RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions

(2017) Edik M. Blais et al.   Nature Communications

Systems approach to characterize the metabolism of liver cancer stem cells expressing CD133

(2017) Wonhee Hur et al.   Scientific Reports

Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

(2017) Anush Chiappino-Pepe et al.   PLoS Computational Biology

Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome

(2016) R. Adam Thompson et al.   Biotechnology for Biofuels

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

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom

(2016) Jennifer Levering et al.   PLoS One

Using Genome-scale Models to Predict Biological Capabilities

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

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

(2015) Saeed Shoaie et al.   Cell Metabolism

Genome-scale modeling for metabolic engineering

(2015) Evangelos Simeonidis et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

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

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

(2015) Stepan Tymoshenko et al.   PLoS Computational Biology

Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community

(2015) Joshua J. Hamilton et al.   PLoS Computational Biology

Reconstruction of a high-quality metabolic model enables the identification of gene overexpression targets for enhanced antibiotic production inStreptomyces coelicolorA3(2)

(2014) Minsuk Kim et al.   Biotechnology Journal

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling

(2014) R. Agren et al.   Molecular Systems Biology

Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes

(2014) H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

(2014) Adil Mardinoglu et al.   Nature Communications

Assimilating genome-scale metabolic reconstructions with modelBorgifier

(2013) John T. Sauls et al.   BIOINFORMATICS

Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites

(2013) Kyu-Sang Hwang et al.   BIOTECHNOLOGY ADVANCES

Genome scale metabolic modeling of the riboflavin overproducer Ashbya gossypii

(2013) Rodrigo Ledesma-Amaro et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genome-scale modeling of human metabolism - a systems biology approach

(2013) Adil Mardinoglu et al.   Biotechnology Journal

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Exploitation of the Streptomyces coelicolor A3(2) genome sequence for discovery of new natural products and biosynthetic pathways

(2013) Gregory L. Challis   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren et al.   PLoS Computational Biology

MEMOSys: Bioinformatics platform for genome-scale metabolic models

(2011) Stephan Pabinger et al.   BMC Systems Biology

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

(2011) Jan Schellenberger et al.   Nature Protocols

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

In Silico Identification of Gene Amplification Targets for Improvement of Lycopene Production

(2010) H. S. Choi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

(2010) Mohammad T Alam et al.   BMC GENOMICS

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

(2010) Ines Thiele et al.   Nature Protocols

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

(2010) Sergio Bordel et al.   PLoS Computational Biology

LibSBML: an API Library for SBML

(2008) B. J. Bornstein et al.   BIOINFORMATICS