Published in PLoS Comput Biol on March 13, 2009
What is flux balance analysis? Nat Biotechnol (2010) 9.01
High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol (2010) 6.08
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol (2012) 3.56
Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol (2010) 2.60
The biomass objective function. Curr Opin Microbiol (2010) 2.32
Systematizing the generation of missing metabolic knowledge. Biotechnol Bioeng (2010) 1.85
Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol Syst Biol (2009) 1.69
An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet (2011) 1.62
Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain. J Biol Chem (2009) 1.55
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol (2009) 1.53
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol (2011) 1.50
OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput Biol (2012) 1.48
Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets. PLoS Comput Biol (2016) 1.43
Construction and completion of flux balance models from pathway databases. Bioinformatics (2012) 1.42
Metabolic systems biology. FEBS Lett (2009) 1.40
Synthetic biology of cyanobacteria: unique challenges and opportunities. Front Microbiol (2013) 1.38
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. BMC Syst Biol (2010) 1.35
The evolution of metabolic networks of E. coli. BMC Syst Biol (2011) 1.32
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proc Natl Acad Sci U S A (2014) 1.20
Improving metabolic flux predictions using absolute gene expression data. BMC Syst Biol (2012) 1.19
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Syst Biol (2011) 1.19
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. BMC Syst Biol (2010) 1.17
An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models. PLoS Comput Biol (2010) 1.05
Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142. PLoS Comput Biol (2012) 1.05
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. BMC Syst Biol (2012) 1.04
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model. Nucleic Acids Res (2012) 1.04
Shrinking the metabolic solution space using experimental datasets. PLoS Comput Biol (2012) 1.04
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans. BMC Syst Biol (2011) 0.99
A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database. BMC Syst Biol (2014) 0.99
Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A. J Bacteriol (2011) 0.97
MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks. Genome Biol (2012) 0.97
Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models. PLoS Comput Biol (2014) 0.96
Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis. BMC Syst Biol (2010) 0.96
Systems metabolic engineering: genome-scale models and beyond. Biotechnol J (2010) 0.96
Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS Comput Biol (2013) 0.95
Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. PLoS One (2012) 0.94
Applying systems biology methods to the study of human physiology in extreme environments. Extrem Physiol Med (2013) 0.94
Computational tools for metabolic engineering. Metab Eng (2012) 0.94
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. PLoS Negl Trop Dis (2016) 0.94
Mining high-throughput experimental data to link gene and function. Trends Biotechnol (2011) 0.93
Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis. J Biol Chem (2011) 0.91
A Method to Constrain Genome-Scale Models with 13C Labeling Data. PLoS Comput Biol (2015) 0.90
Model-driven discovery of underground metabolic functions in Escherichia coli. Proc Natl Acad Sci U S A (2015) 0.89
The EcoCyc Database. Ecosal Plus (2014) 0.88
A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. BMC Syst Biol (2012) 0.86
Metabolic network modeling of microbial communities. Wiley Interdiscip Rev Syst Biol Med (2015) 0.83
Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems. Front Microbiol (2016) 0.82
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm. Front Plant Sci (2015) 0.82
FOCAL: an experimental design tool for systematizing metabolic discoveries and model development. Genome Biol (2012) 0.82
MapMaker and PathTracer for tracking carbon in genome-scale metabolic models. Biotechnol J (2016) 0.81
Metabolic constraint-based refinement of transcriptional regulatory networks. PLoS Comput Biol (2013) 0.80
Bridging the gap between fluxomics and industrial biotechnology. J Biomed Biotechnol (2011) 0.80
Computational approaches for microalgal biofuel optimization: a review. Biomed Res Int (2014) 0.79
BioMog: a computational framework for the de novo generation or modification of essential biomass components. PLoS One (2013) 0.79
Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth. BMC Syst Biol (2012) 0.78
Functional genomics of Plasmodium falciparum using metabolic modelling and analysis. Brief Funct Genomics (2013) 0.77
Linking genome-scale metabolic modeling and genome annotation. Methods Mol Biol (2013) 0.77
Systematic applications of metabolomics in metabolic engineering. Metabolites (2012) 0.77
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti. BMC Syst Biol (2013) 0.76
Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Syst (2016) 0.75
