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List of works by William P. Hanage

1165. Comparing Patient Risk Factors, Sequence Type, and Resistance Loci Identification Approaches for Predicting Antibiotic Resistance in Escherichia coli Bloodstream Infections

scholarly article by Derek MacFadden et al published November 2018 in Open Forum Infectious Diseases

Ability of pneumococcal serotypes and clones to cause acute otitis media: implications for the prevention of otitis media by conjugate vaccines

scientific article

Antibiotics in agriculture and the risk to human health: how worried should we be?

scientific article

Assessing the reliability of eBURST using simulated populations with known ancestry

scientific article

Assigning strains to bacterial species via the internet

scientific article

Association of Pneumococcal Protein Antigen Serology With Age and Antigenic Profile of Colonizing Isolates

scientific article published on 29 December 2016

Bacterial genomes in epidemiology--present and future.

scientific article published on 04 February 2013

Bayesian modeling of recombination events in bacterial populations

scientific article

Biomedical Ph.D. students enrolled in two elite universities in the United kingdom and the United States report adopting multiple learning relationships

scientific article

COVID-19: US federal accountability for entry, spread, and inequities-lessons for the future

scientific article published on 02 November 2020

Carriage burden, multiple colonization and antibiotic pressure promote emergence of resistant vaccine escape pneumococci

scientific article published on June 2015

Carried pneumococci in Massachusetts children: the contribution of clonal expansion and serotype switching.

scientific article

Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen

scientific article

Comparing Patient Risk Factor-, Sequence Type-, and Resistance Locus Identification-Based Approaches for Predicting Antibiotic Resistance in Escherichia coli Bloodstream Infections.

scientific article published on 24 May 2019

Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes

scientific article

Continued impact of pneumococcal conjugate vaccine on carriage in young children.

scientific article published on July 2009

Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

scientific article

Detection of recombination events in bacterial genomes from large population samples

scientific article

Displaying the relatedness among isolates of bacterial species -- the eBURST approach

scientific article published in December 2004

Distribution of pneumococcal surface protein A families 1 and 2 among Streptococcus pneumoniae isolates from children in finland who had acute otitis media or were nasopharyngeal carriers

scientific article published on 27 August 2008

Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening

scientific article published on 04 January 2017

Diversification of bacterial genome content through distinct mechanisms over different timescales.

scientific article

Diversity and Antibiotic Resistance among Nonvaccine Serotypes ofStreptococcus pneumoniaeCarriage Isolates in the Post–Heptavalent Conjugate Vaccine Era

article

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

article

Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis.

scientific article published on 16 April 2015

Effects of Streptococcus pneumoniae strain background on complement resistance

scientific article (publication date: 2011)

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.

scientific article published on 11 February 2017

Emergence of 19A as virulent and multidrug resistant Pneumococcus in Massachusetts following universal immunization of infants with pneumococcal conjugate vaccine

scientific article published in June 2007

Epidemiology and risk factors for Staphylococcus aureus colonization in children in the post-PCV7 era

scientific article

Estimating the hospitalization burden associated with influenza and respiratory syncytial virus in New York City, 2003-2011.

scientific article

Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape

scientific article

Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete

scientific article

Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae.

scientific article

Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti

scientific article

Exploring Genetic Relatedness, Patterns of Evolutionary Descent, and the Population Genetics of Bacterial Pathogens Using Multilocus Sequence Typing

article

Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen

scientific article published on 01 February 2020

Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae

scientific article published on 22 October 2020

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

scientific article published on 16 October 2017

From bacterial genomics to clinical epidemiology: an interview with Bill Hanage

article

Functional characterization of bacteria isolated from ancient arctic soil exposes diverse resistance mechanisms to modern antibiotics

scientific article

Fuzzy species among recombinogenic bacteria

scientific article

Fuzzy species revisited

scientific article

Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States.

scientific article published on 18 January 2017

Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study

scientific article

Genomic epidemiology of meticillin-resistant ST22 widespread in communities of the Gaza Strip, 2009

article

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.

scientific article published on 6 February 2012

Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci

scientific article published on 26 November 2018

Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages

scientific article published on 04 December 2014

HIV-1 transmitting couples have similar viral load set-points in Rakai, Uganda

scientific article

Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution

scientific article

Historical zoonoses and other changes in host tropism of Staphylococcus aureus, identified by phylogenetic analysis of a population dataset

scientific article

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

scientific article

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

scientific article published on 20 May 2020

Host population structure and treatment frequency maintain balancing selection on drug resistance

scientific article

Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity.

scientific article published on 9 May 2015

Identifying currents in the gene pool for bacterial populations using an integrative approach

scientific article

Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus

scientific article published on 13 February 2016

Immunization, Antibiotic Use, and Pneumococcal Colonization Over a 15-Year Period

scientific article published on 4 October 2017

Impact of 13-Valent Pneumococcal Conjugate Vaccination on Streptococcus pneumoniae Carriage in Young Children in Massachusetts.

