Numerous methods have been developed for the constraint-based modeling framework.

Click on the heading in each column to sort by method name, authors, type of method, or year of publication.

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Methods to categorize:

Von Neumann's framework for flux analysis De Martino, et al. 2010
Bilevel dFBA with Monod equations Feng, et al. 2012
Ergodic hypothesis of metabolic networks Li, et al. 2009
Robust flux balance analysis Zavlanos and Julius 2011
Flux balance analysis with flux ratios (FBrAtio) McAnulty, et al. 2012
Integrative Network Inference for Tissues (INIT) Agren, et al. 2012
Improving metabolic flux predictions using absolute gene expression data Lee, et al. 2012
Variations on M-DFBA Kleessen and Nikoloski 2012
MetabOlic Modeling with ENzyme kineTics (MOMENT) Adadi, et al. 2012
Cogne, et al. 2011
Kelk, et al.
flux variability scanning based on enforced objective flux (FVSEOF) with grouping reaction (GR) Park et al.
Jungreuthmayer and Zanghellini
Random sampling of elementary flux modes in large-scale metabolic networks Machado et al.
Stoichiometric capacitance Larhlimi, et al.
Constraining flux with expression data using a reference state Feng, et al.
Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks Acuña, et al. 2012
Simulation of both metabolism and transcription/translation Thiele, et al. 2012
Genetic Design through Multi-Objective (GDMO) Costanza, et al. 2012
Relative Change (RELATCH) Kim and Reed 2012
Framework for network modularization and Bayesian network analysis (FMB) Kim et al. 2011
Minimization of Metabolites Balance (MiMBl) Brochado et al. 2012
ModeScore Hoppe, et al. 2012
MIRAGE Vitkin and Shlomi 2012
TEAM Collins, et al. 2012
GX-FBA Navid and Almaas 2012
mCADRE Wang et al. 2012
FOCAL Tervo and Reed 2012
TFVAMüller and Bockmayr 2013
GMF Zhao and Kurata 2009
CONGA Hamilton and Reed 2012
FASTCORE Vlassis, et al. 2014
Sampling to find best fluxes to measure Megchelenbrink, et al. 2011
GIM3E Schmidt, et al. 2013
Flexible flux balance analysis (flexFBA) objective and time-linked flux balance analysis Birch et al. 2014
k-OptForce Chowdhury, et al. 2014
minimization of flux to expression levels Li, et al. 2012
Economic Flux Analysis (EFA) Liebermeister 2014
COMETS Harcombe, et al. 2014
MOMAKnock Ren et al. 2013

Application papers to add:
OptForce Ranganathan and Maranas
OptForce Xu et al
FBA - kind of Schuetz et al
Superessentiality Barve, et al
Reductive evolution simulation Belda, et al
EFMEvolver and the K-shortest EFM Gebauer et al
FBA and alternate optima Karlstaedt, et al.
Gene deletion? Multiobjective modeling? Byrne et al.
DFBA Ghosh, et al.
DFBA Krauss, et al.

Reviews of interest:
Mathematical Optimization Applications in Metabolic Networks
Mechanistic systems modeling to guide drug discovery and development
Biofuel production improvement with genome-scale models: The role of cell composition
Metabolic network modeling and simulation for drug targeting and discovery
Host-microbe and microbial community modeling
Towards metagenome-scale models for industrial applications — the case of Lactic Acid Bacteria
Genome‐scale modeling of human metabolism–a systems biology approach

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