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

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

(2013) Christian Jungreuthmayer et al.   BIOSYSTEMS

The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway

(2012) Michele Fabris et al.   PLANT JOURNAL

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

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Parallelization of Nullspace Algorithm for the computation of metabolic pathways

(2011) Dimitrije Jevremović et al.   PARALLEL COMPUTING

Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana

(2011) Masaaki Tachibana et al.   PHOTOSYNTHESIS RESEARCH

Predicting novel pathways in genome-scale metabolic networks

(2010) Stefan Schuster et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Which Metabolic Pathways Generate and Characterize the Flux Space? A Comparison among Elementary Modes, Extreme Pathways and Minimal Generators

(2010) Francisco Llaneras et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

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

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

Decomposing complex reaction networks using random sampling, principal component analysis, and basis rotation

(2009) Christian L Barrett et al.   BMC Systems Biology

In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study

(2009) Reed Taffs 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

Genome-scale metabolic networks

(2009) Marco Terzer et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

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

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

Decomposition of complex microbial behaviors into resource-based stress responses

(2008) Ross P. Carlson   BIOINFORMATICS

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

(2008) Marco Terzer et al.   BIOINFORMATICS

A Model for Carbohydrate Metabolism in the Diatom Phaeodactylum tricornutum Deduced from Comparative Whole Genome Analysis

(2008) Peter G. Kroth et al.   PLoS One