Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks

(2011) Siu Hung Joshua Chan et al.   BIOINFORMATICS

Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models

(2011) Jan Schellenberger et al.   BIOPHYSICAL JOURNAL

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data

(2011) Ali R Zomorrodi et al.   BMC Systems Biology

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

(2011) Caroline B Milne et al.   BMC Systems Biology

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

(2011) Aarash Bordbar et al.   BMC Systems Biology

Analysis of complex metabolic behavior through pathway decomposition

(2011) Kuhn Ip et al.   BMC Systems Biology

The role of cellular objectives and selective pressures in metabolic pathway evolution

(2011) Hojung Nam et al.   CURRENT OPINION IN BIOTECHNOLOGY

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA

(2011) Peng Xu et al.   METABOLIC ENGINEERING

Probabilistic pathway construction

(2011) Mona Yousofshahi et al.   METABOLIC ENGINEERING

Predicting selective drug targets in cancer through metabolic networks

(2011) O. Folger et al.   Molecular Systems Biology

Metabolic modeling of endosymbiont genome reduction on a temporal scale

(2011) K. Yizhak et al.   Molecular Systems Biology

Economics of membrane occupancy and respiro-fermentation

(2011) K. Zhuang et al.   Molecular Systems Biology

Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs

(2011) F. Wessely et al.   Molecular Systems Biology

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

(2011) H. U. Kim et al.   Molecular Systems Biology

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

An integrated approach to characterize genetic interaction networks in yeast metabolism

(2011) Balázs Szappanos et al.   NATURE GENETICS

Systems-biology approaches for predicting genomic evolution

(2011) Balázs Papp et al.   NATURE REVIEWS GENETICS

Computational Design of Auxotrophy-Dependent Microbial Biosensors for Combinatorial Metabolic Engineering Experiments

(2011) Naama Tepper et al.   PLoS One

Serine Biosynthesis with One Carbon Catabolism and the Glycine Cleavage System Represents a Novel Pathway for ATP Generation

(2011) Alexei Vazquez et al.   PLoS One

Impact of gene expression noise on organismal fitness and the efficacy of natural selection

(2011) Z. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organization of Intracellular Reactions with Rationally Designed RNA Assemblies

(2011) C. J. Delebecque et al.   SCIENCE

Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis

(2011) Bhushan K. Bonde et al.   PLoS Computational Biology

Flux-Balance Modeling of Plant Metabolism

(2011) Lee J. Sweetlove et al.   Frontiers in Plant Science

Exploring metabolic pathways in genome-scale networks via generating flux modes

(2010) A. Rezola et al.   BIOINFORMATICS

Functional integration of a metabolic network model and expression data without arbitrary thresholding

(2010) Paul A. Jensen et al.   BIOINFORMATICS

Functional Characterization of Alternate Optimal Solutions of Escherichia coli's Transcriptional and Translational Machinery

(2010) Ines Thiele et al.   BIOPHYSICAL JOURNAL

Systematizing the generation of missing metabolic knowledge

(2010) Jeffrey D. Orth et al.   BIOTECHNOLOGY AND BIOENGINEERING

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

Characterization of Proton Production and Consumption Associated with Microbial Metabolism

(2010) Karthikeyan Srinivasan et al.   BMC BIOTECHNOLOGY

Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

(2010) Carola Huthmacher et al.   BMC Systems Biology

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

(2010) Martin I Sigurdsson et al.   BMC Systems Biology

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

(2010) Joonhoon Kim et al.   BMC Systems Biology

Data integration and analysis of biological networks

(2010) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

Which Metabolic Pathways Generate and Characterize the Flux Space? A Comparison among Elementary Modes, Extreme Pathways and Minimal Generators

(2010) Francisco Llaneras et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism

(2010) R.M.T. Fleming et al.   JOURNAL OF THEORETICAL BIOLOGY

Understanding the physiology of Lactobacillus plantarum at zero growth

(2010) Philippe Goffin et al.   Molecular Systems Biology

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

(2010) Christoph Gille et al.   Molecular Systems Biology

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Emergent cooperation in microbial metabolism

