In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling-Reference-Cited by-同舟云学术

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In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

Published:2010-12-06 Issue:1 Volume:9 Page:39-50
ISSN:1740-1526
Container-title:Nature Reviews Microbiology
language:en
Short-container-title:Nat Rev Microbiol

Author:

Mahadevan Radhakrishnan,Palsson Bernhard Ø.,Lovley Derek R.

Publisher

Springer Science and Business Media LLC

Subject

General Immunology and Microbiology,Microbiology,Infectious Diseases

Link

http://www.nature.com/articles/nrmicro2456.pdf

Reference108 articles.

1. Feist, A. M., Herrgard, M. J., Thiele, I., Reed, J. L. & Palsson, B. O. Reconstruction of biochemical networks in microorganisms. Nature Rev. Microbiol. 7, 129–143 (2009).

2. Oberhardt, M. A., Palsson, B. O. & Papin, J. A. Applications of genome-scale metabolic reconstructions. Mol. Syst. Biol. 5, 320 (2009).

3. Thiele, I. & Palsson, B. O. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature Protoc. 5, 93–121 (2010). This paper provides a comprehensive 96-step protocol for reconstructing a metabolic network based on genome sequence and physiology, followed by evaluation of the network through the use of constraint-based modelling.

4. Reed, J. L., Famili, I., Thiele, I. & Palsson, B. O. Towards multidimensional genome annotation. Nature Rev. Genet. 7, 130–141 (2006).

5. Palsson, B. in Systems Biology: Properties of Reconstructed Networks (Cambridge Univ. Press, New York, 2006).

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