Computing

Selected Peer Reviewed Journals

• Dr Martin F Crane. 2012. .
• Marbach, D., Costello, J., Küffner, R., Vega, N., Prill, R., Camacho, D., Allison, K., Aderhold, A, Bonneau, R., Chen, Y., Cordero, F., Crane, M., Dondelinger, F., Drton, M., Esposito, R., Foyge, R., de la Fuente, A., Gertheiss, J., Geurts, P., Greenfield, A., Grzegorczyk, M., Haury, A-C, Holmes, B., Hothorn, T., Husmeier, D., Huynh-Thu, V., Irrthum, A., Karlebach, G., Lèbre, S., De Leo, V., Madar, A., Mani, S., Mordelet, F., Ostrer, H., Ouyang, Z., Pandya, R., Petri, T., Pinna, A., Poultney, C., Rezny, S., Ruskin, H.J., Saeys, Y., Shamir, R., Sîrbu, A., Song, M., Soranzo, N., Statnikov, A., Vega, N., Vera-Licona, P., Vert, J.-P., Visconti, A., Wang, H., Wehenkel, L., Windhager, L., Zhang, Y., Zimmer, R., Kellis, M., Collins, J.J., Stolovitzky, G. 2012. Wisdom of crowds for robust gene network inference. Nature Methods, 9, 8, pp796-804.
• Bezbradica, M., Ruskin, H.J. and Crane, M.. 2011. Modelling drug coatings: A parallel cellular automata model of ethylcellulose-coated microspheres. International Proceedings Of Chemical, Biological And Environmental Engineering, 5,, pp419-424.
• Daly, J., Ruskin, H.J., Crane, M. 2011. Can random matrix filters be used for trading in the foreign exchange market? - A comparison of foreign exchange and stock portfolio filtering. Dynamics Of Socio-economic Systems, Vol 2, 2, pp253-265.
• Sirbu, A., Ruskin, H.J., Crane, M.. 2011. Integrating Heterogeneous Gene Expression Data for Gene Regulatory Network Modelling. Theory In Biosciences,, pp1-8.
• Conlon, T., Ruskin, H.J., Crane, M. 2010. Multi-scaled Cross Correlation Dynamics in Financial Time Series. Advances In Complex Systems, Vol. 12, 4&5, pp439-454.
• Daly, J., Ruskin, H.J., Crane, M. 2010. Random matrix theory filters and currency portfolio optimization. Journal Of Physics : Conference Series, 221, , pp012003-.
• Kerr, G., Perrin, D., Ruskin, H.J., Crane, M. 2010. Edge Weighting of Gene Expression Graphs. Advances In Complex Systems, 13, 2, pp217-238.
• Perrin D., Ruskin H.J., Crane M. 2010. Model refinement through high-performance computing: an agent-based HIV example. Immunome Research, 6(Suppl 1), S3
• Sirbu, A., Ruskin, H.J., Crane, M. 2010. Modelling Gene Regulatory Networks - An Integrative Approach. Ercim News, 81, , pp36-37.
• Sirbu, A., Ruskin, H.J., Crane, M. 2010. Comparison of evolutionary algorithms in gene regulatory network model inference. Bmc Bioinformatics, 11, 59, pp1471-2205.
• Sîrbu A, Ruskin HJ, Crane M. 2010. Cross-Platform Microarray Data Normalisation for Regulatory Network Inference. Plos One, 5, 11
• Conlon, T., Ruskin, H.J., Crane, M. 2009. Cross-Correlation Dynamics in Financial Time Series. Physica A, 388, 5, pp705-714.
• McMahon, N.M., Crane, L.J., Ruskin, H.J., Crane, M., D¿Arcy, D.M., Healy, A.-M., Corrigan, O. 2009. A Numerical Model of a Drug Particle Dissolving in a Dissolution Test Apparatus. Proceedings In Applied Maths And Mechanics (pamm), 9, 1, pp655-656.
• Conlon, T., Ruskin, H.J., Crane, M. 2009. Seizure Characterisation using Frequency Dependent Multivariate Dynamics. Computers In Biology And Medicine, Vol 39, 9, pp760-767.
