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Using Genome-scale Models to Predict Biological Capabilities

Cell, 2015-05, Vol.161 (5), p.971-987

2015

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Constraint-based models predict metabolic and associated cellular functions

Nature reviews. Genetics, 2014-02, Vol.15 (2), p.107-120

2014

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A biochemically-interpretable machine learning classifier for microbial GWAS

Nature communications, 2020-05, Vol.11 (1), p.2580-2580, Article 2580

2020

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Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

Nature communications, 2018-10, Vol.9 (1), p.4306-9, Article 4306

2018

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Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity

BMC genomics, 2022-01, Vol.23 (1), p.7-7, Article 7

2022

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Impact of insertion sequences on convergent evolution of Shigella species

PLoS genetics, 2020-07, Vol.16 (7), p.e1008931-e1008931

2020

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Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

Nature communications, 2018-09, Vol.9 (1), p.3771-12, Article 3771

2018

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Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens

PLoS computational biology, 2020-03, Vol.16 (3), p.e1007608-e1007608

2020

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Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Proceedings of the National Academy of Sciences - PNAS, 2013-12, Vol.110 (50), p.20338-20343

2013

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Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species

Nature communications, 2023-11, Vol.14 (1), p.7690-7690, Article 7690

2023

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BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

PLoS computational biology, 2019-04, Vol.15 (4), p.e1006971-e1006971

2019

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Rapid resistance development to three antistaphylococcal therapies in antibiotic-tolerant staphylococcus aureus bacteremia

PloS one, 2021-10, Vol.16 (10), p.e0258592-e0258592

2021

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High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

BMC bioinformatics, 2022-12, Vol.23 (1), p.566-566, Article 566

2022

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A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

PLoS computational biology, 2019-01, Vol.15 (1), p.e1006644-e1006644

2019

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Genome-scale metabolic network reconstructions of diverse Escherichia strains reveal strain-specific adaptations

Philosophical transactions of the Royal Society of London. Series B. Biological sciences, 2022-10, Vol.377 (1861), p.20210236

Monk, Jonathan M

2022

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Model-driven discovery of underground metabolic functions in Escherichia coli

Proceedings of the National Academy of Sciences - PNAS, 2015-01, Vol.112 (3), p.929-934

2015

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Metabolic and behavioral features of acute hyperpurinergia and the maternal immune activation mouse model of autism spectrum disorder

PloS one, 2021-03, Vol.16 (3), p.e0248771-e0248771

2021

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Metabolic features of Gulf War illness

PloS one, 2019-07, Vol.14 (7), p.e0219531

2019

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Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes

BMC bioinformatics, 2020-04, Vol.21 (1), p.162-162, Article 162

2020

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Improved Dried Blood Spot-Based Metabolomics: A Targeted, Broad-Spectrum, Single-Injection Method

Metabolites, 2020-02, Vol.10 (3), p.82

2020

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Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection

PLoS computational biology, 2019-12, Vol.15 (12), p.e1007562-e1007562

2019

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Genome‐scale metabolic modeling reveals key features of a minimal gene set

Molecular systems biology, 2021-07, Vol.17 (7), p.e10099-n/a

2021

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Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

Cell systems, 2016-09, Vol.3 (3), p.238-251.e12

2016

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Predicting Antimicrobial Resistance and Associated Genomic Features from Whole-Genome Sequencing

Journal of clinical microbiology, 2019-02, Vol.57 (2)

2019

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iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE

Frontiers in genetics, 2018-04, Vol.9, p.121-121

2018

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Using Genome-scale Models to Predict Biological Capabilities

Constraint-based models predict metabolic and associated cellular functions

A biochemically-interpretable machine learning classifier for microbial GWAS

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity

Impact of insertion sequences on convergent evolution of Shigella species

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Rapid resistance development to three antistaphylococcal therapies in antibiotic-tolerant staphylococcus aureus bacteremia

High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

Genome-scale metabolic network reconstructions of diverse Escherichia strains reveal strain-specific adaptations

Model-driven discovery of underground metabolic functions in Escherichia coli

Metabolic and behavioral features of acute hyperpurinergia and the maternal immune activation mouse model of autism spectrum disorder

Metabolic features of Gulf War illness

Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes

Improved Dried Blood Spot-Based Metabolomics: A Targeted, Broad-Spectrum, Single-Injection Method

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection

Genome‐scale metabolic modeling reveals key features of a minimal gene set

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

Predicting Antimicrobial Resistance and Associated Genomic Features from Whole-Genome Sequencing

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE

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