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

ages_tests

Age distribution of COVID-19 cases in San Diego County

| Data | No Comments
To understand the spread of COVID-19 in San Diego, we looked at the age distribution of COVID-19 over time (Figure 1). Data for this analysis was provided by the Epidemiology and Immunization Services Branch of the County of San Diego Health and Human Services agency through the San Diego Open GIS Data Portal. The visualization was inspired by Gytis Dudas's…
narrative

Narrative 2 | Cross-border virus transmission

| Data, Narrative | No Comments
English: To gain insights into the the emergence, spread, and transmission of COVID-19 in our community, we are working with a large number of partners to sequence SARS-CoV-2 samples from patients in San Diego and across the border in Tijuana. In this preliminary analysis we look at the how the outbreaks are connected between California, USA and Baja California, (more…)
narrative

Narrative 1 | Genomic Epi in San Diego

| Data, Narrative | No Comments
To gain insights into the the emergence, spread, and transmission of COVID-19 in our community, we are working with a large number of partners to sequence SARS-CoV-2 samples from infected patients in San Diego. This is our first preliminary analysis. (more…)

Recent Publications

Cell abstract

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…
Cell 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 nature commentary

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…