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The Alpha Project: a model system for systems biology research

Yu, R. C. and Resnekov, O. and Abola, A. P. and Andrews, S. S. and Benjamin, K. R. and Bruck, J. and Burbulis, I. E. and Colman-Lerner, A. and Endy, D. and Gordon, A. and Holl, M. and Lok, L. and Pesce, C. G. and Serra, E. and Smith, R. D. and Thomson, T. M. and Tsong, A. E. and Brent, R. (2008) The Alpha Project: a model system for systems biology research. IET Systems Biology, 2 (5). pp. 222-233. ISSN 1751-8849. https://resolver.caltech.edu/CaltechAUTHORS:20090728-082033135

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Abstract

One goal of systems biology is to understand how genome-encoded parts interact to produce quantitative phenotypes. The Alpha Project is a medium-scale, interdisciplinary systems biology effort that aims to achieve this goal by understanding fundamental quantitative behaviours of a prototypic signal transduction pathway, the yeast pheromone response system from Saccharomyces cerevisiae. The Alpha Project distinguishes itself from many other systems biology projects by studying a tightly bounded and well-characterised system that is easily modified by genetic means, and by focusing on deep understanding of a discrete number of important and accessible quantitative behaviours. During the project, the authors have developed tools to measure the appropriate data and develop models at appropriate levels of detail to study a number of these quantitative behaviours. The authors have also developed transportable experimental tools and conceptual frameworks for understanding other signalling systems. In particular, the authors have begun to interpret system behaviours and their underlying molecular mechanisms through the lens of information transmission, a principal function of signalling systems. The Alpha Project demonstrates that interdisciplinary studies that identify key quantitative behaviours and measure important quantities, in the context of well-articulated abstractions of system function and appropriate analytical frameworks, can lead to deeper biological understanding. The authors’ experience may provide a productive template for systems biology investigations of other cellular systems.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1049/iet-syb:20080127DOIUNSPECIFIED
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4648904&isnumber=4648901PublisherUNSPECIFIED
Additional Information:© The Institution of Engineering and Technology 2008. The work was made possible by grants P50 HG002370 from NHGRI (PI, R.B.) and R33 CA114306 from NCI (PI, R.B.), and we are grateful for this support. The assertions in this article are solely the responsibility of the authors. We thank three anonymous reviewers for their helpful comments on the manuscript. Special Issue, Selected papers from the First q-bio Conference on Cellular Information Processing.
Funders:
Funding AgencyGrant Number
National Human Genome Research InstituteP50 HG002370
National Cancer InstituteR33 CA114306
Issue or Number:5
Record Number:CaltechAUTHORS:20090728-082033135
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20090728-082033135
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14688
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:07 Aug 2009 22:36
Last Modified:03 Oct 2019 00:51

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