Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Logical transformation of genome-scale metabolic models for gene level applications and analysis

(2015) Cheng Zhang et al.   BIOINFORMATICS

Predicting internal cell fluxes at sub-optimal growth

(2015) André Schultz et al.   BMC Systems Biology

Next-generation genome-scale models for metabolic engineering

(2015) Zachary A King et al.   CURRENT OPINION IN BIOTECHNOLOGY

Quantitative prediction of genome-wide resource allocation in bacteria

(2015) Anne Goelzer et al.   METABOLIC ENGINEERING

In SilicoConstraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

(2015) Paulo Maia et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data

(2015) Luca Gerosa et al.   Cell Systems

An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli

(2014) J. Carrera et al.   Molecular Systems Biology

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Network-level architecture and the evolutionary potential of underground metabolism

(2014) R. A. Notebaart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks

(2014) Hojung Nam et al.   PLoS Computational Biology

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks

(2014) Axel von Kamp et al.   PLoS Computational Biology

Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering

(2013) Cameron Cotten et al.   Biotechnology Journal

Somewhat in control—the role of transcription in regulating microbial metabolic fluxes

(2013) Karl Kochanowski et al.   CURRENT OPINION IN BIOTECHNOLOGY

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

(2013) R. L. Chang et al.   SCIENCE

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Random sampling of elementary flux modes in large-scale metabolic networks

(2012) Daniel Machado et al.   BIOINFORMATICS

Designing optimal cell factories: integer programming couples elementary mode analysis with regulation

(2012) Christian Jungreuthmayer et al.   BMC Systems Biology

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks

(2012) Ana Rita Brochado et al.   PLoS Computational Biology

Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

(2012) Roi Adadi et al.   PLoS Computational Biology

Chapter 11: Genome-Wide Association Studies

(2012) William S. Bush et al.   PLoS Computational Biology

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

(2011) Paul A Jensen et al.   BMC Systems Biology

EMILiO: A fast algorithm for genome-scale strain design

(2011) Laurence Yang et al.   METABOLIC ENGINEERING

Predicting selective drug targets in cancer through metabolic networks

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

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

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

(2010) Joonhoon Kim et al.   BMC Systems Biology

CASOP: A Computational Approach for Strain Optimization aiming at high Productivity

(2010) Oliver Hädicke et al.   JOURNAL OF BIOTECHNOLOGY

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord 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

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

Computing the shortest elementary flux modes in genome-scale metabolic networks

(2009) Luis F. de Figueiredo et al.   BIOINFORMATICS

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

(2009) Caroline Colijn et al.   PLoS Computational Biology

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

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

Use of Randomized Sampling for Analysis of Metabolic Networks

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

Context-Specific Metabolic Networks Are Consistent with Experiments

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