Prediction of intracellular metabolic states from extracellular metabolomic data

A Fresh View of Glycolysis and Glucokinase Regulation: History and Current Status

(2014) Sigurd Lenzen   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells

(2013) Swagatika Sahoo 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

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Predicting Network Activity from High Throughput Metabolomics

(2013) Shuzhao Li et al.   PLoS Computational Biology

Metabolic Associations of Reduced Proliferation and Oxidative Stress in Advanced Breast Cancer

(2012) L. Jerby et al.   CANCER RESEARCH

Predicting Drug Targets and Biomarkers of Cancer via Genome-Scale Metabolic Modeling

(2012) L. Jerby et al.   CLINICAL CANCER RESEARCH

Pharmaceutical research and metabolomics in the newborn

(2012) Roberto Antonucci et al.   Journal of Maternal-Fetal & Neonatal Medicine

Systems biology of stored blood cells: Can it help to extend the expiration date?

(2012) Giuseppe Paglia et al.   Journal of Proteomics

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

HMDB 3.0—The Human Metabolome Database in 2013

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

M2 isoform of pyruvate kinase is dispensable for tumor maintenance and growth

(2012) M. Cortes-Cros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Pathways and Subcellular Compartmentation of NAD Biosynthesis in Human Cells

(2011) Andrey Nikiforov 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

Predicting selective drug targets in cancer through metabolic networks

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

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis

(2011) Jason W Locasale et al.   NATURE GENETICS

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

(2011) Jan Schellenberger et al.   Nature Protocols

Targeting cancer metabolism: a therapeutic window opens

(2011) Matthew G. Vander Heiden   NATURE REVIEWS DRUG DISCOVERY

Serine Biosynthesis with One Carbon Catabolism and the Glycine Cleavage System Represents a Novel Pathway for ATP Generation

(2011) Alexei Vazquez et al.   PLoS One

Optical measurement of cycle-dependent cell growth

(2011) Mustafa Mir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

Energy metabolism of leukemia cells: glycolysisversusoxidative phosphorylation

(2010) Kazuto Suganuma et al.   LEUKEMIA & LYMPHOMA

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

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

Determination of Reduced Nicotinamide Adenine Dinucleotide Phosphate Concentration Using High-Performance Liquid Chromatography with Fluorescence Detection: Ratio of the Reduced Form as a Biomarker of Oxidative Stress

(2009) Yuki Ogasawara et al.   BIOLOGICAL & PHARMACEUTICAL BULLETIN

Quantitative assignment of reaction directionality in constraint-based models of metabolism: Application to Escherichia coli

(2009) R.M.T. Fleming et al.   BIOPHYSICAL CHEMISTRY

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

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

HIF-1α Modulates Energy Metabolism in Cancer Cells by Inducing Over-Expression of Specific Glycolytic Isoforms

(2009) Alvaro Marin-Hernandez et al.   MINI-REVIEWS IN MEDICINAL CHEMISTRY

Use of Randomized Sampling for Analysis of Metabolic Networks

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

Context-Specific Metabolic Networks Are Consistent with Experiments

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