List of works by Trevor Bedford

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

scientific article published on 31 March 2020

A Novel SARS-CoV-2 Variant of Concern, B.1.526, Identified in New York

scientific article

ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL. ⬇️

scientific article published on June 2015

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

scientific article published on 23 August 2021

Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster

scientific article

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

scientific article published on 07 January 2021

Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza

scientific article published on 18 January 2017

Canalization of the evolutionary trajectory of the human influenza virus

scientific article

Characterising the epidemic spread of Influenza A/H3N2 within a city through phylogenetics

scientific article published on 29 April 2020

Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics

scientific article published on 19 November 2020

Characteristics of COVID-19 in Homeless Shelters : A Community-Based Surveillance Study

scientific article published on 15 September 2020

Clustered Mutations at the Murine and Human IgH Locus Exhibit Significant Linkage Consistent with Templated Mutagenesis

scientific article published on 02 August 2019

Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans

scientific article published on 30 April 2019

Comprehensive mapping of avian influenza polymerase adaptation to the human host

Correction: MERS-CoV spillover at the camel-human interface.

scientific article

CpG-creating mutations are costly in many human viruses

scientific article published on 24 April 2020

Cross-Sectional Prevalence of SARS-CoV-2 Among Skilled Nursing Facility Employees and Residents Across Facilities in Seattle

scientific article published on 01 September 2020

Cryptic transmission of SARS-CoV-2 in Washington State

scientific article published on 06 April 2020

Cryptic transmission of SARS-CoV-2 in Washington state

scientific article published on 10 September 2020

Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants

article published in the Proceedings of the National Academy of Sciences of the United States of America

Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants

Dengue genetic divergence generates within-serotype antigenic variation, but serotypes dominate evolutionary dynamics

scientific article published on 06 August 2019

Did a Single Amino Acid Change Make Ebola Virus More Virulent?

scientific article published on November 2016

Early Detection of Covid-19 through a Citywide Pandemic Surveillance Platform

scientific article published on 01 May 2020

Early prediction of antigenic transitions for influenza A/H3N2

scientific article published on 18 February 2020

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

scientific article

Effects of weather-related social distancing on city-scale transmission of respiratory viruses

scientific article (preprint)

Eight challenges in phylodynamic inference.

scientific article

Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas

scientific article

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

scientific article (publication date: 24 May 2017)

Estimating Vaccine-Driven Selection in Seasonal Influenza

article

Evidence for Limited Early Spread of COVID-19 Within the United States, January-February 2020

scientific article published on 05 June 2020

Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e

scientific article

Evolvability of Hsp70 expression under artificial election for inducible thermotolerance in independent populations of Drosophila melanogaster.

scientific article published in July 2002

Explaining the geographical origins of seasonal influenza A (H3N2).

scientific article published in September 2016

Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster

scientific article

Gene conversion as a source of nucleotide diversity in Plasmodium falciparum

scientific article published on 2 April 2003

Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine

scientific article published on 21 October 2015

Genetic characterization of the Zika virus epidemic in the US Virgin Islands

scientific article (publication date: 3 March 2017)

Genome-wide evolutionary dynamics of influenza B viruses on a global scale

scientific article published on 28 December 2017

Genomic epidemiology reveals multiple introductions of Zika virus into the United States ⬇️

scientific article

Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

article

Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia. ⬇️

scientific article published on 12 November 2019

Genomic heterogeneity in the density of noncoding single-nucleotide and microsatellite polymorphisms in Plasmodium falciparum

scientific article published on 14 August 2006

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California ⬇️

scientific article published on 08 June 2020

Geography and host species shape the evolutionary dynamics of U genogroup infectious hematopoietic necrosis virus

scientific article published in July 2016

Global circulation patterns of seasonal influenza viruses vary with antigenic drift

scientific article published on 8 June 2015

Global migration dynamics underlie evolution and persistence of human influenza A (H3N2)

scientific article published in May 2010

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations

scientific article

Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypes

scientific article published on 28 December 2020

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

scientific article published on 05 April 2020

Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses.

