Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

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

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

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

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

(2013) Brian J. Schmidt et al.   BIOINFORMATICS

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Multiscale Metabolic Modeling: Dynamic Flux Balance Analysis on a Whole-Plant Scale

(2013) E. Grafahrend-Belau et al.   PLANT PHYSIOLOGY

RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing

(2012) Markus Krupp et al.   BIOINFORMATICS

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee 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 omics data with genome-scale models of metabolism

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

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

Construction of anE. Coligenome-scale atom mapping model for MFA calculations

(2011) Prabhasa Ravikirthi et al.   BIOTECHNOLOGY AND BIOENGINEERING

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

(2011) Paul A Jensen et al.   BMC Systems Biology

Strategies for investigating the plant metabolic network with steady-state metabolic flux analysis: lessons from an Arabidopsis cell culture and other systems

(2011) N. J. Kruger et al.   JOURNAL OF EXPERIMENTAL BOTANY

Mapping photoautotrophic metabolism with isotopically nonstationary 13C flux analysis

(2011) Jamey D. Young et al.   METABOLIC ENGINEERING

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

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

C4GEM, a Genome-Scale Metabolic Model to Study C4 Plant Metabolism

(2010) C. G. de Oliveira Dal'Molin et al.   PLANT PHYSIOLOGY

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

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