B. (2003) Persistence Measures for 2D Soap Froth. International Journal of Modern Physics C, Vol. 14, No. 9, Pg1-8, November 2003, World Scientific Publishing Co.


• Horgan J.M. (2003) A List-Sequential Sampling Scheme with Applications in Financial Auditing, IMA: J. of Mang. Maths, 14(1) Pg 31-48.


• Horgan J.M. (2003) A Criterion for an Efficient Ratio Estimator with Poisson sampling, Pakistan Journal of Information and Technology (PJIT), Vol. 2, No. 1, Pg1-18.


• McMahon N., Crane M., Ruskin H.J. and Crane L. (2003) The Mechanics of Drug-Dissolution. Proceedings in Applied mathematics and Mechanics (PAMM), Vol. 3, Issue 1, December 2003, p. 392-393.


• Quinn N., Killen L., Buckley F. (2003) The Factors affecting lactation curves of Irish Dairy Cows. Proceedings of Agricultural Research Forum 2003, Tullamore, Co.Offaly. Pg 20.


• Shamaie, A. and Sutherland, A., Learning and Understanding Bimanual Movements, ERCIM News, European Research Consortium for Informatics and Mathematics, No. 55, October 2003


• Shamaie, A. and Sutherland, A., A Dynamic Model for Real-time Tracking of Hands in Bimanual Movements, 5th International Workshop on Gesture and Sign Language based Human-Computer Interaction, Genova, Italy, 15-17 April 2003.


• Shamaie, A. and Sutherland, A., Accurate Recognition of Large Number of Hand Gestures", 2nd Iranian Conference on Machine Vision and Image Processing, K.N. Toosi University of Technology, Tehran, Iran, 13-15 February 2003.


• Sharifi, S., Shamaie, A., and Crane, M., Noise in the Correlation Matrix: A Simulation Approach", 23rd Conference on Applied Statistics in Ireland, Mullingar, Ireland, May 2003.


• Wang, R. and Ruskin, H. J. (2003) Modelling Traffic Flow at a Multilane Intersection, Proceedings of International Conference on Computational Science and its Applications 2003, (May18-21, 2003. Montreal, Canada), Lecture Notes in Computer Science (LNCS), Springer-Verlag Heidelberg. ISSN: 0302-9743. Vol. 2667 / 2003. Pg 577- 586.


• Wang, R. and Ruskin, H. J. (2003) Modelling Traffic Flow at a Two-lane Roundabout, Proceedings of International Conference on Computer Science, Software Engineering, Information Technology, e-Business and Applications, (June 5-7, 2003, Rio de Janeiro, Brazil) Pg 575-580 ISBN: 0-9742059-0-7.



 
 
 
 
 
 

2002
 

• Feng Y., Ruskin H.J. and Zhu B. (2002) Virtual Phase Dynamics for Constrained Geometries in a Soap Froth. ICCS 2002, (Ed. Sloot P.M. A. et al.) pub. in LNCS (2002) 2329, 399. Springer-Verlag, ISBN 3-540-43592, ISSN 0302-9743


• Horgan, J., Waldron, J. (2002), The Unexpected Properties of Expectation, Indian Journal of Pure and Applied Mathematics, Vol 133/9, Pg1373-8


• Liu Y. and Ruskin H. J. (2002) A Mesoscopic Approach to Modelling Immunological Memory. International Conference on Computational Science ICCS 2002, (Ed. Sloot P.M. A. et al.) pub. in Lecture Notes in Computer Science, LNCS (2002) 2329, 127. Springer-Verlag ISBN 3-540-43592, ISSN 0302-9743


• Mannion R., Ruskin H.J. and Pandey R.B. (2002) Effects of Viral Mutation on Cellular Dynamics in a Monte Carlo Simulation of HIV Immune Response Model in Three Dimensions, Theory in Biosciences 121, 237, Elsevier


• Ruskin H.J. and Feng Y. (2002) Constrained geometries in soap froth dynamics. Physica A 314, 362, Elsevier


• Ruskin H.J. and Wang R. (2002) Modelling Traffic Flow at an Urban Unsignalised Intersection. ICCS 2002, (Ed. Sloot P.M. A. et al.) pub. in LNCS (2002) 2329, 381 Springer-Verlag., ISBN 3-540-43592, ISSN 0302-9743


• Ruskin H.J. and Wang R. (2002) Effect of Driver Behaviour on Cross-Traffic. Proc. IASTED Intl. Conf. Proceedings on Modelling, Identification and Control (Ed. Hamza M.H.), p.54


• Ruskin H.J. , Pandey R.B. and Liu Y. (2002) Viral load and stochastic mutation in a Monte Carlo simulation of HIV. Physica A 311, 213, Elsevier


• Tuohey, W.G. (2002). Benefits & Effective Application of Software Engineering Standards, Software Quality Journal, Vol. 10, Issue 1, 47-68.


