Biology related ABM Papers

Click on a paper for abstract:

Before 2001:: 2002:: 2003:: 2004:: 2005:: 2006:: 2007:: 2008

2008

Gary An (2008). Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation. Theoretical Biology and Medical Modelling, 5:11.

Bentley, K., Gerhardt, H. and Bates, P. A. (2008). Agent-based simulation of notch mediated tip cell selection in angiogenic sprout initialisation. Journal of Theoretical Biology, 250(1):25-36.

2007

Zhihui Wang, Le Zhang, Jonathan Sagotsky, Thomas S Deisboeck (2007). Simulating non-small cell lung cancer with a multiscale agent-based modelTheoretical Biology and Medical Modelling 2007, 4:50.

Qi Mi, Beatrice Rivière, Gilles Clermont, David L. Steed (2007). Yoram Vodovotz Agent-based model of inflammation and wound healing: insights into diabetic foot ulcer pathology and the role of transforming growth factor. Wound Repair and Regeneration, 15(5):671-682.

Bryan C. Thorne, Alexander M. Bailey, Shayn M. (2007). Combining experiments with multi-cell agent-based modeling to study biological tissue patterning. Peirce Briefings in Bioinformatics, 8(4):245-257.

Alexander M. Bailey, Bryan C. Thorne, Shayn M. Peirce (2007). Multi-cell Agent-based Simulation of the Microvasculature to Study the Dynamics of Circulating Inflammatory Cell Trafficking. Annals of Biomedical Engineering, 35(6):916-936.

I. Stamatopoulou, P. Kefalas, M. Gheorghe (2007). Modelling the dynamic structure of biological state-based systems. Biosystems, 87(2-3):142-149.

2006

Mark Pogson, Rod Smallwood, Eva Qwarnstrom, Mike Holcombe (2005). Formal agent-based modelling of intracellular chemical interactions. BioSystems, 85:37-45.

Dawn Walker, Steven Wood, Jennifer Southgate, Mike Holcombe, Rodney Smallwood (2006). An integrated agent-mathematical model of the effect of intercellular signalling via the epidermal growth factor receptor on cell proliferation. Journal of Theoretical Biology, 242:774-789.

Smallwood, R. Holcombe, M. (2006). The Epitheliome Project: multiscale agent-based modeling of epithelial cells. 3rd IEEE International Symposium on Biomedical Imaging: Nano to Macro, 2006. 816- 819.

2005

Bentley, K., Cox, E. J., Bentley, P. J. (2005). Nature's Batik: A Computer Evolution Model of Diatom Valve Morphogenesis. Journal of Nanoscience and Nanotechnology 5(1): 25-34.

Bentley, K and Clack, C. (2005). Morphological Plasticity: Environmentally Driven Morphogenesis. In Advances in Artificial Life (Lecture notes in AI series) Proceedings of the Eighth European Conference on Artificial Life (ECAL '05). Capcarrere, M. et al. (eds). 118-127.

Grabe N, Neuber K. (2005). A multicellular systems biology model predicts epidermal morphology, kinetics and Ca²⁺ flow. Bioinformatics, 21(17):3541-7.

Hédi Soula, Céline Robardet, François Perrin, Sébastien Gripon, Guillaume Beslon, Olivier Gandrillon (2005). Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software. BMC Bioinformatics, 6:228.

Kefalas, P. and Eleftherakis, G. and Holcombe, M. and Stamatopoulou, I. (2005). Formal Modelling of the Dynamic Behaviour of Biology-Inspired Agent-Based Systems. Molecular Computational Models: Unconventional Approaches, 243-276.

Ken Webb, Tony White (2005). UML as a cell and biochemistry modeling language. BioSystems 80:283-302.

Arancha Casal, Cenk Sumen, Timothy E. Reddy, Mark S. Alber, Peter P. Lee (2005). Agent-based modeling of the context dependency in T cell recognition. Journal of Theoretical Biology, 236:376-391.

