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 |