• Barat, A., Crane, M., Ruskin, H.J. 2008. Quantitative multi-agent models for simulating protein release from PLGA bioerodible nano- and microspheres. Journal Of Pharmaceutical And Biomedical Analysis, 48, 2, pp361-368.
• Conlon, T., Crane, M., Ruskin, H.J. 2008. Wavelet Multiscale Analysis of Hedge Funds: Scaling and Strategies. Physica A, 387, 21, pp5197-5204.
• Barat A, Ruskin HJ, Crane M. 2008. 3D Multi-agent models for protein release from PLGA spherical particles with complex inner morphologies. Theory In Biosciences, 127, 2, pp95-105.
• Daly, J., Crane, M., Ruskin, H.J. 2008. Random Matrix Theory Filters in Portfolio Optimization: A Stability and Risk Assessment. Physica A, 387, 16-17, pp4248-4260.
• Matos,J.-A., Gama,S., Ruskin,H.J.,Al Sharkasi,A., Crane, M. 2008. Time and scale Hurst exponent analysis for financial markets. Physica A, 387, 15 , pp3910-3915.
• Kerr, G., Ruskin, H.J., Crane, M., Doolan, P. 2008. Techniques for Clustering Gene Expression Data. Computers In Biology And Medicine, 38, 3, pp283-293.
• Hecquet, D., Ruskin, H.J., Crane, M. 2008. 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, 38, 2, pp282-282.
• Conlon, T., Ruskin, H.J., Crane, M.,. 2007. Random Matrix Theory and Fund of Funds Portfolio Optimization. Physica A, 382, 2, pp565-576.
• Hecquet, D., Ruskin, H.J., Crane, M. 2007. Optimisation and parallelisation strategies for Monte Carlo simulation of HIV Infection. Computers In Biology And Medicine, 37, 5, pp691-699.
• Perrin, D., McMahon, N., Crane,M., Ruskin, H.J.,Crane, L., Hurley, B. 2007. The effect of a meteorological tower on its top-mounted anemometer. Applied Energy, 84, 4, pp413-424.
• N. McMahon, M. Crane, H.J. Ruskin and L. Crane. 2007. The importance of boundary conditions in the simulation of dissolution in the USP dissolution apparatus. 15, 3, pp247-255.
• Barat, A., Ruskin, H.J., Crane, M. 2006. Probabilistic models for drug dissolution. Part 1. Review of Monte Carlo and stochastic cellular automata approaches. 14, 7, pp843-856.
• Barat, A., Ruskin, H.J., Crane, M. 2006. Probabilistic methods for drug dissolution. Part 2. Modelling a soluble binary drug delivery system dissolving in vitro. 14, 7, pp857-873.
• Sharkasi, A., Crane, M., Ruskin, H.J., Matos, J.-A.,. 2006. The Reaction of Stock Markets to Crashes: A Comparison Study between Emerging and Mature Markets using Wavelet Transforms. Physica A, 368, 2, pp512-521.
• Sharkasi, A., Ruskin, H.J, Crane, M. 2005. Interrelationships among International Stock Market Indices: Europe, Asia and the Americas. International Journal Of Theoretical And Applied Finance, 8, 5, pp1-18.
• 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. Vol. 12/6,, pp397-411.
• 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. Simulation Modelling Practice And Theory, 12/2,, pp147-158.
• Sharifi, S., Crane, M., Shamaie, A., Ruskin, H. 2004. Random Matrix Theory for Portfolio Optimization: A Stability Approach. Physica A, Vol. 335(3-4),, pp629-643.
• Crane, M. and Boyle, J.T.,. 1996. The Calculation of Interlaminar Stresses in Laminar Plates using Walsh Transforms. Journal Of American Institute Of Aeronautics And Astron, 34(8),, pp1-4.
• Crane, M, Byrne,J, Glynn, T, Boyle, J. 1995. Causality and the complex modulus model of damping. Zamm, 75,, pp807-808.
