redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

(2017) Meric Ataman et al.   PLoS Computational Biology

Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

(2016) Stefano Andreozzi et al.   METABOLIC ENGINEERING

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

(2016) Ali Khodayari et al.   Nature Communications

An algorithm for the reduction of genome-scale metabolic network models to meaningful core models

(2015) Philipp Erdrich et al.   BMC Systems Biology

Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes

(2015) Ljubisa Miskovic et al.   CURRENT OPINION IN BIOTECHNOLOGY

Heading in the right direction: thermodynamics-based network analysis and pathway engineering

(2015) Meric Ataman et al.   CURRENT OPINION IN BIOTECHNOLOGY

Dynamic metabolic models in context: biomass backtracking

(2015) Katja Tummler et al.   Integrative Biology

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

(2015) N. Hadadi et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

(2015) Stepan Tymoshenko et al.   PLoS Computational Biology

Data-driven integration of genome-scale regulatory and metabolic network models

(2015) Saheed Imam et al.   Frontiers in Microbiology

Reducing Recon 2 for steady-state flux analysis of HEK cell culture

(2014) Lake-Ee Quek et al.   JOURNAL OF BIOTECHNOLOGY

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data

(2014) Ali Khodayari et al.   METABOLIC ENGINEERING

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints

(2013) Anirikh Chakrabarti et al.   Biotechnology Journal

The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum

(2013) William R. Harcombe et al.   PLoS Computational Biology

The evolution of metabolic networks of E. coli

(2011) David J Baumler et al.   BMC Systems Biology

Recent advances in reconstruction and applications of genome-scale metabolic models

(2011) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism

(2011) Mohammad Tauqeer Alam et al.   FEBS LETTERS

From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks

(2011) Keng Cher Soh et al.   FEMS YEAST RESEARCH

Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli

(2011) B. R. B. Haverkorn van Rijsewijk et al.   Molecular Systems Biology

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Dispensability of Escherichia coli's latent pathways

(2011) S. P. Cornelius et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

(2010) Karin Radrich et al.   BMC Systems Biology

Network thermodynamics in the post-genomic era

(2010) Keng Cher Soh et al.   CURRENT OPINION IN MICROBIOLOGY

Dynamic modeling of Escherichia coli metabolic and regulatory systems for amino-acid production

(2010) Yoshihiro Usuda et al.   JOURNAL OF BIOTECHNOLOGY

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Production of biofuels and biochemicals: in need of an ORACLE

(2010) Ljubisa Miskovic et al.   TRENDS IN BIOTECHNOLOGY

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

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

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

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

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

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

A critical examination of stoichiometric and path-finding approaches to metabolic pathways

(2008) F. J. Planes et al.   BRIEFINGS IN BIOINFORMATICS