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.


Top

Foreword

Computational cellular dynamics: a network�physics integral

Hiroaki Kitano

doi:10.1038/nrm1904

Nature Reviews Molecular Cell Biology 7, 163


Top

Research highlights

Proteomics: The yeast proteome: say cheese!

Sharon Ahmad

doi:10.1038/nrm1902

Nature Reviews Molecular Cell Biology 7, 156

In the news

MIRIAM, for fine modelling

Ekat Kritikou

doi:10.1038/nrm1906

Nature Reviews Molecular Cell Biology 7, 158

Reviews

Cell-signalling dynamics in time and space

Boris N. Kholodenko

doi:10.1038/nrm1838

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

doi:10.1038/nrm1860

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

doi:10.1038/nrm1859

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

doi:10.1038/nrm1857

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

doi:10.1038/nrm1858

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.


Top

Perspectives

Innovation: A visual approach to proteomics

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

doi:10.1038/nrm1861

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.

Top

Extra navigation

Supported by

naturejobs

natureevents

Advertisement