• Crane, M. 1993. The simulation of a simple chaotic dynamical system using Walsh functions. Zamm, 73,, pp161-164.

Selected Chapters

• Perrin, D., Bezbradica, M., Crane, M., Ruskin, H. J., Duhamel, C. 2012. High-Performance Computing for Data Analytics. , pp234-242.
• Bezbradica, M., Crane, M. and Ruskin, H.J. 2012. Parallelisation strategies for large scale cellular automata frameworks in pharmaceutical modellings. , pp223-230.
• Matos, J.-A., Gama, S., Ruskin, H.J., Sharkasi, Crane, M. 2011. A Study of Correlation and Entropy for Multiple Time Series. , pp245-254.
• Shakya, K., Ruskin, H.J., Kerr, G., Crane, M., Becker, J. 2010. Comparison of Microarray Pre-Processing Methods. Advances in Computational Biology
• Sirbu, A., Ruskin, H.J., Crane, M. 2010. Stages of Gene Regulatory Network Inference: the Evolutionary Algorithm Role. Evolutionary Algorithms
• Perrin, D., Ruskin, H.J., Crane, M.,. 2009. In Silico Biology: Making the most of parallel computing,. Handbook of Research on Biocomputation and Biomedical Informatics: Case Studies and Applications
• Kerr, G., Ruskin, H.J., Crane, M. 2007. Pattern Discovery in Gene Expression Data. Intelligent Data Analysis: Developing New Methodologies Through Pattern Discovery and Recovery

Selected Non-peer Reviewed Journals

• Crane, M. & Sievers, F. 1998. Assessment of MPP as an Option for Small & Medium-Sized Enterprises. Hitachi Internal Technical Report, HDL-TR-98-197,
• Talbot, L., Lawless, E., Hurley, N., & Crane, M. 1998. Implementation Issues for a Finite Element Moving Boundary Code for the PSUDO Project. Hitachi Internal Technical Report, HDL-TR-98-207,
• Vanessa Houlder. 1998. Data models hit the spot by Vanessa Houlder in Financial Times, 6/10/98. Financial Times,
• Dick Ahlstrom. 1998. "Computer used as guinea pig" by Dick Ahlstrom in Irish Times, 24/8/98. Irish Times,
• Dick Ahlstrom. 1998. "Hitachi targets `virtual laboratory' for drug trials" in Irish Times, 21/8/98. Irish Times,
• John von Radowitz. 1998. "Scientists launch `virtual laboratory' drug research" by John von Radowitz in PA News, 21/8/98. PA News,
• Jonathan Birt. 1998. "Virtual guinea pigs" by Jonathan Birt in Reuters, 20/8/98. Reuters,
• Rachel Oldroyd. 1998. "The virtual patient" by Rachel Oldroyd in Mail on Sunday, 23/8/98. Mail on Sunday,
• . 1998. "Drug trials is inhuman" The Guardian, 27/8/98. The Guardian,
• Crane, M. 1997. Discretisation and Pressure Correction Schemes for Steady-State Convection-Diffusion problems. Hitachi Internal Technical Report, HDL-TR-97-182,
• Crane, M. 1997. Convergence of the Conjugate Gradient Solution of the Pressure Equation from the SPRAY code. Hitachi Internal Technical Report, HDL-TR-97-171,
• Crane, M. 1997. Important Optimisation Aspects in CINDER code. Hitachi Internal Research Note, HDL-RN-97-005,
• Crane, M., Cahill, E. and Field, M. 1997. Parallel Iterative Solvers for the Distributed CINDER Combustion code. Hitachi Internal Technical Report, HDL-TR-97-174,
• Hurley, N., Crane, M., Fallon, M. and Mulvey, P. 1996. Parallel Direct Solvers. Hitachi Internal Technical Report, HDL-TR-96-168,
• Mackenzie, D., Crane, M., Boyle, J.T. and Banks, W.M. 1995. Composite Lamina Failure Criteria. University of Strathclyde Dept. of Mechanical Engineering Internal Report, 1995, *,
