From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline

Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism

(2019) Daniel R. Weilandt et al.   BIOPHYSICAL JOURNAL

Metabolic flux responses to deletion of 20 core enzymes reveal flexibility and limits of E. coli metabolism

(2019) Christopher P. Long et al.   METABOLIC ENGINEERING

Advances in analytical tools for high throughput strain engineering

(2018) Esteban Marcellin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures

(2018) Hiroyuki Kurata et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Elucidation of photoautotrophic carbon flux topology in Synechocystis PCC 6803 using genome-scale carbon mapping models

(2018) Saratram Gopalakrishnan et al.   METABOLIC ENGINEERING

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

(2018) Meike T. Wortel et al.   PLoS Computational Biology

Genome-scale fluxome of Synechococcus elongatus UTEX 2973 using transient 13C-labeling data

(2018) John I. Hendry et al.   PLANT PHYSIOLOGY

Quantifying enzyme activity in living cells

(2017) Agnes Zotter et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Engineering biological systems using automated biofoundries

(2017) Ran Chao et al.   METABOLIC ENGINEERING

Enzyme I facilitates reverse flux from pyruvate to phosphoenolpyruvate in Escherichia coli

(2017) Christopher P. Long et al.   Nature Communications

Automated multiplex genome-scale engineering in yeast

(2017) Tong Si et al.   Nature Communications

Fully Automated One-Step Synthesis of Single-Transcript TALEN Pairs Using a Biological Foundry

(2017) Ran Chao et al.   ACS Synthetic Biology

Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity

(2017) Ed Reznik et al.   Cell Reports

Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli

(2017) Pierre Millard et al.   PLoS Computational Biology

Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism

(2016) Christopher P. Long et al.   METABOLIC ENGINEERING

Optimal tracers for parallel labeling experiments and 13 C metabolic flux analysis: A new precision and synergy scoring system

(2016) Scott B. Crown et al.   METABOLIC ENGINEERING

Metabolite concentrations, fluxes and free energies imply efficient enzyme usage

(2016) Junyoung O Park et al.   Nature Chemical Biology

BRENDA in 2017: new perspectives and new tools in BRENDA

(2016) Sandra Placzek et al.   NUCLEIC ACIDS RESEARCH

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

(2016) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Systems-level analysis of mechanisms regulating yeast metabolic flux

(2016) S. R. Hackett et al.   SCIENCE

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

(2016) Ali Khodayari et al.   Nature Communications

Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach

(2016) Pedro A. Saa et al.   Scientific Reports

Macromolecular crowding explains overflow metabolism in cells

(2016) Alexei Vazquez et al.   Scientific Reports

The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

(2016) Elad Noor et al.   PLoS Computational Biology

Gobal optimization of hybrid kinetic/FBA models via outer-approximation

(2015) Carlos Pozo et al.   COMPUTERS & CHEMICAL ENGINEERING

13C metabolic flux analysis at a genome-scale

(2015) Saratram Gopalakrishnan et al.   METABOLIC ENGINEERING

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

Building biological foundries for next-generation synthetic biology

(2015) Ran Chao et al.   Science China-Life Sciences

Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics

(2015) Aarash Bordbar et al.   Cell Systems

13C-MFA delineates the photomixotrophic metabolism ofSynechocystissp. PCC 6803 under light- and carbon-sufficient conditions

(2014) Le You et al.   Biotechnology Journal

Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook

(2014) Christopher P Long et al.   CURRENT OPINION IN BIOTECHNOLOGY

Macromolecular Crowding Effect upon in Vitro Enzyme Kinetics: Mixed Activation–Diffusion Control of the Oxidation of NADH by Pyruvate Catalyzed by Lactate Dehydrogenase

(2014) Cristina Balcells et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Systematic metabolic engineering of Escherichia coli for high-yield production of fuel bio-chemical 2,3-butanediol

(2014) Youqiang Xu et al.   METABOLIC ENGINEERING

Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways

(2014) Yun Lee et al.   METABOLIC ENGINEERING

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

(2014) Ali Khodayari et al.   METABOLIC ENGINEERING

Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks

(2013) Ali R. Zomorrodi et al.   Biotechnology Journal

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

(2013) Kieran Smallbone et al.   FEBS LETTERS

COMPLETE-MFA: Complementary parallel labeling experiments technique for metabolic flux analysis

(2013) Robert W. Leighty et al.   METABOLIC ENGINEERING

Phosphoketolase Pathway for Xylose Catabolism in Clostridium acetobutylicum Revealed by 13C Metabolic Flux Analysis

(2012) L. Liu et al.   JOURNAL OF BACTERIOLOGY

Parallel labeling experiments with [U-13C]glucose validate E. coli metabolic network model for 13C metabolic flux analysis

(2012) Robert W. Leighty et al.   METABOLIC ENGINEERING

Metabolic engineering and flux analysis of Corynebacterium glutamicum for L-serine production

(2012) ShuJuan Lai et al.   Science China-Life Sciences

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA

(2011) Peng Xu et al.   METABOLIC ENGINEERING

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

(2010) Neema Jamshidi et al.   BIOPHYSICAL JOURNAL

Escherichia coli W as a new platform strain for the enhanced production of L-Valine by systems metabolic engineering

(2010) Jin Hwan Park et al.   BIOTECHNOLOGY AND BIOENGINEERING

Resolving the TCA cycle and pentose-phosphate pathway of Clostridium acetobutylicum ATCC 824: Isotopomer analysis, in vitro activities and expression analysis

(2010) Scott B. Crown et al.   Biotechnology Journal

Evaluation of Genetic Manipulation Strategies on d-Lactate Production by Escherichia coli

(2010) Li Zhou et al.   CURRENT MICROBIOLOGY

Metabolic flux analysis in eukaryotes

(2010) Jens Niklas et al.   CURRENT OPINION IN BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Non-linear effects of macromolecular crowding on enzymatic activity of multi-copper oxidase

(2009) Irina Pozdnyakova et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Evaluation of 13C isotopic tracers for metabolic flux analysis in mammalian cells

(2009) Christian M. Metallo et al.   JOURNAL OF BIOTECHNOLOGY

Metabolic flux analysis in mammalian cell culture

(2009) Lake-Ee Quek et al.   METABOLIC ENGINEERING

Production of Glucaric Acid from a Synthetic Pathway in Recombinant Escherichia coli

(2008) T. S. Moon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic engineering of Escherichia coli for the production of malic acid

(2008) Soo Yun Moon et al.   BIOCHEMICAL ENGINEERING JOURNAL

Ensemble Modeling of Metabolic Networks

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

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

(2008) Neema Jamshidi et al.   Molecular Systems Biology

Metabolic flux analysis inEscherichia coli by integrating isotopic dynamic and isotopic stationary13C labeling data

(2007) Jochen Schaub et al.   BIOTECHNOLOGY AND BIOENGINEERING