Systems biology primer: the basic methods and approaches

I Tavassoly, J Goldfarb, R Iyengar - Essays in biochemistry, 2018 - portlandpress.com
Systems biology is an integrative discipline connecting the molecular components within a
single biological scale and also among different scales (eg cells, tissues and organ systems) …

Multiscale cancer modeling

TS Deisboeck, Z Wang, P Macklin… - Annual review of …, 2011 - annualreviews.org
Simulating cancer behavior across multiple biological scales in space and time, ie,
multiscale cancer modeling, is increasingly being recognized as a powerful tool to refine …

Comparing individual-based approaches to modelling the self-organization of multicellular tissues

JM Osborne, AG Fletcher, JM Pitt-Francis… - PLoS computational …, 2017 - journals.plos.org
The coordinated behaviour of populations of cells plays a central role in tissue growth and
renewal. Cells react to their microenvironment by modulating processes such as movement …

Simulating cancer growth with multiscale agent-based modeling

Z Wang, JD Butner, R Kerketta, V Cristini… - Seminars in cancer …, 2015 - Elsevier
There have been many techniques developed in recent years to in silico model a variety of
cancer behaviors. Agent-based modeling is a specific discrete-based hybrid modeling …

Multi-scale modelling and simulation in systems biology

JO Dada, P Mendes - Integrative Biology, 2011 - academic.oup.com
The aim of systems biology is to describe and understand biology at a global scale where
biological functions are recognised as a result of complex mechanisms that happen at …

Modeling formalisms in systems biology

D Machado, RS Costa, M Rocha, EC Ferreira, B Tidor… - AMB express, 2011 - Springer
Abstract Systems Biology has taken advantage of computational tools and high-throughput
experimental data to model several biological processes. These include signaling, gene …

High performance cellular level agent-based simulation with FLAME for the GPU

P Richmond, D Walker, S Coakley… - Briefings in …, 2010 - academic.oup.com
Driven by the availability of experimental data and ability to simulate a biological scale
which is of immediate interest, the cellular scale is fast emerging as an ideal candidate for …

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

NA Cilfone, DE Kirschner, JJ Linderman - Cellular and molecular …, 2015 - Springer
Biologically related processes operate across multiple spatiotemporal scales. For
computational modeling methodologies to mimic this biological complexity, individual scale …

Multi-scale modeling of the cardiovascular system: disease development, progression, and clinical intervention

Y Zhang, VH Barocas, SA Berceli, CE Clancy… - Annals of biomedical …, 2016 - Springer
Cardiovascular diseases (CVDs) are the leading cause of death in the western world. With
the current development of clinical diagnostics to more accurately measure the extent and …

[HTML][HTML] Systems biology of kidney diseases

JC He, PY Chuang, A Ma'Ayan, R Iyengar - Kidney international, 2012 - Elsevier
Kidney diseases manifest in progressive loss of renal function, which ultimately leads to
complete kidney failure. The mechanisms underlying the origins and progression of kidney …