Elementary flux modes in a nutshell: Properties, calculation and applications

regEfmtool: Speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic

(2013) Christian Jungreuthmayer et al.   BIOSYSTEMS

Random sampling of elementary flux modes in large-scale metabolic networks

(2012) Daniel Machado et al.   BIOINFORMATICS

Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis

(2012) Yan Zhu et al.   BIOTECHNOLOGY AND BIOENGINEERING

Designing optimal cell factories: integer programming couples elementary mode analysis with regulation

(2012) Christian Jungreuthmayer et al.   BMC Systems Biology

Detecting and investigating substrate cycles in a genome-scale human metabolic network

(2012) Juliane Gebauer et al.   FEBS Journal

Predicting the adaptive evolution of Thermoanaerobacterium saccharolyticum

(2012) Pornkamol Unrean et al.   JOURNAL OF BIOTECHNOLOGY

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

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

Redesigning Escherichia coli Metabolism for Anaerobic Production of Isobutanol

(2011) Cong T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks

(2011) Siu Hung Joshua Chan et al.   BIOINFORMATICS

Do elementary flux modes combine linearly at the “atomic” level? Integrating tracer-based metabolomics data and elementary flux modes

(2011) Jon Pey et al.   BIOSYSTEMS

A new computational method to split large biochemical networks into coherent subnets

(2011) Wynand S Verwoerd   BMC Systems Biology

Analysis of complex metabolic behavior through pathway decomposition

(2011) Kuhn Ip et al.   BMC Systems Biology

Metabolic networks evolve towards states of maximum entropy production

(2011) Pornkamol Unrean et al.   METABOLIC ENGINEERING

From zero to hero—Design-based systems metabolic engineering of Corynebacterium glutamicum for l-lysine production

(2011) Judith Becker et al.   METABOLIC ENGINEERING

Parallelization of Nullspace Algorithm for the computation of metabolic pathways

(2011) Dimitrije Jevremović et al.   PARALLEL COMPUTING

ACoM: A classification method for elementary flux modes based on motif finding

(2010) S. Pérès et al.   BIOSYSTEMS

OptFlux: an open-source software platform for in silico metabolic engineering

(2010) Isabel Rocha et al.   BMC Systems Biology

A Statistical Thermodynamical Interpretation of Metabolism

(2010) Friedrich Srienc et al.   Entropy

On Algebraic Properties of Extreme Pathways in Metabolic Networks

(2010) Dimitrije Jevremovic et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Computing complex metabolic intervention strategies using constrained minimal cut sets

(2010) Oliver Hädicke et al.   METABOLIC ENGINEERING

Metabolic Engineering of Escherichia coli for Efficient Conversion of Glycerol to Ethanol

(2009) C. T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Computing the shortest elementary flux modes in genome-scale metabolic networks

(2009) Luis F. de Figueiredo et al.   BIOINFORMATICS

A note on the complexity of finding and enumerating elementary modes

(2009) Vicente Acuña et al.   BIOSYSTEMS

Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties

(2009) Guido Melzer et al.   BMC Systems Biology

Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns

(2009) C. Kaleta et al.   GENOME RESEARCH

Rational design and construction of an efficient E. coli for production of diapolycopendioic acid

(2009) Pornkamol Unrean et al.   METABOLIC ENGINEERING

Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses

(2008) C. T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Large-scale computation of elementary flux modes with bit pattern trees

(2008) Marco Terzer et al.   BIOINFORMATICS

Modes and cuts in metabolic networks: Complexity and algorithms

(2008) Vicente Acuña et al.   BIOSYSTEMS

Structural robustness of metabolic networks with respect to multiple knockouts

(2007) Jörn Behre et al.   JOURNAL OF THEORETICAL BIOLOGY