Paul Simon Andrews

Search results

• 2018

  Macrophage transactivation for chemokine production identified as a negative regulator of granulomatous inflammation using agent-based modeling

  Moyo, D., Beattie, L., Andrews, P. S., Moore, J. W. J., Timmis, J. I., Sawtell, A. K., Hoehme, S., Sampson, A. T. & Kaye, P., 27 Mar 2018, In: Frontiers in immunology. 9, 637, 10 p., 637.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Strategies for calibrating models of biology

  Read, M. N., Alden, K., Timmis, J. & Andrews, P. S., 18 Sept 2018, (E-pub ahead of print) In: Briefings in bioinformatics. 44 p., bby092.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
• 2015

  A Metamodel for the Evolution of Evolution

  Andrews, P. S. & Stepney, S., 2015, European Conference of Artificial Life 2015. MIT Press , p. 621-628

  Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed) › peer-review

• Correction: Determining Disease Intervention Strategies Using Spatially Resolved Simulations

  Read, M., Andrews, P. S., Timmis, J., Williams, R. A., Greaves, R. B., Sheng, H., Coles, M. & Kumar, V., 9 May 2015, In: PLoS ONE. 10, 5, e0128170.

  Research output: Contribution to journal › Article › peer-review

• Using argument notation to engineer biological simulations with increased confidence

  Alden, K. J., Andrews, P. S., Polack, F. A. C., Veiga-Fernandes, H., Coles, M. C. & Timmis, J., 6 Mar 2015, (E-pub ahead of print) In: Interface. 12, 104, 11 p., 20141059.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Utilising a simulation platform to understand the effect of domain model assumptions

  Alden, K., Andrews, P. S., Veiga-Fernandes, H., Timmis, J. & Coles, M., Mar 2015, In: Natural Computing. 14, 1, p. 99-107 9 p.

  Research output: Contribution to journal › Article › peer-review
• 2014

  Applying spartan to Understand Parameter Uncertainty in Simulations

  Alden, K. J., Read, M. N., Andrews, P. S., Timmis, J. & Coles, M. C., Dec 2014, In: R Journal. 6, 2, p. 63-80 18 p.

  Research output: Contribution to journal › Article › peer-review

• Modelling biological behaviours with the unified modelling language: an immunological case study and critique

  Read, M. N., Andrews, P. S., Timmis, J. & Kumar, V., 6 Oct 2014, In: Interface. 11, 99, 20140704.

  Research output: Contribution to journal › Article › peer-review
• 2013

  Determining Disease Intervention Strategies Using Spatially Resolved Simulations

  Read, M. N., Andrews, P. S., Timmis, J., Williams, R. A., Greaves, R. B., Sheng, H., Coles, M. C. & Kumar, V., 14 Nov 2013, In: PLoS ONE. 8, 11, e80506.

  Research output: Contribution to journal › Article › peer-review

• Functional complexity of the Leishmania granuloma and the potential of in silico modelling

  Moore, J. W. J., Moyo, D., Beattie, L., Andrews, P. S., Timmis, J. & Kaye, P., 15 Feb 2013, In: Frontiers in immunology. 4, FRB, 35.

  Research output: Contribution to journal › Article › peer-review

• In silico investigation into dendritic cell regulation of CD8Treg mediated killing of Th1 cells in murine experimental autoimmune encephalomyelitis

  Williams, R. A., Greaves, R., Read, M., Timmis, J., Andrews, P. S. & Kumar, V., Apr 2013, In: BMC Bioinformatics. 14, SUPPL6, S9.

  Research output: Contribution to journal › Article › peer-review

• In silico investigation of novel biological pathways: The role of CD200 in regulation of T cell priming in experimental autoimmune encephalomyelitis

  Greaves, R. B., Read, M., Timmis, J., Andrews, P. S., Butler, J. A., Gerckens, B. O. & Kumar, V., May 2013, In: Biosystems. 112, 2, p. 107-121 15 p.

  Research output: Contribution to journal › Article › peer-review

• In Silico investigtation into dendrtic cell regulation of CD8Treg mediated killing of Th1 cells in murine experimental autoimmune encephalomyelitis

  Williams, R. A., Greaves, R. B., Read, M. N., Andrews, P. S., Timmis, J. & Kumar, V., 2013, In: BMC Bioinformatics.

  Research output: Contribution to journal › Article › peer-review

• Spartan: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems

  Alden, K. J., Read, M. N., Timmis, J., Andrews, P. S., Viega-Fernandes, H. & Coles, M. C., Feb 2013, In: PLoS Computational Biology. 9, 2, p. 1-9 e1002916.

