May 19, 2010

Publications and Presentations

Here is a list of my publications and presentations. I try to keep this list as exhaustive, and as up-to-date, as possible, but there may sometimes be some delays.
If, for some reason, you need the latest list, please contact me directly.

In addition to the publications below, there are two articles and one conference submission currently under review. For practical reasons, these are not listed here.

May 19, 2010

Publications

  1. 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.
  2. 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.
  3. Perrin, D., and Ohsaki, H. (2011). Decentralised communication in autonomous agent swarms. Technical report CQ2011-30, Institute of Electronics, Information and Communication Engineers.
  4. Raghavan, K., Ruskin, H. J., and Perrin, D. (2011). Computational analysis of epigenetic information in human DNA sequences. Proceedings of the International Conference on Bioscience, Biochemistry and Bioinformatics, IEEE.
  5. 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.
  6. 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.
  7. Raghavan, K., Ruskin, H. J., Perrin, D., Goasmat, F., and Burns, J. (2010). Computational micromodel for epigenetic mechanisms. PLoS One 5(11):e14031.
  8. Perrin, D., Ruskin H. J., and Crane, M. (2010). Model refinement through high-performance computing: an agent-based HIV example. Immunome Research 6(S1):S3.
  9. Perrin, D., and Ruskin, H. J. (2010). Cell type-dependent, infection-induced, aberrant DNA methylation in gastric cancer. Journal of Theoretical Biology 264(2):570-577.
  10. Kerr, G., Perrin, D., Ruskin H. J., and Crane, M. (2010). Edge weighting of gene expression graphs. Advances in Complex Systems 13(2):217-238.
  11. Perrin, D., Ruskin H. J., and Crane, M. (2009). In silico Biology: making the most of parallel computing. In A. Lazakidou (editor), Handbook of Research on Biocomputation and Biomedical Informatics: Case Studies and Applications. Medical Information Science Reference.
  12. Claude, B., Perrin, D., and Ruskin, H. J. (2009). Considerations for a social and geographical framework for agent-based epidemics. In Proceedings of the International Conference on Computational Aspects of Social Networks, CASoN 2009:149-154, IEEE Computer Society.
  13. Burns, J., Ruskin, H. J., Perrin, D., and Walsh, J. (2009). Visualization of Complex Biological Systems: An Immune Response Model Using OpenGL. Complex 1(4):671-679.
  14. Perrin, D., and Ruskin, H. J. (2009). From bio-inspired computing to e-Biology. In Proceedings of the seventh International Conference on Creating, Connecting and Collaborating Through Computing C5-2009:111-118, IEEE Computer Society.
  15. Perrin, D., and Burns, J. (2008). Large-scale immune models and visualization. ERCIM News 74:33-34.
  16. Duhamel, C., and Perrin, D. (2008). Genetic Algorithms to compute a set of bicliques in microarray biclustering. Technical report RR-08-07, LIMOS.
  17. Perrin, D., Ruskin, H. J., Crane, M., and Walshe, R. (2008). Epigenetic modelling. ERCIM News 72:46.
  18. 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(2007):413-424.
  19. Perrin, D., Ruskin, H. J., and Crane, M. (2006). HIV Modelling - A Parallel Implementation of a Lymph Network. Selected proceedings of the Third International Conference on Cluster and Grid Computing Systems (CGCS 2006), pp. 84-89.
  20. Perrin, D., Ruskin, H. J., and Crane, M. (2006). An agent-based approach to immune modelling: Priming individual response. Selected proceedings of the Third International Conference on Modeling and Simulation (ICMS06), pp. 81-86.
  21. Perrin, D., Ruskin, H. J., Burns, J. and Crane, M. (2006). An agent-based approach to immune modelling. Lecture Notes in Computer Science 3980:612-621.
  22. Perrin, D. (2006). Agent-Based Modelling of Viral Infection. ERCIM News 64:50-51.
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May 19, 2010

