Open question for anyone that develops/maintains of bioinformatics tools, especially those used for public health - what do you think is the right way to fund this long term?
Grants are great for new research directions, but aren't really appropriate for most tool dev/maintenance.
A screenshot of the new Pathoplexus homepage showing all viruses now supported, including Dengue and Yellow Fever, which are circled in red
1/ 🦟 Big news: #Pathoplexus now supports Dengue virus & Yellow Fever virus - two arboviruses responsible for over 400 million infections and up to 94,000 deaths per year.
Here's what’s new in our latest update 👇🏻
Read the full update: pathoplexus.org/news/2026-03... 📰
@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs).
If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you.
In 2025, GISAID cut off access to many critical SARS-CoV-2 resources, incl. our outbreak.info.
A month ago, GISAID leveled accusations against us, Cov-Spectrum, Nextstrain, and members of COG-UK, which are false and misrepresent known facts.
Our joint response:
blog.outbreak.info/joint-respon...
A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
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RFK says basically every infectious disease came from a lab or vaccine.
We need a better way to get the 3800+ kids out of ICE detention than this. We know Liam’s name and we can advocate on his behalf, but that isn’t true of almost any of the other people stuck in detention centers.
We have to stop ICE on a systemic level.
I am wondering if any of the loudest proponents of "learning loss" in the context of the COVID-19 pandemic have spoken up about what ICE is doing to students' ability to learn, safety, etc. I'll wait...I'm sure they're on it.
www.chalkbeat.org/2026/01/28/e...
This must be that radical transparency I keep hearing about.
The majority of organizing happening in Minnesota isn’t just peaceful, it’s INVISIBLE. Moms showing up who won’t be interviewed on TV, people whose ICE patrols don’t turn into viral video. The grocery runs, the donations, the people filming bc they happen to be there. Please remember this.
Yup - here's a good resource where they could pop the data right over: pathoplexus.org/measles/.
And, it would take about a full two minutes to figure out how these outbreaks may be connected via e.g.,: nextstrain.org/measles/genome.
This line graph illustrates the percentage change in agency staff levels from the previous year for nine major U.S. federal scientific and health organizations between the fiscal years 2016 and 2025. The agencies tracked include the CDC, Department of Energy, EPA, FDA, NASA, NIH, NIST, NOAA, and NSF. For the majority of the timeline between 2016 and 2023, the agencies show relatively stable fluctuations, generally staying within a range of +5% to -5% change per year. However, there is a dramatic and uniform plummet starting in the 2024–25 period. Every agency depicted shows a sharp downward trajectory, with staffing losses ranging from approximately -15% to over -25%. The Environmental Protection Agency (EPA) shows the most significant decline, dropping to roughly -26%, while the National Institute of Standards and Technology (NIST) shows the least severe but still substantial drop at approximately -15%.
This is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again.
www.nature.com/immersive/d4...
An article today in @natmed.nature.com lays out a "New Vision" for NIAID, stating that following Covid "much of the American public lost trust in the NIAID, the National Institutes of Health (...), and in the greater scientific community"
Let's have a look at what they cite in support of that 1/n
Just because the US is pretending that viruses only come from labs & we shouldn't bother with prevention otherwise, H5N1 is still here & is still a huge pandemic threat.
Join me & my expert colleagues Mar 3-4 in DC as we figure out what to do about it.
www.eventbrite.com/e/johns-hopk...
Today, Minneapolis. Tomorrow, it could be my town, your town, anywhere. The good news is that people in all the towns care about their neighbors and are organizing to resist this. It will stop when enough of us say no.
We are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬
Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
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As wastewater has become a core part of infectious disease surveillance worldwide, new guidance from WHO, GLOWACON, ASTHO, and others has laid key foundations for public health. But in practice, it’s not always obvious how to apply these recommendations or choose among available tools.
A screenshot of the front page of Pathoplexus' website, showing the addition of a tile for Marburg Virus.
1/ 🚀 Pathoplexus now supports Marburg virus (MARV) and Ravn virus (RAVN) (sister viruses in the same genus). MARV has two main clades and causes severe disease with reported fatality rates of 24–88%.
You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...
Today we woke up to our public health allies telling the public that they can't trust CDC anymore More than a little demoralizing Because it's complicated The actual scientists at CDC - the ones you should trust - are not in control of public-facing webpages The conspiracy theorists are running the messaging And yet, most of us scientists... are still doing good science It's just not making it out We're still supporting local health departments We're still running our disease surveillance systems We're still on call for emergencies 24/7 Despite intense staffing shortages from multiple waves of RIFs And chronically being under-resourced Those of us left are still working hard to keep everything going We are proud of our mission And we persist, goddammit Yet We can also say... read the CDC webpages with skepticism Don't treat them as the gold standard. Corroborate the information with other trusted, independent sources. Many are still fine, but even we don't know when the political appointees are going to change their content And this is a painful thing for us to say So we just ask that, if you read or say "Don't trust the CDC!" You remember that we're here still trying to serve the nation, throw sand in the gears, and weather the storm
Hard day today
Here's what we think about trusting CDC
The CDC website has been lobotomized. Where it once presented the decades of evidence debunking the false claims of a link between vaccines and autism, that has now been replaced with junk science.
Pathoplexus is growing not only in terms of new sequences, but also integrating into the larger ecosystem of pathogen surveillance by joining WHO's IPSN and expanding membership. This is the way a pathogen sequence database should work! (Lessons learned from GISAID/SARS-CoV-2...)
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
Well, I suppose they renamed the Department of Defense to the Department of War, so probably about time to rename the Department of Health to the Department of Disease.
The Humphrey series (author Betty G. Birney) is wonderful for elementary school aged kids.
If you have to get permission to teach in your area of expertise from people who are definitionally not qualified to adjudicate your expertise then you are no longer working at a university.
You’re working at a state propaganda factory.
🚨Dept. of Education proposes to exclude public health degrees from the “professional degree” category.
That means new public health experts could lose access to key higher ed resources, like loan limits & reimbursement.
A bold strategy to let infectious diseases win! 🦠
aspph.org/department-o...
Defunding scientists for the nationality of who they co-author with or who they train.
One of the most radical attack on freedom of speech in US history. A far right nationalist destruction of US science. Such a shameful time to be an American that this racist stupidity has become mainstream.
🚨🚨
🧵1/6 #FedFam, reporters - urgent help needed
🚨CDC Museum (a Smithsonian affiliate) is being shuttered🚨
Staff are being “un-RIFed” just to close the museum permanently — then RIFed again in Jan
This is bureaucratic cruelty & cultural vandalism
CDC Library is a national treasure
#SaveCDCLibrary
Like… people want affordable groceries, housing, and healthcare, *And* they want their friends and loved ones the be alive and safe and free from persecution.
These are not mutually exclusive ideas. They are in fact bound up together.
