A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism

Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models

(2018) Samuel Y. Ng et al.   Nature Communications

Targeting MYC dependency in ovarian cancer through inhibition of CDK7 and CDK12/13

(2018) Mei Zeng et al.   eLife

Genome scale metabolic modeling of cancer

(2017) Avlant Nilsson et al.   METABOLIC ENGINEERING

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines

(2017) Maike K. Aurich et al.   PLoS Computational Biology

Analysing Algorithms and Data Sources for the Tissue-Specific Reconstruction of Liver Healthy and Cancer Cells

(2017) Jorge Ferreira et al.   Interdisciplinary Sciences-Computational Life Sciences

Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism

(2017) Daniel C. Zielinski et al.   Scientific Reports

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

(2016) André Schultz et al.   PLoS Computational Biology

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

(2016) Maike K. Aurich et al.   Frontiers in Physiology

Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network

(2015) Maria Pires Pacheco et al.   BMC GENOMICS

Reconstruction of genome-scale human metabolic models using omics data

(2015) Jae Yong Ryu et al.   Integrative Biology

Modeling cancer metabolism on a genome scale

(2015) K. Yizhak et al.   Molecular Systems Biology

NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings

(2015) Omer An et al.   NUCLEIC ACIDS RESEARCH

fastGapFill: efficient gap filling in metabolic networks

(2014) Ines Thiele et al.   BIOINFORMATICS

Reconstruction of a generic metabolic network model of cancer cells

(2014) Mahdieh Hadi et al.   Molecular BioSystems

A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration

(2014) K. Yizhak et al.   Molecular Systems Biology

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

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

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

(2014) Adil Mardinoglu et al.   Nature Communications

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

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

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

A Genome-Wide Systematic Analysis Reveals Different and Predictive Proliferation Expression Signatures of Cancerous vs. Non-Cancerous Cells

(2013) Yedael Y. Waldman et al.   PLoS Genetics

The evolution of genome-scale models of cancer metabolism

(2013) Nathan E. Lewis et al.   Frontiers in Physiology

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

(2012) Yuliang Wang et al.   BMC Systems Biology

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

(2012) L. Jerby et al.   CANCER RESEARCH

CellMiner: A Web-Based Suite of Genomic and Pharmacologic Tools to Explore Transcript and Drug Patterns in the NCI-60 Cell Line Set

(2012) W. C. Reinhold et al.   CANCER RESEARCH

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

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

Post-transcriptional regulatory networks play a key role in noise reduction that is conserved from micro-organisms to mammals

(2012) Anagha Joshi et al.   FEBS Journal

Analysis of omics data with genome-scale models of metabolism

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

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

Recurrent Hemizygous Deletions in Cancers May Optimize Proliferative Potential

(2012) N. L. Solimini et al.   SCIENCE

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

Ensemble Modeling of Cancer Metabolism

(2012) Tahmineh Khazaei et al.   Frontiers in Physiology

Predicting selective drug targets in cancer through metabolic networks

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

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

(2011) Jan Schellenberger et al.   Nature Protocols

Frozen robust multiarray analysis (fRMA)

(2010) M. N. McCall et al.   BIOSTATISTICS

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

Analysis of Food and Drug Administration-Approved Anticancer Agents in the NCI60 Panel of Human Tumor Cell Lines

(2010) S. L. Holbeck et al.   MOLECULAR CANCER THERAPEUTICS

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

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

(2010) Livnat Jerby et al.   Molecular Systems Biology

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes

(2010) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH

The Control of the Metabolic Switch in Cancers by Oncogenes and Tumor Suppressor Genes

(2010) A. J. Levine et al.   SCIENCE

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

Cancer Cell Metabolism: Warburg and Beyond

(2008) Peggy P. Hsu et al.   CELL

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Context-Specific Metabolic Networks Are Consistent with Experiments

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