Angie Hinrichs
@angieshinrichs.bsky.social
Working on the UCSC Genome Browser since 2002, SARS-Cov-2 phylogenetics since 2020. Opinions my own not employer's. she/her
Reposted by Angie Hinrichs
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.
December 10, 2025 at 7:54 PM
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.
Reposted by Angie Hinrichs
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...
You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...
November 28, 2025 at 12:37 PM
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...
You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...
Reposted by Angie Hinrichs
Hard day today
Here's what we think about trusting CDC
Here's what we think about trusting CDC
November 21, 2025 at 1:24 AM
Hard day today
Here's what we think about trusting CDC
Here's what we think about trusting CDC
Reposted by Angie Hinrichs
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.
November 20, 2025 at 6:23 PM
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...)
1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻
Read the full update: pathoplexus.org/news/2025-11...
Read the full update: pathoplexus.org/news/2025-11...
November 18, 2025 at 7:32 PM
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...)
Reposted by Angie Hinrichs
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.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 17, 2025 at 1:32 PM
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.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
Reposted by Angie Hinrichs
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.
RFK Jr says he will end the "war" on saturated fats, contradicting decades of evidence-based dietary recommendations.
"We’re ending the war on saturated fats in this country. So, we’re going to publish dietary guidelines that are going to stress the importance of protein and saturated fats."
"We’re ending the war on saturated fats in this country. So, we’re going to publish dietary guidelines that are going to stress the importance of protein and saturated fats."
November 17, 2025 at 10:20 PM
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.
Reposted by Angie Hinrichs
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.
You’re working at a state propaganda factory.
COLLEGE STATION, Texas (AP) — Texas A&M adopts policy requiring professors to get OK from school president to discuss certain race and gender issues.
November 13, 2025 at 11:48 PM
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.
You’re working at a state propaganda factory.
Reposted by Angie Hinrichs
🚨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...
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...
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.
aspph.org
November 13, 2025 at 3:57 PM
🚨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...
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...
Reposted by Angie Hinrichs
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.
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.
“The prohibited activities would include joint research, co-authorship on papers, and advising a foreign graduate student or postdoctoral fellow. The language is retroactive, meaning any interactions during the previous 5 years could make a scientist ineligible for future federal funding.”
U.S. Congress considers sweeping ban on Chinese collaborations
Researchers speak out against proposal that would bar funding for U.S. scientists working with Chinese partners or training Chinese students
www.science.org
November 14, 2025 at 3:32 AM
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.
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.
Reposted by Angie Hinrichs
🚨🚨
🧵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
🧵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
The David J. Sencer CDC Museum: In Association with the Smithsonian
Free museum exhibiting public health topics and the history of CDC.
www.cdc.gov
November 13, 2025 at 7:09 PM
🚨🚨
🧵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
🧵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
Reposted by Angie Hinrichs
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.
These are not mutually exclusive ideas. They are in fact bound up together.
Too many news outlets & pols framing Tuesday as affordability *Instead Of* "woke"/"DEI"/whatever the fuck when Mamdani & Sherrill both *explicitly* embraced trans & other LGBTQ+ rights, VA solidly rejected Republicans' virulent anti-trans attack adz, & a PA elected their 1st trans mayor. Be serious.
Pro-Equality Candidates Win, Anti-Trans Campaigns Lose Again, in Election 2025 | GLAAD
History was made, and repeated, in the 2025 election, with significant impacts for LGBTQ Americans and candidates who campaigned to support LGBTQ people. Virginia voters elected the Commonwealth’s fir...
glaad.org
November 9, 2025 at 3:35 PM
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.
These are not mutually exclusive ideas. They are in fact bound up together.
Reposted by Angie Hinrichs
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.
The thing is, it's pretty hard to transmit COVID if you don't get infected in the first place.
November 9, 2025 at 7:53 PM
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.
The thing is, it's pretty hard to transmit COVID if you don't get infected in the first place.
Reposted by Angie Hinrichs
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
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
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...
apply.refline.ch
October 25, 2025 at 1:03 PM
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
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
Reposted by Angie Hinrichs
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.
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.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 7, 2025 at 2:41 PM
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.
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.
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. 🧵👇
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 7, 2025 at 5:03 AM
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. 🧵👇
Reposted by Angie Hinrichs
A List of Things Said to Have Been Ruined by Women
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🧵
November 6, 2025 at 8:43 PM
A List of Things Said to Have Been Ruined by Women
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🧵
Reposted by Angie Hinrichs
Colorado shows that feeding children is still a popular notion. All school meals should be free.
BREAKING: Colorado voters approved a ballot measure that would raise state income taxes on higher-earning households to fund free meals for all public school students.
Follow AP for live updates.
Follow AP for live updates.
Live updates: US voters head to the polls in first general election since Trump's return to power
One year after Donald Trump retook the presidency, 2025 Election Day includes closely watched races for New York City mayor, New Jersey governor and California's Proposition 50.
bit.ly
November 5, 2025 at 4:10 AM
Colorado shows that feeding children is still a popular notion. All school meals should be free.
Reposted by Angie Hinrichs
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.
This makes us less safe, as live tracking of viral evolution remains critical for assessment of emerging threats. This needs to be escalated.
Bad. No justification, no communication, no standard procedures for making changes—just arbitrary pronouncements cutting off access to some of the most valuable resources we have.
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.
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.
October 30, 2025 at 10:53 PM
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.
This makes us less safe, as live tracking of viral evolution remains critical for assessment of emerging threats. This needs to be escalated.
Reposted by Angie Hinrichs
Since Greg Abbott made Houston remove the rainbow crosswalk. Rainbows are being painted on homes and businesses all over the city.
November 2, 2025 at 4:40 AM
Since Greg Abbott made Houston remove the rainbow crosswalk. Rainbows are being painted on homes and businesses all over the city.
Reposted by Angie Hinrichs
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
I'm aware of at least 2 stores that had offered struggling customers a discount, then withdrew it after receiving this email
November 2, 2025 at 7:01 PM
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
I'm aware of at least 2 stores that had offered struggling customers a discount, then withdrew it after receiving this email
Reposted by Angie Hinrichs
@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...
Please consider filling out this VERY SHORT survey about your interest and/or concerns.
docs.google.com/forms/d/e/1F...
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...
docs.google.com
October 30, 2025 at 8:11 PM
@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...
Please consider filling out this VERY SHORT survey about your interest and/or concerns.
docs.google.com/forms/d/e/1F...
Reposted by Angie Hinrichs
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-...
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-...
October 24, 2025 at 3:37 PM
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-...
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-...
Reposted by Angie Hinrichs
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...
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...
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.
www.nature.com
October 25, 2025 at 1:42 PM
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...
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...
Reposted by Angie Hinrichs
"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 👏🏾👏🏼👏
@joann-trejo.bsky.social, @marymunson4.bsky.social and I have a commentary in @natcellbio.nature.com on recent attacks on DEI in biomedical research: "If scientific research, especially biomedical research, is meant to serve everyone, then it requires that everyone has an opportunity to participate"
Scaling back DEI programmes and the loss of scientific talent
Nature Cell Biology - Programmes that support diversity, equity and inclusion (DEI) in science are under attack in the USA. Data indicate that diversity in the scientific workforce increases...
www.nature.com
October 23, 2025 at 10:22 PM
"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 👏🏾👏🏼👏