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COBRApy: COnstraints-Based Reconstruction and Analysis for Python

BMC systems biology, 2013-08, Vol.7 (1), p.74-74, Article 74

2013

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Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction

Molecular systems biology, 2013, Vol.9 (1), p.693-n/a

2013

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Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs

Proceedings of the National Academy of Sciences - PNAS, 2017-12, Vol.114 (51), p.E10881-E10889

2017

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Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water

Critical reviews in toxicology, 2015-01, Vol.45 (1), p.1-43

2015

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A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks

PLoS computational biology, 2014-09, Vol.10 (9), p.e1003837-e1003837

2014

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Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells

Environmental and molecular mutagenesis, 2015-07, Vol.56 (6), p.505-519

2015

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AMP-activated protein kinase promotes human prostate cancer cell growth and survival

Molecular cancer therapeutics, 2009-04, Vol.8 (4), p.733-741

2009

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Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli

Proceedings of the National Academy of Sciences - PNAS, 2007-05, Vol.104 (20), p.8484-8489

2007

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

Nature protocols, 2011-09, Vol.6 (9), p.1290-1307

2011

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Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland

Radiation oncology (London, England), 2012-12, Vol.7 (1), p.205-205, Article 205

2012

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Nitric Oxide is Consumed, Rather Than Conserved, by Reaction with Oxyhemoglobin under Physiological Conditions

Proceedings of the National Academy of Sciences - PNAS, 2002-08, Vol.99 (16), p.10341-10346

2002

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Trimming of mammalian transcriptional networks using network component analysis

BMC bioinformatics, 2010-10, Vol.11 (1), p.511-511, Article 511

2010

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Analysis of omics data with genome-scale models of metabolism

Molecular bioSystems, 2013-02, Vol.9 (2), p.167-174

2013

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

Nature communications, 2012-07, Vol.3 (1), p.929-929, Article 929

2012

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Modulation of Nitric Oxide Bioavailability by Erythrocytes

Proceedings of the National Academy of Sciences - PNAS, 2001-09, Vol.98 (20), p.11771-11776

2001

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

Bioinformatics (Oxford, England), 2013-11, Vol.29 (22), p.2900-2908

2013

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Determination of the Escherichia coli S-Nitrosoglutathione Response Network Using Integrated Biochemical and Systems Analysis

The Journal of biological chemistry, 2008-02, Vol.283 (8), p.5148-5157

2008

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Towards genome-scale signalling network reconstructions

Nature reviews. Genetics, 2010-04, Vol.11 (4), p.297

2010

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Nitric Oxide Reaction with Red Blood Cells and Hemoglobin under Heterogeneous Conditions

Proceedings of the National Academy of Sciences - PNAS, 2002-05, Vol.99 (11), p.7763-7768

2002

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Pore Size Analysis of Activated Carbons from Argon and Nitrogen Porosimetry Using Density Functional Theory

Langmuir, 2000-05, Vol.16 (11), p.5041-5050

2000

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A predictive toxicogenomics signature to classify genotoxic versus non-genotoxic chemicals in human TK6 cells

Data in brief, 2015-12, Vol.5 (C), p.77-83

2015

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Comparison of mouse urinary metabolic profiles after exposure to the inflammatory stressors γ radiation and lipopolysaccharide

Radiation research, 2012-02, Vol.177 (2), p.187

2012

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

Molecular systems biology, 2012-06, Vol.8 (1), p.558-n/a

2012

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Regulation of Nitric Oxide Consumption by Hypoxic Red Blood Cells

Proceedings of the National Academy of Sciences - PNAS, 2003-10, Vol.100 (21), p.12504-12509

2003

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Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells

Environmental and molecular mutagenesis, 2015-07, Vol.56 (6), p.520-534

2015

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COBRApy: COnstraints-Based Reconstruction and Analysis for Python

Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction

Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs

Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water

A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks

Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells

AMP-activated protein kinase promotes human prostate cancer cell growth and survival

Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli

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

Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland

Nitric Oxide is Consumed, Rather Than Conserved, by Reaction with Oxyhemoglobin under Physiological Conditions

Trimming of mammalian transcriptional networks using network component analysis

Analysis of omics data with genome-scale models of metabolism

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

Modulation of Nitric Oxide Bioavailability by Erythrocytes

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

Determination of the Escherichia coli S-Nitrosoglutathione Response Network Using Integrated Biochemical and Systems Analysis

Towards genome-scale signalling network reconstructions

Nitric Oxide Reaction with Red Blood Cells and Hemoglobin under Heterogeneous Conditions

Pore Size Analysis of Activated Carbons from Argon and Nitrogen Porosimetry Using Density Functional Theory

A predictive toxicogenomics signature to classify genotoxic versus non-genotoxic chemicals in human TK6 cells

Comparison of mouse urinary metabolic profiles after exposure to the inflammatory stressors γ radiation and lipopolysaccharide

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

Regulation of Nitric Oxide Consumption by Hypoxic Red Blood Cells

Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells

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