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

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

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

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

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

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

(2017) Woosung Chung et al.   Nature Communications

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

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

Zooming-in on cancer metabolic rewiring with tissue specific constraint-based models

(2016) Marzia Di Filippo et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Recon 2.2: from reconstruction to model of human metabolism

(2016) Neil Swainston et al.   Metabolomics

Metabolomics: Small molecules, single cells

(2016) Marissa Fessenden   NATURE

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

(2016) André Schultz et al.   PLoS Computational Biology

Lipid metabolic reprogramming in cancer cells

(2016) S Beloribi-Djefaflia et al.   Oncogenesis

Single-Cell Transcriptomics Bioinformatics and Computational Challenges

(2016) Olivier B. Poirion et al.   Frontiers in Genetics

Cancer associated fibroblasts transfer lipids and proteins to cancer cells through cargo vesicles supporting tumor growth

(2015) Alice Santi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Impact of Metabolic Heterogeneity on Tumor Growth, Invasion, and Treatment Outcomes

(2015) M. Robertson-Tessi et al.   CANCER RESEARCH

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Modeling cancer metabolism on a genome scale

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

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Statistics requantitates the central dogma

(2015) J. J. Li et al.   SCIENCE

Inhibitors of glutamate release from breast cancer cells; new targets for cancer-induced bone-pain

(2015) Jennifer Fazzari et al.   Scientific Reports

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

(2015) Kyu-Tae Kim et al.   GENOME BIOLOGY

Tumor-stroma metabolic relationship based on lactate shuttle can sustain prostate cancer progression

(2014) Patrizia Sanità et al.   BMC CANCER

An ensemble evolutionary constraint-based approach to understand the emergence of metabolic phenotypes

(2014) Chiara Damiani et al.   Natural Computing

Cancer Cells Differentially Activate and Thrive on De Novo Lipid Synthesis Pathways in a Low-Lipid Environment

(2014) Veerle W. Daniëls et al.   PLoS One

Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells

(2014) J. H. van Heerden et al.   SCIENCE

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

(2014) Daniel Machado et al.   PLoS Computational Biology

Influence of tumour micro-environment heterogeneity on therapeutic response

(2013) Melissa R. Junttila et al.   NATURE

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

(2013) Ruchir A. Khandelwal et al.   PLoS One

Single-Cell Metabolomics: Analytical and Biological Perspectives

(2013) R. Zenobi   SCIENCE

Lysophosphatidic Acid Inhibits CD8 T-cell Activation and Control of Tumor Progression

(2013) S. K. Oda et al.   Cancer Immunology Research

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee et al.   BMC Systems Biology

Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach

(2012) Ali Navid et al.   BMC Systems Biology

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

(2012) Yuliang Wang et al.   BMC Systems Biology

Analysis of glutamine dependency in non-small cell lung cancer

(2012) A. Pieter J. van den Heuvel et al.   CANCER BIOLOGY & THERAPY

Metabolic Reprogramming: A Cancer Hallmark Even Warburg Did Not Anticipate

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

Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

(2012) Aaron Brandes et al.   PLoS One

Cancer Cell Metabolism: One Hallmark, Many Faces

(2012) Jason R. Cantor et al.   Cancer Discovery

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

Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia

(2012) Xin Fang et al.   PLoS Computational Biology

Integration of expression data in genome-scale metabolic network reconstructions

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

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

The reverse Warburg effect: Aerobic glycolysis in cancer associated fibroblasts and the tumor stroma

(2011) Stephanos Pavlides et al.   CELL CYCLE

Cancer cells metabolically "fertilize" the tumor microenvironment with hydrogen peroxide, driving the Warburg effect

(2011) Ubaldo E. Martinez-Outschoorn et al.   CELL CYCLE

Evidence for a stromal-epithelial “lactate shuttle” in human tumors

(2011) Diana Whitaker-Menezes et al.   CELL CYCLE

Cell–cell interaction and diversity of emergent behaviours

(2011) C. Damiani et al.   IET Systems Biology

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

Functional integration of a metabolic network model and expression data without arbitrary thresholding

(2010) Paul A. Jensen et al.   BIOINFORMATICS

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

(2010) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Ammonia: A Diffusible Factor Released by Proliferating Cells That Induces Autophagy

(2010) G. Marino et al.   Science Signaling

Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p

(2009) J. F. Moxley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Context-Specific Metabolic Networks Are Consistent with Experiments

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