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

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

(2012) Ida Schomburg et al.   NUCLEIC ACIDS RESEARCH

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

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

(2011) Jan Schellenberger et al.   Nature Protocols

Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation

(2011) Joshua Lequieu et al.   PLoS Computational Biology

Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models

(2010) Neema Jamshidi et al.   BIOPHYSICAL JOURNAL

Modeling of uncertainties in biochemical reactions

(2010) Ljubiša Mišković et al.   BIOTECHNOLOGY AND BIOENGINEERING

Towards a genome-scale kinetic model of cellular metabolism

(2010) Kieran Smallbone et al.   BMC Systems Biology

Network thermodynamics in the post-genomic era

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

Kinetic and Thermodynamic Aspects of Enzyme Control and Regulation†

(2010) Johann M. Rohwer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Production of biofuels and biochemicals: in need of an ORACLE

(2010) Ljubisa Miskovic et al.   TRENDS IN BIOTECHNOLOGY

Industrial systems biology

(2009) José Manuel Otero et al.   BIOTECHNOLOGY AND BIOENGINEERING

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

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

Growth-limiting Intracellular Metabolites in Yeast Growing under Diverse Nutrient Limitations

(2009) Viktor M. Boer et al.   MOLECULAR BIOLOGY OF THE CELL

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

(2009) Christopher S Henry et al.   GENOME BIOLOGY

Ensemble Modeling of Metabolic Networks

(2008) Linh M. Tran et al.   BIOPHYSICAL JOURNAL

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

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

Separation and mass spectrometry in microbial metabolomics

(2008) David E Garcia et al.   CURRENT OPINION IN MICROBIOLOGY

Formulating genome-scale kinetic models in the post-genome era

(2008) Neema Jamshidi et al.   Molecular Systems Biology

Reconstruction of biochemical networks in microorganisms

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