October 23, 2024

The lab went out to dinner to celebrate the newest member of the lab, Stephen Shank, who is joining us as a full time bioinformatician/computational biologist. We had dim sum on got a mostly complete lab picture. Welcome Stephen!


October 16, 2024

I did a webinar with Aliza Simeone, Cheryl Bettigole, and Kathleen Hall Jamieson on highly pathogenic avian influenza in North America. It was a great discussion, with lots of great questions, and the webinar was covered by Penn Today!

July 2024: The lab goes to the CEIRR Annual meeting

In July, almost the entire lab went to New York for the CEIRR annual meeting. Maria presented a poster on her work characterizing influenza evolution in different species and Jordan presented both a poster and a talk on his NextClade dataset. It was really exciting to have the lab presenting data, and they were both very well received. We also continued our quest to get a fully up to date lab photo and got close, but not all the way there.


Jordan presenting his work at the Computational Modeling Core Showcase, and the lab relaxing in Central Park.



July 16, 2024: Spring recap

It was a busy spring! We were thrilled to have Clara rotate and join the lab, and are excited to have her working on avian ecology and H5 transmission. Louise was named a Pew Biomedical Scholar, and Maria and Jordan passed their prelims. Congrats to everyone!

It was also a busy spring for avian influenza. H5N1 started spreading in dairy cattle, necessitating new visualizations, builds, and updates to Nextstrain/avian-flu, which would not have been possible without a tremendous amount of help from Trevor, Jover, James, and John on the Nextstrain team. We also made some commentary/interpretations to news outlets about the cattle outbreak, which you can peruse at NPR, All Things Considered, Vox, Nature News, and New York Times here and here.

Jordan also released his H5 Nextclade dataset onto the main Nextclade site, providing a tool for rapid, drag and drop clade assignment that the community can use. This is really exciting, and will be hopefully be useful to the field. Congrats Jordan!

December 12, 2023: Lab field trip!

The lab took a field trip! We went to see our friends and collaborators based out to Penn Vet’s large animal campus at New Bolton Center. We had a research update with investigators with the Wildlife Futures Program, picked up samples, and got to meet some alpacas!



October 15, 2023: TWIV 1053: Bird flu in Baltimore

During the CEIRR meeting in Baltimore, I sat down with Vincent Racaniello, Ron Fouchier, and Rafael Medina to chat about the ongoing H5Nx avian influenza outbreak in the Americas or a live recording for This Week in Virology! You can listen to the podcast here.

August 28, 2023: The lab goes to the CEIRR Network Meeting

Jordan, Lambo, and I went to the CEIRR Annual Network meeting this year in Baltimore, MD. Lambo gave a poster on some work from his PhD using generalized additive models to model seasonal influenza circulation and transmission patterns, and Jordan got to meet some new people and hear about a lot of cool research! I did a demo of the avian flu Nextstrain builds for the Computational Modeling Core showcase, and gave a talk on our work using new structured coalescent models to study H5Nx cross-species transmission. It was really fun to see old friends and meet some new people as well.

August 25, 2023

Today we celebrated all of the lab’s summer successes and said goodbye to Alex, who is off to start a new job at AstraZeneca. This summer, both Jordan and Maria joined the lab as PhD students, and Lambo won a Verena Fellowship to work with Barbara Han on modeling canine influenza. To celebrate these successes and Alex’s time in the lab, we went out in West Philly and finally took a lab photo!


August 8, 2023: Bird flu has never done this before

I talked to Katie Wu at the Atlantic about the ongoing H5 avian influenza outbreak in North America. We talked about the recent, widespread infections in mammals in Europe and South America, and about the difficulty in assigning risk to new viruses when they emerge. Katie covered a lot of important information in this article and got commentary from a lot of amazing researchers, and it was fun to contribute to.

June 14, 2023

The summer is off to a good start! I taught for a day in Fort Collins, CO for the Genomics of Disease in Wildlife Workshop. I lectured and lead two lab activities about phylodynamics, BEAST, and Nextstrain. The participants and co-instructors were awesome, and Fort Collins was beautiful. All the course materials (lectures and lab activities) are publicly available on the course github page, as well as on my github page here. Here are some pictures from the workshop hike!


February 14, 2023: A Bird Flu Pandemic Hovering on the Horizon?

A Bird Flu Pandemic Hovering on the Horizon
I did an interview for the Naked Scientist (a BBC podcast series) on the ongoing avian influenza outbreak in North America, why it’s distinct from past outbreaks, and what we should be thinking about going forward. Also featured in this are some of my all-time favorite virologists (Wendy Barclay!), giving great commentary.

November 30, 2022: What is bird flu and how deadly is it?

What is bird flu and how deadly is it?
I provided a quote for Helen Briggs, who was writing an article about the ongoing avian influenza outbreak for BBC News. The article discusses why this outbreak is distinct from past outbreaks, and possible reasons why this one is so widespread.

October 21, 2022: Why is bird flu so bad right now?

Why is bird flu so bad right now?
Saima Sidik from Nature News chatted with me about the ongoing H5N1 avian influenza outbreak that is happening in the US and Europe, which is causing devastating impacts on wild and domestic birds. We talked about why this outbreak is different from past outbreaks, and what we still need to learn about H5N1 going forward.

July 29, 2022: A podcast with TWiEVO!

TWiEVO 80: Viruses of a feather bottleneck together
I had a great time doing this podcast with Vincent Racaniello and Nels Elde for their podcast This Week in Evolution (TWiEVO). We talked about our work looking at H5N1 cross-species transmission, SARS-CoV-2 within-host diversity, and mumps transmission in Washington State, and swapped notes on the excellent ASV (American Society for Virology) meeting in July 2022 in Madison, WI.