• Wang R. and Ruskin H.J. (2002) Modelling traffic flow at a single-lane urban roundabout. Computer Physics Communications 147, 570, Elsevier



 
 
 
 
 
 

2001
 

• Daly, C., Horgan, J., (2001), Automatic Plagiarism Detection, Applied Informatics, Pg255-259


• Horgan J.M. (2000) Auditing Y2K: A Sampling Fig Leaf, Aus. CPA, Nov., Pg 46-47.


• Hurley, N., Crane, L., Crane, M., Healy, A.M., Corrigan, O.I., Gallagher, K.M. and McCarthy, L.G., Modelling drug delivery systems using finite element analysis, in Proceedings of the 4th International Eurosim 2001 Congress, Delft, June 2001 (ISBN: 90-806441-1-0).


• Ruskin H.J., Feng Y. and Zhu B. (2001) Modelling froth dynamics; persistence measures. Physica A 293, 315, Elsevier


• Shamaie, A, Wu Hai, and Sutherland, A., Hand Gesture Recognition for Human Computer Interaction", ERCIM News, European Research Consortium for Informatics and Mathematics, No. 46, July 2001.


• Shamaie, A., and Sutherland, A., Graph-based Matching of Occluded Hand Gestures", IEEE Applied Imagery Pattern Recognition Workshop (AIPR 2001), Washington DC, USA, 10-12 October 2001.


• Walshe, R., (2001) The Origin of the Speeches: language evolution through collaborative reinforcement learning, in Proceedings of Intelligent Virtual Agents, Third International Workshop, IVA 2001, A. de Antonio, R. Aylett \& D. Ballin (Eds.), LNCS 2190, ISBN 3-540-42570-5, Springer


• Wang, R., and Ruskin, H. J. (2001) Modeling Traffic Flow at a Single-lane Urban Roundabout, Abstracts of Europhysics Conference on Computational Physics (CCP2001), September 5th-8th, Aachen, Germany, ISBN 3-00-008236-0.

 

 
 
 
 

2012
 
• Shakya, K., O' Connell, M. J. and Ruskin, H. J., Content Evaluation and Tool Development for Knowledge Management Systems, Poster, O'Hare Presentation Ceremony, DCU, Dublin, Ireland, 4th April 2012.


• Perrin, D. and Ohsaki, H., Decentralised communication in autonomous agent swarms, Twenty-sixth IEEE International Conference on Advanced Information Networking and Applications (AINA 2012), Fukuoka, Japan, 2012.


• Bezbradica, M., Crane, M. and Ruskin, H. J., Modelling controlled DDS: A probabilistic model for ethylcellulose-coated beads, Poster, 8th World Meeting on Pharmaceutics, Biopharmaceutics and Pharmaceutical Technology, Istanbul, Turkey, 19th-22nd March 2012.

2011
 
• Perrin, D. and Ohsaki, H., Impact of randomness on information diffusion in Mobile Ad-Hoc Networks, Workshop of the IPSJ Technical Committee on Radio Communication Systems (RCS), Asahikawa, Japan, 2011.


• Perrin, D. and Ohsaki, H., Decentralised communication in autonomous agent swarms, Workshop of the IPSJ Technical Committee on Communication Quality (CQ), Otaru, Japan, 2011.


• Perrin, D. and Ohsaki, H., Applications of epidemic diffusion to complex systems: from communication networks to autonomous exploratory robots, Eight International Conference on Complex Systems (ICCS 2011), Boston, USA, 2011.


• Perrin, D. and Ohsaki, H., A parallel approach to social network generation and agent-based epidemic simulation, Ninth Australasian Symposium on Parallel and Distributed Computing (AusPDC 2011), Perth, Australia, 2011.


• Bezbradica, M., Ruskin, H.J. and Crane, M., Probabilistic modelling of drug delivery systems, Computational Biology and Innovation - PhD Symposium, UCD, Dublin, Ireland, 6th-7th December 2011.


• Roznovăţ, I. and Ruskin, H.J., Complexity of Interdependent Epigenetic Signals in Cancer Initiation, Poster, Computational Biology and Innovation - PhD Symposium, UCD, Dublin, Ireland, 6th-7th December 2011.


• Shakya, K., O' Connell, M. J. and Ruskin, H. J., Data mining in Colon Cancer Research, Poster, Computational Biology and Innovation - PhD Symposium, UCD, Dublin, Ireland, 6th-7th December 2011.


• Ioudinkova, E. S., Barat, A., Pichugin, A., Markova, E., Pirozhkova, I., Lipinski, M., Ogryzko, V., Vassetzky, Y.S. and Razin, S.V., Comparative analysis of histone variants H2A.Bbd and macroH2A in open and closed chromatin domains suggest a distinct distribution, Poster, Histone Variants and Genome Regulation, Strasbourg, France, 12th-14th October 2011.


