Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models

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

(2017) Sylvain Prigent et al.   PLoS Computational Biology

The bioleaching potential of a bacterial consortium

(2016) Mauricio Latorre et al.   BIORESOURCE TECHNOLOGY

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans

(2016) Hadi Nazem-Bokaee et al.   Microbial Cell Factories

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus

(2016) Alexandre Cormier et al.   NEW PHYTOLOGIST

Updates in Rhea – an expert curated resource of biochemical reactions

(2016) Anne Morgat et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Comparative genome-scale modelling ofStaphylococcus aureusstrains identifies strain-specific metabolic capabilities linked to pathogenicity

(2016) Emanuele Bosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PSAMM: A Portable System for the Analysis of Metabolic Models

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

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

(2016) Derrick E. Fouts et al.   PLoS Neglected Tropical Diseases

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

(2016) Emily B. Graham et al.   Frontiers in Microbiology

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

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

Transparency in metabolic network reconstruction enables scalable biological discovery

(2015) Benjamin D Heavner et al.   CURRENT OPINION IN BIOTECHNOLOGY

Do genome-scale models need exact solvers or clearer standards?

(2015) A. Ebrahim et al.   Molecular Systems Biology

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

(2015) Sébastien Moretti et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Ron Caspi 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

A refined genome-scale reconstruction ofChlamydomonasmetabolism provides a platform for systems-level analyses

(2015) Saheed Imam et al.   PLANT JOURNAL

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Using a Genome-Scale Metabolic Model of Enterococcus faecalis V583 To Assess Amino Acid Uptake and Its Impact on Central Metabolism

(2014) Nadine Veith et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

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

(2014) Sylvain Prigent et al.   PLANT JOURNAL

Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model

(2014) M. Simons et al.   PLANT PHYSIOLOGY

Comparative Transcriptome of Wild Type and Selected Strains of the Microalgae Tisochrysis lutea Provides Insights into the Genetic Basis, Lipid Metabolism and the Life Cycle

(2014) Gregory Carrier et al.   PLoS One

Sulfobacillus thermosulfidooxidans strain Cutipay enhances chalcopyrite bioleaching under moderate thermophilic conditions in the presence of chloride ion

(2014) Roberto A Bobadilla-Fazzini et al.   AMB Express

Genome and metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae

(2014) Simon M. Dittami et al.   Frontiers in Genetics

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Extracting reaction networks from databases-opening Pandora's box

(2013) L. G. Fearnley et al.   BRIEFINGS IN BIOINFORMATICS

Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii

(2013) Harish Nagarajan et al.   Microbial Cell Factories

Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803

(2013) Henning Knoop 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-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in-silico evaluation of their potentials

(2012) Luis Caspeta et al.   BMC Systems Biology

Semantic Web meets Integrative Biology: a survey

(2012) H. Chen et al.   BRIEFINGS IN BIOINFORMATICS

Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

(2012) Rajib Saha et al.   PLoS One

Biocurators and Biocuration: surveying the 21st century challenges

(2012) S. Burge et al.   Database-The Journal of Biological Databases and Curation

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

(2011) Ines Thiele et al.   BMC Systems Biology

Bioactive compounds in seaweed: functional food applications and legislation

(2011) Susan Løvstad Holdt et al.   JOURNAL OF APPLIED PHYCOLOGY

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism

(2011) R. L. Chang et al.   Molecular Systems Biology

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

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

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

(2011) H. U. Kim et al.   Molecular Systems Biology

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

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

(2011) Jan Schellenberger et al.   Nature Protocols

Consistency, comprehensiveness, and compatibility of pathway databases

(2010) Donny Soh et al.   BMC BIOINFORMATICS

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

(2010) Arnau Montagud et al.   BMC Systems Biology

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

AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis

(2010) C. G. de Oliveira Dal'Molin et al.   PLANT PHYSIOLOGY

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology