A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks

SDH Mutations Establish a Hypermethylator Phenotype in Paraganglioma

(2013) Eric Letouzé et al.   CANCER CELL

MYC-driven accumulation of 2-hydroxyglutarate is associated with breast cancer prognosis

(2013) Atsushi Terunuma et al.   JOURNAL OF CLINICAL INVESTIGATION

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

An Inhibitor of Mutant IDH1 Delays Growth and Promotes Differentiation of Glioma Cells

(2013) D. Rohle et al.   SCIENCE

Targeted Inhibition of Mutant IDH2 in Leukemia Cells Induces Cellular Differentiation

(2013) F. Wang et al.   SCIENCE

Metabolic Reprogramming: A Cancer Hallmark Even Warburg Did Not Anticipate

(2012) Patrick S. Ward et al.   CANCER CELL

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

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

Inhibition of  -KG-dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors

(2012) M. Xiao et al.   GENES & DEVELOPMENT

IDH mutation impairs histone demethylation and results in a block to cell differentiation

(2012) Chao Lu et al.   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Assignment of EC Numbers to Enzymatic Reactions with Reaction Difference Fingerprints

(2012) Qian-Nan Hu et al.   PLoS One

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

The emerging role of fumarate as an oncometabolite

(2012) Ming Yang et al.   Frontiers in Oncology

Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds

(2011) Fangping Mu et al.   BIOINFORMATICS

RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity

(2011) Q.-N. Hu et al.   BIOINFORMATICS

Fifteen years of large scale metabolic modeling of yeast: Developments and impacts

(2011) Tobias Österlund et al.   BIOTECHNOLOGY ADVANCES

Oncometabolite 2-Hydroxyglutarate Is a Competitive Inhibitor of α-Ketoglutarate-Dependent Dioxygenases

(2011) Wei Xu et al.   CANCER CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

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

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

Metabolism unhinged: IDH mutations in cancer

(2011) John R Prensner et al.   NATURE MEDICINE

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

(2011) Jan Schellenberger et al.   Nature Protocols

MACiE: exploring the diversity of biochemical reactions

(2011) Gemma L. Holliday et al.   NUCLEIC ACIDS RESEARCH

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Tomer Shlomi et al.   PLoS Computational Biology

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

(2010) Olga Khersonsky and Dan S. Tawfik   Annual Review of Biochemistry

What makes an enzyme promiscuous?

(2010) Ann Babtie et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Metabolite and reaction inference based on enzyme specificities

(2009) M. J. L. de Groot et al.   BIOINFORMATICS

Computational framework for predictive biodegradation

(2009) Stacey D. Finley et al.   BIOTECHNOLOGY AND BIOENGINEERING

Assignment of EC Numbers to Enzymatic Reactions with MOLMAP Reaction Descriptors and Random Forests

(2009) Diogo A. R. S. Latino et al.   Journal of Chemical Information and Modeling

Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation

(2009) M. G. Vander Heiden et al.   SCIENCE

Use of Randomized Sampling for Analysis of Metabolic Networks

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

HMDB: a knowledgebase for the human metabolome

(2008) D. S. Wishart et al.   NUCLEIC ACIDS RESEARCH

Highly parallel identification of essential genes in cancer cells

(2008) B. Luo 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