Literature DB >> 22052476

Modelling complex biological systems using an agent-based approach.

Mike Holcombe1, Salem Adra, Mesude Bicak, Shawn Chin, Simon Coakley, Alison I Graham, Jeffrey Green, Chris Greenough, Duncan Jackson, Mariam Kiran, Sheila MacNeil, Afsaneh Maleki-Dizaji, Phil McMinn, Mark Pogson, Robert Poole, Eva Qwarnstrom, Francis Ratnieks, Matthew D Rolfe, Rod Smallwood, Tao Sun, David Worth.   

Abstract

Many of the complex systems found in biology are comprised of numerous components, where interactions between individual agents result in the emergence of structures and function, typically in a highly dynamic manner. Often these entities have limited lifetimes but their interactions both with each other and their environment can have profound biological consequences. We will demonstrate how modelling these entities, and their interactions, can lead to a new approach to experimental biology bringing new insights and a deeper understanding of biological systems. This journal is © The Royal Society of Chemistry 2012

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Year:  2011        PMID: 22052476     DOI: 10.1039/c1ib00042j

Source DB:  PubMed          Journal:  Integr Biol (Camb)        ISSN: 1757-9694            Impact factor:   2.192


  22 in total

1.  Cell-intrinsic adaptation of lipid composition to local crowding drives social behaviour.

Authors:  Mathieu Frechin; Thomas Stoeger; Stephan Daetwyler; Charlotte Gehin; Nico Battich; Eva-Maria Damm; Lilli Stergiou; Howard Riezman; Lucas Pelkmans
Journal:  Nature       Date:  2015-05-25       Impact factor: 49.962

2.  An agent-based simulation of extirpation of Ceratitis capitata applied to invasions in California.

Authors:  Nicholas C Manoukis; Kevin Hoffman
Journal:  J Pest Sci (2004)       Date:  2013-06-29       Impact factor: 5.918

3.  Counter-propagating wave patterns in a swarm model with memory.

Authors:  Angelika Manhart
Journal:  J Math Biol       Date:  2018-08-28       Impact factor: 2.259

4.  Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems.

Authors:  Nicholas A Cilfone; Denise E Kirschner; Jennifer J Linderman
Journal:  Cell Mol Bioeng       Date:  2015-03       Impact factor: 2.321

Review 5.  Cancer systems immunology.

Authors:  Nathan E Reticker-Flynn; Edgar G Engleman
Journal:  Elife       Date:  2020-07-13       Impact factor: 8.140

6.  BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.

Authors:  Thomas E Gorochowski; Antoni Matyjaszkiewicz; Thomas Todd; Neeraj Oak; Kira Kowalska; Stephen Reid; Krasimira T Tsaneva-Atanasova; Nigel J Savery; Claire S Grierson; Mario di Bernardo
Journal:  PLoS One       Date:  2012-08-24       Impact factor: 3.240

7.  Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework.

Authors:  Gael Pérez-Rodríguez; Martín Pérez-Pérez; Daniel Glez-Peña; Florentino Fdez-Riverola; Nuno F Azevedo; Anália Lourenço
Journal:  Biomed Res Int       Date:  2015-03-22       Impact factor: 3.411

8.  Multi-scale computational models of the airways to unravel the pathophysiological mechanisms in asthma and chronic obstructive pulmonary disease (AirPROM).

Authors:  K S Burrowes; J De Backer; R Smallwood; P J Sterk; I Gut; R Wirix-Speetjens; S Siddiqui; J Owers-Bradley; J Wild; D Maier; C Brightling
Journal:  Interface Focus       Date:  2013-04-06       Impact factor: 3.906

Review 9.  Spatial simulations in systems biology: from molecules to cells.

Authors:  Michael Klann; Heinz Koeppl
Journal:  Int J Mol Sci       Date:  2012-06-21       Impact factor: 6.208

10.  Mechanical properties of growing melanocytic nevi and the progression to melanoma.

Authors:  Alessandro Taloni; Alexander A Alemi; Emilio Ciusani; James P Sethna; Stefano Zapperi; Caterina A M La Porta
Journal:  PLoS One       Date:  2014-04-07       Impact factor: 3.240

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