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Angie Hinrichs

@angieshinrichs.bsky.social
637 followers 283 following 34 posts

Working on the UCSC Genome Browser since 2002, SARS-Cov-2 phylogenetics since 2020. Opinions my own not employer's. she/her

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Reposted by Angie Hinrichs
Pathoplexus @pathoplexus.org · 09/05/2026
1/ 🚀 Pathoplexus now supports the Andes variant of Hantavirus (ANDV). ANDV is the variant identified in the recent MV Hondius cases, & the Hantavirus variant previously identified as having occasional human-to-human transmission. pathoplexus.org/andv #hantavirus #hondius
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Josh Levy @josh-levy.bsky.social · 10/03/2026
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.
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Pathoplexus @pathoplexus.org · 12/03/2026
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... 📰
A screenshot of the new Pathoplexus homepage showing all viruses now supported, including Dengue and Yellow Fever, which are circled in red
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Russ Corbett-Detig @russcd.bsky.social · 24/02/2026
@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.
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Reposted by Angie Hinrichs
Kristian G. Andersen @kgandersen.bsky.social · 24/02/2026
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...
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Zamin Iqbal @zaminiqbal.bsky.social · 09/02/2026
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... (thread 1/n)
nature.com
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods
This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.
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Jonathan Howard @joho.bsky.social · 07/02/2026
RFK says basically every infectious disease came from a lab or vaccine.
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Nicole Bedera @nbedera.bsky.social · 31/01/2026
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.
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Gregg Gonsalves @gregggonsalves.bsky.social · 31/01/2026
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...
chalkbeat.org
‘People are living in fear’: Education groups demand changes to immigration enforcement
Critics are pushing to condition funding for the Department of Homeland Security on changes to immigration enforcement agents’ aggressive tactics, like detaining parents and children on their way to s...
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Walker Bragman @walkerbragman.bsky.social · 30/01/2026
This must be that radical transparency I keep hearing about.
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Ana Marie Cox @anamariecox.com · 25/01/2026
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.
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Kristian G. Andersen @kgandersen.bsky.social · 21/01/2026
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.
pathoplexus.org
Pathoplexus | Measles Virus - Browse
Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.
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David Ho @davidho.bsky.social · 20/01/2026
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...
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%.
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Bill Hanage @billhanage.bsky.social · 16/01/2026
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
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Angie Rasmussen @angierasmussen.bsky.social · 14/01/2026
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...
eventbrite.com
Johns Hopkins H5N1 Influenza Preparedness & Response Forum
Join us at Johns Hopkins for a hands-on forum on tackling H5N1 flu outbreaks and response strategies!
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Angie Hinrichs @angieshinrichs.bsky.social · 13/01/2026
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.
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Ed Cunningham-Oakes @edcoakes.bsky.social · 16/12/2025
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) (1/7)
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Josh Levy @josh-levy.bsky.social · 10/12/2025
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.
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Pathoplexus @pathoplexus.org · 28/11/2025
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...
A screenshot of the front page of Pathoplexus' website, showing the addition of a tile for Marburg Virus.
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Alt CDC (they/them) @altcdc.altgov.info · 21/11/2025
Hard day today Here's what we think about trusting CDC
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
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Atul Gawande @agawande.bsky.social · 20/11/2025
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.
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Angie Hinrichs @angieshinrichs.bsky.social · 18/11/2025
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...)
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Bede Constantinides @bede.im · 17/11/2025
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.
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Dr Duncan Robertson @duncanrobertson.bsky.social · 17/11/2025
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.
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Victor Ray @victorerikray.bsky.social · 13/11/2025
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.
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Alt CDC (they/them) @altcdc.altgov.info · 13/11/2025
🚨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...
aspph.org
Department of Education Proposal Excludes Public Health Degrees from “Professional Degree” Definition
Discover the new results and implications of Dept of Ed consensus regarding professional degree programs and public health education.
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Alex Crits-Christoph @acritschristoph.bsky.social · 14/11/2025
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.
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Alt CDC (they/them) @altcdc.altgov.info · 13/11/2025
🚨🚨 🧵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
cdc.gov
The David J. Sencer CDC Museum: In Association with the Smithsonian
Free museum exhibiting public health topics and the history of CDC.
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Dr. Damien P. Williams, dread portent down from a mountain cave @wolven.blacksky.app · 09/11/2025
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.
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Adam Kucharski @adamjkucharski.bsky.social · 09/11/2025
To back up their (incorrect) argument that COVID vaccines didn't affect transmission of the early variants, someone just sent me a paper showing that vaccines 'only' prevented infection... The thing is, it's pretty hard to transmit COVID if you don't get infected in the first place.
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Tanja Stadler @tanjastadler.bsky.social · 25/10/2025
Open position at the Swiss Institute of Bioinformatics: We are looking for a Director of the Center of Pathogen Bioinformatics apply.refline.ch/499599/0346/... I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
