MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models

Improved metabolite identification with MIDAS and MAGMa through MS/MS spectral dataset-driven parameter optimization

(2016) Dries Verdegem et al.   Metabolomics

Transparency in metabolic network reconstruction enables scalable biological discovery

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

Updates in metabolomics tools and resources: 2014-2015

(2015) Biswapriya B. Misra et al.   ELECTROPHORESIS

Global Profiling of Metabolic Adaptation to Hypoxic Stress in Human Glioblastoma Cells

(2015) Paulina Kucharzewska et al.   PLoS One

Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling

(2015) Pouyan Ghaffari et al.   Scientific Reports

Pathomx: an interactive workflow-based tool for the analysis of metabolomic data

(2014) Martin A Fitzpatrick et al.   BMC BIOINFORMATICS

Getting the right answers: understanding metabolomics challenges

(2014) Stephan Beisken et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Defining the Human Adipose Tissue Proteome To Reveal Metabolic Alterations in Obesity

(2014) Adil Mardinoglu et al.   JOURNAL OF PROTEOME RESEARCH

Prediction of intracellular metabolic states from extracellular metabolomic data

(2014) Maike K. Aurich et al.   Metabolomics

Exometabolome analysis reveals hypoxia at the up-scaling of a Saccharomyces cerevisiae high-cell density fed-batch biopharmaceutical process

(2014) Zhibiao Fu et al.   Microbial Cell Factories

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

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

Integrating Transcriptomics with Metabolic Modeling Predicts Biomarkers and Drug Targets for Alzheimer's Disease

(2014) Shiri Stempler et al.   PLoS One

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

(2014) Adil Mardinoglu et al.   Nature Communications

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2

(2014) Hulda S Haraldsdóttir et al.   Journal of Cheminformatics

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

(2014) Nikos Vlassis et al.   PLoS Computational Biology

Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer

(2014) Keren Yizhak et al.   eLife

Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease

(2014) Swagatika Sahoo et al.   Frontiers in Physiology

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

(2013) Brian J. Schmidt et al.   BIOINFORMATICS

Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits

(2013) Ann-Kristin Petersen et al.   HUMAN MOLECULAR GENETICS

Integration of clinical data with a genome-scale metabolic model of the human adipocyte

(2013) A. Mardinoglu et al.   Molecular Systems Biology

Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia

(2013) J. Fan et al.   Molecular Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

The dynamic range of the human metabolome revealed by challenges

(2012) Susanne Krug et al.   FASEB JOURNAL

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

(2012) Aarash Bordbar et al.   Molecular Systems Biology

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

HMDB 3.0—The Human Metabolome Database in 2013

(2012) David S. Wishart et al.   NUCLEIC ACIDS RESEARCH

Contextualization Procedure and Modeling of Monocyte Specific TLR Signaling

(2012) Maike K. Aurich et al.   PLoS One

Metabolite Profiling Identifies a Key Role for Glycine in Rapid Cancer Cell Proliferation

(2012) M. Jain et al.   SCIENCE

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

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole–time of flight mass spectrometry (UPLC–Q–ToF-MS)

(2011) Giuseppe Paglia et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks

(2011) S. G. Thorleifsson et al.   BIOINFORMATICS

Individualized therapy of HHT driven by network analysis of metabolomic profiles

(2011) Neema Jamshidi et al.   BMC Systems Biology

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

Linkage of Organic Anion Transporter-1 to Metabolic Pathways through Integrated “Omics”-driven Network and Functional Analysis

(2011) Sun-Young Ahn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2011) A. Bordbar et al.   JOURNAL OF INTERNAL MEDICINE

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

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

(2011) Jan Schellenberger et al.   Nature Protocols

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

Cell culture metabolomics: applications and future directions

(2010) Miroslava Čuperlović-Culf et al.   DRUG DISCOVERY TODAY

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

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

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

(2010) L. Cottret et al.   NUCLEIC ACIDS RESEARCH

Metabolomics for Functional Genomics, Systems Biology, and Biotechnology

(2009) Kazuki Saito et al.   Annual Review of Plant Biology

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

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

Use of Randomized Sampling for Analysis of Metabolic Networks

(2008) Jan Schellenberger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY