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

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

A mathematical framework for yield ( vs. rate) optimization in constraint-based modeling and applications in metabolic engineering

(2018) Steffen Klamt et al.   METABOLIC ENGINEERING

Use of CellNetAnalyzer in biotechnology and metabolic engineering

(2017) Axel von Kamp et al.   JOURNAL OF BIOTECHNOLOGY

Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks

(2017) A. Kiparissides et al.   METABOLIC ENGINEERING

EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model

(2017) Oliver Hädicke et al.   Scientific Reports

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

(2017) Steffen Klamt et al.   PLoS Computational Biology

Sugar Synthesis from CO2 in Escherichia coli

(2016) Niv Antonovsky et al.   CELL

Which sets of elementary flux modes form thermodynamically feasible flux distributions?

(2016) Matthias P. Gerstl et al.   FEBS Journal

A synthetic pathway for the fixation of carbon dioxide in vitro

(2016) Thomas Schwander et al.   SCIENCE

Elementary Vectors and Conformal Sums in Polyhedral Geometry and their Relevance for Metabolic Pathway Analysis

(2016) Stefan Müller et al.   Frontiers in Genetics

Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy

(2016) Michael Volpers et al.   PLoS One

tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks

(2015) Matthias P. Gerstl et al.   BIOINFORMATICS

Heading in the right direction: thermodynamics-based network analysis and pathway engineering

(2015) Meric Ataman et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computational methods in metabolic engineering for strain design

(2015) Matthew R Long et al.   CURRENT OPINION IN BIOTECHNOLOGY

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Microbial electron transport and energy conservation – the foundation for optimizing bioelectrochemical systems

(2015) Frauke Kracke et al.   Frontiers in Microbiology

Escherichia coli pyruvate:flavodoxin oxidoreductase, YdbK - regulation of expression and biological roles in protection against oxidative stress

(2015) Takayuki Nakayama et al.   GENES & GENETIC SYSTEMS

Metabolic states with maximal specific rate carry flux through an elementary flux mode

(2014) Meike T. Wortel et al.   FEBS Journal

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

Fast thermodynamically constrained flux variability analysis

(2013) Arne C. Müller et al.   BIOINFORMATICS

Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes

(2013) Stefan Müller et al.   JOURNAL OF THEORETICAL BIOLOGY

Consistent Estimation of Gibbs Energy Using Component Contributions

(2013) Elad Noor et al.   PLoS Computational Biology

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

(2012) Elad Noor et al.   BIOINFORMATICS

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Integrated Electromicrobial Conversion of CO2 to Higher Alcohols

(2012) H. Li et al.   SCIENCE

System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes

(2012) Stefan J. Jol et al.   PLoS Computational Biology

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

An application programming interface for CellNetAnalyzer

(2011) Steffen Klamt et al.   BIOSYSTEMS

A survey of carbon fixation pathways through a quantitative lens

(2011) Arren Bar-Even et al.   JOURNAL OF EXPERIMENTAL BOTANY

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

eQuilibrator--the biochemical thermodynamics calculator

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

Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design

(2010) Brett A Boghigian et al.   BMC Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Cross-species analysis traces adaptation of Rubisco toward optimality in a low-dimensional landscape

(2010) Yonatan Savir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative assignment of reaction directionality in constraint-based models of metabolism: Application to Escherichia coli

(2009) R.M.T. Fleming et al.   BIOPHYSICAL CHEMISTRY

Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism

(2008) Cong T. Trinh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

(2008) Nicola Zamboni et al.   BMC BIOINFORMATICS