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Face mask use in the general population and optimal resource allocation during the COVID-19 pandemic

Nature communications, 2020-08, Vol.11 (1), p.4049-4049, Article 4049

2020

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Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data

PLoS computational biology, 2014-03, Vol.10 (3), p.e1003549

2014

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Bayesian reconstruction of transmission within outbreaks using genomic variants

PLoS computational biology, 2018-04, Vol.14 (4), p.e1006117-e1006117

2018

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Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data

American journal of epidemiology, 2017-11, Vol.186 (10), p.1209-1216

2017

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THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites

PLoS computational biology, 2017-01, Vol.13 (1), p.e1005348-e1005348

2017

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Establishing the role of the gut microbiota in susceptibility to recurrent urinary tract infections

The Journal of clinical investigation, 2022-03, Vol.132 (5)

2022

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StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities

Genome Biology, 2022-03, Vol.23 (1), p.74-27, Article 74

2022

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'SEEDY' (Simulation of Evolutionary and Epidemiological Dynamics): An R Package to Follow Accumulation of Within-Host Mutation in Pathogens

PloS one, 2015-06, Vol.10 (6), p.e0129745-e0129745

2015

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On the relative role of different age groups in influenza epidemics

Epidemics, 2015-12, Vol.13 (C), p.10-16

2015

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Microbial Genomics of Ancient Plagues and Outbreaks

Trends in microbiology (Regular ed.), 2016-12, Vol.24 (12), p.978-990

2016

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Model diagnostics and refinement for phylodynamic models

PLoS computational biology, 2019-04, Vol.15 (4), p.e1006955-e1006955

2019

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Dynamics of microbiome and resistome in a poultry burger processing line

Food research international, 2024-10, Vol.193, p.114842, Article 114842

2024

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Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

Nature communications, 2024-11, Vol.15 (1), p.9466-15, Article 9466

2024

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On the Relative Role of Different Age Groups During Epidemics Associated With Respiratory Syncytial Virus

The Journal of infectious diseases, 2018-01, Vol.217 (2), p.238-244

2018

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The distribution of pairwise genetic distances: a tool for investigating disease transmission

Genetics (Austin), 2014-12, Vol.198 (4), p.1395-1404

2014

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Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes

Briefings in bioinformatics, 2023-03, Vol.24 (2)

2023

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Clinical and Genomic Characterization of a Cohort of Patients With Klebsiella pneumoniae Bloodstream Infection

Clinical infectious diseases, 2024-01, Vol.78 (1), p.31-39

2024

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Penicillin Resistance of Nonvaccine Type Pneumococcus before and after PCV13 Introduction, United States

Emerging infectious diseases, 2017-06, Vol.23 (6), p.1012-1015

2017

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Intrinsic Resistance to Colistin in the Genus Hafnia

Journal of clinical microbiology, 2023-05, Vol.61 (5), p.e0132622

2023

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Examining the role of different age groups and of vaccination during the 2012 Minnesota pertussis outbreak

Scientific reports, 2015-08, Vol.5 (1), p.13182-13182, Article 13182

2015

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Impact of mupirocin resistance on the transmission and control of healthcare-associated MRSA

Journal of antimicrobial chemotherapy, 2015-12, Vol.70 (12), p.3366-3378

2015

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Transmission of SARS-CoV-2 before and after symptom onset: impact of nonpharmaceutical interventions in China

European journal of epidemiology, 2021-04, Vol.36 (4), p.429-439

2021

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Phylogeography of rubella virus in Asia: Vaccination and demography shape synchronous outbreaks

Epidemics, 2019-09, Vol.28, p.100346-100346, Article 100346

2019

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Face mask use in the general population and optimal resource allocation during the COVID-19 pandemic

Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data

Bayesian reconstruction of transmission within outbreaks using genomic variants

Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data

THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites

Establishing the role of the gut microbiota in susceptibility to recurrent urinary tract infections

StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities

'SEEDY' (Simulation of Evolutionary and Epidemiological Dynamics): An R Package to Follow Accumulation of Within-Host Mutation in Pathogens

On the relative role of different age groups in influenza epidemics

Microbial Genomics of Ancient Plagues and Outbreaks

Model diagnostics and refinement for phylodynamic models

Dynamics of microbiome and resistome in a poultry burger processing line

Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

On the Relative Role of Different Age Groups During Epidemics Associated With Respiratory Syncytial Virus

The distribution of pairwise genetic distances: a tool for investigating disease transmission

Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes

Clinical and Genomic Characterization of a Cohort of Patients With Klebsiella pneumoniae Bloodstream Infection

Penicillin Resistance of Nonvaccine Type Pneumococcus before and after PCV13 Introduction, United States

Intrinsic Resistance to Colistin in the Genus Hafnia

Examining the role of different age groups and of vaccination during the 2012 Minnesota pertussis outbreak

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

Impact of mupirocin resistance on the transmission and control of healthcare-associated MRSA

Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women

Transmission of SARS-CoV-2 before and after symptom onset: impact of nonpharmaceutical interventions in China

Phylogeography of rubella virus in Asia: Vaccination and demography shape synchronous outbreaks

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