The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren et al.   PLoS Computational Biology

von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models

(2010) R. M. T. Fleming et al.   BIOINFORMATICS

Use of genome-scale metabolic models for understanding microbial physiology

(2010) Liming Liu et al.   FEBS LETTERS

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

BioMet Toolbox: genome-wide analysis of metabolism

(2010) M. Cvijovic et al.   NUCLEIC ACIDS RESEARCH

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

(2010) Sergio Bordel et al.   PLoS Computational Biology

Industrial systems biology

(2009) José Manuel Otero et al.   BIOTECHNOLOGY AND BIOENGINEERING

Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

(2008) Wanwipa Vongsangnak et al.   BMC GENOMICS

The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

(2008) Intawat Nookaew et al.   BMC Systems Biology

Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger

(2008) Mikael Rørdam Andersen et al.   Molecular Systems Biology

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

(2008) Marco A van den Berg et al.   NATURE BIOTECHNOLOGY

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

(2008) A. Funahashi et al.   PROCEEDINGS OF THE IEEE