• Crane, M. and Rahman, D. 1995. A Semi-Analytical Approach to the Problem of the Response of a Composite Plate to Blast Loading. Dept. of Mech. Eng., University of Strathclyde Internal Report, 1995, *,
• Crane, M. 1993. Practical Models of Damping for the Plate Vibration Problem. Ph.D. Thesis 1993, Dept. of Comp. Sci., Trinity College Dublin, Ireland, *,
• Crane, M. 1989. Flow-Induced Vibration on a Cylinder Column in Cross-Flow. Dept. of Mech. Eng. Technical Report 1989, Trinity College Dublin, Ireland, *,

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• Bezbradica, M., Ruskin, H.J, Crane, M., Agent based modelling in prediction of environmental influence on drug release, European Conference on Complex Systems (ECCS'11), 12-SEP-11 - 16-SEP-11, Vienna, Austria
• Sirbu, A., Ruskin, H.J., Crane, M., An integrative framework for gene regulatory network inference, European Conference on Complex Systems (ECCS'11), 12-SEP-11 - 16-SEP-11, Vienna, Austria
• Sirbu, A., Ruskin, H.J., Crane, M., Gene regulatory network inference by integrative evolutionary computation, Eighth International Symposium on Networks in Bioinformatics, 14-APR-11 - 15-APR-11, Amsterdam, The Netherlands
• Bezbradica, M., Ruskin, H.J, Crane, M., Ethylcellulose/ Pectin-coated Microspheres in Controlled Drug Delivery: Agent-Based Modelling, UK & Ireland Controlled Release Society (UKIRS) Symposium, 13-APR-11 - 13-APR-11, Belfast, UK
• Bezbradica, M., Ruskin, H.J, Crane, M., Modelling Drug Coatings: A parallel Cellular Automata Model of Ethylcellulose-coated Microspheres, International Conference on Bioscience, Biochemistry and Bioinformatics, ICBBB 2011, 26-FEB-11 - 28-FEB-11, Singapore
• Bezbradica, M., Barat, A., Ruskin, H.J, Crane, M.,, Probabilistic models for dissolution of ethylcellulose coated microspheres, European Simulation & Modelling Conference ESM'2010, 25-OCT-10 - 27-OCT-10, Hasselt, Belgium
• Perrin D., Ruskin H.J., Crane M., Local Properties and Large-Scale Agent-Based HIV Simulations, International Conference on Bioinformatics, InCoB, 26-SEP-10 - 28-SEP-10, Tokyo, Japan
• Sirbu, A., Ruskin, H.J., Crane, M., Integrating Heterogeneous Gene Expression Data for Gene Regulatory Network Modelling, European Conference on Complex Systems ECCS2010, 13-SEP-10 - 17-SEP-10, Lisbon, Portugal
• Sirbu, A., Ruskin, H.J., Crane, M., Gene regulatory network modelling: an integrative approach, COST Action MP0801 Second Annual Meeting "Physics of Competition and Conflicts", 26-MAY-10 - 29-MAY-10, Sunny Beach, Bulgaria
• Sirbu, A., Ruskin, H.J., Crane, M., Integrating heterogeneous microarray data for regulatory network modelling, 6th Annual Advances in Microarray Technology Conference, 25-MAY-10 - 26-MAY-10, Dublin, Ireland
• Sirbu, A., Ruskin, H.J., Crane, M., Evolutionary algorithms in genetic regulatory network modelling with microarray data, Complex 09 ¿ How to Manage Complexity, 04-NOV-09 - 07-NOV-09, Tokyo, Japan
• McGuinness, E.D., Ruskin, H.J., Crane, M., Increasing biological accuracy in models of HIV progression while minimising complexity, 7th IFAC Symposium on Modelling and Control in Biomedical Systems, (MCBMS'09), 12-AUG-09 - 14-AUG-09, Aalborg, Denmark
• Daly, J., Crane, M., Ruskin, H.J., Random matrix theory filters and currency portfolio optimization, Applications of Physics in Financial Analysis 2009 (APFA09), 01-MAR-09 - 05-MAR-09, Tokyo, Japan