  Research output: Contribution to journal › Article › peer-review
• 2012

  Differential RET Signaling Pathways Drive Development of the Enteric Lymphoid and Nervous Systems

  Patel, A., Harker, N., Moreira-Santos, L., Alden, K. J., Timmis, J., Foster, K., Andrews, P. S., Pachnis, P., Garefalaki, A., Coles, M. C., Enomoto, H., Milbrandt, J., Pachnis, V., Kioussis, D. & Veiga-Fernandes, H., 31 Jul 2012, In: Science Signaling. 5, 235, p. ra55

  Research output: Contribution to journal › Article › peer-review

• Engineering simulations for cancer systems biology

  Bown, J. L., Andrews, P. S., Deeni, Y., Goltsov, A., Idowu, M., Polack, F. A. C., Sampson, A. T., Shovman, M. & Stepney, S., Nov 2012, In: Current Drug Targets. 13, 12, p. 1560-1574

  Research output: Contribution to journal › Article › peer-review

• Extending an estabished simulation: exploration of the possible effects using a case study in Experimental Autoimmune Encephalomyelitis

  Greaves, R. B., Read, M. N., Timmis, J., Andrews, P. S. & Kumar, V., 2012, Information processing in cells and tissues. Springer, p. 150-161 (Lecture Notes in Computer Science; vol. 7223).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Pairing experimentation and computational modelling to understand the role of tissue inducer cells in the development of lymphoid organs.

  Alden, K. J., Timmis, J., Andrews, P. S., Veiga-Fernandes, H. & Coles, M. C., 2012, In: Frontiers in immunology. 3, 172

  Research output: Contribution to journal › Article › peer-review

• 2011

  CoSMoS process, models, and metamodels

  Andrews, P. S., Stepney, S., Hoverd, T., Polack, F. A. C., Sampson, A. T. & Timmis, J., 2011.

  Research output: Contribution to conference › Paper

• Editorial for special issue on the interaction between computation and biology

  Timmis, J., Andrews, P. & Stepney, S., Mar 2011, In: Natural Computing. 10, 1, p. 187-188 2 p.

  Research output: Contribution to journal › Editorial › peer-review

• Preface

  Timmis, J., Andrews, P. S. & Hone, A., 2011, In: Electronic Notes in Theoretical Computer Science. 412, 6, p. 500-501 2 p.

  Research output: Contribution to journal › Article › peer-review

• Techniques for Grounding Agent-Based Simulations in the Real Domain: a case study in Experimental Autoimmune Encephalomyelisis

  Timmis, J., Read, M. N., Andrews, P. S. & Kumar, V., 1 Dec 2011, In: Journal of Mathematical and Computational Modelling of Dynamical Systems. 18, 1, p. 296-302 20 p.

  Research output: Contribution to journal › Article › peer-review

• Towards Argument-Driven Validation of an in silico Model of Immune Tissue Organogenesis

  Alden, K. J., Andrews, P. S., Timmis, J., Viega-Fernandes, H. & Coles, M. C., 2011, Proceedings of 10th International Conference on Artificial Immune Systems. Springer, p. 66-70 5 p. (Lecture Notes in Computer Science; vol. 6825).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• 2010

  A Petri Net Model of Granulomatous Inflammation

  Albergante, L., Timmis, J., Andrews, P. S., Beattie, L. & Kaye, P. M., 2010, p. 1-3.

  Research output: Contribution to conference › Paper › peer-review

• On artificial immune systems and swarm intelligence

  Timmis, J., Andrews, P. S. & Hart, E., 2010, In: Swarm Intelligence. 4, 4, p. 247-273 27 p.

  Research output: Contribution to journal › Article › peer-review

• Reflections on the Simulation of Complex Systems for Science

  Polack, F. A. C., Andrews, P. S., Ghetiu, T., Read, M., Stepney, S., Timmis, J. & Sampson, A. T., 2010, Engineering of Complex Computer Systems (ICECCS), 2010 15th IEEE International Conference on . IEEE, p. 276-285 9 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Special issue on artificial immune systems

  Timmis, J., Andrews, P. S. & Hart, E., 2010, In: Swarm Intelligence. 4, 4, p. 245-246 2 p.

  Research output: Contribution to journal › Article › peer-review

• The CoSMoS Process, Version 0.1: A Process for the Modelling and Simulation of Complex Systems

  Andrews, P. S., Polack, F. A. C., Sampson, A. T., Stepney, S. & Timmis, J., 1 Mar 2010.

  Research output: Working paper
• 2009

  Artificial Immune Systems, 8th International Conference, ICARIS 2009, York, UK, August 9-12, 2009. Proceedings

  Andrews, P. S. (Editor), Timmis, J. (Editor), Owens, N. D. L. (Editor), Aickelin, U. (Editor), Hart, E. (Editor), Hone, A. (Editor) & Tyrrell, A. M. (Editor), 2009, Springer. (Lecture Notes in Computer Science; vol. 5666)

  Research output: Book/Report › Book

• Equivalence Arguments for Complex Systems Simulations: A Case-Study

  Ghetiu, T., Alexander, R., Andrews, P., Polack, F. & Bown, J., 2009.

  Research output: Contribution to conference › Paper

• Modelling and simulation of granuloma formation in visceral leishmaniasis

  Flugge, A. J., Timmis, J., Andrews, P. S., Moore, J. W. J. & Kaye, P. M., 2009, p. 3052-3059.