apply.refline.ch
Director, Center for Pathogen Bioinformatics
The Centre for Pathogen Bioinformatics (CPB) is a unit of SIB which offers expertise and services in pathogen bioinformatics, computational molecular epidemiology and related multi-site project manage...
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Dr Emma Hodcroft @firefoxx66.bsky.social · 07/11/2025
I want to spell this out in case the implications aren't clear: This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited. The file allowed this. Cut that - cut off all tools the public & others were using.
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Angie Hinrichs @angieshinrichs.bsky.social · 07/11/2025
Nextstrain's daily-updated tree of SARS-CoV-2 genomes was my gateway into the world of viral phylogenetics in early 2020, and Nextstrain's beautiful interactive tree display is crucial to making usher.bio results usable. GISAID cutting off data harms global surveillance efforts. 🧵👇
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Paul Fairie @paulisci.bsky.social · 06/11/2025
A List of Things Said to Have Been Ruined by Women 🧵
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Alt CDC (they/them) @altcdc.altgov.info · 05/11/2025
Colorado shows that feeding children is still a popular notion. All school meals should be free.
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JPWeiland @jpweiland.bsky.social · 30/10/2025
GISAID is now blocking genomic sequencing access to critical resources like Nextstrain, Covspectrum, Outbreak-info, & others. This makes us less safe, as live tracking of viral evolution remains critical for assessment of emerging threats. This needs to be escalated.
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Blue Texas @turntexasblue.bsky.social · 02/11/2025
Since Greg Abbott made Houston remove the rainbow crosswalk. Rainbows are being painted on homes and businesses all over the city.
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Catherine Rampell @crampell.bsky.social · 02/11/2025
The USDA sent an email to grocery stores telling them they are prohibited from offering special discounts to customers affected by the SNAP funding lapse. I'm aware of at least 2 stores that had offered struggling customers a discount, then withdrew it after receiving this email
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Nathan Grubaugh @nathangrubaugh.bsky.social · 30/10/2025
@andersonfbrito.bsky.social and I are seeking input from the community on hosting/sharing arbovirus sequencing data (DENV, CHIKV, OROV, ZIKV, & YFV) on @pathoplexus.org. Please consider filling out this VERY SHORT survey about your interest and/or concerns. docs.google.com/forms/d/e/1F...
docs.google.com
Community survey on the addition of Dengue, Chikungunya, Oropouche, Zika and Yellow fever virus to Pathoplexus
Pathoplexus is a new platform for sharing pathogen sequence data, launched in August 2024 [1], with the primary aim of making sharing and accessing pathogen genomic data easier, faster, and more effic...
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Don Moynihan @donmoyn.bsky.social · 24/10/2025
You know the situation is bad when the national media is publishing guides to recognize which armed forces might be in your neighborhood. Trump is ensuring that all parts of the omniforce will be paid during the shutdown, unlike their civilian peers. donmoynihan.substack.com/p/the-risks-...
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BK. Titanji @boghuma.bsky.social · 25/10/2025
Finally read the paper and it's worth the buzz. mRNA vaccines saved 20 million lives in a global pandemic and the technology is opening up new avenues for the treatment of deadly cancers. This is really one of the most impactful scientific developments of our time. www.nature.com/articles/s41...
nature.com
SARS-CoV-2 mRNA vaccines sensitize tumours to immune checkpoint blockade - Nature
mRNA vaccines targeting SARS-CoV-2 also sensitize tumours to immune checkpoint inhibitors.
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UC Santa Cruz Science @ucscscience.bsky.social · 23/10/2025
"Data shows that expansion of those who participate in academic science produces better science that has a wider impact." From a new research-backed defense of DEI programs published today by Needhi Bhalla @ucsantacruz.bsky.social and peers @ucsdmedschool.bsky.social and @uofmass.bsky.social 👏🏾👏🏼👏
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Alt CDC (they/them) @altcdc.altgov.info · 23/10/2025
🗓️ June 5, 1981: five cases of Pneumocystis Pneumonia, one report, a global awakening. 💙 The MMWR gave voice to what became the HIV/AIDS epidemic—and countless public-health moments since. 🕯️ Honoring the science and reporting that save lives. www.cdc.gov/mmwr/preview... #MMWR #CDCSavesLives
cdc.gov
Pneumocystis Pneumonia -- Los Angeles
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Eric Topol @erictopol.bsky.social · 21/10/2025
From a new @thelancet.com article today entitled "Health care in the USA: money has become the mission" www.thelancet.com/journals/lan...
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Michele Tobias, PhD @micheletobias.bsky.social · 19/10/2025
The estimate of the Davis, CA #NoKings protest was over 4,500! #DavisCA
People holding signs fill a four lane wide street lined with trees.
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Kristian G. Andersen @kgandersen.bsky.social · 16/10/2025
And now NextStrain as well. Next up, will GISAID start charging open-source community tools to have access? That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
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Louise H. Moncla @lhmoncla.bsky.social · 15/10/2025
Our lab's first paper is out! Led by Jordan Ort, we developed NextClade datasets that enable rapid H5 clade assignment via NextClade. We deployed these during the start of the H5 cattle outbreak, and we finally published the paper in Virus Evolution academic.oup.com/ve/article/1...
academic.oup.com
Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment
Abstract. The 2022 panzootic of highly pathogenic avian influenza (HPAI) A(H5) viruses has led to unprecedented transmission to multiple mammalian species.
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Aaron Rupar @atrupar.com · 15/10/2025
Trump: "We're just at the start. We're going to go into other cities that we're not talking about purposely. We're getting ready to go in."
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BK. Titanji @boghuma.bsky.social · 14/10/2025
Awesome public health news: Maldives becomes the first country to achieve ‘triple elimination’ of 1. mother-to-child transmission of HIV, 2. Syphilis and 3. Hepatitis B www.who.int/news/item/13...
who.int
Maldives becomes the first country to achieve ‘triple elimination’ of mother-to-child transmission of HIV, syphilis and hepatitis B
In a landmark public health achievement, WHO has validated the Maldives for eliminating mother-to-child transmission (EMTCT) of hepatitis B, while maintaining its earlier validation (in 2019) for EMTCT of HIV and syphilis. This makes the Maldives the first country in the world to achieve ‘triple elimination’.
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