E-Flux2 and SPOT: Validated Methods for Inferring Intracellular Metabolic Flux Distributions from Transcriptomic Data

Recent advances in the reconstruction of metabolic models and integration of omics data

(2014) Rajib Saha et al.   CURRENT OPINION IN BIOTECHNOLOGY

Prediction of Metabolic Flux Distribution from Gene Expression Data Based on the Flux Minimization Principle

(2014) Hyun-Seob Song et al.   PLoS One

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

(2014) Daniel Machado et al.   PLoS Computational Biology

Methods for integration of transcriptomic data in genome-scale metabolic models

(2014) Min Kyung Kim et al.   Computational and Structural Biotechnology Journal

A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation

(2012) Magalie Celton et al.   BMC GENOMICS

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee et al.   BMC Systems Biology

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

(2012) Benjamin D Heavner et al.   BMC Systems Biology

Analysis of omics data with genome-scale models of metabolism

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

Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

(2012) Aaron Brandes et al.   PLoS One

Shrinking the Metabolic Solution Space Using Experimental Datasets

(2012) Jennifer L. Reed   PLoS Computational Biology

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

Comparison between elementary flux modes analysis and 13C-metabolic fluxes measured in bacterial and plant cells

(2011) Marie Beurton-Aimar et al.   BMC Systems Biology

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

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

Metabolic and Transcriptional Response to Cofactor Perturbations in Escherichia coli

(2010) Anders K. Holm et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Making Informed Choices about Microarray Data Analysis

(2010) Mark Reimers   PLoS Computational Biology

Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae

(2009) Eija Rintala et al.   BMC GENOMICS

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

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

Flux balance analysis of biological systems: applications and challenges

(2009) K. Raman et al.   BRIEFINGS IN BIOINFORMATICS

Flux balance analysis: A geometric perspective

(2009) Kieran Smallbone et al.   JOURNAL OF THEORETICAL BIOLOGY

Integrating multiple 'omics' analysis for microbial biology: application and methodologies

(2009) W. Zhang et al.   MICROBIOLOGY-SGM

13C-based metabolic flux analysis

(2009) Nicola Zamboni et al.   Nature Protocols

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

(2009) Caroline Colijn et al.   PLoS Computational Biology

Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A

(2008) Paula Jouhten et al.   BMC Systems 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