• Vasić, J. and Ruskin, H.J., Combined motorised and bicycle traffic on a one-way road intersection - simulation and analysis. Complexity and the Future of Transportation Systems, Satellite Meeting of ECCS'11 (European Conference on Complex Systems 2011), Vienna, Austria, 15th September 2011.


• Sîrbu, A., Ruskin, H. J. and Crane, M., An integrative framework for gene regulatory network inference, ECCS'11, Vienna, Austria, September 2011 (Presentation).


• Bezbradica, M., Ruskin, H.J. and Crane, M., Agent-based modelling in prediction of environmental influence on drug release, Poster, ECCS'11 (European Conference on Complex Systems 2010), Vienna, 12th - 16th September 2011.


• Vasić, J. and Ruskin, H.J., A cellular automaton based network meta-model for mixed city traffic simulation. Poster Presentation, ECCS'11 (European Conference on Complex Systems 2011), Vienna, Austria, 12th - 16th September 2011.


• Vasić, J. and Ruskin, H.J., Throughput and delay in a discrete simulation model for traffic including bicycles on urban networks. Irish Transport Research Network Conference, Cork, Ireland, 31th August - 1st September 2011. Best session paper.


• Shakya, K., O' Connell, M. J. and Ruskin, H. J., Colon Cancer Research: Knowledge Discovery/ Data Mining and Phylogenetic Perspective, Poster, SCI-SYM Research Day (sci-sym.dcu.ie), DCU, Dublin, Ireland 24th June 2011.


• Raghavan, K. and Ruskin, H.J., Computational Epigenetic Micromodel - Framework for Parallel Implementation and Information Flow. International Conference on Complex Systems 2011 (ICCS) , Boston, USA, June 2011


• Bezbradica, M., Ruskin, H.J. and Crane, M., Agent-based modelling of controlled drug release from ethylcellulose/pectin coated beads, Poster, DCU Research Day, Dublin, 12th May 2011.


• Raghavan, K., Ruskin, H. J. and Perrin, D., Computational Analysis of Epigenetic Information in Human DNA Sequences. International Conference on Bioscience, Biochemistry and Bioinformatics 2011, February 2011.


• Bezbradica, M., Ruskin, H.J. and Crane, M., Ethylcellulose/pectin coated microspheres in controlled drug delivery: agent based modelling, UKICRS (UK & Ireland Controlled Release Society) Symposium, Belfast April 13th, 2011.


• Sîrbu, A., Ruskin, H. J. and Crane, M., Gene regulatory network inference by integrative evolutionary computation, 8th Symposium for Networks in Bioinformatics, Amsterdam University, Netherlands, April 2011 (Presentation)

2010
 
• Ruskin, H. J., Perrin, D., Raghavan, K. and Goasmat, F., Modelling Complex Epigenetic Changes. Poster Presentation, ECCS 2010, Lisbon, Portugal, September 2010.


• Bezbradica, M., Ruskin, H.J. and Crane, M., Drug Dissolution Modelling Using Monte Carlo and Cellular Automata, Poster, Globe Forum, Dublin, 17th - 18th November 2010


• Vasić, J., and Ruskin, H.J., Traffic Simulation with Focus on Pedal-Bicycles, Poster, ECCS'10 (European Conference on Complex Systems 2010), Lisbon, 13th - 17th September 2010.


• Vasić, J., and Ruskin, H.J., Simulation of Traffic Including Bicycles, Poster, Globe Forum, Dublin, 17th - 18th November 2010


• Sîrbu, A., Ruskin, H.J. and Crane, M. Gene Regulatory Network Modelling with Evolutionary algorithms - An Integrative Approach, Poster, Globe Forum, Dublin, 17th - 18th November 2010


• McGuinness E.D., Ruskin, H.J., Crane M., Effect of cell infection delay on treatment interruption models of within-host HIV progression, 3rd International Workshop on Systems Biology, NUI Maynooth, 2010


• Murphy, J.T., Walshe, R. and Devocelle, M. Computer simulations of resistance mechanisms in antibiotic-resistant bacterial populations, submitted to 8th Louis Pasteur Conference, Institut Pasteur, Paris, 2010


• Perrin D., Ruskin H.J., Crane M., Local Properties and Large-Scale Agent-Based HIV Simulations, International Conference on Bioinformatics, InCoB, September 26-28, 2010


• Perrin, D., Ruskin H. J., and Crane, M. Model refinement through high-performance computing: an agent-based HIV example. International Conference on Bioinformatics (InCoB 2010). Tokyo, Japan. September 26-28, 2010


• Perrin, D., and Ruskin H. J. Modelling Complex Epigenetic Changes. Epigenetics Europe. Dublin, Ireland. September 13-13, 2010


• Sîrbu, A., Ruskin, H.J. and Crane, M. Integrating Heterogeneous Gene Expression Data for Gene Regulatory Network Modelling , ECCS, September 2010, Lisbon.


• Sîrbu, A., Ruskin, H.J. and Crane, M. Integrating Heterogenous Microarray Data for Regulatory Network modelling , Advances in Microarray Technology, May 2010, Dublin.


