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The changing epidemiology of SARS-CoV-2

Science (American Association for the Advancement of Science), 2022-03, Vol.375 (6585), p.1116-1121

2022

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Viral phylodynamics

PLoS computational biology, 2013-03, Vol.9 (3), p.e1002947-e1002947

2013

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Transmission-clearance trade-offs indicate that dengue virulence evolution depends on epidemiological context

Nature communications, 2018-06, Vol.9 (1), p.2355-11, Article 2355

2018

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Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

Nature communications, 2020-11, Vol.11 (1), p.5518-5518, Article 5518

2020

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Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration

PLoS computational biology, 2014-12, Vol.10 (12), p.e1003919-e1003919

2014

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Epochal Evolution Shapes the Phylodynamics of Interpandemic Influenza A (H3N2) in Humans

Science (American Association for the Advancement of Science), 2006-12, Vol.314 (5807), p.1898-1903

2006

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Lineage-specific protection and immune imprinting shape the age distributions of influenza B cases

Nature communications, 2021-07, Vol.12 (1), p.4313-4313, Article 4313

2021

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Decreases in dengue transmission may act to increase the incidence of dengue hemorrhagic fever

Proceedings of the National Academy of Sciences - PNAS, 2008-02, Vol.105 (6), p.2238-2243

2008

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Epidemiological inference for emerging viruses using segregating sites

Nature communications, 2023-05, Vol.14 (1), p.3105-3105, Article 3105

2023

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Identifying Malaria Transmission Foci for Elimination Using Human Mobility Data

PLoS computational biology, 2016-04, Vol.12 (4), p.e1004846-e1004846

2016

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Drivers of Inter-individual Variation in Dengue Viral Load Dynamics

PLoS computational biology, 2016-11, Vol.12 (11), p.e1005194-e1005194

2016

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SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent

PLoS computational biology, 2016-09, Vol.12 (9), p.e1005130-e1005130

2016

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Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread

Nature communications, 2020-11, Vol.11 (1), p.5558-5558, Article 5558

2020

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The Effect of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Mitigation Strategies on Seasonal Respiratory Viruses: A Tale of 2 Large Metropolitan Centers in the United States

Clinical infectious diseases, 2021-03, Vol.72 (5), p.e154-e157

2021

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The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans

eLife, 2015-09, Vol.4, p.e07361-e07361

2015

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Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models

PLoS computational biology, 2018-08, Vol.14 (8), p.e1006211-e1006211

2018

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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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Inference for nonlinear epidemiological models using genealogies and time series

PLoS computational biology, 2011-08, Vol.7 (8), p.e1002136-e1002136

2011

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Real-time decision-making during emergency disease outbreaks

PLoS computational biology, 2018-07, Vol.14 (7), p.e1006202-e1006202

2018

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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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Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

PLoS pathogens, 2021-08, Vol.17 (8), p.e1009849-e1009849

2021

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Indirect benefits are a crucial consideration when evaluating SARS-CoV-2 vaccine candidates

Nature medicine, 2021-01, Vol.27 (1), p.4-5

2021

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Forecasting Influenza Epidemics in Hong Kong

PLoS computational biology, 2015-07, Vol.11 (7), p.e1004383-e1004383

2015

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Phylodynamic inference for structured epidemiological models

PLoS computational biology, 2014-04, Vol.10 (4), p.e1003570-e1003570

2014

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Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck

PLoS pathogens, 2021-02, Vol.17 (2), p.e1009373-e1009373

2021

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The changing epidemiology of SARS-CoV-2

Viral phylodynamics

Transmission-clearance trade-offs indicate that dengue virulence evolution depends on epidemiological context

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration

Epochal Evolution Shapes the Phylodynamics of Interpandemic Influenza A (H3N2) in Humans

Lineage-specific protection and immune imprinting shape the age distributions of influenza B cases

Decreases in dengue transmission may act to increase the incidence of dengue hemorrhagic fever

Epidemiological inference for emerging viruses using segregating sites

Identifying Malaria Transmission Foci for Elimination Using Human Mobility Data

Drivers of Inter-individual Variation in Dengue Viral Load Dynamics

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent

Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread

The Effect of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Mitigation Strategies on Seasonal Respiratory Viruses: A Tale of 2 Large Metropolitan Centers in the United States

The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans

Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models

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

Inference for nonlinear epidemiological models using genealogies and time series

Real-time decision-making during emergency disease outbreaks

Bayesian reconstruction of transmission within outbreaks using genomic variants

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

Indirect benefits are a crucial consideration when evaluating SARS-CoV-2 vaccine candidates

Forecasting Influenza Epidemics in Hong Kong

Phylodynamic inference for structured epidemiological models

Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck

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