title: Next-generation genome-scale models for metabolic engineering.
abstract: Constraint-based reconstruction and analysis (COBRA) methods have become widely used tools for metabolic engineering in both academic and industrial laboratories. By employing a genome-scale in silico representation of the metabolic network of a host organism, COBRA methods can be used to predict optimal genetic modifications that improve the rate and yield of chemical production. A new generation of COBRA models and methods is now being developed--encompassing many biological processes and simulation strategies-and next-generation models enable new types of predictions. Here, three key examples of applying COBRA methods to strain optimization are presented and discussed. Then, an outlook is provided on the next generation of COBRA models and the new types of predictions they will enable for systems metabolic engineering.
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Zachary A
authors.initials: ZA
authors.lastname: King
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Colton J
authors.initials: CJ
authors.lastname: Lloyd
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark.
authors.forename: Adam M
authors.initials: AM
authors.lastname: Feist
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. Electronic address: palsson@ucsd.edu.
authors.forename: Bernhard O
authors.initials: BO
authors.lastname: Palsson
mesh_terms: D018533:Biomass; D017353:Gene Deletion; D016678:Genome; D006801:Humans; D060847:Metabolic Engineering; D053858:Metabolic Networks and Pathways; D008954:Models, Biological