• Sîrbu, A., Ruskin, H.J. and Crane, M. Wavelets for analysis of time series gene expression data , 2nd COST Action MP0801 “Physics of Competition and Conflicts”, May 2010, Bulgaria, poster presentation.


• Sîrbu, A., Ruskin, H.J. and Crane, M. Modelling Gene Regulatory Networks: an Integrative Approach , 2nd COST Action MP0801 “Physics of Competition and Conflicts”, May 2010, Bulgaria.


• Sîrbu, A., Ruskin, H.J. and Crane, M. Integrating heterogenous Gene Expression data for Regulatory Network modelling , VIBE, January 2010, Dublin, poster presentation.

2009
 

• Perrin, D., Ruskin, H.J. and Claude, B. Computer-based city model and control of epidemic spreads , The 9th Asia-Pacific Complex Systems Conference (Complex'09), Tokyo, Japan, November 4-7, 2009, presented by D. Perrin


• Sîrbu, A., Ruskin, H.J. and Crane, M. Evolutionary algorithms in genetic regulatory network modelling with microarray data , The 9th Asia-Pacific Complex Systems Conference (Complex'09), Tokyo, Japan, November 4-7, 2009, presented by A. Sîrbu


• Daly, J., Ruskin, H.J., Crane, M., Can random matrix filters be used for trading in the foreign exchange market?- A comparison of foreign exchange and stock portfolio filtering using forward validation, 1st COST Action MP0801 “Physics of Competition and Conflicts”, Rome, May 2009 – poster presented by J. Daly.


• McMahon, N.M., Crane, L.J., Ruskin, H.J., Crane, M., D’Arcy, D.M., Healy, A.-M., Corrigan, O. A Numerical Model of a Drug Particle Dissolving in a Dissolution Test Apparatus, GAMM 2009, Gdansk, Poland, February 2009.


• McGuinness, E.D., Ruskin, H.J., Crane, M. Increasing biological accuracy in models of HIV progression while minimising complexity, presentation as Invited Talk, at the 7th IFAC Symposium on Modelling and Control in Biomedical Systems, (MCBMS'09), Aalborg, Denmark, August 12 - 14, 2009.


• A. Barat Web Resources for Cancer Epigenetics – Comparison, Advantages and Disadvantages, Institute de Cancerologie Gustave Roussy, Paris, France, April, 2009.


• A. Barat, H.J. Ruskin, Data Curation for PathEpigen – a Novel Knowledge Management System on the Genetic and Epigenetic Determinants of Cancer Development, 3rd International Biocuration Conference, Berlin, 17th -20th of April, 2009 – presented by A. Barat.


• A. Barat, H.J. Ruskin PathEpigen – A Novel Knowledge Management Platform for the Molecular Determinants of Colon Cancer, ICTBSB 2009 - International Conference on Trends in Bioanalytical Sciences and Biosensors, Dublin, 26th-28th January, 2009 – presented by A. Barat.


• J.Daly, M. Crane, H. J. Ruskin,Random matrix theory filters and currency portfolio optimisation,7th International Conference on Applications of Physics in Financial Analysis, (Tokyo, March 2009)



2008
 

• Burns J., Perrin D. and Ruskin H.J., Network stability and susceptibility in computational epigenetics, presented at the second annual Symposium on Biological Complexity: Genes, Circuits and Behavior, (Salk Institute for Biological Studies, La Jolla, California, USA, January 2008).


• Kumar, B., Delaure, Y.,Crane, M.,"VOF (PLIC) Method for Tracking Sharp Fluid Interfaces",Irish Society for Scientific \& Engineering Computations and Irish Mechanics Society: Joint Symposium on Advances in Mechanics, (University College Dublin, Ireland,15-16 May, 2008)


• Perrin D. and Ruskin H.J., The case for epigenetic modelling, accepted for the XX International Congress of Genetics (Berlin, Germany, July 2008).


• Porwal J., Ruskin H.J., Perrin D. and Roche D., Microscopic model of epigenetic mechanisms, the XX International Congress of Genetics (Berlin, Germany, July 2008).


• Perrin D., Ruskin H.J. and Crane M., Inclusion of localised patterns in a large-scale agent-based model of the immune response to HIV infection, accepted for the 16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB2008, Toronto, Canada, July 2008).


• Perrin D., Ruskin H.J. and Crane M., Towards epigenetic modelling: an initial map, IET BioSysBio Event 2008, Synthetic Biology, Systems Biology and Bioinformatics, London, UK, April 20-22, 2008.



2007
 

• Barat A., Ruskin H.J. and Crane M., 3D Multi-Agent Models for Protein Release from PLGA Spherical Particles with Complex Inner Morphologies, European Conference on Complex Systems (ECCS), Dresden, Germany, 1-5 October 2007.


