Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines

Improving the metabolic fidelity of cancer models with a physiological cell culture medium

(2019) Johan Vande Voorde et al.   Science Advances

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism

(2019) Chiara Damiani et al.   PLoS Computational Biology

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

Quantification of microenvironmental metabolites in murine cancers reveals determinants of tumor nutrient availability

(2019) Mark R Sullivan et al.   eLife

Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli

(2019) Mattia Zampieri et al.   Nature Communications

Assessing key decisions for transcriptomic data integration in biochemical networks

(2019) Anne Richelle et al.   PLoS Computational Biology

Integrating Proteomic or Transcriptomic Data into Metabolic Models Using Linear Bound Flux Balance Analysis

(2018) Mingyuan Tian et al.   BIOINFORMATICS

Recon3D enables a three-dimensional view of gene variation in human metabolism

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

The nutrient environment affects therapy

(2018) Alexander Muir et al.   SCIENCE

Microenvironmental regulation of cancer cell metabolism: implications for experimental design and translational studies

(2018) Alexander Muir et al.   Disease Models & Mechanisms

Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power

(2018) Alex Graudenzi et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Systems analysis of intracellular pH vulnerabilities for cancer therapy

(2018) Erez Persi et al.   Nature Communications

Stearoyl-CoA desaturase regulates sorafenib resistance via modulation of ER stress-induced differentiation

(2017) Mark Kin Fai Ma et al.   JOURNAL OF HEPATOLOGY

Modulating the therapeutic response of tumours to dietary serine and glycine starvation

(2017) Oliver D. K. Maddocks et al.   NATURE

Genome-scale metabolic models applied to human health and disease

(2017) Daniel J Cook et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect

(2017) Chiara Damiani et al.   PLoS Computational Biology

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models

(2017) Sjoerd Opdam et al.   Cell Systems

The Emerging Facets of Non-Cancerous Warburg Effect

(2017) Alyaa M. Abdel-Haleem et al.   Frontiers in Endocrinology

Reexamining cancer metabolism: lactate production for carcinogenesis could be the purpose and explanation of the Warburg Effect

(2016) Iñigo San-Millán et al.   CARCINOGENESIS

Environment Dictates Dependence on Mitochondrial Complex I for NAD+ and Aspartate Production and Determines Cancer Cell Sensitivity to Metformin

(2016) Dan Y. Gui et al.   Cell Metabolism

The Emerging Hallmarks of Cancer Metabolism

(2016) Natalya N. Pavlova et al.   Cell Metabolism

Environment Impacts the Metabolic Dependencies of Ras-Driven Non-Small Cell Lung Cancer

(2016) Shawn M. Davidson et al.   Cell Metabolism

Recon 2.2: from reconstruction to model of human metabolism

(2016) Neil Swainston et al.   Metabolomics

Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers

(2016) J. R. Mayers et al.   SCIENCE

The Warburg Effect: How Does it Benefit Cancer Cells?

(2016) Maria V. Liberti et al.   TRENDS IN BIOCHEMICAL SCIENCES

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

(2016) André Schultz et al.   PLoS Computational Biology

Lactate Contribution to the Tumor Microenvironment: Mechanisms, Effects on Immune Cells and Therapeutic Relevance

(2016) Susana Romero-Garcia et al.   Frontiers in Immunology

Fundamentals of cancer metabolism

(2016) R. J. DeBerardinis et al.   Science Advances

Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond

(2015) Thomas Pfau et al.   BRIEFINGS IN BIOINFORMATICS

Metabolic and mind shifts

(2015) Cyril Corbet et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

MERAV: a tool for comparing gene expression across human tissues and cell types

(2015) Yoav D. Shaul et al.   NUCLEIC ACIDS RESEARCH

PARP14 promotes the Warburg effect in hepatocellular carcinoma by inhibiting JNK1-dependent PKM2 phosphorylation and activation

(2015) Valeria Iansante et al.   Nature Communications

Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism

(2015) Katja N. Rybakova et al.   PLoS Computational Biology

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

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

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

(2014) Nikos Vlassis et al.   PLoS Computational Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

(2013) Kieran Smallbone et al.   FEBS LETTERS

Glutamine and cancer: cell biology, physiology, and clinical opportunities

(2013) Christopher T. Hensley et al.   JOURNAL OF CLINICAL INVESTIGATION

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Allosteric Regulation of PKM2 Allows Cellular Adaptation to Different Physiological States

(2013) D. Y. Gui et al.   Science Signaling

Analysis of omics data with genome-scale models of metabolism

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

Proliferative activity in hepatocellular carcinoma is closely correlated with glucose metabolism but not angiogenesis

(2011) Koji Kitamura et al.   JOURNAL OF HEPATOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Glutamine addiction: a new therapeutic target in cancer

(2010) David R. Wise et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2009) Caroline Colijn et al.   PLoS Computational Biology

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Glucose metabolism inhibits apoptosis in neurons and cancer cells by redox inactivation of cytochrome c

(2008) Allyson E. Vaughn et al.   NATURE CELL BIOLOGY

Context-Specific Metabolic Networks Are Consistent with Experiments

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