Chapter 9: Extending constraint-based approaches #
Analysis of optimality in natural and perturbed metabolic networks
Segre et al. (2002) Proceedings of the National Academy of Sciences USAThe classic paper on quadratic programming applied to COBRA: Minimisation of Metabolic Adjustment (MoMA).
Using Genome-scale Models to Predict Biological Capabilities
O' Brien et al. (2015) CellAn excellent review covering various applications of metabolic modelling.
Regulatory on-off minimization of metabolic flux changes after genetic perturbations
Shlomi et al. (2005) Proceedings of the National Academy of Sciences USAThis paper describes ROOM, an MILP-based method for constraint-based analysis of metabolic networks.
In Silico Identification of Gene Amplification Targets for Improvement of Lycopene Production
Choi et al. (2010) Applied and Environmental MicrobiologyThis paper describes FSEOF, for identifying over-expression targets in metabolic networks, for metabolic engineering.
Computational identification of gene over-expression targets for metabolic engineering of taxadiene production
Boghigian et al. (2012) Applied Microbiology and BiotechnologyA nice illustration of computational approaches to identify over-expression targets for metabolic engineering.
Predicting Gene Essentiality Using Genome-Scale in silico Models
Joyce and Palsson (2008) Methods in Molecular BiologyA nice review, detailing the strengths and limitations of constraint-based modelling, especially for predicting gene deletions/phenotypes.