Related references
Note: Only part of the references are listed.Heading in the right direction: thermodynamics-based network analysis and pathway engineering
Meric Ataman et al.
CURRENT OPINION IN BIOTECHNOLOGY (2015)
Reply to Do genome-scale models need exact solvers or clearer standards?
Leonid Chindelevitch et al.
MOLECULAR SYSTEMS BIOLOGY (2015)
Do genome-scale models need exact solvers or clearer standards?
Ali Ebrahim et al.
MOLECULAR SYSTEMS BIOLOGY (2015)
A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration
K. Yizhak et al.
Molecular Systems Biology (2014)
Constraint-based models predict metabolic and associated cellular functions
Aarash Bordbar et al.
NATURE REVIEWS GENETICS (2014)
An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models
Leonid Chindelevitch et al.
NATURE COMMUNICATIONS (2014)
Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach
Ali Navid et al.
BMC SYSTEMS BIOLOGY (2012)
Multidimensional Optimality of Microbial Metabolism
Robert Schuetz et al.
SCIENCE (2012)
Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters
Roi Adadi et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011
Jeffrey D. Orth et al.
MOLECULAR SYSTEMS BIOLOGY (2011)
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
Harry Yim et al.
NATURE CHEMICAL BIOLOGY (2011)
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Jan Schellenberger et al.
NATURE PROTOCOLS (2011)
A protocol for generating a high-quality genome-scale metabolic reconstruction
Ines Thiele et al.
NATURE PROTOCOLS (2010)
Context-specific metabolic networks are consistent with experiments
Scott A. Becker et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
Q. K. Beg et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
Robert Schuetz et al.
MOLECULAR SYSTEMS BIOLOGY (2007)
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
Adam M. Feist et al.
MOLECULAR SYSTEMS BIOLOGY (2007)
Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation
Jin Hwan Park et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Phenotypic variation in bacteria: the role of feedback regulation
WK Smits et al.
NATURE REVIEWS MICROBIOLOGY (2006)
Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli
A Nanchen et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)
Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling
R Mahadevan et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)
Robust optimization for intensity modulated radiation therapy treatment planning under uncertainty
M Chu et al.
PHYSICS IN MEDICINE AND BIOLOGY (2005)
The activity reaction core and plasticity of metabolic networks
Eivind Almaas et al.
PLOS COMPUTATIONAL BIOLOGY (2005)
Cell individuality: the bistability of competence development
SV Avery
TRENDS IN MICROBIOLOGY (2005)
Optimality and evolutionary tuning of the expression level of a protein
E Dekel et al.
NATURE (2005)
Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli
A Perrenoud et al.
JOURNAL OF BACTERIOLOGY (2005)
Global organization of metabolic fluxes in the bacterium Escherichia coli
E Almaas et al.
NATURE (2004)
Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
SS Fong et al.
NATURE GENETICS (2004)
OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
AP Burgard et al.
BIOTECHNOLOGY AND BIOENGINEERING (2003)
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
JL Reed et al.
GENOME BIOLOGY (2003)
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
RU Ibarra et al.
NATURE (2002)
Metabolic network structure determines key aspects of functionality and regulation
J Stelling et al.
NATURE (2002)
Analysis of optimality in natural and perturbed metabolic networks
D Segrè et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Regulation of gene expression in flux balance models of metabolism
MW Covert et al.
JOURNAL OF THEORETICAL BIOLOGY (2001)
Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments
AP Burgard et al.
BIOTECHNOLOGY PROGRESS (2001)