Challenges in experimental data integration within genome-scale metabolic models. Algorithms Mol Biol (2010) 0.75
Systems approach to characterize the metabolism of liver cancer stem cells expressing CD133. Sci Rep (2017) 0.75
Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods. Front Microbiol (2015) 0.75
Computational Methods for Modification of Metabolic Networks. Comput Struct Biotechnol J (2015) 0.75
Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973. Sci Rep (2017) 0.75
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA. PLoS Comput Biol (2017) 0.75
Discovering missing reactions of metabolic networks by using gene co-expression data. Sci Rep (2017) 0.75
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Comput Biol (2017) 0.75
Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach. PLoS One (2015) 0.75
Efficient Reconstruction of Predictive Consensus Metabolic Network Models. PLoS Comput Biol (2016) 0.75
From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model. Front Microbiol (2016) 0.75
In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions. Sci Rep (2017) 0.75
The Proteome of a Healthy Human during Physical Activity under Extreme Conditions. Acta Naturae (2014) 0.75
Thermodynamic Constraints Improve Metabolic Networks. Biophys J (2017) 0.75
iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol (2017) 0.75
More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes. Microbiome (2017) 0.75
The KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05
KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol (2006) 40.15
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A (2003) 14.01
Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A (2007) 11.46
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol (2007) 11.03
EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res (2005) 11.01
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res (2007) 10.62
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol (2003) 10.46
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol (2001) 8.88
Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A (2002) 8.41
Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science (2004) 7.75
Integrating high-throughput and computational data elucidates bacterial networks. Nature (2004) 7.72
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci U S A (2000) 7.70
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature (2002) 7.38
Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol (2003) 7.32
Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A (2006) 6.31
Comprehensive identification of conditionally essential genes in mycobacteria. Proc Natl Acad Sci U S A (2001) 6.22
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res (2004) 6.21
Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr Biol (2001) 6.05
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics (2004) 5.90
MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res (2006) 5.79
Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol (2003) 4.91
Towards multidimensional genome annotation. Nat Rev Genet (2006) 4.44
Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res (2004) 3.61
Systems approach to refining genome annotation. Proc Natl Acad Sci U S A (2006) 3.58
Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci U S A (2005) 2.99
Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol (2006) 2.93
Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics (2007) 2.74
Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophys J (2005) 2.70
Plasticity of genetic interactions in metabolic networks of yeast. Proc Natl Acad Sci U S A (2007) 2.40
Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Res (2002) 2.28
Identification of essential genes in Streptococcus pneumoniae by allelic replacement mutagenesis. Mol Cells (2005) 2.20
Exploring the diversity of complex metabolic networks. Bioinformatics (2004) 1.93
Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. PLoS Comput Biol (2005) 1.82
Predicting synthetic rescues in metabolic networks. Mol Syst Biol (2008) 1.82
Filling gaps in a metabolic network using expression information. Bioinformatics (2004) 1.69
Predicting genes for orphan metabolic activities using phylogenetic profiles. Genome Biol (2006) 1.68
Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics (2006) 1.65
A metabolic network in the evolutionary context: multiscale structure and modularity. Proc Natl Acad Sci U S A (2006) 1.59
Predicting biological system objectives de novo from internal state measurements. BMC Bioinformatics (2008) 1.42
Homocysteine toxicity in Escherichia coli is caused by a perturbation of branched-chain amino acid biosynthesis. J Bacteriol (2005) 0.99
Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst Biol (2008) 0.91
Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng (2003) 5.53
Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res (2004) 3.61
OptStrain: a computational framework for redesign of microbial production systems. Genome Res (2004) 2.80
Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics (2007) 2.74
In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng (2005) 2.63
A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189. PLoS Comput Biol (2009) 2.02
