Methods for automated genome-scale metabolic model reconstruction

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

A Genome Scale Model of Geobacillus thermoglucosidasius (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate

(2017) Ahmad Ahmad et al.   JOURNAL OF BIOTECHNOLOGY

Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal

(2017) Claus Jonathan Fritzemeier et al.   PLoS Computational Biology

Modeling central metabolism and energy biosynthesis across microbial life

(2016) Janaka N. Edirisinghe et al.   BMC GENOMICS

Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction

(2016) Christopher S. Henry et al.   JOURNAL OF CELLULAR PHYSIOLOGY

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

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

A genome-scale metabolic network reconstruction of tomato (Solanum lycopersicumL.) and its application to photorespiratory metabolism

(2016) Huili Yuan et al.   PLANT JOURNAL

Reconstructing genome-scale metabolic models with merlin

(2015) Oscar Dias et al.   NUCLEIC ACIDS RESEARCH

fastGapFill: efficient gap filling in metabolic networks

(2014) Ines Thiele et al.   BIOINFORMATICS

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

(2014) Oscar Dias et al.   Biotechnology Journal

Efficiently gap-filling reaction networks

(2014) Mario Latendresse   BMC BIOINFORMATICS

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

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

(2014) Nikos Vlassis et al.   PLoS Computational Biology

A systematic comparison of the MetaCyc and KEGG pathway databases

(2013) Tomer Altman et al.   BMC BIOINFORMATICS

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

(2013) Ross Overbeek 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

Construction and completion of flux balance models from pathway databases

(2012) Mario Latendresse et al.   BIOINFORMATICS

Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering

(2012) Chiam Yu Ng et al.   Microbial Cell Factories

A metabolic network approach for the identification and prioritization of antimicrobial drug targets

(2012) Arvind K. Chavali et al.   TRENDS IN MICROBIOLOGY

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions

(2011) Ottar Rolfsson et al.   BMC Systems Biology

Genetically engineered bacteria: An emerging tool for environmental remediation and future research perspectives

(2011) Jay Shankar Singh et al.   GENE

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

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

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

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

(2010) Isabel Rocha et al.   BMC Systems Biology

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

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