Integrating –omics data into genome-scale metabolic network models: principles and challenges

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

(2018) Mingyuan Tian et al.   BIOINFORMATICS

Exploring candidate biomarkers for lung and prostate cancers using gene expression and flux variability analysis

(2018) Yazdan Asgari et al.   Integrative Biology

How to deal with parameters for whole-cell modelling

(2017) Ann C. Babtie et al.   Journal of the Royal Society Interface

An integrated computational and experimental study uncovers FUT9 as a metabolic driver of colorectal cancer

(2017) Noam Auslander et al.   Molecular Systems Biology

An analytic approximation of the feasible space of metabolic networks

(2017) Alfredo Braunstein et al.   Nature Communications

Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity

(2017) Ed Reznik et al.   Cell Reports

Population FBA predicts metabolic phenotypes in yeast

(2017) Piyush Labhsetwar et al.   PLoS Computational Biology

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

(2017) Sjoerd Opdam et al.   Cell Systems

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

(2017) Aarash Bordbar et al.   Scientific Reports

ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks

(2016) Pedro A. Saa et al.   BIOINFORMATICS

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

Current state and challenges for dynamic metabolic modeling

(2016) Eleni Vasilakou et al.   CURRENT OPINION IN MICROBIOLOGY

Metabolite concentrations, fluxes and free energies imply efficient enzyme usage

(2016) Junyoung O Park et al.   Nature Chemical Biology

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli

(2016) Minseung Kim et al.   Nature Communications

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

(2015) Maria Pires Pacheco et al.   BMC GENOMICS

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

How to measure metabolic fluxes: a taxonomic guide for 13 C fluxomics

(2015) Sebastian Niedenführ et al.   CURRENT OPINION IN BIOTECHNOLOGY

Dynamic exometabolome analysis reveals active metabolic pathways in non-replicating mycobacteria

(2015) Michael Zimmermann et al.   ENVIRONMENTAL MICROBIOLOGY

Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

(2015) Ahmad A. Mannan et al.   PLoS One

Uniform Sampling of Steady States in Metabolic Networks: Heterogeneous Scales and Rounding

(2015) Daniele De Martino et al.   PLoS One

Prediction of intracellular metabolic states from extracellular metabolomic data

(2014) Maike K. Aurich et al.   Metabolomics

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

(2014) Daniel Machado et al.   PLoS Computational Biology

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

(2014) Anupam Chowdhury et al.   PLoS Computational Biology

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

(2013) Cameron Cotten et al.   BMC BIOINFORMATICS

A note on the kinetics of enzyme action: A decomposition that highlights thermodynamic effects

(2013) Elad Noor et al.   FEBS LETTERS

Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis

(2013) V. Chubukov et al.   Molecular Systems Biology

Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo

(2013) Hannes Link et al.   NATURE BIOTECHNOLOGY

Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism

(2013) M. Sunnaker et al.   Science Signaling

Model-based identification of drug targets that revert disrupted metabolism and its application to ageing

(2013) Keren Yizhak et al.   Nature Communications

Consistent Estimation of Gibbs Energy Using Component Contributions

(2013) Elad Noor et al.   PLoS Computational Biology

Analysis of omics data with genome-scale models of metabolism

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

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Metabolite Profiling Identifies a Key Role for Glycine in Rapid Cancer Cell Proliferation

(2012) M. Jain et al.   SCIENCE

Integration of expression data in genome-scale metabolic network reconstructions

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

Predicting selective drug targets in cancer through metabolic networks

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

Yeast Dynamic Metabolic Flux Measurement in Nutrient-Rich Media by Hplc and Accelerator Mass Spectrometry

(2010) Benjamin J. Stewart et al.   ANALYTICAL CHEMISTRY

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

Classic and contemporary approaches to modeling biochemical reactions

(2010) W. W. Chen et al.   GENES & DEVELOPMENT

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

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Messy biology and the origins of evolutionary innovations

(2010) Dan S Tawfik   Nature Chemical 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

Inferring Signaling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species

(2010) T.-R. Xu et al.   Science Signaling

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

Quantitative Evaluation of Intracellular Metabolite Extraction Techniques for Yeast Metabolomics

(2009) André B. Canelas et al.   ANALYTICAL CHEMISTRY

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

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

Novel biological insights through metabolomics and 13C-flux analysis

(2009) Nicola Zamboni et al.   CURRENT OPINION IN MICROBIOLOGY

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

Genome-scale metabolic networks

(2009) Marco Terzer et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

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

(2009) Caroline Colijn et al.   PLoS Computational Biology

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

(2008) Markus W. Covert et al.   BIOINFORMATICS

Metabolomics and fluxomics approaches

(2008) Marta Cascante et al.   Essays in Biochemistry

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

(2008) T. Toni et al.   Journal of the Royal Society Interface

Allostery: an illustrated definition for the ‘second secret of life’

(2008) Aron W. Fenton   TRENDS IN BIOCHEMICAL SCIENCES