| 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 |