Using Genome-scale Models to Predict Biological Capabilities

Edward J O'Brien; Jonathan M Monk; Bernhard O Palsson

doi:10.1016/j.cell.2015.05.019

Using Genome-scale Models to Predict Biological Capabilities

Cell. 2015 May 21;161(5):971-987. doi: 10.1016/j.cell.2015.05.019.

Authors

Edward J O'Brien¹, Jonathan M Monk², Bernhard O Palsson³

Affiliations

¹ Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA.
² Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA.
³ Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark. Electronic address: palsson@ucsd.edu.

Abstract

Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have been under development since the first whole-genome sequences appeared in the mid-1990s. A few years ago, this approach began to demonstrate the ability to predict a range of cellular functions, including cellular growth capabilities on various substrates and the effect of gene knockouts at the genome scale. Thus, much interest has developed in understanding and applying these methods to areas such as metabolic engineering, antibiotic design, and organismal and enzyme evolution. This Primer will get you started.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review

MeSH terms

Computer Simulation
Escherichia coli / genetics
Humans
Metabolic Engineering
Models, Genetic*
Protein Interaction Maps
Systems Biology / methods*
Thermotoga maritima / genetics
Yeasts / genetics

Grants and funding

R01 GM057089/GM/NIGMS NIH HHS/United States