Method name and description page Lead author / paper link Method group Year
Elementary modes Schuster and Hilgetag EFM 1994
Enzyme subsets Pfeiffer, et al. EFM 1999
Minimal cut sets Klamt, et al. EFM 2004
Duality framework for minimal cut sets Ballerstein, et al. EFM 2012
Estimation of Elementary Mode Coefficients by the maximum entropy principle Zhao, et al. EFM 2009
Elementary Flux Patterns Kaleta, et al. EFM 2009
Minimal generating elementary flux modes Rezola, et al. EFM 2011
Projection to latent pathways (PLP) Ferreira, et al. EFM 2011
Flux Design Melzer, et al. EFM / Strain Design 2009
CASOP: computational approach for strain optimization aiming at high productivity Hädicke and Klamt EFM / Strain Design 2010
Thermodynamically-weighted elementary modes Boghigian, et al. EFM / Strain Design 2010
Constrained Minimal Cut Sets Hädicke and Klamt EFM / Strain Design 2011
Systematic multiple enzyme targeting (SMET) Flowers et al. EFM / Strain Design 2013
FastPros Ohno, et al. EFM / Strain Design 2013
Extreme pathways (ExPas) Schilling, et al. ExPas 2000
Alpha-spectrum Wiback, et al. ExPas 2003
Extreme currents Clarke ExPas/EFM 1980
Fermentation equation Papoutsakis FBA precusor 1984
Flux Balance Analysis M.R. Watson Flux Balance Analysis 1984
Phenotypic phase plane Varma and Palsson Flux Balance Analysis 1993
Dynamic FBA (DFBA) Varma and Palsson Flux Balance Analysis 1994
Delineation of all alternate optimal solutions (AOS) Lee, et al. Flux Balance Analysis 2000
Flux variability analysis Burgard, et al. Flux Balance Analysis 2001
Minimal reaction sets Burgard, et al. Flux Balance Analysis 2001
Multi-product trade-off analysis Oh, et al. Flux Balance Analysis 2004
Flux coupling finder Burgard, et al. Flux Balance Analysis 2004
M-DFBA Luo, et al. Flux Balance Analysis 2006
Minimal flux modes (MinModes or MFM) Hoffmann, et al. Flux Balance Analysis 2006
FBAwMC Beg, et al. Flux Balance Analysis 2007
Metabolic flux ratios Choi, et al. Flux Balance Analysis 2007
Optimal capacity constraint identification (OCCI) Yang, et al. Flux Balance Analysis 2007
Minimization of active reactions Ponce de Leon, et al. Flux Balance Analysis 2008
Structural sensitivity analysis Uhr and Stelling Flux Balance Analysis 2008
Geometric FBA Smallbone and Simeonidis Flux Balance Analysis 2009
COBRA without mass balance Martelli, et al. Flux Balance Analysis 2009
Flux-sum analysis Chung and Lee Flux Balance Analysis 2009
Search for Minimal Media (SMM) Suthers, et al. Flux Balance Analysis 2009
Alternate optimal patterns of the minimal subnetwork Murabito, et al. Flux Balance Analysis 2009
Possibilistic framework for constraint-based metabolic flux analysis Llaneras, et al. Flux Balance Analysis 2009
CoupledFBA Thiele, et al. Flux Balance Analysis 2010
Genomic context analysis Park et al. Flux Balance Analysis 2010
MD-FBA Benyamini, et al. Flux Balance Analysis 2010
Parsimonious enzyme usage FBA (pFBA) Lewis, et al. Flux Balance Analysis 2010
Dynamic multi-species metabolic modeling (DMMM) Zhuang et al. Flux Balance Analysis 2010
Minimal substrate and product sets Gevorgyan, et al. Flux Balance Analysis 2010
FastFVA Gudmundsson and Thiele Flux Balance Analysis 2010
FBAwMC with ribosome, compartment, and uptake constraints Vazquez, et al. Flux Balance Analysis 2011
Feasibility-based Flux Coupling Analysis (FFCA) David, et al. Flux Balance Analysis 2011
FBAME Zhuang, et al. Flux Balance Analysis 2011
Differential Producibility Analysis Bonde, et al. Flux Balance Analysis 2011
Comprehensive Polyhedra Enumeration FBA (CoPE-FBA) Kelk, et al. Flux Balance Analysis 2012
Flux variability analysis with target flux minimization (FATMIN) Mao and Verwoerd Flux Balance Analysis 2013
Flux balance impact degree (FBID) Zhao, et al. Flux Balance Analysis 2013
Search for Interaction-Inducing Media (SIM) Klitgord and Segre Flux Balance Analysis / Community modeling 2010
Search for Exchanged Metabolites (SEM) Klitgord and Segre Flux Balance Analysis / Community modeling 2010
