4.6 Article

Avoiding the Enumeration of Infeasible Elementary Flux Modes by Including Transcriptional Regulatory Rules in the Enumeration Process Saves Computational Costs

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition

Kristopher A. Hunt et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks

Axel von Kamp et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Review Biochemical Research Methods

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

Juergen Zanghellini et al.

BIOTECHNOLOGY JOURNAL (2013)

Article Biochemical Research Methods

Comparison and improvement of algorithms for computing minimal cut sets

Christian Jungreuthmayer et al.

BMC BIOINFORMATICS (2013)

Article Biochemical Research Methods

Fast Computation of Minimal Cut Sets in Metabolic Networks with a Berge Algorithm That Utilizes Binary Bit Pattern Trees

Christian Jungreuthmayer et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2013)

Article Biochemical Research Methods

Boolean modeling of biological regulatory networks: A methodology tutorial

Assieh Saadatpour et al.

METHODS (2013)

Article Biochemical Research Methods

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

Daniel Machado et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks

Abdelhalim Larhlimi et al.

BMC BIOINFORMATICS (2012)

Article Mathematical & Computational Biology

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

Christian Jungreuthmayer et al.

BMC SYSTEMS BIOLOGY (2012)

Article Mathematics, Applied

New modification of the double description method for constructing the skeleton of a polyhedral cone

N. Yu. Zolotykh

COMPUTATIONAL MATHEMATICS AND MATHEMATICAL PHYSICS (2012)

Article Biochemistry & Molecular Biology

Boolean modeling in systems biology: an overview of methodology and applications

Rui-Sheng Wang et al.

PHYSICAL BIOLOGY (2012)

Article Mathematical & Computational Biology

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

Paul A. Jensen et al.

BMC SYSTEMS BIOLOGY (2011)

Article Biotechnology & Applied Microbiology

Computing complex metabolic intervention strategies using constrained minimal cut sets

Oliver Haedicke et al.

METABOLIC ENGINEERING (2011)

Article Computer Science, Theory & Methods

Parallelization of Nullspace Algorithm for the computation of metabolic pathways

Dimitrije Jevremovic et al.

PARALLEL COMPUTING (2011)

Article Biochemical Research Methods

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

Marco Terzer et al.

BIOINFORMATICS (2008)

Article Mathematical & Computational Biology

Structural and functional analysis of cellular networks with CellNetAnalyzer

Steffen Klamt et al.

BMC SYSTEMS BIOLOGY (2007)

Article Biochemical Research Methods

Metatool 5.0: fast and flexible elementary modes analysis

Axel von Kamp et al.

BIOINFORMATICS (2006)

Article Biochemical Research Methods

Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis

Jean-Marc Schwartz et al.

BMC BIOINFORMATICS (2006)

Article Biochemical Research Methods

Computation of elementary modes: a unifying framework and the new binary approach

J Gagneur et al.

BMC BIOINFORMATICS (2004)

Article Multidisciplinary Sciences

Integrating high-throughput and computational data elucidates bacterial networks

MW Covert et al.

NATURE (2004)

Article Biochemistry & Molecular Biology

Combinatorial complexity of pathway analysis in metabolic networks

S Klamt et al.

MOLECULAR BIOLOGY REPORTS (2002)

Article Biochemistry & Molecular Biology

Identification and functions of new transporters in yeast mitochondria

L Palmieri et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2000)