Using the reconstructed genome-scale human metabolic network to study physiology and pathology

A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data

(2011) Pedro R Costa et al.   BMC GENOMICS

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

Predicting selective drug targets in cancer through metabolic networks

(2011) O. Folger et al.   Molecular Systems Biology

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

(2011) Tomer Shlomi et al.   PLoS Computational Biology

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

(2010) Mohammad T Alam et al.   BMC GENOMICS

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

(2010) Martin I Sigurdsson et al.   BMC Systems Biology

Deep epistasis in human metabolism

(2010) Marcin Imielinski et al.   CHAOS

Genome-scale network analysis of imprinted human metabolic genes

(2010) Martin Sigurdsson et al.   Epigenetics

Copy Number Alterations among Mammalian Enzymes Cluster in the Metabolic Network

(2010) M. Bekaert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconstruction annotation jamborees: a community approach to systems biology

(2010) Ines Thiele et al.   Molecular Systems Biology

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

(2010) Christoph Gille et al.   Molecular Systems Biology

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

(2010) Livnat Jerby et al.   Molecular Systems Biology

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

(2010) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Messy biology and the origins of evolutionary innovations

(2010) Dan S Tawfik   Nature Chemical Biology

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

(2010) Ines Thiele et al.   Nature Protocols

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

(2010) Radhakrishnan Mahadevan et al.   NATURE REVIEWS MICROBIOLOGY

Interpreting Metabolomic Profiles using Unbiased Pathway Models

(2010) Rahul C. Deo et al.   PLoS Computational Biology

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model

(2010) Roger L. Chang et al.   PLoS Computational Biology

Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes

(2010) Aleksej Zelezniak et al.   PLoS Computational Biology

Reconstruction of metabolic pathways for the cattle genome

(2009) Seongwon Seo et al.   BMC Systems Biology

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

(2009) Anu Raghunathan et al.   BMC Systems Biology

Genome-scale constraint-based modeling of Geobacter metallireducens

(2009) Jun Sun et al.   BMC Systems Biology

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

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

Macrophages and Adipocytes in Human Obesity: Adipose Tissue Gene Expression and Insulin Sensitivity During Calorie Restriction and Weight Stabilization

(2009) F. Capel et al.   DIABETES

Comparative Genome-Scale Metabolic Reconstruction and Flux Balance Analysis of Multiple Staphylococcus aureus Genomes Identify Novel Antimicrobial Drug Targets

(2009) D.-S. Lee et al.   JOURNAL OF BACTERIOLOGY

Genome Scale Reconstruction of a Salmonella Metabolic Model

(2009) Manal AbuOun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic Flux Correlations, Genetic Interactions, and Disease

(2009) Balaji Veeramani et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genome-scale modeling and in silico analysis of mouse cell metabolic network

(2009) Suresh Selvarasu et al.   Molecular BioSystems

Predicting metabolic biomarkers of human inborn errors of metabolism

(2009) Tomer Shlomi et al.   Molecular Systems Biology

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima

(2009) Y. Zhang et al.   SCIENCE

MouseCyc: a curated biochemical pathways database for the laboratory mouse

(2009) Alexei V Evsikov et al.   GENOME BIOLOGY

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

(2009) Christopher S Henry et al.   GENOME BIOLOGY

Impact of the solvent capacity constraint on E. coli metabolism

(2008) Alexei Vazquez et al.   BMC Systems Biology

Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis

(2008) Anne Goelzer et al.   BMC Systems Biology

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

McKusick's Online Mendelian Inheritance in Man (OMIM(R))

(2008) J. Amberger et al.   NUCLEIC ACIDS RESEARCH

The implications of human metabolic network topology for disease comorbidity

(2008) D.- S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology

Modeling Hybridoma Cell Metabolism Using a Generic Genome-Scale Metabolic Model of Mus musculus

(2005) Kashif Sheikh et al.   BIOTECHNOLOGY PROGRESS