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

Novel algorithms and the benefits of comparative validation

(2013) R. Smith et al.   BIOINFORMATICS

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

(2013) Brian J. Schmidt et al.   BIOINFORMATICS

Flux-coupled genes and their use in metabolic flux analysis

(2013) Hyun Uk Kim et al.   Biotechnology Journal

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

(2013) Cameron Cotten et al.   BMC BIOINFORMATICS

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

(2013) Tobias Österlund et al.   BMC Systems Biology

Somewhat in control—the role of transcription in regulating microbial metabolic fluxes

(2013) Karl Kochanowski et al.   CURRENT OPINION IN BIOTECHNOLOGY

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements

(2013) Sergio Rossell et al.   PLoS Computational Biology

Ten Simple Rules for Reproducible Computational Research

(2013) Geir Kjetil Sandve et al.   PLoS Computational Biology

Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli

(2012) Nadine Töpfer et al.   BMC Systems Biology

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

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Analysis of omics data with genome-scale models of metabolism

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

The expanding scope of DNA sequencing

(2012) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

(2012) Aaron Brandes et al.   PLoS One

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

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

Temporal Expression-based Analysis of Metabolism

(2012) Sara B. Collins et al.   PLoS Computational Biology

Shrinking the Metabolic Solution Space Using Experimental Datasets

(2012) Jennifer L. Reed   PLoS Computational Biology

Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia

(2012) Xin Fang et al.   PLoS Computational Biology

Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

(2012) Roi Adadi et al.   PLoS Computational Biology

RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations

(2012) Joonhoon Kim et al.   GENOME BIOLOGY

Integration of expression data in genome-scale metabolic network reconstructions

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

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

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

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Modeling formalisms in Systems Biology

(2011) Daniel Machado et al.   AMB Express

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

(2010) Paul A. Jensen et al.   BIOINFORMATICS

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

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

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

(2010) Sergio Bordel et al.   PLoS Computational Biology

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

(2009) Eija Rintala et al.   BMC GENOMICS

Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints

(2009) Rogier J P van Berlo et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Metabolic reconfiguration precedes transcriptional regulation in the antioxidant response

(2009) Markus Ralser et al.   NATURE BIOTECHNOLOGY

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

Strategies for systems-level metabolic engineering

(2008) Tae Yong Kim et al.   Biotechnology Journal

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

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Context-Specific Metabolic Networks Are Consistent with Experiments

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