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congratulations to Dr. Brent Allman on his amazing PhD defense! i've been very lucky to get to co-advise brent with Koelle Lab

For the second preprint announcement of the day, we’ve updated our earlier manuscript on using segregating sites trajectories of viral sequence data for epidemiological inference, which was led by Yeongseon Park. biorxiv.org/content/10.110…

Second PhD defended from the Koelle lab this week was from Michael Martin. Mike not only did a phenomenal quantity of work, but it was of high quality as well! Mike collaborated with many folks, SternLab @sternadi.bsky.social @AnnePiantadosi Ahmed Babiker أحمد بابكر among others. Congrats!!

This week's EEB Thurs Seminar features ALUM Dr Katia Koelle Koelle Lab presenting Using genetic data at multiple scales to understand constraints on viral adaptation. 3pm, 1010 Bio Sci Bldg and Zoom live, see poster #eventalanche #Genetics #diseases

Our paper on influenza reassortment in mammals is out now on Nature Communications! Congratulations to all our collaborators!rdcu.be/cZtAo Anice Lowen Lucas Ferreri 🇦🇷 ☮️ Koelle Lab @CRP_FLU_UGA Joaquín Cáceres Silvia Carnaccini Juergen Richt CEIRRNetwork #LoveVirology

And now with a more accurate title! Also a gift link, so it should not be behind a paywall. nytimes.com/2023/05/10/sci…

#eeid2023 Transmission bottleneck and disease severity

Congratulations Yeongseon Park and Michael Martin 🎉

We just posted a preprint on a new approach for estimating transmission bottleneck sizes. Spoiler alert: we confirm bottleneck sizes for influenza virus and SARS-CoV-2 to be tiny using the new approach: biorxiv.org/cgi/content/sh…

(We think this new approach is preferable to existing approaches - some of which we've developed - because it uses a different subset of viral sites to estimate transmission bottleneck sizes and is less prone to underestimation of bottleneck sizes.)

Congratulations to Dr. Yeongseon Park for her successful PhD defense on Friday, March 7, 2025!

And while I'm on tweeter (once in a blue moon), here are some relatively recent papers from our group!

A fun analysis with David Rasmussen focused on seeing if incomplete purifying selection impacts/biases our estimates of epidemiological parameters in phylodynamic analyses: royalsocietypublishing.org/doi/pdf/10.109… (thankfully, it doesn't bias estimates much at all!)

Fortunate to collaborate with Rustom Antia and Jim Bull on an analysis focused on the question: Why do respiratory viruses evolve antigenically while viruses undergoing systemic replication do not? watermark.silverchair.com/eoaf002.pdf?to…

Collaboration with Lucas Ferreri and the Lowen lab at Emory to look at influenza virus evolution and dispersal during infection within a host: pnas.org/doi/abs/10.107…

Hope to post again in less than a year :)

Excited to share our recent preprint on quantifying pandemic potential from experimental transmission studies, spearheaded by grad student Elizabeth Somsen in my group and in collab with Troy Sutton & lab at Penn State and Anice Lowen at Emory: biorxiv.org/content/10.110….