Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models

In-situ generation of large numbers of genetic combinations for metabolic reprogramming via CRISPR-guided base editing

(2021) Yu Wang et al.   Nature Communications

Automatic construction of metabolic models with enzyme constraints

(2020) Pavlos Stephanos Bekiaris et al.   BMC BIOINFORMATICS

Growth of E. coli on formate and methanol via the reductive glycine pathway

(2020) Seohyoung Kim et al.   Nature Chemical Biology

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

(2020) Pierre Salvy et al.   Nature Communications

An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli

(2020) Hai He et al.   METABOLIC ENGINEERING

High-throughput enrichment of temperature-sensitive argininosuccinate synthetase for two-stage citrulline production in E. coli

(2020) Thorben Schramm et al.   METABOLIC ENGINEERING

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

(2020) David Heckmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BRENDA, the ELIXIR core data resource in 2021: new developments and updates

(2020) Antje Chang et al.   NUCLEIC ACIDS RESEARCH

Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

(2019) Ilaria Massaiu et al.   Microbial Cell Factories

Constructing a synthetic pathway for acetyl-coenzyme A from one-carbon through enzyme design

(2019) Xiaoyun Lu et al.   Nature Communications

Regulation of arginine biosynthesis, catabolism and transport in Escherichia coli

(2019) Daniel Charlier et al.   AMINO ACIDS

Novel biosynthesis of L-malate based on overflow metabolism in Escherichia coli

(2019) Jiangfeng Ma et al.   BIOCHEMICAL ENGINEERING JOURNAL

Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum

(2019) Satyakam Dash et al.   METABOLIC ENGINEERING

Energy metabolism controls phenotypes by protein efficiency and allocation

(2019) Yu Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of an engineered carbamoyl phosphate synthetase with released sensitivity to feedback inhibition by site-directed mutation and casting error-prone PCR

(2019) Su Shen et al.   ENZYME AND MICROBIAL TECHNOLOGY

Metabolic control analysis of L-tryptophan production with Escherichia coli based on data from short-term perturbation experiments

(2019) Julia Tröndle et al.   JOURNAL OF BIOTECHNOLOGY

Systematic design and in vitro validation of novel one-carbon assimilation pathways

(2019) Xue Yang et al.   METABOLIC ENGINEERING

Exploring the combinatorial space of complete pathways to chemicals

(2018) Lin Wang et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method

(2018) Bin Du et al.   BIOPHYSICAL JOURNAL

Modeling the multi-scale mechanisms of macromolecular resource allocation

(2018) Laurence Yang et al.   CURRENT OPINION IN MICROBIOLOGY

Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential

(2018) Johannes Asplund-Samuelsson 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

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

(2018) Colton J. Lloyd et al.   PLoS Computational Biology

A Bird’s-Eye View of Enzyme Evolution: Chemical, Physicochemical, and Physiological Considerations

(2018) Dan Davidi et al.   CHEMICAL REVIEWS

OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli

(2018) Oliver Hädicke et al.   PLoS Computational Biology

Design and in vitro realization of carbon-conserving photorespiration

(2018) Devin L. Trudeau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating Metabolic Equilibrium Constants: Progress and Future Challenges

(2018) Bin Du et al.   TRENDS IN BIOCHEMICAL SCIENCES

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

(2018) David Heckmann et al.   Nature Communications

Engineering Escherichia coli for poly-(3-hydroxybutyrate) production guided by genome-scale metabolic network analysis

(2017) Yangyang Zheng et al.   ENZYME AND MICROBIAL TECHNOLOGY

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Coupling between d-3-phosphoglycerate dehydrogenase and d-2-hydroxyglutarate dehydrogenase drives bacterial l-serine synthesis

(2017) Wen Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic Models of Protein Allocation Call for the Kinetome

(2017) Avlant Nilsson et al.   Cell Systems

Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitrokcatmeasurements

(2016) Dan Davidi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Elad Noor et al.   PLoS Computational Biology

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

(2016) Jonathan M. Monk et al.   Cell Systems

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

Metabolic engineering ofCorynebacterium glutamicumfor the production of L-ornithine

(2014) Seo Yun Kim et al.   BIOTECHNOLOGY AND BIOENGINEERING

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

(2014) Joanne K Liu et al.   BMC Systems Biology

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

(2014) Elad Noor et al.   PLoS Computational Biology

Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins

(2013) Kaspar Valgepea et al.   Molecular BioSystems

Glycolytic strategy as a tradeoff between energy yield and protein cost

(2013) A. Flamholz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biosynthesis of ethylene glycol in Escherichia coli

(2012) Huaiwei Liu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes

(2012) Arren Bar-Even et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage

(2012) Elad Noor et al.   BIOINFORMATICS

PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life

(2012) M. Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Systems metabolic engineering of microorganisms for natural and non-natural chemicals

(2012) Jeong Wook Lee et al.   Nature Chemical Biology

Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

(2012) Roi Adadi et al.   PLoS Computational Biology

Recommendations for terminology and databases for biochemical thermodynamics

(2011) Robert A. Alberty et al.   BIOPHYSICAL CHEMISTRY

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

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

eQuilibrator--the biochemical thermodynamics calculator

(2011) A. Flamholz et al.   NUCLEIC ACIDS RESEARCH

Network thermodynamics in the post-genomic era

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

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

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

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

How mitochondria produce reactive oxygen species

(2008) Michael P. Murphy   BIOCHEMICAL JOURNAL