2004

Bentley, K and Clack, C. (2004). The Artificial Cytoskeleton for Lifetime Adaptation in Morphology. In Workshop Proceedings of the 9th International Conference on the Simulation and Synthesis of Living Systems (Alife IX). Bedau, M., Husbands, P., Hutton, T., Kumar, S., Suzuki, H.(Eds.) 13-16.

Walker, D.C., Hill, G., Wood, S.M., Smallwood, R.H., Southgate, J. (2004). Agent-based computational modeling of wounded epithelial cell monolayers. NanoBioscience, 3(3):153-163.

Gabhann, F.M. Karagiannis, E.D. Popel, A.S.(2004).Building blocks for computational models of angiogenesis. Conference record of the Thirty-eighth Asilomar Conference on Signals, Systems & Computers, 1:739-745.

Yoram Vodovotz, Gilles Clermont, Carson Chow, Gary An (2004). Mathematical models of the acute inflammatory response. Current Opinion in Critical Care 10(5):383-390.

Shayn M. Peirce, Eric J. Van Gieson, Thomas C. Skalak (2004). Multicellular simulation predicts microvascular patterning and in silico tissue assembly. The FASEB Journal, (6):731-3.

D.C. Walker, J. Southgate, G. Hill, M. Holcombe, D.R. Hosea, S.M. Wood, S. Mac Neil, R.H. Smallwood (2004). The epitheliome: agent-based modelling of the social behaviour of cells. BioSystems, 76:89-100.

2003

Pedro Pablo Gonzalez, Maura Cardenas, David Camacho, Armando Franyuti, Octavio Rosas, Jaime Lagunez-Otero, (2003). Cellulat: an agent-based intracellular signalling model. Biosystems, 68(2-3):171-185.

R Smallwood, M Holcombe, D Walker, D R Hose, S Wood, S Mac Neil, J Southgate (2003). Modelling emergent order: from individual cell to tissue Biosystems

2002

Jose L. Segovia-Juarez, Suman Ganguli, Denise Kirschner (2004). Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model Journal of Theoretical Biology 231:357-376.

Yuri Mansury, Mark Kimura, Jose Lobo, Thomas S. Deisboeck (2002). Emerging Patterns in Tumor Systems: Simulating the Dynamics of Multicellular Clusters with an Agent-based Spatial Agglomeration Model Journal of Theoretical Biology, 219:343-370.

Before 2001

Kreft, JU, Booth, G, Wimpenny, JW (1998). BacSim, a simulator for individual-based modelling of bacterial colony growth. Microbiology 144:3275-3287.

Ferber, J. Gutknecht, O.(1998). A meta-model for the analysis and design of organizations in multi-agent systems. Proceedings. International Conference on Multi Agent Systems, 1998. 128-135.

Researchers

• Katie Bentley. - Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute
• Paul A. Bates - Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute
• Alexander M. Bailey - Department of Biomedical Engineering, University of Virginia
• Thomas S Deisboeck - Complex Biosystems Modeling Laboratory (CBML), Harvard
• Shayn M. Peirce - Department of Biomedical Engineering, University of Virginia
• Rod Smallwood - Computational Systems Biology, University of Sheffield
• Mike Holcombe - Computational Systems Biology, University of Sheffield
• D.C. Walker - Department of Computer Science, University of Sheffield
• Petros Kefalas - Intelligence, Modelling & Computation Research Group, CITY College
• J. Southgate - Jack Birch Unit for Molecular Carcinogenesis, The University of York

ABM Biology Websites

Websites

• Agent-Based Models in Biology and Medicine - An introduction to ABM in this area with a short selection of papers.
• Agent-based modelling - a tool for replicating biological systems - A good description of ABM from the team in Sheffield.
• AGENT-BASED MODELLING FOR SYSTEMS BIOLOGY - An introduction to ABM in this field from a few years ago. Also contains a list of software.
• Individual based models - A nine year old site, but nevertheless a very comprehensive list of ABM applications from the time.
• Agent based model - A decent article from Wikipedia serving as an introduction to ABM in general. Also contains some history of its uses and development.

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©2008 Katie Bentley, David Barr, Paul Bates