Systems biology primer: the basic methods and approaches.

@article{Tavassoly2018SystemsBP,
  title={Systems biology primer: the basic methods and approaches.},
  author={Iman Tavassoly and Joseph Goldfarb and Ravi Iyengar},
  journal={Essays in biochemistry},
  year={2018},
  volume={62 4},
  pages={
          487-500
        }
}
Systems biology is an integrative discipline connecting the molecular components within a single biological scale and also among different scales (e.g. cells, tissues and organ systems) to physiological functions and organismal phenotypes through quantitative reasoning, computational models and high-throughput experimental technologies. Systems biology uses a wide range of quantitative experimental and computational methodologies to decode information flow from genes, proteins and other… 
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References

SHOWING 1-10 OF 120 REFERENCES
The nature of systems biology.
Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology
TLDR
A Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB, which contains a large number of analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis.
Systems Biology: A Brief Overview
To understand biology at the system level, we must examine the structure and dynamics of cellular and organismal function, rather than the characteristics of isolated parts of a cell or organism.
Systems pharmacology: network analysis to identify multiscale mechanisms of drug action.
TLDR
Network analyses based on publicly available databases allow us to develop an initial understanding of the context within which molecular-level drug-target interactions can lead to distal effectors in a process that results in adverse phenotypes at the organ and organismal levels.
Scale-free networks in cell biology
TLDR
The observed topologies of cellular networks give clues about their evolution and how their organization influences their function and dynamic responses, and the opportunity to describe quantitatively a network of hundreds or thousands of interacting components is offered.
Systems approaches to polypharmacology and drug discovery.
TLDR
The current state of the systems-level understanding of diseases and both the therapeutic and adverse mechanisms of drug actions are discussed, with the discovery of new drug therapies for complex diseases greatly aided by systems biology.
Systems pharmacology and genome medicine: a future perspective
TLDR
A perspective on the questions and approaches that drive the development of these new interrelated fields of genetics, pathophysiology and pharmacology are provided.
Merging Systems Biology with Pharmacodynamics
TLDR
The concept of enhanced pharmacodynamic (ePD) models, which synergistically combine the desirable features of systems biology and current PD models within the framework of ordinary or partial differential equations, are introduced.
A new approach to decoding life: systems biology.
TLDR
The emergence of systems biology is described, as well as several examples of specific systems approaches.
...
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2
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5
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