scientific article published on 03 October 2013

Impact of Host Heterogeneity on the Efficacy of Interventions to Reduce Staphylococcus aureus Carriage

scientific article published on 24 November 2015

Inference on population histories by approximating infinite alleles diffusion

scientific article published on 19 September 2012

Interim results of an ecological experiment - Conjugate vaccination against the pneumococcus and serotype replacement

scientific article

Invasiveness of serotypes and clones of Streptococcus pneumoniae among children in Finland ⬇️

scientific article

Low effective dispersal of asexual genotypes in heterogeneous landscapes by the endemic pathogen Penicillium marneffei

scientific article

Making sense of differences in pneumococcal serotype replacement

scientific article published on 29 January 2019

Mechanisms of genome evolution of Streptococcus

scientific article

Microbiology: Microbiome science needs a healthy dose of scepticism

scientific article

Modelling bacterial speciation

scientific article

Modelling infectious disease - time to think outside the box?

scientific article

Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks

scientific article published on 17 January 2017

Navigating the future of bacterial molecular epidemiology.

scientific article published on 16 September 2010

Neutral microepidemic evolution of bacterial pathogens

scientific article

No coexistence for free: neutral null models for multistrain pathogens

scientific article

Nontypeable pneumococcal isolates among navajo and white mountain apache communities: are these really a cause of invasive disease?

scientific article

Not So Simple After All: Bacteria, Their Population Genetics, and Recombination

scientific article

Origin and proliferation of multiple-drug resistance in bacterial pathogens

scientific article

Pandemic potential of a strain of influenza A (H1N1): early findings

scientific article

Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination

article

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

scientific article

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

scientific article published on 10 December 2020

Phylogenetic interpretation during outbreaks requires caution

scientific article published on 19 May 2020

Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus

scientific article published on 27 December 2012

Pneumococcal carriage and antibiotic resistance in young children before 13-valent conjugate vaccine

scientific article published on March 2012

Pneumococcal conjugate vaccines in different settings - Authors' reply

scientific article published on 01 December 2019

Pneumococcal sequence type replacement among American Indian children: A comparison of pre- and routine-PCV7 eras

scientific article published in March 2012

Population biology of Gram-positive pathogens: high-risk clones for dissemination of antibiotic resistance

scientific article published on 4 July 2011

Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi ⬇️

scientific article published on 12 July 2017

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae

scientific article

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

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

scientific article published in 2019

Population genomics of post-vaccine changes in pneumococcal epidemiology.

scientific article published on 05 May 2013

Population structure in the Neisseria, and the biological significance of fuzzy species

scientific article

Potential for Erosion of Efficacy in Noninferiority Trials of Decreasing Duration of Antibiotic Therapy

scientific article published on 01 September 2019

Prediction of post-vaccine population structure of Streptococcus pneumoniae using accessory gene frequencies

article

Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing

scientific article published on 04 February 2020

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing

scientific article published on 10 February 2020

Re-emergence of the type 1 pilus among Streptococcus pneumoniae isolates in Massachusetts, USA.

scientific article

Recombination and the nature of bacterial speciation

scientific article published on January 2007

Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule

scientific article published on 27 September 2016

Recombination produces coherent bacterial species clusters in both core and accessory genomes.

scientific article published on 5 November 2015

Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany

scientific article

Restricted gene flow among hospital subpopulations of Enterococcus faecium.

scientific article

Selective and genetic constraints on pneumococcal serotype switching

scientific article published on 31 March 2015

Sequences, sequence clusters and bacterial species

scientific article published on November 2006

Serotype specific invasive capacity and persistent reduction in invasive pneumococcal disease

scientific article published on 26 October 2010

Serotype-specific problems associated with pneumococcal conjugate vaccination

scientific article published on February 2008

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

scientific article published in November 2017

Speciation trajectories in recombining bacterial species

scientific article

Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced

scientific article

Streptococcus pneumoniae contains 3 rlrA pilus variants that are clonally related

scientific article published in March 2008

Streptococcus pyogenes with reduced susceptibility to β-lactams: how big an alarm bell?

scientific article published on 20 October 2019

Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms.

scientific article

The Next Pandemic: On the Front Lines Against Humankind’s Gravest Dangers.

scientific article published in December 2017

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

scientific article

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

scientific article (preprint)

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

scientific article

The impact of homologous recombination on the generation of diversity in bacteria

scientific article published on 19 October 2005

The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.

scientific article published on 4 April 2018

The important role of nontypable Streptococcus pneumoniae international clones in acute conjunctivitis

scientific article published on 28 July 2006

The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci

scientific article published on 14 July 2021

Two Health or Not Two Health? That Is the Question

article

Understanding pneumococcal serotype 1 biology through population genomic analysis

scientific article published on 8 November 2016

Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15.

scientific article published in March 2018

Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli

scientific article published on 09 March 2020

Using multilocus sequence data to define the pneumococcus

scientific article

Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone

scientific article published on 23 June 2014

Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis

scientific article

Wastewater surveillance of SARS-CoV-2 across 40 U.S. states from February to June 2020

scientific article published in September 2021

Weak Epistasis May Drive Adaptation in Recombining Bacteria

scientific article published on 12 January 2018

What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae?

scientific article

Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157.

scientific article

Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints

scientific article published in 2022

Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission

article

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

scientific article published on 27 March 2014

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