(2010) Edwin H Wintermute et al.   Molecular Systems Biology

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

(2010) Livnat Jerby et al.   Molecular Systems Biology

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

(2010) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

(2010) Radhakrishnan Mahadevan et al.   NATURE REVIEWS MICROBIOLOGY

Blueprint for antimicrobial hit discovery targeting metabolic networks

(2010) Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design and analysis of synthetic carbon fixation pathways

(2010) A. Bar-Even et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model

(2010) Roger L. Chang et al.   PLoS Computational Biology

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

(2010) Sergio Bordel et al.   PLoS Computational Biology

An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models

(2010) Dipak Barua et al.   PLoS Computational Biology

Flux balance analysis accounting for metabolite dilution

(2010) Tomer Benyamini et al.   GENOME BIOLOGY

Network-based prediction of metabolic enzymes' subcellular localization

(2009) S. Mintz-Oron et al.   BIOINFORMATICS

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

(2009) N. Tepper et al.   BIOINFORMATICS

Quantitative assignment of reaction directionality in constraint-based models of metabolism: Application to Escherichia coli

(2009) R.M.T. Fleming et al.   BIOPHYSICAL CHEMISTRY

Decomposing complex reaction networks using random sampling, principal component analysis, and basis rotation

(2009) Christian L Barrett et al.   BMC Systems Biology

In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study

(2009) Reed Taffs et al.   BMC Systems Biology

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology

Systems-Level Engineering of Nonfermentative Metabolism in Yeast

(2009) C. J. Kennedy et al.   GENETICS

Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns

(2009) C. Kaleta et al.   GENOME RESEARCH

Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints

(2009) Rogier J P van Berlo et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Capturing the essence of a metabolic network: A flux balance analysis approach

(2009) Ettore Murabito et al.   JOURNAL OF THEORETICAL BIOLOGY

Improving NADPH availability for natural product biosynthesis in Escherichia coli by metabolic engineering

(2009) Joseph A. Chemler et al.   METABOLIC ENGINEERING

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

(2009) Adam M. Feist et al.   METABOLIC ENGINEERING

Genome-scale gene/reaction essentiality and synthetic lethality analysis

(2009) Patrick F Suthers et al.   Molecular Systems Biology

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Automatic policing of biochemical annotations using genomic correlations

(2009) Tzu-Lin Hsiao et al.   Nature Chemical Biology

Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima

(2009) Y. Zhang et al.   SCIENCE

Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation

(2009) Bas Teusink et al.   PLoS Computational Biology

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

(2009) Ines Thiele et al.   PLoS Computational Biology

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses

(2008) C. T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism

(2008) Cong T. Trinh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

DESHARKY: automatic design of metabolic pathways for optimal cell growth

(2008) Guillermo Rodrigo et al.   BIOINFORMATICS

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

(2008) Markus W. Covert et al.   BIOINFORMATICS

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

(2008) Matthew D. Jankowski et al.   BIOPHYSICAL JOURNAL

Estimating the size of the solution space of metabolic networks

(2008) Alfredo Braunstein et al.   BMC BIOINFORMATICS

Predicting biological system objectives de novo from internal state measurements

(2008) Erwin P Gianchandani et al.   BMC BIOINFORMATICS

Exploiting the pathway structure of metabolism to reveal high-order epistasis

(2008) Marcin Imielinski et al.   BMC Systems Biology

Use of Randomized Sampling for Analysis of Metabolic Networks

(2008) Jan Schellenberger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Strategy to Calculate the Patterns of Nutrient Consumption by Microorganisms Applying a Two-Level Optimisation Principle to Reconstructed Metabolic Networks

(2008) Miguel Ponce de León et al.   JOURNAL OF BIOLOGICAL PHYSICS

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

(2008) Jong Min Lee et al.   PLoS Computational Biology

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology

Is maximization of molar yield in metabolic networks favoured by evolution?

(2007) Stefan Schuster et al.   JOURNAL OF THEORETICAL BIOLOGY