Analysis of omics data with genome-scale models of metabolism

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Cellular Noise Regulons Underlie Fluctuations in Saccharomyces cerevisiae

(2012) Jacob Stewart-Ornstein et al.   MOLECULAR CELL

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

(2012) Aarash Bordbar et al.   Molecular Systems Biology

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

Integrative Genomic Analysis Identifies Isoleucine and CodY as Regulators of Listeria monocytogenes Virulence

(2012) Lior Lobel et al.   PLoS Genetics

Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus

(2011) Oksana Sorokina et al.   BMC Systems Biology

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

(2011) Aarash Bordbar et al.   BMC Systems Biology

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

(2011) Ines Thiele et al.   BMC Systems Biology

Transcript amplification from single bacterium for transcriptome analysis

(2011) Y. Kang et al.   GENOME RESEARCH

Linkage of Organic Anion Transporter-1 to Metabolic Pathways through Integrated “Omics”-driven Network and Functional Analysis

(2011) Sun-Young Ahn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

An integrated approach to characterize genetic interaction networks in yeast metabolism

(2011) Balázs Szappanos et al.   NATURE GENETICS

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

(2010) Paul A. Jensen et al.   BIOINFORMATICS

Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

(2010) Carola Huthmacher et al.   BMC Systems Biology

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

(2010) Christoph Gille et al.   Molecular Systems Biology

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar 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

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

(2010) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

Towards genome-scale signalling-network reconstructions

(2010) Daniel R. Hyduke et al.   NATURE REVIEWS GENETICS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

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

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model

(2010) Roger L. Chang et al.   PLoS Computational Biology

Industrial systems biology

(2009) José Manuel Otero et al.   BIOTECHNOLOGY AND BIOENGINEERING

UOK 262 cell line, fumarate hydratase deficient (FH−/FH−) hereditary leiomyomatosis renal cell carcinoma: in vitro and in vivo model of an aberrant energy metabolic pathway in human cancer

(2009) Youfeng Yang et al.   CANCER GENETICS AND CYTOGENETICS

Metabolic systems biology

(2009) Bernhard Palsson   FEBS LETTERS

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

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

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

An integrative approach towards completing genome-scale metabolic networks

(2009) Nils Christian et al.   Molecular BioSystems

Applications of genome-scale metabolic reconstructions

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

The transcription unit architecture of the Escherichia coli genome

(2009) Byung-Kwan Cho et al.   NATURE BIOTECHNOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

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

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

Learning biological networks: from modules to dynamics

(2008) Richard Bonneau   Nature Chemical Biology

Cascading failure and robustness in metabolic networks

(2008) A. G. Smart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Context-Specific Metabolic Networks Are Consistent with Experiments

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

Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

(2008) Evan S Snitkin et al.   GENOME BIOLOGY