  Research output: Contribution to conference › Paper › peer-review

• Modelling and Simulation of Granuloma Formation in Visceral Leishmaniasis

  Fluegge, A. J., Timmis, J., Andrews, P., Moore, J. W. J. & Kaye, P., 2009, 2009 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION, VOLS 1-5. NEW YORK: IEEE, p. 3052-3059 8 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• The CoSMoS Process: Simulations for Scientific Exploration (extended abstract)

  Andrews, P. S., Stepney, S., Timmis, J. & Polack, F., 2009.

  Research output: Contribution to conference › Abstract › peer-review

• The engineering of concurrent simulations of complex systems

  Polack, F. A. C., Andrews, P. S. & Sampson, A. T., 2009, 2009 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION. NEW YORK: IEEE, p. 217-224 8 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Using UML to Model EAE and Its Regulatory Network

  Read, M., Timmis, J., Andrews, P. S. & Kumar, V., 2009, p. 4-6.

  Research output: Contribution to conference › Paper › peer-review

• Using UML to Model EAE and Its Regulatory Network

  Read, M., Timmis, J., Andrews, P. S. & Kumar, V., 2009, ARTIFICIAL IMMUNE SYSTEMS, PROCEEDINGS. Andrews, P., Timmis, J., Owens, N., Aickelin, U., Hart, E., Hone, A. & Tyrrell, A. (eds.). BERLIN: Springer, Vol. 5666 LNCS. p. 46 3 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• 2008

  Adaptable lymphocytes for artificial immune systems

  Andrews, P. S. & Timmis, J., 2008, ARTIFICIAL IMMUNE SYSTEMS, PROCEEDINGS. Bentley, P., Lee, D. & Jung, S. (eds.). BERLIN: Springer, Vol. 5132 LNCS. p. 376-386 11 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Adaptable Lymphocytes for Artificial Immune Systems

  Andrews, P. S. & Timmis, J., 2008, p. 376-386.

  Research output: Contribution to conference › Paper › peer-review

• An interdisciplinary perspective on artificial immune systems

  Timmis, J., Andrews, P., Owens, N. & Clark, E., 2008, In: Evolutionary Intelligence. 1, 1, p. 5-26 22 p.

  Research output: Contribution to journal › Article › peer-review

• Empirical investigation of an Artificial Cytokine Network

  Read, M., Timmis, J. & Andrews, P. S., 2008, ARTIFICIAL IMMUNE SYSTEMS, PROCEEDINGS. Bentley, P., Lee, D. & Jung, S. (eds.). BERLIN: Springer, Vol. 5132 LNCS. p. 340-351 12 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Empirical Investigation of an Artificial Cytokine Network

  Read, M., Timmis, J. & Andrews, P. S., 2008, p. 340-351.

  Research output: Contribution to conference › Paper › peer-review

• Immune Systems and Computation: An Interdisciplinary Adventure

  Timmis, J., Andrews, P. S., Owens, N. D. L. & Clark, E., 2008, p. 8-18.

  Research output: Contribution to conference › Paper › peer-review

• Immune systems and computation: An interdisciplinary adventure

  Timmis, J., Andrews, P., Owens, N. & Clark, E., 2008, UNCONVENTIONAL COMPUTATION, PROCEEDINGS. Calude, C., Costa, J., Freund, R., Oswald, M. & Rozenberg, G. (eds.). BERLIN: Springer, Vol. 5204 LNCS. p. 818 11 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Investigating Patterns for the Process-Oriented Modelling and Simulation of Space in Complex Systems

  Andrews, P. S., Sampson, A. T., Bjørndalen, J. M., Stepney, S., Timmis, J., Warren, D. N. & Welch, P. H., 2008, p. 17-24.

  Research output: Contribution to conference › Paper

• Simulating biology: towards understanding what the simulation shows

  Andrews, P. S., Polack, F., Sampson, A. T., Timmis, J. & Coles, M., 2008, p. 93-123.

  Research output: Contribution to conference › Paper

• 2007

  The Immune System in Pieces: Computational Lessons from Degeneracy in the Immune System

  Mendoa, M., Timmis, J., Andrews, P. & Davies, M., 2007, p. 394-400.

  Research output: Contribution to conference › Other

• 2006

  A computational model of degeneracy in a lymph node

  Andrews, P. S. & Timmis, J., 2006, ARTIFICIAL IMMUNE SYSTEMS, PROCEEDINGS. Bersini, H. & Carneiro, J. (eds.). BERLIN: Springer, p. 164-177 14 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• A Computational Model of Degeneracy in a Lymph Node

  Andrews, P. & Timmis, J., 2006, p. 164-177.

  Research output: Contribution to conference › Other

• An investigation into mutation operators for Particle Swarm Optimization

  Andrews, P. S., 2006, 2006 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION, VOLS 1-6. NEW YORK: IEEE, p. 1029-1036 8 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Computer-Driven Persuasive Dialogue: A Multi-Layer Reasoning Framework

  Andrews, P., Manandhar, S. & Boni, M. D., 2006, p. 787-788.

  Research output: Contribution to conference › Paper › peer-review