Allison Black

Google Scholar

I’m a PhD student in the Department of Epidemiology at the University of Washington. My research focuses on using evolutionary analysis of viral genome sequences to explore how diseases move around, whether that be from person-to-person or country-to-country.

Most of my work so far has focused on understanding the Zika epidemic in the Americas. I’ve been involved in estimating when Zika was introduced to Brazil and investigating how frequently Zika was introduced to the US Virgin Islands. While joint analysis of sequence data and surveillance data is a relatively new domain for infectious disease epidemiologists, these analyses can help us better define populations at risk, investigate factors associated with disease spread, and evaluate infection control measures, all of which are critical components of epidemiology.

I received my Bachelor’s of Arts and Sciences from Quest University in British Columbia, Canada, studying health sciences, and did a post-baccalaureate year at the University of Manitoba studying microbiology. I have a Master’s in Genetic Epidemiology from the University of Washington.


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

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

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

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

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

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

Ebola virus transmission initiated by relapse of systemic Ebola virus disease

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

Ten recommendations for supporting open pathogen genomic analysis in public health

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

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

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

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

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

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


zika-usvi - Evolutionary analysis of USVI Zika epidemic

zika-colombia - Genetic analysis of the Zika epidemic in Colombia

zika-seq - Pipelines to do MinION sequencing of Zika virus

roka - Evolutionary and epidemiological analysis of Roka HIV outbreak


How can we improve support for open pathogen genomic analysis in public health settings?

A concrete example of the value of data sharing

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

Multiple introductions of mumps virus into Washington State

Characterization of 27 mumps virus genomes from the Washington state outbreak

The Bedford lab becomes a sequencing lab...

Evolutionary dynamics of infectious hematopoietic necrosis virus in Pacific salmon

Postcard from Brazil