Reconstructing genome-scale metabolic models with merlin

iOD907, the first genome-scale metabolic model for the milk yeastKluyveromyces lactis

(2014) Oscar Dias et al.   Biotechnology Journal

Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis

(2014) Daniel Gomes et al.   BMC GENOMICS

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

(2014) Esa Pitkänen et al.   PLoS Computational Biology

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

Genome-wide metabolic (re-) annotation of Kluyveromyces lactis

(2012) Oscar Dias et al.   BMC GENOMICS

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

(2012) Xueyang Feng et al.   BMC Systems Biology

FAME, the Flux Analysis and Modeling Environment

(2012) Joost Boele et al.   BMC Systems Biology

JSBML: a flexible Java library for working with SBML

(2011) Andreas Dräger et al.   BIOINFORMATICS

BKM-react, an integrated biochemical reaction database

(2011) Maren Lang et al.   BMC BIOCHEMISTRY

MEMOSys: Bioinformatics platform for genome-scale metabolic models

(2011) Stephan Pabinger et al.   BMC Systems Biology

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

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

(2010) Isabel Rocha et al.   BMC Systems Biology

AIBench: A rapid application development framework for translational research in biomedicine

(2010) D. Glez-Peña et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

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

(2010) Ines Thiele et al.   Nature Protocols

BRENDA, the enzyme information system in 2011

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

Annotation and merging of SBML models with semanticSBML

(2009) F. Krause et al.   BIOINFORMATICS

UniProtJAPI: a remote API for accessing UniProt data

(2008) S. Patient et al.   BIOINFORMATICS

BioJava: an open-source framework for bioinformatics

(2008) R. C. G. Holland et al.   BIOINFORMATICS

Reconstruction of biochemical networks in microorganisms

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