• Barat A., Ruskin H.J. and Crane M., Multi-Agent Models for Simulating Protein Release from PLGA Bioerodible Nano- and Microspheres, the 12th International Meeting on Recent Developments in Pharmaceutical Analysis (RDPA), Island of Elba, Italy, 23-26 September 2007.


• Perrin D., Duhamel C., Ruskin H.J. and Crane M., Microarray biclustering: mathematical model and metaheuristic alternatives, International Conference on Computational Methods (ICCM2007), Hiroshima, Japan, April 4-6 2007.


• Perrin D., Biocomputation Research: a two-way street between Biology and Computer Science, at the Research Institute for Microbial Diseases, Osaka University, Japan, April 10, 2007.


• Perrin D., Ruskin H.J., Crane M., The case for epigenetic modelling, poster presented at the second IARC meeting on cancer and epigenetics, International Agency for Research on Cancer, Lyon, France, December 6-7, 2007.


• Tuohey W.G., Closed-form approximation as a basis for a lightweight radiative transfer model, First Irish Earth Observation Researchers Symposium, November 14 2007, Teagasc (Kinsealey).


• Yu D., Ghita O., Sutherland A. and Whelan P.F. A New Manifold Representation for Visual Speech Recognition, IMVIP 2007 - The International Machine Vision and Image Processing Conference 2007, 5-7 September, National University of Ireland, Maynooth, Co. Kildare, Ireland.


• Yu D., Ghita O., Sutherland A. and Whelan P.F. A PCA- based Manifold Representation for Visual Speech Recognition, China-Ireland International Conference on Information and Communications Technologies (CIICT2007), page(247-254), August 28th - 29th, 2007 [Microsoft Best Paper Award].


• Yu D., Ghita O., Sutherland A. and Whelan P.F. A New Manifold Representation for Visual Speech Recognition, 12th International Conference on Computer Analysis of Images and Patterns (CAIP07), Vienna, Austria, 2007.



2006
 

• Awad G., Han J. and Sutherland A., A Unified System for Segmentation and Tracking of Face and Hands in Sign Language Recognition, ICPR 2006 - 18th International Conference on Pattern Recognition, Hong Kong, 20-24 August 2006.


• Coogan T., Awad G. and Han J., Real-Time Gesture Segmentation, Tracking and Recognition, Demonstration at European Conference on Computer Vision, ECCV, Graz, Vienna, 2006.


• Coogan T., Awad G., Han J. and Sutherland A., Real Time Hand Gesture Recognition Including Hand Segmentation and Tracking, ISVC 2006 - 2nd International Symposium on Visual Computing, Lake Tahoe, Nevada, USA, 6-8 November 2006.


• Coogan T. and Sutherland A., Transformation Invariance in Hand Shape Recognition, ICPR 2006 - International Conference on Pattern Recognition 2006, Hong Kong, China, 20-24 August 2006.


• Conlon T., Ruskin H.J., Crane M., Random matrix theory and hedge fund strategy identification, 4th INFINITI Conference on International Finance, Dublin, June 2006.


• Daly, J., Ruskin, H. J. and Crane, M., Exponentially Weighted Volatility, Random-Matrix-Theory Filters and Stability in Portfolio Optimisation, Econophysics Colloquium 2006 and Third Bonzenfreies Colloquium, Tokyo, November 2006.


• Deo P. and Ruskin H.J., Comparison of Homogeneous and Heterogeneous Motorised Traffic at Signalised and Two-way Stop control Single lane Intersection, 2006 International Conference on Computational Science and its Applications (ICCSA 2006), Glasgow, UK, May 8-11 2006.


• Deo P. and Ruskin H.J., Heterogeneous traffic flow at a single lane T-intersection: traffic responsive signalisation, accepted for presentation at Econophysics Colloquium, Tokyo, Japan, November 23-25, 2006.


• Han J., Awad G., Sutherland A. and Wu H., Automatic Skin Segmentation for Gesture Recognition Combining Region and Support Vector Machine Active Learning, FGR 2006 - The 7th International Conference on Automatic Face and Gesture Recognition, Southampton, U.K., 10-12 April 2006.


• Matos J.A.O., Gama S.M.A., Ruskin H., Sharkasi A. and Crane M. (2006). Correlation of worldwide markets’ entropies, Perspectivas of Econophysics Workshop, 27 January 2006, Evora University, Portugal.


• Murphy J.T. and Walshe R., Micro-Gen: An Agent-Based Model of Bacteria-Antibiotic Interactions in Batch Culture, European Simulation and Modelling Conference, Eurosis-ETI, Toulouse, France, 2006.


• Perrin D., Ruskin H.J., Burns J. and Crane M., An agent-based approach to immune modelling, 2006 International Conference on Computational Science and its Applications (ICCSA 2006), Glasgow, UK, May 8-11 2006.


• Perrin D. and Ruskin H.J., Agent-Based Modelling of Viral Infection: An Introduction, poster presented at the BioNet 2006 conference, Tallaght, Ireland, January 18-19 2006.