• Kumar, B., Crane, M., Delaure, Y., On the development of Object Oriented Parallel Pentadiagonal Preconditioned Krylov Subspace (K-S) Solvers, In: Bertelle, C. and Ayesh, A. ed.Proceedings of the European Multidisciplinary Society for Modelling and Simulation Technology (ESM08), 27-OCT-08 - 29-OCT-08, Le Havre, France, 348 - 352
• Barat, A., Ruskin, H.J, Crane, M., Reconstruction of Particle Size Distributions of Particulate Polydisperse Systems from in vitro Experimental Data, 21st Annual European Simulation and Modelling Conference (ESM'2007), 22-OCT-07 - 24-OCT-07, St.Julians, Malta
• Barat, A., Ruskin, H.J, Crane, M., 3D Multi-Agent Models for Protein Release from PLGA Spherical Particles with Complex Inner Morphologies, European Conference on Complex Systems (ECCS07), 01-OCT-07 - 05-OCT-07, Dresden, Germany
• Barat A., Ruskin H.J. and Crane M., Multi-Agent Models for Simulating Protein Release from PLGA Bioerodible nano- and microspheres, Twelfth International Meeting on Recent Developments in Pharmaceutical Analysis (RDPA07), 23-SEP-07 - 26-SEP-07, Island of Elba, Italy
• Perrin, D., Duhamel, C., Ruskin, H.J., Crane, M., Microarray biclustering: mathematical model and metaheuristic alternatives, International Conference on Computational Methods (ICCM 2007), 04-APR-07 - 06-APR-07, Hiroshima, Japan
• Perrin, D., Ruskin, H.J., Crane, M., An agent-based approach to immune modelling: Priming individual response, Third International Conference on Modeling and Simulation (ICMS06), 08-DEC-06 - 10-DEC-06, Cairo, Egypt, 81 - 86
• Perrin, D., Ruskin, H.J., Crane, M., HIV Modelling - A Parallel Implementation of a Lymph Network, The Third International Conference on Cluster and Grid Computing Systems (CGCS 2006), 24-NOV-06 - 26-NOV-06, Venice, Italy, 84 - 89
• Daly, J., Crane, M., Ruskin, H.J., Exponentially Weighted Volatility and Random Matrix Theory Filters in Portfolio Optimisation, Econophysics Colloquium 2006/ Third Bonzenfreies Colloquium, 23-NOV-06 - 25-NOV-06, Tokyo, Japan
• Matos, J-A, Gama, S., Ruskin, H.J., Sharkasi, A., Crane M., Correlation of worldwide markets¿ entropies, Applications of Physics in Financial Analysis (APFA06), 29-JUN-06 - 01-JUL-06, Turin, Italy
• Conlon, T., Ruskin, H.J., Crane, M., Random Matrix Theory and Hedge Fund Strategy Identification, 4th INFINITI Conference on International Finance, 12-JUN-06 - 13-JUN-06, Trinity College, Dublin
• Sharkasi, A., Ruskin, H.J., Crane, M., Stock Market Behaviour for Different Time Intervals with Different Volatility Levels, 3rd Annual Meeting COST Action P10 "Physics of Risk", 13-MAY-06 - 16-MAY-06, Vilnius, Lithuania
• Perrin, D., Ruskin, H.J., Burns, J., Crane, M., An Agent-Based Approach to Immune Modelling, In: M. Gavrilova et al (Eds.) ed.International Conference on Computational Science and its Applications (ICCSA 2006), 08-MAY-06 - 11-MAY-06, Glasgow, Scotland, 612 - 621
• Sharkasi, A., Crane, M., Ruskin, H.J., Matos, J.-A., Measuring the Degree of Maturity in Developed Markets, Condensed Matter and Materials Physics (CMMP06), 19-APR-06 - 21-APR-06, University of Exeter, UK
• McMahon, N., Crane, M., Ruskin, H.J, Crane, L.,, Particle Tracking: from Raindrops in 1940 to Drug Dissolution in 2005, Third MIT Conference on Computational Fluid and Solid Mechanics, 01-JUN-05 - 05-JUN-05, Cambridge, Mass.
