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Public Library of Science, PLoS ONE, 4(9), p. e95326, 2014

DOI: 10.1371/journal.pone.0095326

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Inferring Cell-Scale Signalling Networks via Compressive Sensing

Journal article published in 2014 by Lei Nie, Xian Yang, Ian Adcock ORCID, Zhiwei Xu, Yike Guo
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Signalling network inference is a central problem in system biology. Previous studies investigate this problem by independently inferring local signalling networks and then linking them together via crosstalk. Since a cellular signalling system is in fact indivisible, this reductionistic approach may have an impact on the accuracy of the inference results. Preferably, a cell-scale signalling network should be inferred as a whole. However, the holistic approach suffers from three practical issues: scalability, measurement and overfitting. Here we make this approach feasible based on two key observations: 1) variations of concentrations are sparse due to separations of timescales; 2) several species can be measured together using cross-reactivity. We propose a method, CCELL, for cell-scale signalling network inference from time series generated by immunoprecipitation using Bayesian compressive sensing. A set of benchmark networks with varying numbers of time-variant species is used to demonstrate the effectiveness of our method. Instead of exhaustively measuring all individual species, high accuracy is achieved from relatively few measurements.