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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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The specious art of single-cell genomics

PLoS computational biology, 2023-08, Vol.19 (8), p.e1011288-e1011288

2023

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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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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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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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Hypertrophy and/or Hyperplasia: Dynamics of Adipose Tissue Growth

PLoS computational biology, 2009-03, Vol.5 (3), p.e1000324-e1000324

2009

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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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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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Quantifying critical states of complex diseases using single-sample dynamic network biomarkers

PLoS computational biology, 2017-07, Vol.13 (7), p.e1005633-e1005633

2017

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Using the concordance of in vitro and in vivo data to evaluate extrapolation assumptions

PloS one, 2019-05, Vol.14 (5), p.e0217564

2019

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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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Perspective: Dimensions of the scientific method

PLoS computational biology, 2019-09, Vol.15 (9), p.e1007279

2019

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Environments that induce synthetic microbial ecosystems

PLoS computational biology, 2010-11, Vol.6 (11), p.e1001002-e1001002

2010

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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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Predicting antimicrobial resistance using conserved genes

PLoS computational biology, 2020-10, Vol.16 (10), p.e1008319

2020

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There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk

PLoS computational biology, 2022-02, Vol.18 (2), p.e1009795-e1009795

2022

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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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MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra

PloS one, 2020-01, Vol.15 (1), p.e0226770-e0226770

2020

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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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Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production

PLoS computational biology, 2009-08, Vol.5 (8), p.e1000489

2009

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Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery

PLoS computational biology, 2024-10, Vol.20 (10), p.e1012530

2024

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History of antibiotic adaptation influences microbial evolutionary dynamics during subsequent treatment

The specious art of single-cell genomics

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

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

Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation

Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

Hypertrophy and/or Hyperplasia: Dynamics of Adipose Tissue Growth

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

Ten simple rules for biologists learning to program

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

Quantifying critical states of complex diseases using single-sample dynamic network biomarkers

Using the concordance of in vitro and in vivo data to evaluate extrapolation assumptions

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

Perspective: Dimensions of the scientific method

Environments that induce synthetic microbial ecosystems

Integration of expression data in genome-scale metabolic network reconstructions

Predicting antimicrobial resistance using conserved genes

There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk

Ten simple rules for launching an academic research career

Applications of genome-scale metabolic reconstructions

MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra

Collaborating with our community to increase code sharing

Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery

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