2024

Inferring variant-specific effective reproduction numbers from combined case and sequencing data

Figgins and Bedford. 2024. medRxiv.

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2

Nanduri et al. 2024. Virus Evol.

Clinical and genomic epidemiology of coxsackievirus A21 and enterovirus D68 in homeless shelters, King County, Washington, USA, 2019–2021

Cox et al. 2024. Emerg Infect Dis.

High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains

Loes et al. 2024. J Virol.

Timely vaccine strain selection and genomic surveillance improves evolutionary forecast accuracy of seasonal influenza A/H3N2

Huddleston et al. 2024. medRxiv.

Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency

Abousamra et al. 2024. PLoS Comput Biol.

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

Welsh et al. 2024. Cell Host Microbe.

Spike deep mutational scanning helps predict success of SARS-CoV-2 clades

Dadonaite et al. 2024. Nature.

Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences

Tran Kiem et al. 2024. medRxiv.

Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years

Perofsky et al. 2024. Nat Commun.

Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution

Wagner et al. 2024. Nat Commun.

Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences

Tran Kiem and Bedford. 2024. Proc Natl Acad Sci USA.

Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county

Paredes et al. 2024. PLoS Pathog.

Comparative diagnostic utility of SARS-CoV-2 rapid antigen and molecular testing in a community setting

Kim et al. 2024. J Infect Dis.

Seasonal influenza circulation patterns and projections for February 2024 to February 2025

Huddleston et al. 2024. Zenodo.

Integrating dynamical modeling and phylogeographic inference to characterize global influenza circulation

Parino et al. 2024. medRxiv.

MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions

Müller et al. 2024. bioRxiv.

SARS-CoV-2 diversity and transmission on a university campus across two academic years during the pandemic

Casto et al. 2024. medRxiv.

Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic

Paredes et al. 2024. Cell.

Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States

Perofsky et al. 2024. eLife.

Changing genomic epidemiology of COVID-19 in long-term care facilities during the 2020–2022 pandemic, Washington State

Oltean et al. 2024. BMC Public Health.

2023

An atlas of continuous adaptive evolution in endemic human viruses

Kistler and Bedford. 2023. Cell Host Microbe.

Tracking the horizontal transfer of plasmids in Shigella sonnei and Shigella flexneri using phylogenetics

Müller et al. 2023. bioRxiv.

Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition

Lee and Hadfield et al. 2023. Front. Bioinform.

State-dependent evolutionary models reveal modes of solid tumor growth

Lewinsohn et al. 2023. Nat Ecol Evol.

Fitting stochastic epidemic models to gene genealogies using linear noise approximation

Tang et al. 2023. Ann Appl Stat.

Sentinel surveillance system implementation and evaluation for SARS-CoV-2 genomic data, Washington, USA, 2020–2021

Oltean et al. 2023. Emerg Infect Dis.

2022

Trends in risk factors and symptoms associated with SARS-CoV-2 and rhinovirus test positivity in King County, Washington: A test-negative design study of the greater Seattle Coronavirus Assessment Network

Hansen et al. 2022. JAMA Netw.

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Tegally et al. 2022. Science.

Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus

Weil et al. 2022. Nat Commun.

Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus

Happi et al. 2022. PLoS Biol.

A Bayesian approach to infer recombination patterns in coronaviruses

Müller et al. 2022. Nat Commun.

Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study

Paredes et al. 2022. Clin Infect Dis.

Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2

Kistler et al. 2022. Cell Host Microbe.

Diagnostic accuracy of an at-home, rapid self-test for influenza: prospective comparative accuracy study

Geyer et al. 2022. JMIR Public Health Surveill.

Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data

Burstein et al. 2022. medRxiv.

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

Srivatsan et al. 2022. Clin Chem.

2021

Tracing the origin, spread, and molecular evolution of Zika virus, Puerto Rico, 2016–2017

Santiago et al. 2021. Emerg Infect Dis.

SARS-CoV-2 epidemiology on a public university campus in Washington State

Weil et al. 2021. Open Forum Infect Dis.

Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York

Annavajhala et al. 2021. Nature.

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

Braun et al. 2021. PLoS Pathog.

SARS-CoV-2 variants in patients with immunosuppression

Corey et al. 2021. N Engl J Med.

Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State

Perchetti et al. 2021. J Med Virol.

Comparison of symptoms and RNA levels in children and adults With SARS-CoV-2 infection in the community setting

Chung et al. 2021. JAMA Pediatr.

