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

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

(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

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

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

(2015) Noushin Hadadi et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

(2015) Stepan Tymoshenko et al.   PLoS Computational Biology

The Functional Structure of Central Carbon Metabolism in Pseudomonas putida KT2440

(2014) Suresh Sudarsan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Advances in metabolic engineering of yeastSaccharomyces cerevisiaefor production of chemicals

(2014) Irina Borodina et al.   Biotechnology Journal

Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model

(2014) M. Simons et al.   PLANT PHYSIOLOGY

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

(2013) Anirikh Chakrabarti et al.   Biotechnology Journal

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

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

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

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

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

The biomass objective function

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

Intracellular characterization of aerobic glucose metabolism in seven yeast species by 13C flux analysis and metabolomics

(2010) Stefan Christen et al.   FEMS YEAST RESEARCH

Central Carbon Metabolism as a Minimal Biochemical Walk between Precursors for Biomass and Energy

(2010) Elad Noor et al.   MOLECULAR CELL

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

Correlation between TCA cycle flux and glucose uptake rate during respiro-fermentative growth of Saccharomyces cerevisiae

(2009) J. Heyland et al.   MICROBIOLOGY-SGM