Author: William Hanage

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Preprints

Characterizing features of outbreak duration for novel SARS-CoV-2 variants of concern

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ASSESSING THE AGE SPECIFICITY OF INFECTION FATALITY RATES FOR COVID-19: META-ANALYSIS & PUBLIC POLICY IMPLICATIONS

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Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events

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SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

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The effect of human mobility and control measures on the COVID-19 epidemic in China

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Rapid heuristic inference of antibiotic resistance and susceptibility by genomic neighbor typing

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Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts

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COVID-19 vaccine impact on rates of SARS-CoV-2 cases and post vaccination strain sequences among healthcare workers at an urban academic medical center: a prospective cohort study

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Population impact of SARS-CoV-2 variants with enhanced transmissibility and/or partial immune escape

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Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification

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Efficient inference of recent and ancestral recombination within bacterial populations

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The risk of SARS-CoV-2 transmission in the healthcare setting and potential impact of cohorting strategies

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Predicting evolution using frequency-dependent selection in bacterial populations

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Choosing Your Battles: Which Resistance Genes Warrant Global Action?

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Wastewater Surveillance of SARS-CoV-2 across 40 U.S. states

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Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen

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Metrics to relate COVID-19 wastewater data to clinical testing dynamics

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The impact of host metapopulation structure on the population genetics of colonizing bacteria

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Optimal SARS-CoV-2 vaccine allocation using real-time seroprevalence estimates in Rhode Island and Massachusetts

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Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages

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SARS-CoV-2 epidemic after social and economic reopening in three US states reveals shifts in age structure and clinical characteristics

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Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci

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Previously undetected superspreading of Mycobacterium tuberculosis revealed by deep sequencing

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The role of interspecies recombinations in the evolution of antibiotic resistant pneumococci

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Population genomics of pneumococcal carriage in Massachusetts children following PCV-13 introduction

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Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae

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Leveraging pathogen sequence and contact tracing data to enhance vaccine trials in emerging epidemics

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Speciation trajectories in recombining bacterial species

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

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Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures

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Using the Association Between Antibiotic Susceptibility and Genetic Relatedness to Rescue Old Drugs for Empiric Use

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Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in Two Cohorts of High-Risk Military Trainees

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SARS-CoV-2 attack rate and population immunity in southern New England, March 2020 - May 2021

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Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data

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