• Perrin D., Ruskin H.J. and Crane M. (2006). HIV Modelling - Parallel Implementation Strategies, 3rd International Conference on Cluster and Grid Computing Systems (CGCS'06), Venice, Italy, November 2006.


• Perrin D., Ruskin H.J. and Crane M., 2006. An agent-based approach to immune modelling, Priming individual response, 3rd International Conference on Modeling and Simulation (ICMS'06), Cairo, Egypt, December 2006.


• Ruskin, H.J., The Work of the Biocomputation Research Lab., at Waterford Inst. Technology, Ireland, January 25th.


• Ruskin, H.J., Biocomputation: Cell to System, at National University of Ireland Maynooth, Feb. 24th.


• Sharkasi A., Crane M., Ruskin H., Matos J.A.O. and Gama S.M.A. (2006). Measuring the Degree of Maturity in Developed Markets, accepted for the Condensed Matter and Materials Physics Conference (CMMP 2006), University of Exeter, UK, April 20-21 2006.


• Sharkasi, A., Ruskin, H. and Crane, M. (2006). Stock Market Behaviour for Different Time Intervals with Different Volatility Levels, accepted for the Third Annual Meeting of the COST P10 Action 'Physics of Risk', 13 - 16 May 2006, Vilnius, Lithuania.


• Sharkasi, A., Ruskin, H. and Crane, M. (2006). Long-Term Memory in the Irish Market (ISEQ): Evidence from Wavelet Analysis, accepted for the International Conference ‘Applications of Physics in Financial Analysis’, 29 June- 1 July 2006, Torino, Italy.


• Yu D., Ghita O., Sutherland A. and Whelan P.F., Dictionary Based Lip Reading Classification, China-Ireland International Conference on Information and Communications Technologies (CIICT 06), Hangzhou, China, 2006.


• Yu D., Ghita O., Sutherland A. and Whelan P.F., Dictionary Based Lip Reading Classification, Irish Machine Vision & Image Processing Conference (IMVIP06), Dublin City University, Ireland, 2006.



2005
 

• Barat, A., Ruskin, H.J, Crane, M., Modelling the in vitro Dissolution of Soluble Binary Drug Delivery Systems using Direct Monte Carlo techniques, accepted for presentation at First Open International Conference on Modelling and Simulation, Clermont-Ferrand, France, June 2005


• McMahon, N., Crane, M., Ruskin, H.J, Crane, L., Particle Tracking: from Raindrops in 1940 to Drug Dissolution in 2005 accepted for presentation at Third MIT Conference on Computational Fluid and Solid Mechanics, Cambridge, Mass., June 2005


• Quinn N., (w. L. Killen , F. Buckley), March 2005, at Young Statisticians Meeting 2005, Trinity College, Dublin. Modelling the Fat and Protein Percentage Curves for Irish Dairy Cows


• Quinn N., (w. L. Killen , F. Buckley), March 2005, at Agricultural Research Forum 2005, Tullamore, Co. Offaly. Modelling Liveweight for Irish Dairy Cows


• Quinn N., (w. L. Killen , F. Buckley), May 2005, at Conference of Applied Statistics in Ireland 2005, Manor House Hotel, Enniskillen, Co. Fermanagh. Statistical Modelling of Liveweight for Irish Dairy Cows


• Quinn N., (w. L. Killen , F. Buckley), May 2005, at Annual Meeting of the European Association of Animal Production, Uppsala Sweden. Modelling Liveweight change over a Lactation in Irish Dairy Cows.


• Quinn N., Killen L., Buckley F., 2005. Statistical Modelling of Fat and Protein Content Curves for Irish Dairy Cows , 25^th European Meeting of Statisticians 24^th – 28^th July 2005, Oslo, Norway.


• Ruskin, H.J., February 16th 2005. BioComputation: Imitation and Inspiration, Speaker at Bioinformatics Inform 2005, DCU.


• Ruskin, H.J., February 17th 2005. Speaker at Virtual Inst. Bioinformatics_Eire Bi-Annual Meeting, Biocomputation Group, DCU.


• Ruskin, H.J., June 7th 2005. Chip, Bytes and Bio: Computational and Mathematical Modelling of Complex Biosystems, Weill Medical College, Cornell University, NY, USA


• Ruskin, H.J., Crane, M., Walshe, R., June 7th 2005. Biocomputation at DCU, Albert Einstein Medical College, NY, USA.


• Sharkasi A., (H. J. Ruskin. and M. Crane), March 2005, at Young Statisticians Meeting 2005, Trinity College, Dublin. Long-Term Memory in the Irish Market (ISEQ): Additional Insight from Wavelet Transform".