Conference presentations and invited talks

  1. Perrin, D., and Ohsaki, H. (2011). Impact of randomness on information diffusion in Mobile Ad-Hoc Networks. Workshop of the IPSJ Technical Committee on Radio Communication Systems (RCS), Asahikawa, Japan.
  2. Perrin, D., and Ohsaki, H. (2011). Decentralised communication in autonomous agent swarms. Workshop of the IPSJ Technical Committee on Communication Quality (CQ), Otaru, Japan.
  3. Perrin, D., and Ohsaki, H., (2011). Applications of epidemic diffusion to complex systems: from communication networks to autonomous exploratory robots. Eight International Conference on Complex Systems (ICCS 2011), Boston, USA.
  4. Perrin, D., and Ohsaki, H. (2011). A parallel approach to social network generation and agent-based epidemic simulation. Ninth Australasian Symposium on Parallel and Distributed Computing (AusPDC 2011), Perth, Australia.
  5. Perrin, D., Ruskin H. J., and Crane, M. (2010). Model refinement through high-performance computing. International Conference on Bioinformatics (InCoB 2010), Tokyo, Japan.
  6. Perrin, D., and Ruskin, H. J. (2010). Modelling complex epigenetic changes. Epigenetics Europe 2010, Dublin, Ireland.
  7. Perrin, D., Ruskin, H. J., and Claude, B. (2009). Computer-based city model and control of epidemic spreads. Ninth Asia-Pacific Complex Systems Conference (Complex'09), Tokyo, Japan.
  8. Perrin, D. (2009). Agent-based models of epidemic outbreaks. Invited talk at the National Centre for Geocomputation, National University of Ireland, Maynooth, Ireland.
  9. Claude, B., Perrin, D., and Ruskin, H. J. (2009). Considerations for a social and geographical framework for agent-based epidemics. International Conference on Computational Aspects of Social Networks (CASoN 2009), Fontainebleau, France.
  10. Perrin, D., and Ruskin, H. J. (2009). Agent-based epidemiological models and assessment of intervention policies. International Workshop on Coping with Crises in Complex Socio-Economic Systems, Zurich, Switzerland.
  11. Perrin, D., and Ruskin, H. J. (2009). From bio-inspired computing to e-Biology. International Conference on Creating, Connecting and Collaborating through Computing (C5 2009), Kyoto, Japan.
  12. Perrin, D., Ruskin, H. J., and Crane, M. (2008). Inclusion of localised patterns in a large-scale agent-based model of the immune response to HIV infection (poster). Sixteenth Annual International Conference Intelligent Systems for Molecular Biology (ISMB2008), Toronto, Canada.
  13. Porwal, J., Ruskin, H. J., Perrin, D., and Roche, D. (2008). Microscopic model of epigenetic mechanisms (poster). Twentieth International Congress of Genetics, Berlin, Germany.
  14. Perrin, D., and Ruskin, H. J. (2008). The case for epigenetic modelling (poster). Twentieth International Congress of Genetics, Berlin, Germany.
  15. Perrin, D., Ruskin, H. J. and Crane, M. (2008). Towards epigenetic modelling: an initial map. IET BioSysBio 2008, Synthetic Biology, Systems Biology and Bioinformatics, London, UK.
  16. Burns, J., Perrin, D., and Ruskin, H. J. (2008). Network stability and susceptibility in computational epigenetics (poster). Second annual Symposium on Biological Complexity: Genes, Circuits and Behavior, Salk Institute for Biological Studies, La Jolla, California, USA.
  17. Perrin, D., Ruskin, H. J., and Crane, M. (2007). The case for epigenetic modelling (poster). IARC meeting on cancer and epigenetics, International Agency for Research on Cancer, Lyon, France.
  18. Perrin, D. (2007). Biocomputation Research: a two-way street between Biology and Computer Science. Invited talk at the Research Institute for Microbial Diseases, Osaka University, Japan.
  19. Perrin, D., Duhamel, C., Ruskin, H. J., and Crane, M. (2007). Microarray biclustering: mathematical model and metaheuristic alternatives. International Conference on Computational Methods (ICCM 2007), Hiroshima, Japan.
  20. Perrin, D., Ruskin, H. J., and Crane, M. (2006). An agent-based approach to immune modelling - Priming individual response. Third International Conference on Modeling and Simulation (ICMS 06), Cairo, Egypt.
  21. Perrin, D., Ruskin, H. J., and Crane, M. (2006). HIV Modelling - Parallel Implementation Strategies. Third International Conference on Cluster and Grid Computing Systems (CGCS 06), Venice, Italy.
  22. Perrin, D., Ruskin, H. J., and Crane, M. (2006). Computer-based model of the immune response to {HIV} infection (poster). Immunology masterclass, Maynooth, Ireland.
  23. 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), Glasgow, UK.
  24. Perrin, D., and Ruskin, H. J. (2006). Agent-based modelling of viral infection: an introduction (poster). BioNet 2006 conference, Tallaght, Ireland.
  25. Perrin, D., and Ruskin, H. J. (2005). Modelling the dynamics of viral infection; an agent-based approach (poster). National Symposium of the Irish Research Council for Science, Engineering and Technology, Dublin, Ireland.
  26. Perrin, D., McMahon, N., Crane, L. J., Hurley, B. (2004). The Influence of mounting booms and towers on wind speed measured by anemometers (poster). International Technical Wind Energy Conference (DEWEK 2004), Wilhelmshaven, Germany.
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This page was last updated on February 6th, 2012.