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, Narrative | 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

Catie Anderson

SARS-CoV-2 early epidemic study out in Cell

| Publications | No Comments
Our study investigating one of the most explosive early COVID-19 outbreaks in the United States has been published in Cell. The emergence of the COVID-19 epidemic in the U.S. went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in…
Congo River

Ebola relapse study out in NEJM

| Publications | No Comments
Our study investigating a rare case of Ebola relapse has been published in the New England Journal of Medicine. Together with our colleagues at INDR in the Democratic Republic of Congo, the University of Nebraska Medical Center in Omaha, and several other institutions, we investigated a case of a vaccinated man who had already been sick with Ebola fell ill with…
graphical abstract

Study on B.1.1.7 out in Cell

| Publications | No Comments
Our study investigating the spread of the B.1.1.7 SARS-CoV-2 variant first discovered in the UK has been published in the journal Cell. Together with our colleagues at the San Diego-based company Helix, we used testing data, genomics, and modeling to answer two simple questions - when was B.1.1.7 introduced into the US and how is it currently spreading in this country?…