• Sharkasi A., (H. J. Ruskin. and M. Crane), 17 June 2005, at Applied Mathematics, Porto University, Port, Portugal. Long Memory in Irish Market


• Sharkasi A., (H. J. Ruskin. and M. Crane), 23 June 2005, at Applied Mathematics, Porto University, Port, Portugal. Interrelationship among international stock market Indices



 
 

2004
 

• Quinn N., Killen L., Buckley F., 2004. Statistical Modelling of Lactation Curve Data, CompStat 2004, Prague, Czech Republic


• Quinn N., Killen L., Buckley F., 2004. Modelling Lactation Curves for Irish Dairy Cows, 34^th ICAR Session, Sousse, Tunisia. 1^st - 3^rd June 2004.


• Quinn N., Killen L., Buckley F., 2004. A Statistical Analysis of Lactation Curve Data, Agricultural Research Forum 2004, Tullamore, Co.Offaly.


• December 2004, Kerr, G., (w. R. Walshe, M. Duggan, C. Pender, R. Winters), at Annual BioNet Conference, Institute of Technology Carlow, The BAIT Simulation: Bacteria Antibiotic Interaction Tool


• November 2004, Barat, A., (w. M. Crane, & H.J. Ruskin), at Irish Association for High Performance Computing Symposium, Monte Carlo and Cellular Automata Techniques in Simulating Drug Dissolution


• November 2004, Sharkasi, A., (w. M. Crane, & H.J. Ruskin), at Third Nikkei Econophysics Symposium - Practical Fruits of Econophysics, Nihon Keisai Shimbun,Tokyo, Japan, Apples and Oranges: the Difference Between the Reaction of Emerging and Mature Markets to Crashes


• October 2004, J. Burns, (w. H. Ruskin) at Sixth International conference on Cellular Automata for Research and Industry (ACRI 04), Amsterdam, The Netherlands,  A Stochastic Model of the Effector T Cell Lifecycle". 


• July 2004, A. Barat (w. M. Crane, H.J. Ruskin & A.-M. Healy) at EXYSTENCE Thematic Institute: From Many-Particle Physics to Multi-Agent Systems, Max Planck Institute for the Physics of Complex Systems (MPIPKS), Dresden, Germany, Monte-Carlo models of dissolution of multi-component tablets in the USP paddle apparatus


• May 2004, Y. Feng, (w. H.J. Ruskin, Y. Liu) at International Conference on Computational Science & Applications (ICCSA04), Assisi, Italy, Multiple Parameterisation of Human Immune Response in HIV: Many-Cell Models.


• May 2004, K. Podesta (w. M. Crane, H.J. Ruskin) at International Conference on Computational Science & Applications (ICCSA04), Assisi, Italy, Running EMBOSS on a cluster of workstations


• March 2004, Horgan, J.,  Invited talk to Facultad de Contaduria y Administacion, A New method for Stratifying Skewed Data: Applications in Auditing



 
 
 

2003
 

• Nov 2003 - K. Podesta (w. M. Crane, H.J. Ruskin) at IAHPC meeting, Irish Association for High Performance Computing, Dublin City University. The Biologist does not compute


• June 2003 - J. Burns (w. H. Ruskin) at IASTED International Conference on Biomedical Engineering, Saltzburg, Austria. Viral Strain Diversity and Immune Response - a Computational Model


• June 2003 - J. Burns (w. H. Ruskin) at International Conference on Computational Science, St. Petersburg, Russia. A Model of Immune Suppression and Repertoire Evolution


• May 2003 - J.M. Horgan (w. C. Daly) at Conference of Applied Statistics in Ireland, Mullingar, Ireland. Automated Learning Systems: What the Statistics Say


• May 2003 - S. Sharifi (w. A. Shamaie, M. Crane) at Conference of Applied Statistics in Ireland, Mullingar, Ireland. Noise in the Correlation Matrix


• May 2003 - Y. Bimpeh (w. J.M. Horgan) at Conference of Applied Statistics in Ireland, Mullingar, Ireland. Inference on Rare Errors Using Asymptotic Expansion for Studenttized Compound Poisson Process


• May 2003 - W. G. Tuohey at Conference of Applied Statistics in Ireland, Mullingar, Ireland. Approach to the Inversion Problem in Radiative Transfer


• May 2003 - N. Quinn (w. L. Killen, F. Buckley) at Conference of Applied Statistics in Ireland, Mullingar, Ireland. Modelling Lactation Curves for Irish Dairy Cows


• May 2003 - P. Gunning (w J.M. Horgan, W. Yancey) at Conference of Applied Statistics in Ireland, Mullingar, Ireland. A new method of stratification by size for skewed populations


• May 2003 - undecided (H. Ruskin, R. Wang) at Int. Conf. on Computational Science and its Applications, Montreal, Canada. Modelling Traffic Flow at a Multilane Intersection


• April 2003 - A. Shamaie (w A. Sutherland) at 5th International Workshop on Gesture and Sign Language based Human-Computer Interaction, Genova, Italy - A Dynamic Model for Real-time Tracking of Hands in Bimanual Movements