scientific article

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty

scientific article (publication date: September 2012)

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

scientific article published on 02 September 2020

Integrating influenza antigenic dynamics with molecular evolution

scientific article

LB21. The Seattle Flu Study: A Community-Based Study of Influenza

scientific article published on 23 October 2019

Lorenzo-Redondo et al. reply

scientific article published in November 2017

MERS-CoV spillover at the camel-human interface

scientific article published on 16 January 2018

MERS-CoV spillover at the camel-human interface

scientific article published on 11 August 2017

Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin

scientific article published on 27 August 2019

Massive Iatrogenic Outbreak of Human Immunodeficiency Virus Type 1 in Rural Cambodia, 2014-2015.

scientific article published on 4 December 2017

Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission

scientific article published on 3 July 2017

Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

scientific article

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

scientific article (publication date: 9 January 2017)

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.

scientific article

Nextstrain: real-time tracking of pathogen evolution.

scientific article

Optimization of gene expression by natural selection

scholarly article

Overdispersion of the molecular clock varies between yeast, Drosophila and mammals

scientific article published on 27 May 2008

Overdispersion of the molecular clock: temporal variation of gene-specific substitution rates in Drosophila

scientific article published on 13 May 2008

Persistent HIV-1 replication maintains the tissue reservoir during therapy

scientific article published on 27 January 2016

Phylowood: interactive web-based animations of biogeographic and phylogeographic histories

scientific article

Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages

scientific article

Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses. ⬇️

scientific article

Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology.

scientific article published on 30 October 2017

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference ⬇️

scientific article

Quantifying evolutionary constraints on B-cell affinity maturation

scientific article

Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia

scientific article published on 17 January 2020

Real-time analysis and visualization of pathogen sequence data

scientific article published on 25 October 2018

Reassortment between influenza B lineages and the emergence of a coadapted PB1-PB2-HA gene complex

scientific article

Remote Household Observation for Non-influenza Respiratory Viral Illness

scientific article published on 17 November 2020

Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State

scientific article published on 19 April 2021

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

scientific article published in 2021

Seasonal influenza circulation patterns and projections for 2016-2017

Seasonal influenza circulation patterns and projections for 2017-2018

Seasonal influenza circulation patterns and projections for Sep 2017 to Sep 2018

Seasonality in the migration and establishment of H3N2 Influenza lineages with epidemic growth and decline

scientific article

Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution

scientific article

Spatial guilds in the Serengeti food web revealed by a Bayesian group model

scientific article (publication date: December 2011)

Strength and tempo of selection revealed in viral gene genealogies

scientific article

Ten recommendations for supporting open pathogen genomic analysis in public health

scientific article published on 11 June 2020

The Seattle Flu Study: a multi-arm community-based prospective study protocol for assessing influenza prevalence, transmission, and genomic epidemiology

scientific article published on 07 March 2020

The Seattle Flu Study: a multiarm community-based prospective study protocol for assessing influenza prevalence, transmission and genomic epidemiology

scientific article published on 07 October 2020

The ability of single genes vs full genomes to resolve time and space in outbreak analysis

scientific article published on 26 December 2019

The ability of single genes vs full genomes to resolve time and space in outbreak analysis

scientific article published on 24 March 2019

The roles of competition and mutation in shaping antigenic and genetic diversity in influenza

scientific article

Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak.

scientific article

Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain

scientific article published on 31 October 2019

Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2.

scientific article

Viral Phylodynamics

scientific article published on 21 March 2013

Viral factors in influenza pandemic risk assessment.

scientific article

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

scientific article published on 30 September 2020

Virus genomes reveal factors that spread and sustained the Ebola epidemic

scientific article (publication date: 12 April 2017)

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

article published in 2016

Within-Host Evolution of Human Influenza Virus.

scientific article

dms-view: Interactive visualization tool for deep mutational scanning data

scientific article

nextflu: real-time tracking of seasonal influenza virus evolution in humans

scientific article

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