OptCom Zomorrodi and Maranas Flux Balance Analysis / Community modeling 2012
Community Flux Balance Analysis (cFBA) Khandelwal et al. Flux Balance Analysis / Community modeling 2013
Pruning for consistent ad functionem networks Hoffmann, et al. Flux Balance Analysis / Model refinement 2007
Systematic assessment of FBA objective functions Savinell and Palsson Flux Balance Analysis / Objective Function Approximation 1992
Representative minimal flux modes (rMFM) Hoffmann, et al. Flux Balance Analysis / Objective function approximation 2009
Bayesian FBA Heino, et al. Flux Balance Analysis / Sampling 2007
Sampling for transcriptional regulation prediction Bordel, et al. Flux Balance Analysis / Sampling 2010
Normalized Constraint Energy and Flux Balance Analysis (NCEFBA) Nagrath, et al. Flux Balance Analysis / Thermodynamics 2007
Optimal metabolic network identification (OMNI) Herrgard et al. Gap-filling 2006
Algorithmic Gap-Filling (Smiley) Reed, et al. Gap-filling 2006
GapFill / GapFind Satish Kumar, et al. Gap-filling 2007
Structurally Consistent Automatic Reconstruction (SCAR) Pitkänen, et al. Gap-filling 2008
Synthetic Lethal (SL) Finder Suthers et al. Gap-filling 2009
Network-based enzyme localization Mintz-Oron, et al. Gap-filling 2009
Automated model refinement using genetic interaction data Szappanos, et al. Gap-Filling 2011
GrowMatch Kumar, et al. Gap-filling / Objective function approximation 2009
GrowMatch with gene perturbation Zomorrodi and Maranas Gap-filling / Objective function approximation 2010
Gene deletion analysis Edwards and Palsson Gene/Reaction Perturbation 1999
MOMA Segre, et al. Gene/Reaction Perturbation 2002
ROOM Shlomi, et al. Gene/Reaction Perturbation 2005
Reductive evolution simulation Pal, et al. Gene/Reaction Perturbation 2006
Metabolite essentiality Kim, et al. Gene/Reaction Perturbation 2007
Gene-Nutrient Interactions (GNI) Diamant, et al. Gene/Reaction Perturbation 2009
Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model Chang et al. Gene/Reaction Perturbation 2010
Evolutionary SA search for likely environment and biomass Yizhak, et al. Gene/Reaction Perturbation / Objective function approximation 2011
Reaction correlation coefficients Poolman, et al. Network-based Pathway Analysis 2007
Minimal metabolic behaviors Larhlimi and Bockmayr Network-based Pathway Analysis 2009
Symbolic flux analysis Schryer, et al. Network-based Pathway Analysis 2011
ObjFind Burgard and Maranas Objective function approximation 2003
Data reconciliation and parameter estimation in FBA Raghunathan, et al. Objective function approximation 2003
Bayesian-based selection of metabolic objective functions Knorr, et al. Objective function approximation 2007
BOSS Gianchandani, et al. Objective function approximation 2008
Soft constraints based linear physical programming-based flux balance analysis (LPPFBA) Nagrath, et al. Objective function approximation 2010
Identification of distributed metabolic objectives by FBA and EBA Nolan, et al. Objective function approximation / EFM / Thermodynamics 2006
Noninferior set estimation (NISE) for multiobjective balancing Oh, et al. Objective function approximation / Flux Balance Analysis 2009
Approximating an objective function with transcriptomic data Bordbar, et al. Objective function approximation / Sampling 2010
Constraining flux through integration of gene expression data Akesson, et al. Omic constraints/Flux Balance Analysis 2005
Gene Inactivity Moderated by Metabolism and Expression (GIMME) Becker and Palsson Omic constraints 2008
Shlomi_NBT_08 Shlomi, et al. Omic constraints 2008
E-flux Colijn, et al. Omic constraints/Flux Balance Analysis 2009
Model building algorithm (MBA) Jerby, et al. Omic constraints 2010
Integrative omics-metabolic analysis (IOMA) Yizhak, et al. Omic constraints 2010
Metabolic Adjustment by Differential Expression (MADE) Jensen and Papin Omic constraints 2011