• March 2003 - N. McMahon (w. H. Ruskin, M. Crane, L. Crane.) at GAMM, Padua, Italy - Drug Dissolution Models


• Feb 2003 - N. Quinn (w. L. Killen, F. Buckley) at the Agricultural Research Forum 2003, Tullamore, Co. Offaly, Ireland - The Factors affecting lactation curves of Irish Dairy Cows


• Feb 2003 - A. Shamaie (w A. Sutherland) at 2nd Iranian Conference on Machine Vision and Image Processing, K.N. Toosi University of Technology, Tehran, Iran - Accurate Recognition of Large Number of Hand Gestures



 
 
 

2002
 

• Nov 2002 - K. Podesta (w. M. Crane, H.J. Ruskin) at IAHPC meeting, Irish Association for High Performance Computing, University College Dublin


• Nov 2002 - H. Ruskin (w. M. Crane, G. Keogh, S. Sharifi) at the 2nd Nikkei Workshop and Symposium, Tokyo, Japan - Leverage and Cross-Asset Volatility Correlation-Empirical or Optimistic?


• Sep 2002 - J. Burns (w. Heather Ruskin) at the 7th Granada Seminar on Complex Systems, Spain - MC model of Immune Suppression and T-cell receptor cross-reactivity during primary response


• May/June 2002 - H. Ruskin (translation Y. Feng) at Dalian University of Technology, Dept. of Computer Science. 3 invited lectures on Modelling & Scientific Computing in CA" and related topics


• May/June 2002 - H. Ruskin at Beijing Software Centre, China - ICT Sector in Ireland.


• April 2002 - Y. Feng (w. B. Zhu, H. Ruskin) at the International Conference on Computational Science, Amsterdam, the Netherlands - Virtual Phase Dynamics for Constrained Geometries in Soap Froth


• April 2002 - R. Wang (w. H. Ruskin) at the International Conference on Computational Science, Amsterdam, the Netherlands - Modelling Traffic Flow at Urban Unsignalized Intersection.


• April 2002 - Y. Liu (w. H. Ruskin) at the International Conference on Computational Science, Amsterdam, The Netherlands - A Mesoscopic Approach to modelling Immunological Memory


• Feb 2002 - R. Wang (w. H. Ruskin) at the IASTED Intl. Conf. on Modelling, Identification and Control, Innsbruck, Austria - Effects of Driver Behaviour on Cross-Traffic



 
 
 

2001
 

• Dec 2001 - Y. Feng (w. H. Ruskin) at Horizons in Complex Systems, Messina, Sicily - 2D Froth Dynamics for Constrained Geometries


• Oct 2001 - A. Shamaie (w. A. Sutherland) at IEEE Applied Imagery Pattern Recognition Workshop (AIPR 2001), Washington DC, USA - Graph-based Matching of Occluded Hand Gestures


• Sep 2001 - A. Shamaie (w. A. Sutherland) at Machine Vision and Image Processing Conference (IMVIP 2001), National University of Ireland, Maynooth, Ireland - Classification of Coarticulated and Partly Occluded Hand Gestures


• Sep 2001 - R. Wang (w. H. Ruskin) at the Europhysics Conference on Computational Physics, Aachen, Germany - Modelling traffic flow for a single-lane urban roundabout


• May 2001 - J.M. Horgan at American Accounting Association Western Region Meeting - A Fixed-Sample-Size Without-Replacement Plan for Substantive Tests

The MODSCI recommended format for listing publications and presentations is Elsevier Harvard Format. Examples follow:

Conference/proceedings papers

Ribba, B., Alarcon, T., Marron, K., Maini, P., Agur, Z., 2004. The Use of Hybrid Cellular Automaton Models for Improving Cancer Therapy. In: P.M.A. Sloot and Bastien Chopard and Alfons G. Hoekstra (Ed.), Cellular Automata. Vol. 3305 of Lecture Notes in Computer Science. Springer- Verlag, Berlin Heidelberg, pp. 444-453.

Journal papers

Selin, L. K., Varga, S. M., Wong, I. C., Welsh, R. M., 1998. Protective Het- erologous Antiviral Immunity and Enhanced Immunopathogenesis Mediated by Memory T Cell Populations. J. Exp. Med. 188, 1705-1715.

Books

Nowak, M. A., May, R. M., 2000. Virus Dynamics. Oxford Univ. Press, Oxford New York, Ch. 14, pp. 149-181.

Additional Notes

1. Journal abbreviations need to follow the approved international naming standards.


2. For LaTeX users, the required file (elsart-harv.bst) is available from Elseview website, just follow the links for information for authors. You will need the line: \bibliographystyle{elsart-harv} in your latex files to obtain this format automatically (of course, you'll still need a bibTeX file).


3. The conference format is a little fussy, but if you have the info in your bibTeX file, its a simple matter to extract it.


4. Italics and bold have been omitted in the examples above, in keeping with the Elsevier Harvard style.

Compiled by John Burns, 2005.