An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng (2005) 1.90
Optimization-based framework for inferring and testing hypothesized metabolic objective functions. Biotechnol Bioeng (2003) 1.89
Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol Syst Biol (2009) 1.69
Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain. J Biol Chem (2009) 1.55
OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput Biol (2010) 1.51
OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput Biol (2012) 1.48
Predicting biological system objectives de novo from internal state measurements. BMC Bioinformatics (2008) 1.42
Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions. Biophys J (2004) 1.42
Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metab Eng (2011) 1.42
Synthetic biology of cyanobacteria: unique challenges and opportunities. Front Microbiol (2013) 1.38
Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock. Biotechnol Bioeng (2003) 1.34
Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism. PLoS One (2011) 1.31
Metabolic flux elucidation for large-scale models using 13C labeled isotopes. Metab Eng (2007) 1.31
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinformatics (2012) 1.26
OptCircuit: an optimization based method for computational design of genetic circuits. BMC Syst Biol (2008) 1.24
Mathematical optimization applications in metabolic networks. Metab Eng (2012) 1.19
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. BMC Syst Biol (2010) 1.17
Analysis of NADPH supply during xylitol production by engineered Escherichia coli. Biotechnol Bioeng (2009) 1.17
A computational framework for the topological analysis and targeted disruption of signal transduction networks. Biophys J (2006) 1.12
FamClash: a method for ranking the activity of engineered enzymes. Proc Natl Acad Sci U S A (2004) 1.06
d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities. ACS Synth Biol (2014) 1.05
Computational design of Candida boidinii xylose reductase for altered cofactor specificity. Protein Sci (2009) 1.02
IPRO: an iterative computational protein library redesign and optimization procedure. Biophys J (2006) 1.02
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans. BMC Syst Biol (2011) 0.99
An integrated computational and experimental study for overproducing fatty acids in Escherichia coli. Metab Eng (2012) 0.98
Recent advances in computational protein design. Curr Opin Struct Biol (2011) 0.97
Identification of optimal measurement sets for complete flux elucidation in metabolic flux analysis experiments. Biotechnol Bioeng (2008) 0.94
Computational tools for metabolic engineering. Metab Eng (2012) 0.94
Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. PLoS One (2012) 0.94
Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity. Biophys J (2007) 0.94
Using multiple sequence correlation analysis to characterize functionally important protein regions. Protein Eng (2003) 0.92
Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach. Proc Natl Acad Sci U S A (2003) 0.92
Review of the BRENDA Database. Metab Eng (2003) 0.91
Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites. Bioinformatics (2005) 0.91
Improved computational performance of MFA using elementary metabolite units and flux coupling. Metab Eng (2009) 0.90
Using a residue clash map to functionally characterize protein recombination hybrids. Protein Eng (2003) 0.88
A computational procedure for optimal engineering interventions using kinetic models of metabolism. Biotechnol Prog (2006) 0.87
Optimal protein library design using recombination or point mutations based on sequence-based scoring functions. Protein Eng Des Sel (2007) 0.87
OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold. Protein Sci (2009) 0.87
eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments. Nucleic Acids Res (2002) 0.86
Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks. PLoS Comput Biol (2012) 0.85
Construction of an E. Coli genome-scale atom mapping model for MFA calculations. Biotechnol Bioeng (2011) 0.85
Systems metabolic engineering design: fatty acid production as an emerging case study. Biotechnol Bioeng (2014) 0.85
MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies. BMC Bioinformatics (2013) 0.83
Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions. Biotechnol J (2010) 0.81
Predicting out-of-sequence reassembly in DNA shuffling. J Theor Biol (2002) 0.80
DEMSIM: a discrete event based mechanistic simulation platform for gene expression and regulation dynamics. J Theor Biol (2005) 0.79
CLCA: maximum common molecular substructure queries within the MetRxn database. J Chem Inf Model (2014) 0.79
Design of combinatorial protein libraries of optimal size. Proteins (2005) 0.79
Methane oxidation by anaerobic archaea for conversion to liquid fuels. J Ind Microbiol Biotechnol (2014) 0.78
Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks. Biotechnol J (2013) 0.76
The Iterative Protein Redesign and Optimization (IPRO) suite of programs. J Comput Chem (2014) 0.76
OptZyme: computational enzyme redesign using transition state analogues. PLoS One (2013) 0.75
Orchestrating hi-fi annotations. Nat Chem Biol (2012) 0.75