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

Konings et al. 2021. Nat Microbiol.

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

Müller et al. 2021. Sci Transl Med.

A remote household-based approach to influenza self-testing and antiviral treatment

Heimonen et al. 2021. Influenza Other Respir Viruses.

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

Moncla et al. 2021. eLife.

Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo

Kinganda-Lusamaki et al. 2021. Nat Med.

Ebola virus transmission initiated by relapse of systemic Ebola virus disease

Mbala-Kingebeni et al. 2021. N Engl J Med.

Effects of weather-related social distancing on city-scale transmission of respiratory viruses: a retrospective cohort study

Jackson et al. 2021. BMC Infect Dis.

Limited predictability of amino acid substitutions in seasonal influenza viruses

Barrat-Charlaix et al. 2021. Mol Biol Evol.

Evaluating specimen quality and results from a community-wide, home-based respiratory surveillance study

Kim et al. 2021. J Clin Microbiol.

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

Kistler and Bedford. 2021. eLife.

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

Huddleston et al. 2021. J Open Source Softw.

Remote household observation for non-influenza respiratory viral illness

Emanuels et al. 2021. Clin Infect Dis.

2020

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

Jackson et al. 2020. PLoS Pathog.

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

Müller et al. 2020. PLoS Pathog.

Viral genome sequencing places White House COVID-19 outbreak into phylogenetic context

Bedford et al. 2020. medRxiv.

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

Chu et al. 2020. BMJ Open.

Characteristics of COVID-19 in homeless shelters: A community-based surveillance study

Rogers et al. 2020. Ann Intern Med.

Cryptic transmission of SARS-CoV-2 in Washington State

Bedford et al. 2020. Science.

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

Huddleston et al. 2020. eLife.

Cross-sectional prevalence of SARS-CoV-2 among skilled nursing facility employees and residents across facilities in Seattle

Weil et al. 2020. J Gen Intern Med.

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

Hilton et al. 2020. J Open Source Softw.

Ten recommendations for supporting open pathogen genomic analysis in public health

Black et al. 2020. Nat Med.

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

Deng et al. 2020. Science.

Evidence for limited early spread of COVID-19 within the United States, January–February 2020

CDC COVID-19 Response Team et al. 2020. Morb Mortal Wkly Rep.

Early detection of Covid-19 through a citywide pandemic surveillance platform

Chu et al. 2020. N Engl J Med.

CpG-creating mutations are costly in many human viruses

Caudill et al. 2020. Evol Ecol.

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

Egli et al. 2020. bioRxiv.

Early prediction of antigenic transitions for influenza A/H3N2

Castro et al. 2020. PLoS Comput Biol.

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

Moncla et al. 2020. PLoS Pathog.

2019

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

Dudas and Bedford. 2019. BMC Evol Biol.

Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

Potter et al. 2019. Virus Evol.

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

Black et al. 2019. BMC Infect Dis.

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

Hadfield et al. 2019. PLoS Pathog.

Seasonal influenza circulation patterns and projections for September 2019 to September 2020

Bedford et al. 2019. bioRxiv.

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

Lee et al. 2019. eLife.

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

Bell et al. 2019. eLife.

Clustered mutations at the murine and human IgH locus exhibit significant linkage consistent with templated mutagenesis

Dale et al. 2019. J Immunol.

Comprehensive mapping of avian influenza polymerase adaptation to the human host

Soh et al. 2019. eLife.

2018

Estimating vaccine-driven selection in seasonal influenza

Wen et al. 2018. Viruses.

Real-time analysis and visualization of pathogen sequence data

Neher and Bedford. 2018. J Clin Microbiol.

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

Lee et al. 2018. Proc Natl Acad Sci USA.

Nextstrain: real-time tracking of pathogen evolution

Hadfield et al. 2018. Bioinformatics.

Massive iatrogenic outbreak of human immunodeficiency virus type 1 in rural Cambodia, 2014-2015

Rouet et al. 2018. Clin Infect Dis.

Within-host evolution of human influenza virus

Xue et al. 2018. Trends Microbiol.

Seasonal influenza circulation patterns and projections for Feb 2018 to Feb 2019

Bedford and Neher. 2018. bioRxiv.

Predictive modeling of influenza shows the promise of applied evolutionary biology

Morris et al. 2018. Trends Microbiol.

MERS-CoV spillover at the camel-human interface

Dudas et al. 2018. eLife.

Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza

Cybis et al. 2018. Stat Med.

2017

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

Langat et al. 2017. PLoS Pathog.

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

Bedford and Neher. 2017. bioRxiv.

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

Bell and Bedford. 2017. PLoS Pathog.

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

Quick et al. 2017. Nat Protoc.

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

Grubaugh et al. 2017. Nature.

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

Faria et al. 2017. Nature.

Virus genomes reveal factors that spread and sustained the Ebola epidemic

Dudas et al. 2017. Nature.

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

Black et al. 2017. bioRxiv.

Seasonal influenza circulation patterns and projections for 2017-2018

Bedford and Neher. 2017. bioRxiv.

2016

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

Black et al. 2016. Virus Evol.

Viral factors in influenza pandemic risk assessment

Lipsitch et al. 2016. eLife.

Did a single amino acid change make Ebola virus more virulent?

Bedford and Malik. 2016. Cell.

Seasonal influenza circulation patterns and projections for 2016-2017

Bedford and Neher. 2016. bioRxiv.

Explaining the geographical origins of seasonal influenza A (H3N2)

Wen et al. 2016. Proc R Soc B.

Identification of low- and high-impact hemagglutinin amino acid substitutions that drive antigenic drift of influenza A(H1N1) viruses

Harvey et al. 2016. PLoS Pathog.

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

Neher et al. 2016. Proc Natl Acad Sci USA.

Quantifying and mitigating the effect of preferential sampling on phylodynamic inference

Karcher et al. 2016. PLoS Comput Biol.

Persistent HIV-1 replication maintains the tissue reservoir during therapy

Lorenzo-Redondo et al. 2016. Nature.

2015

Genetic diversity and protective efficacy of the RTS,S/AS01 malaria vaccine

Neafsey et al. 2015. N Engl J Med.

Positive selection in CD8+ T-cell epitopes of influenza nucleoprotein revealed by a comparative analysis of human and swine viral lineages

Machovech et al. 2015. J Virol.

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

Meyer et al. 2015. Virus Evol.

Assessing phenotypic correlation through the multivariate phylogenetic latent liability model

Cybis et al. 2015. Ann Appl Stat.

Quantifying evolutionary constraints on B cell affinity maturation

McCoy et al. 2015. Phil Trans R Soc B.

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

Neher and Bedford. 2015. Bioinformatics.

Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone

Park et al. 2015. Cell.

Global circulation patterns of seasonal influenza viruses vary with antigenic drift

Bedford et al. 2015. Nature.

Eight challenges in phylodynamic inference

Frost et al. 2015. Epidemics.

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

Vrancken et al. 2015. Methods Ecol Evol.

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

Dudas et al. 2015. Mol Biol Evol.

2014

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

Zinder et al. 2014. BMC Evol Biol.

Epidemiological and evolutionary analysis of the 2014 Ebola virus outbreak

Łuksza et al. 2014. arXiv.

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

Faria et al. 2014. Science.

Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses

Roche et al. 2014. PLoS Biol.

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

Lemey et al. 2014. PLoS Pathog.

Integrating influenza antigenic dynamics with molecular evolution

Bedford et al. 2014. eLife.

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

Landis and Bedford. 2014. Bioinformatics.

2013 and earlier

Viral phylodynamics

Volz et al. 2013. PLoS Comput Biol.

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

Zinder et al. 2013. PLoS Pathog.

Canalization of the evolutionary trajectory of the human influenza virus

Bedford et al. 2012. BMC Biol.

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

Baele et al. 2012. Mol Biol Evol.

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

Baskerville et al. 2011. PLoS Comput Biol.

Strength and tempo of selection revealed in viral gene genealogies

Bedford et al. 2011. BMC Evol Biol.

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

Bedford et al. 2010. PLoS Pathog.

Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster

Rogers et al. 2010. Proc Natl Acad Sci USA.

Optimization of gene expression by natural selection

Bedford and Hartl. 2009. Proc Natl Acad Sci USA.

Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster

Rogers et al. 2009. Genetics.

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

Bedford and Hartl. 2008. Mol Biol Evol.

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

Bedford et al. 2008. Genetics.

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

Volkman et al. 2007. Gene.

Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites

Castillo-Davis et al. 2004. Mol Biol Evol.

Gene conversion as a source of nucleotide diversity in Plasmodium falciparum

Nielsen et al. 2003. Mol Biol Evol.

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

Feder et al. 2002. Phys Biochem Zool.