Stimulus Design for Model Selection and Validation in Cell Signaling

Joshua F Apgar; Jared E Toettcher; Drew Endy; Forest M White; Bruce Tidor

doi:10.1371/journal.pcbi.0040030

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Open Access

Peer-reviewed

Research Article

Stimulus Design for Model Selection and Validation in Cell Signaling

Joshua F Apgar,

Affiliations Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America , Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Jared E Toettcher,

Affiliations Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America , Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Drew Endy,

Affiliation Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Forest M White,

Affiliations Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America , Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Bruce Tidor

*To whom correspondence should be addressed. E-mail: tidor@mit.edu

Affiliations Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America , Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America , Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Stimulus Design for Model Selection and Validation in Cell Signaling

Joshua F Apgar,
Jared E Toettcher,
Drew Endy,
Forest M White,
Bruce Tidor

Published: February 15, 2008
https://doi.org/10.1371/journal.pcbi.0040030

About the Authors

Joshua F Apgar

Jared E Toettcher

Drew Endy

Affiliation Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

Forest M White

Affiliations Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America , Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

Bruce Tidor

*To whom correspondence should be addressed. E-mail: tidor@mit.edu

Affiliations Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America , Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America , Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

JFA conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, and wrote the paper. JET contributed reagents/materials/analysis tools and wrote the paper. DE and FMW conceived and designed the experiments and wrote the paper. BT conceived and designed the experiments, analyzed the data, and wrote the paper.

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Experimental design
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EGFR signaling
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MAPK signaling cascades
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Optimization
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Protein kinase signaling cascade
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Differential equations
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Phosphatases
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Phosphorylation
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