• Barat, A., Ruskin, H.J, Crane, M., Modelling the in vitro Dissolution of Soluble Binary Drug Delivery Systems using Direct Monte Carlo techniques, In: Pf David R.C. HILL, Dr. Vincent BARRA, Dr. Mamadou K. TRAORE, (Eds) ed.First Open International Conference on Modelling and Simulation, 01-JUN-05 - 05-JUN-05, Clermont-Ferrand, France
• Sharkasi, A., Crane, M., Ruskin, H.J., Apples and Oranges: the Difference Between the Reaction of Emerging and Mature Markets to Crashes, The Third Nikkei Econophysics Research Workshop & Symposium, 08-NOV-04 - 12-NOV-04, Tokyo
• Sharkasi, A., Ruskin, H., Crane, M., Interdependence between Emerging and Major Markets, In: Antoch, Jaromir ed.16th Symposium of International Association for Statistical Computing, IASC (COMPSTAT04), 24-AUG-04 - 28-AUG-04, Prague
• Barat, A., Crane, M., Ruskin, H., Healy, A.-M., Monte-Carlo models of dissolution of multi-component tablets in the USP paddle apparatus, EXYSTENCE Thematic Institute: From Many-Particle Physics to Multi-Agent Systems, Max Planck Institute for the Physics of Complex Systems (MPIPKS), 21-JUL-04 - 24-JUL-04, Dresden, Germany
• Podesta, K., Crane, M., Ruskin, H., Running EMBOSS on a cluster of workstations, International Conference on Computational Science & Applications (ICCSA04), 25-MAY-04 - 29-MAY-04, Assisi, Italy
• McMahon, N., Crane, L., Crane, M., Ruskin, H., INVESTIGATIONS INTO THE MECHANICS OF DRUG COMPACT DISSOLUTION IN THE US PHARMACOPEIA DISSOLUTION APPARATUS, Gesellshaft Fuer Angewandte Mathematik und Mechanik Jahrestagung (Institute for Applied Maths and Mechanics Annual Meeting, 27-MAR-03 - 30-MAR-03, Padua, Italy
• Crane, M., Keogh, G., Ruskin, H., Sharifi, S., Leverage & Cross-Asset Volatility Correlation - Empirical or Optimistic?, 2nd Nikkei Conference on Econophysics, published in Proceedings of the 2nd Nikkei Econophysics Symposium - Application of Econophysics, H. Takayasu (Ed.) Lecture Notes in Computer Science, Springer, N, 12-NOV-02 - 14-NOV-02, Tokyo, Japan
• N.J. Hurley L. Crane M. Crane A.M. Healy O.I. Corrigan K.M. Gallagher L.G. McCarthy, Modelling Drug Delivery Systems using Finite Element Analysis, EUROSIM Congress, 22-JUN-01 - 25-JUN-01, Delft, Netherlands
• Gallagher, K., McCarthy, L., Corrigan, O., Crane, LJ, Crane, M., Pinto, C., Hurley, N., Healy, A.M., Drug Dissolution in the Paddle Dissolution Apparatus, World Congress of Pharmacy & Pharmaceutical Sciences/59th Int'l Congress of FIP, 05-SEP-99 - 10-SEP-99, Barcelona, Spain
• Gallagher, K.M., McCarthy, L.G., Corrigan, O.I., Crane, L., Crane, M. and Healy, A.M., Evaluation of the apparent diffusion boundary layer in the paddle dissolution apparatus, Proceedings of the twenty-second TCD/QUB annual joint research seminar, The Queen's University of Belfast, March 1999, P17, 01-MAR-99 - 01-MAR-99, Queen's University of Belfast
• Crane, M. & Cahill, E., Parallel Iterative Solvers for Combustion Modelling, 3rd IMACS Int'l Symposium on Iterative Methods in Scientific Computation, 09-JUL-97 - 12-JUL-97, Jackson Hole WY