Duncan MacCannell

Duncan MacCannell

@drm.bsky.social

Molecular #epidemiology & #publichealth. Pathogen #genomics, #microbiology, #emerginginfections, #AMR, (bio)tech #biosurveillance and #opendata. Personal account. Opinions/dad jokes are my own. 🦅 Low productivity public sector employee. 🔬🦠🧬🖥️💉🌻🍩🐸🥪

4.2K followers548 following972 posts

Duncan MacCannell reposted

Susie Grigson
@susiegriggo.bsky.social

Replying to @susiegriggo.bsky.social

We tested VHAMSTeR on the 24M genomes in the MetaVR database, successfully assigning hosts to an additional 59.5% of the catalog. Exploring these predictions revealed cool ecological patterns, like finding that protist viruses are highly enriched in polar oceans compared to tropical/temperate ones!

Duncan MacCannell
@drm.bsky.social

This stopped me in my tracks. Helen was an incredibly gifted reporter and such a delight to talk to (even as she was pinning you to the wall).

STAT@statnews.com

We are going to miss you very much, Helen. https://www.statnews.com/2026/10/13/helen-branswell-stat-reporter-obituary/

statnews.comHelen Branswell, whose reporting on infectious diseases and public health drew acclaim, dies at 69Helen Branswell, STAT's infectious disease reporter who earned the respect of experts and public health officials with her accessible, prescient dispatches, has died at age 69.

Duncan MacCannell reposted

Dr. Tom Frieden
@drtomfrieden.bsky.social

I had no idea that Helen Branswell was ill. I'm deeply saddened to hear of her passing. When I became CDC director, a very astute member of the CDC press office told me that I wasn't ready for a briefing unless I was ready for questions from Helen Branswell.

statnews.comHelen Branswell, whose reporting on infectious diseases and public health drew acclaim, dies at 69Helen Branswell, STAT's infectious disease reporter who earned the respect of experts and public health officials with her accessible, prescient dispatches, has died at age 69.

Duncan MacCannell reposted

WHO
@who.int

Disease Outbreak News on Ebola disease caused by Bundibugyo virus - Democratic Republic of the Congo (8 October 2026) https://bit.ly/4zf1z18

Duncan MacCannell
@drm.bsky.social

Reminder that submissions to DHS S&T Ready, set ID the biothreat challenge are due next week. (Oct 14). They are looking for innovative approaches to identify pathogens in environmental metagenomic data. www.dhs.gov/science-and-...

dhs.govReady, Set, ID the Biothreat | Homeland SecurityThe Challenge will focus on the development and demonstration of computational artificially intelligent (AI) algorithms for detecting known, novel, and unknown biological threats in environmental meta...
Duncan MacCannell
@drm.bsky.social

I ran headlong into Claude’s classifiers, and got a gentle downgrade, simply for asking it to put together a fairly vanilla, recurring web/lit search on topics related to AI biorisk.

Duncan MacCannell
@drm.bsky.social

Great paper that describes a generalized Pango-style lineage nomenclature, using chikv as an example. Standard naming conventions are important, yet for most important pathogens, these efforts are community-driven with limited options for sustained funding. www.nature.com/articles/s41...

nature.comA generalized lineage nomenclature for viral genomic epidemiology - Nature MicrobiologyThis study extends the Pango lineage nomenclature system beyond SARS-CoV-2, introducing a dynamic framework for tracking and communicating viral diversity, demonstrated through its application to CHIK...
Duncan MacCannell
@drm.bsky.social

A phylogenetic tree won't tell you who infected whom. The latest module from Pathogen Genomics in Public Health is on Interpretation. It covers the genomic outputs that epidemiologists see most — and their limits. Free, 90 min. learn.hms.harvard.edu/programs/pat... #GenomicEpidemiology

learn.hms.harvard.eduPathogen Genomics for Epidemiology: Interpretation | Harvard Medical School Professional, Corporate, and Continuing EducationLearn how to interpret pathogen genomic data to meaningfully inform epidemiological investigations and public health action.
Duncan MacCannell
@drm.bsky.social

Thanks to the kind, and always effervescent person that helpfully pointed out that I missed a qualifier in this post. “…won’t ALWAYS tell you…”

Duncan MacCannell
@drm.bsky.social

This was definitely becoming a problem a few years ago when I lived there. Super dangerous for everyone, especially the cyclists who regularly do the climb up up to La Honda.

San Francisco Chronicle@sfchronicle.com

“In the last three years we’ve had six locals hit by the hobby-racing motorcycle-car community,” said a resident of the Bay Area town where drivers come for a highway’s hairpin turns.

bit.ly‘Not your racetrack’: How a Bay Area mountain town became a destination for speeding drivers“In the last three years we’ve had six locals hit by the hobby-racing motorcycle-car community,” said a resident of the Bay Area town where drivers come for a highway’s hairpin turns.
Duncan MacCannell
@drm.bsky.social

That’s a wrap! AMD Day was smaller this year, but it was inspiring beyond words to see everyone, the exciting innovation and the commitment to the mission of public health.

Duncan MacCannell reposted

Alexis Stamatakis
@stamatak.bsky.social

The RAxML-NG v2.0 preprint is out: www.biorxiv.org/content/10.6... v2.0 features integrated model testing, fast branch support metrics, automatic parallelization, phylogenetic difficulty prediction, genotype evolution models, to name but the most important features. And it is A LOT FASTER of course

biorxiv.orgRAxML-NG 2: Automatic model selection, novel tree search heuristics, and fast branch support metricsRAxML-NG is a widely used tool for maximum likelihood based phylogenetic inference. In the seven years since the last RAxML-NG publication, we have continuously improved and extended the code. Here, w...

Duncan MacCannell reposted

CNN
@cnn.com

Several baby goats at a mobile petting zoo in North Carolina were infected with rabies, and authorities are asking anyone who had contact with the animals to reach out to health officials. Rabies can be deadly if people don’t receive treatment before symptoms begin. https://cnn.it/4zJSsXl

Duncan MacCannell reposted

ARTIC network
@artic.network

Excellent update from @pathoplexus.org this month. Pathoplexus has been central to data sharing during the ongoing Bundibugyo ebolavirus outbreak response, with ARTIC contributing developer time to Loculus, the platform behind it.

Pathoplexus@pathoplexus.org

1/ 🌍 Our June update is here! Two new pathogens added in response to active outbreaks, over 5,700 new sequences, and a growing community of labs from around the world. Here's what's new in #Pathoplexus 👇 Read the full update: pathoplexus.org/news/2026-06... 📰

Duncan MacCannell
@drm.bsky.social

While it might be an epic movie, I’m not sure a 30 year old film reference hits quite right. Especially when people could be forgiven for associating it with another school of thought on pyrotechnic safety. makeagif.com/gif/the-rock...

U.S. Consumer Product Safety Commission@cpsc.gov

You've got to think about that famous scene from 'The Rock' (1996). Stanley Goodspeed is holding the "string of pearls" virus container that he's just removed from its housing. He looks Sean Connery dead in the eye and says, "The second you don't respect this, it kills you." That's the energy.

Duncan MacCannell reposted

The Washington Post
@washingtonpost.com

The Ebola outbreak spreading through the Democratic Republic of Congo and Uganda could become more devastating than the largest Ebola epidemic in history unless efforts to contain it improve, according to modeling released by the CDC.

washingtonpost.comCongo outbreak could rival the largest Ebola epidemic on record, CDC warnsIn one worst-case scenario projected, more than 20,000 cases would occur within three months if only 1 in 5 infected people are identified and isolated within two days.