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History of antibiotic adaptation influences microbial evolutionary dynamics during subsequent treatment

PLoS biology, 2017-08, Vol.15 (8), p.e2001586-e2001586

2017

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

Bioinformatics (Oxford, England), 2011-02, Vol.27 (4), p.541-547

2011

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Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies

PLoS computational biology, 2023-04, Vol.19 (4), p.e1011076

2023

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Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses

PLoS computational biology, 2023-08, Vol.19 (8), p.e1010927

2023

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Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation

PloS one, 2013-10, Vol.8 (10), p.e78011-e78011

2013

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Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

PLoS computational biology, 2017-03, Vol.13 (3), p.e1005413-e1005413

2017

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Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions

Nature communications, 2017-02, Vol.8 (1), p.14250-15, Article 14250

2017

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Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

PLoS computational biology, 2020-04, Vol.16 (4), p.e1007099-e1007099

2020

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Ten simple rules for biologists learning to program

PLoS computational biology, 2018-01, Vol.14 (1), p.e1005871-e1005871

2018

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Integration of expression data in genome-scale metabolic network reconstructions

Frontiers in physiology, 2012-01, Vol.3, p.299-299

2012

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Ten simple rules for launching an academic research career

PLoS computational biology, 2022-12, Vol.18 (12), p.e1010689-e1010689

2022

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Applications of genome-scale metabolic reconstructions

Molecular systems biology, 2009, Vol.5 (1), p.320-n/a

2009

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Collaborating with our community to increase code sharing

PLoS computational biology, 2021-03, Vol.17 (3), p.e1008867-e1008867

2021

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Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis

Nature communications, 2017-03, Vol.8 (1), p.14631-14631, Article 14631

2017

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The blossoming of methods and software in computational biology

PLoS computational biology, 2023-08, Vol.19 (8), p.e1011390-e1011390

2023

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Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome

PLoS computational biology, 2015-06, Vol.11 (5), p.e1004338-e1004338

2015

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Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions

PLoS computational biology, 2022-02, Vol.18 (2), p.e1009341-e1009341

2022

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Improving reproducibility in computational biology research

PLoS computational biology, 2020-05, Vol.16 (5), p.e1007881-e1007881

2020

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Protein- and zinc-deficient diets modulate the murine microbiome and metabolic phenotype

The American journal of clinical nutrition, 2016-11, Vol.104 (5), p.1253-1262

2016

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Reconciling high-throughput gene essentiality data with metabolic network reconstructions

PLoS computational biology, 2019-04, Vol.15 (4), p.e1006507

2019

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Community standards to facilitate development and address challenges in metabolic modeling

Molecular systems biology, 2020-08, Vol.16 (8), p.e9235-n/a

2020

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Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance

BMC genomics, 2017-07, Vol.18 (1), p.543-543, Article 543

2017

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Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions

PLoS computational biology, 2020-04, Vol.16 (4), p.e1007847-e1007847

2020

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Dynamic analysis of integrated signaling, metabolic, and regulatory networks

PLoS computational biology, 2008-05, Vol.4 (5), p.e1000086-e1000086

2008

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Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment

PLoS computational biology, 2024-04, Vol.20 (4), p.e1012031-e1012031

2024

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History of antibiotic adaptation influences microbial evolutionary dynamics during subsequent treatment

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

Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies

Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses

Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation

Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

Ten simple rules for biologists learning to program

Integration of expression data in genome-scale metabolic network reconstructions

Ten simple rules for launching an academic research career

Applications of genome-scale metabolic reconstructions

Collaborating with our community to increase code sharing

Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis

The blossoming of methods and software in computational biology

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome

Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions

Improving reproducibility in computational biology research

Protein- and zinc-deficient diets modulate the murine microbiome and metabolic phenotype

Reconciling high-throughput gene essentiality data with metabolic network reconstructions

Community standards to facilitate development and address challenges in metabolic modeling

Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance

Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions

Dynamic analysis of integrated signaling, metabolic, and regulatory networks

Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment

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