Open Science

Data

We make our data publicly available as soon as possible after data generation. You can find it all here.

Code

Analyses should be reproducible, so we make our tools, scripts and pipelines available. Come grab our code here.

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

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

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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…)

Zika sequence from local Florida transmission

| Data, News | No Comments
Data here. Protocol here. In collaboration with Dr. Diogo Magnani in the Watkins Laboratory in the Dept. of Pathology at the University of Miami's Miller School of Medicine, we recently received plasma and saliva from two people with Zika virus infections living in the Miami area. Using our amplicon-based approach previously used to sequence Zika virus from travel-related Zika virus cases in…

Recent Publications

Malaria paper in Cell

| Publications | No Comments
Hereditary xerocytosis is thought to be a rare genetic condition characterized by red blood cell (RBC) dehydration with mild hemolysis. RBC dehydration is linked to reduced Plasmodium infection in vitro; however, the role of RBC dehydration in protection against malaria in vivo is unknown. Most cases of hereditary xerocytosis are associated with gain-of-function mutations in PIEZO1, a mechanically activated ion channel. We…

Zika genomics commentary in Cell

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The emergence and spread of Zika virus in the Americas continues to challenge our disease surveillance systems. Virus genome sequencing during the epidemic uncovered the timescale of Zika virus transmission and spread. Yet, we are only beginning to explore how genomics can enhance our responses to emerging viruses. Together with our colleagues Nuno Faria and Oliver Pybus at the University…

Zika papers in Nature

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In a series of papers in the journals Nature and Nature Protocols, we used Zika virus sequencing from patients and mosquitos to show how the virus has spread across South America and into Florida. This work was performed as a large (huge!) collaboration of national and international institutions, which was made possible because of open science and open data. (more…)