Transcriptional-controlled FBA (tFBA) van Berlo, et al. Omic constraints 2011
Gene Inactivity Moderated by Metabolism and Expression by Proteome (GIMMEp) Bordbar, et al. Omic constraints 2012
Regulatory FBA (rFBA) Covert, et al. Regulation 2001
Genetically-constrained metabolic flux analysis Cox, et al. Regulation 2005
R-matrix Gianchandani, et al. Regulation 2006
Steady-state rFBA (SR-FBA) Shlomi, et al. Regulation 2007
Integrated dynamic FBA (idFBA) Lee, et al. Regulation 2008
Integrated FBA (iFBA) Covert, et al. Regulation 2008
GeneForce Barua, et al. Regulation 2010
Probabilistic Regulation of Metabolism (PROM) Chandrasekaran and Price Regulation 2010
Markov-chain Monte Carlo sampling (MCMC) Almaas, et al. Sampling 2004
K-cone analysis Famili, et al. Sampling 2005
ACHR sampling Thiele, et al. Sampling 2005
Message-passing technique or Solution space assessment with the Bethe approximation Braunstein, et al. Sampling 2008
Sample, SVD, and rotate Barrett, et al. Sampling 2009
Exometabalome effect on internal states Mo, et al. Sampling 2009
Reaction Minimizing Expected Volume Megchelenbrink, et al. Sampling 2011
Gene expression change with Flux space shift (FSS) Nam, et al. Sampling 2012
Stoichiometric matrix Grütter and Messikommer Stoichiometric matrix 1961
OptKnock Burgard, et al. Strain Design 2003
OptStrain Pharkya, et al. Strain Design 2004
OptGene Patil, et al. Strain Design 2005
OptReg Pharkya and Maranas Strain Design 2006
Strain design with Set-based Evolutionary Algorithms (SEAs) Rocha, et al. Strain Design 2008
Strain design with Simulated Annealing (SA) Rocha, et al. Strain Design 2008
DESHARKY Rodrigo, et al. Strain Design 2008
GDLS Lun, et al. Strain Design 2009
Cipher of evolutionary design (CiED) Fowler, et al. Strain Design 2009
Objective tilting for OptKnock/OptGene Feist, et al. Strain Design 2010
Flux scanning based on enforced objective flux (FSEOF) Choi, et al. Strain design 2010
RobustKnock Tepper and Shlomi Strain Design 2010
OptKnock-proxy / RobustKnock-proxy for Biosensor design Tepper and Shlomi Strain Design 2010
Probabilistic pathway construction Yousofshahi, et al. Strain Design 2010
OptForce Ranganathan, et al. Strain Design 2010
Enhancing Metabolism with Iterative Linear Optimization (EMILiO) Yang, et al. Strain Design 2011
BioPathway Predictor/OptKnock Yim, et al. Strain Design 2011
BiMOMA Kim, et al. Strain Design 2011
SimOptStrain Kim, et al. Strain Design 2011
Bees Algorithm and Flux Balance Analysis (BAFBA) Choon et al. Strain Design 2012
Genetic Design through Branch and Bound (GDBB) Egen and Lun Strain Design 2012
Redirector Rockwell, et al. Strain Design 2013
OptSwap King and Feist Strain Design 2013
ReacKnock Xu et al. Strain Design 2013
OptORF Kim and Reed Strain design/Regulation 2010
Energy balance analysis (EBA) Beard, et al. Thermodynamics 2002
Flux minimization Holzhütter Thermodynamics 2004
Genome-scale thermodynamic analysis of metabolism Henry, et al. Thermodynamics 2006
Systematic assignment of thermodynamic constraints Kummel, et al. Thermodynamics 2006
Network embedded thermodynamic analysis Kümmel, et al. Thermodynamics 2006
Thermodynamic realizability Hoppe, et al. Thermodynamics 2007
Thermodynamics-based metabolic flux analysis (TMFA) Henry, et al. Thermodynamics 2007
Quantitative assignment of reaction directionality in constraint-based models of metabolism Fleming, et al. Thermodynamics 2009
Integrated stoichiometric, thermodynamic and kinetic modeling Fleming, et al. Thermodynamics 2010
von Bertalanffy Fleming and Thiele Thermodynamics 2010
Constraint finder Bordel and Nielsen Thermodynamics 2010
ll-COBRA Schellenberger, et al. Thermodynamics 2011
Integrated open framework for reaction thermodynamics Noor, et al. Thermodynamics 2012
Scalable Algorithm to Explore the Gibbs Energy Landscape De Martino, et al. Thermodynamics 2012
Sampling-based loop removal Price, et al. Thermodynamics / Sampling 2006