High-throughput technologies now enable the study of cell biology at a systems level — from subcellular systems such as signalling networks, multiprotein complexes and organelles, to cells, tissues and even entire organisms. The diverse systems can be modelled through a combination of high-throughput experimental data and mathematical and computational approaches. This special Focus issue of Nature Reviews Molecular Cell Biology illustrates several cellular systems and describes the different approaches that can be used to model them. The articles of this Focus are freely available for a period of three months.



Computational cellular dynamics: a network�physics integral

Hiroaki Kitano


Nature Reviews Molecular Cell Biology 7, 163


Research highlights

Proteomics: The yeast proteome: say cheese!

Sharon Ahmad


Nature Reviews Molecular Cell Biology 7, 156

In the news

MIRIAM, for fine modelling

Ekat Kritikou


Nature Reviews Molecular Cell Biology 7, 158


Cell-signalling dynamics in time and space

Boris N. Kholodenko


Nature Reviews Molecular Cell Biology 7, p165

Spatial and temporal dynamics of signalling networks control the specificity of cellular responses to receptor stimulation. Computational models now provide insights into the mechanisms that are responsible for signal amplification, as well as the timing, amplitude, duration and spatial distribution of signalling responses.

Building mammalian signalling pathways with RNAi screens

Jason Moffat and David M. Sabatini


Nature Reviews Molecular Cell Biology 7, p177

Recent advances in RNA interference (RNAi)-mediated gene-knockdown technologies have opened up the possibility of large-scale functional discovery in mammalian systems. RNAi screening could help us to delineate the architecture of signalling pathways much faster than by using traditional approaches.

Structural systems biology: modelling protein interactions

Patrick Aloy and Robert B. Russell


Nature Reviews Molecular Cell Biology 7, 117-129

The difficulties that are associated with the experimental determination of atomic structures for interacting proteins mean that predictive methods are needed for progress. Such structural details can be used to turn abstract system representations into models that more accurately reflect biological reality.

The model organism as a system: integrating 'omics' data sets

Andrew R. Joyce and Bernhard �. Palsson


Nature Reviews Molecular Cell Biology 7, p198

Many genome-scale, or 'omics', data sets are becoming available for various model organisms. Although each of these data types is valuable on its own, further insights into whole systems can be gained through the integration of omics data sets.

Capturing complex 3D tissue physiology in vitro

Linda G. Griffith and Melody A. Swartz


Nature Reviews Molecular Cell Biology 7, p211

Tissue engineering has opened up the possibility of studying physiological and pathophysiological processes in vitro. The foundation of this technology is a set of design principles for building three-dimensional tissues that are based on the quantitative analyses of cell and tissue behaviour.



Innovation: A visual approach to proteomics

Stephan Nickell, Christine Kofler, Andrew P. Leis and Wolfgang Baumeister


Nature Reviews Molecular Cell Biology 7, p225

Cryo-electron tomography is an emerging imaging technique that will allow us to map molecular landscapes inside cells. This 'visual proteomics' will complement and extend mass-spectrometry-based inventories, and will provide a quantitative description of the macromolecular interactions that underlie cellular functions.


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