Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

PSAMM: A Portable System for the Analysis of Metabolic Models

(2016) Jon Lund Steffensen et al.   PLoS Computational Biology

Saccharina genomes provide novel insight into kelp biology

(2015) Naihao Ye et al.   Nature Communications

Pantograph: A template-based method for genome-scale metabolic model reconstruction

(2015) Nicolas Loira et al.   Journal of Bioinformatics and Computational Biology

fastGapFill: efficient gap filling in metabolic networks

(2014) Ines Thiele et al.   BIOINFORMATICS

Arsenic hypertolerance in the protistEuglena mutabilisis mediated by specific transporters and functional integrity maintenance mechanisms

(2014) David Halter et al.   ENVIRONMENTAL MICROBIOLOGY

A mathematical approach to emergent properties of metabolic networks: Partial coupling relations, hyperarcs and flux ratios

(2014) Sayed-Amir Marashi et al.   JOURNAL OF THEORETICAL BIOLOGY

A metabolic approach to study algal-bacterial interactions in changing environments

(2014) Simon M. Dittami et al.   MOLECULAR ECOLOGY

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

The genome-scale metabolic network ofEctocarpus siliculosus(EctoGEM): a resource to study brown algal physiology and beyond

(2014) Sylvain Prigent et al.   PLANT JOURNAL

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models

(2014) Matthew N. Benedict et al.   PLoS Computational Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

Conflict-driven answer set solving: From theory to practice

(2012) Martin Gebser et al.   ARTIFICIAL INTELLIGENCE

In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bio-indicator, Euglena mutabilis

(2012) David Halter et al.   ISME Journal

ORCAE: online resource for community annotation of eukaryotes

(2012) Lieven Sterck et al.   NATURE METHODS

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

(2012) David Vallenet et al.   NUCLEIC ACIDS RESEARCH

MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks

(2012) Edward Vitkin et al.   GENOME BIOLOGY

Surface properties and intracellular speciation revealed an original adaptive mechanism to arsenic in the acid mine drainage bio-indicator Euglena mutabilis

(2011) David Halter et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity

(2011) S. Mintz-Oron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

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

The Ectocarpus genome sequence: insights into brown algal biology and the evolutionary diversity of the eukaryotes

(2010) J. Mark Cock et al.   NEW PHYTOLOGIST

Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata

(2010) Ludovic Cottret et al.   PLoS Computational Biology

An integrative approach towards completing genome-scale metabolic networks

(2009) Nils Christian et al.   Molecular BioSystems

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology

Can sugars be produced from fatty acids? A test case for pathway analysis tools

(2008) L. F. de Figueiredo et al.   BIOINFORMATICS