Open Science

Data & Projects

We make our data publicly available as soon as possible after generation.

Tools & Apps

Software packages, tools, and apps from our lab.

Protocols

Here you’ll find the various protocols that we have developed or use in our lab.

Talks

We give talks. Listen, don’t take notes, then come download all of our slides here.

Beer-O-Meter

Overview

We make mistakes. That’s one of the main reasons we make our data publicly available – so others can point it out, and we can correct. For every mistake found, we’re offering a beer – check back here for the tally and leaderboard.

Tally

9
Beers Owed

Leaderboard

Gytis Dudas

50%

Richard Neher

35%

Trevor Bedford

15%

Recent Data-related Blog Posts

Hidden Zika outbreak

| Data | No Comments
Summary: Using local and travel-associated case reporting from American and European public health systems, we identified an unreported Zika outbreak in Cuba during 2017. Virus sequencing from travelers revealed that the Zika outbreak in Cuba was sparked by multiple introductions of the virus from elsewhere in the Caribbean and Central America during 2016 that persisted into 2017. The recent Zika virus…

PAHO Zika numbers

| Data, News | No Comments
Data here. Permanent Andersen Lab project link is here. Most epidemiological investigations of Zika virus during the current epidemic in the Americas requires temporal human case data. The only place to gather this information is is from the Pan American Health Organization (PAHO), an arm of the World Health Organization. They present Zika virus case numbers in two ways: spreadsheets of…

Zika sequences from Miami mosquitoes

| Data, News | No Comments
Data here. Protocol here. Three pools of Aedes aegypti mosquitoes collected in Miami Beach on August 22nd and 23rd, 2016, were found to be infected with Zika virus. Through our collaborators, Scott Michael and Sharon Isern from Florida Gulf Coast University, we recently received samples of these mosquitoes for sequencing using our amplicon-based protocol for MiSeq. (more…)

Recent Publications

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Zika surveillance study in Cell

| Publications | No Comments
Our study investigating smoldering 'hidden' outbreaks of Zika in the Americas was published on the cover of Cell. In this paper we used travel surveillance and genomic epidemiology to answer a simple question - "in 2017, was the epidemic over?". The short answer, is no - read the rest of the study for the long answer. The Zika epidemic in…
abstract

Ebola antibody research

| Publications | No Comments
In two papers published in Cell and Cell Host Microbe together with our collaborators at VIC, CViSB, and VHFC we describe in detail antibody responses to Ebola virus. By systematic analysis of a large set of more than 170 monoclonal antibodies to Ebola virus, we investigated which immunological features play key roles in protection against the virus. This was our first…
holmes

Pandemics: Focus on surveillance

| Publications | No Comments
Over the past 15 years, outbreaks caused by viruses such as Ebola, SARS, and Zika have cost governments billions of US dollars. Combined with a perception among scientists, health workers and citizens that responses to outbreaks have been inadequate, this has fueled what seems like a compelling idea. Namely, that if researchers can identify the next pandemic virus before the…