IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models

Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina

(2015) Chao Ye et al.   BMC Systems Biology

Critical assessment of genome-scale metabolic networks: the need for a unified standard

(2015) A. Ravikrishnan et al.   BRIEFINGS IN BIOINFORMATICS

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Advancing metabolic engineering through systems biology of industrial microorganisms

(2015) Zongjie Dai et al.   CURRENT OPINION IN BIOTECHNOLOGY

MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

(2015) Sébastien Moretti et al.   NUCLEIC ACIDS RESEARCH

ChEBI in 2016: Improved services and an expanding collection of metabolites

(2015) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Transporter Classification Database (TCDB): recent advances

(2015) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Refining metabolic models and accounting for regulatory effects

(2014) Joonhoon Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

A hybrid of bees algorithm and flux balance analysis (BAFBA) for the optimisation of microbial strains

(2014) Yee Wen Choon et al.   International Journal of Data Mining and Bioinformatics

Applications of genome-scale metabolic network model in metabolic engineering

(2014) Byoungjin Kim et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

A genome-scale metabolic model of Methanococcus maripaludis S2 for CO2capture and conversion to methane

(2014) Nishu Goyal et al.   Molecular BioSystems

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Differential Bees Flux Balance Analysis with OptKnock for In Silico Microbial Strains Optimization

(2014) Yee Wen Choon et al.   PLoS One

MediaDB: A Database of Microbial Growth Conditions in Defined Media

(2014) Matthew A. Richards et al.   PLoS One

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks

(2013) M. Ganter et al.   BIOINFORMATICS

Genomically and biochemically accurate metabolic reconstruction ofMethanosarcina barkeriFusaro, iMG746

(2013) Matthew C. Gonnerman et al.   Biotechnology Journal

Prospecting hydrogen production of Escherichia coli by metabolic network modeling

(2013) Jenni J. Seppälä et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network

(2013) Zixiang Xu et al.   PLoS One

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

(2012) Nicolas Loira et al.   BMC Systems Biology

Redirecting carbon flux into malonyl-CoA to improve resveratrol titers: Proof of concept for genetic interventions predicted by OptForce computational framework

(2012) Namita Bhan et al.   CHEMICAL ENGINEERING SCIENCE

Recent advances in reconstruction and applications of genome-scale metabolic models

(2011) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

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

Further developments towards a genome-scale metabolic model of yeast

(2010) Paul D Dobson et al.   BMC Systems Biology

Use of genome-scale metabolic models for understanding microbial physiology

(2010) Liming Liu et al.   FEBS LETTERS

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

(2009) N. Tepper et al.   BIOINFORMATICS