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Identification of stable genetic networks using convex programming

Publication ,  Journal Article
Zavlanos, MM; Julius, AA; Boyd, SP; Pappas, GJ
Published in: Proceedings of the American Control Conference
September 30, 2008

Gene regulatory networks capture interactions between genes and other cell substances, resulting in various models for the fundamental biological process of transcription and translation. The expression levels of the genes are typically measured in mRNA concentrations in micro-array experiments. In a so called genetic perturbation experiment, small perturbations are applied to equilibrium states and the resulting changes in expression activity are measured. This paper develops a novel algorithm that identifies a sparse stable genetic network that explains noisy genetic perturbation experiments obtained at equilibrium. Our identification algorithm can also incorporate a variety of possible prior knowledge of the network structure, which can be either qualitative, specifying positive, negative or no interactions between genes, or quantitative, specifying a range of interaction strength. Our method is based on a convex programming relaxation for handling the sparsity constraint, and therefore is applicable to the identification of genome-scale genetic networks. ©2008 AACC.

Duke Scholars

Published In

Proceedings of the American Control Conference

DOI

ISSN

0743-1619

Publication Date

September 30, 2008

Start / End Page

2755 / 2760
 

Citation

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Zavlanos, M. M., Julius, A. A., Boyd, S. P., & Pappas, G. J. (2008). Identification of stable genetic networks using convex programming. Proceedings of the American Control Conference, 2755–2760. https://doi.org/10.1109/ACC.2008.4586910
Zavlanos, M. M., A. A. Julius, S. P. Boyd, and G. J. Pappas. “Identification of stable genetic networks using convex programming.” Proceedings of the American Control Conference, September 30, 2008, 2755–60. https://doi.org/10.1109/ACC.2008.4586910.
Zavlanos MM, Julius AA, Boyd SP, Pappas GJ. Identification of stable genetic networks using convex programming. Proceedings of the American Control Conference. 2008 Sep 30;2755–60.
Zavlanos, M. M., et al. “Identification of stable genetic networks using convex programming.” Proceedings of the American Control Conference, Sept. 2008, pp. 2755–60. Scopus, doi:10.1109/ACC.2008.4586910.
Zavlanos MM, Julius AA, Boyd SP, Pappas GJ. Identification of stable genetic networks using convex programming. Proceedings of the American Control Conference. 2008 Sep 30;2755–2760.

Published In

Proceedings of the American Control Conference

DOI

ISSN

0743-1619

Publication Date

September 30, 2008

Start / End Page

2755 / 2760