Dr J
@gormanlab.bsky.social
Using structural biology to advance vaccine design.
(Views are my own)
(Views are my own)
Reposted by Dr J
EXCLUSIVE: @laurenweberhp.bsky.social & I have spent the last year collecting school+county-level vaccination data from across the US and found that only about 28% of counties now have herd immunity for kindergartners from measles—that leaves about 5.2mn kids unprotected.
Gift link: wapo.st/49zDc43
Gift link: wapo.st/49zDc43
U.S. vaccination rates are plunging. Look up where your school stands.
Take a look to see what the kindergarten measles vaccination rates are in your area.
wapo.st
December 31, 2025 at 2:29 PM
EXCLUSIVE: @laurenweberhp.bsky.social & I have spent the last year collecting school+county-level vaccination data from across the US and found that only about 28% of counties now have herd immunity for kindergartners from measles—that leaves about 5.2mn kids unprotected.
Gift link: wapo.st/49zDc43
Gift link: wapo.st/49zDc43
Pretty happy with our #Tundra results.
3.55Å for Croatia 2023 H3N2 influenza HA (C3). We're consistently getting better than 4Å and we don't even have the newer camera.
www.ebi.ac.uk/emdb/EMD-74650
3.55Å for Croatia 2023 H3N2 influenza HA (C3). We're consistently getting better than 4Å and we don't even have the newer camera.
www.ebi.ac.uk/emdb/EMD-74650
December 31, 2025 at 5:37 AM
Pretty happy with our #Tundra results.
3.55Å for Croatia 2023 H3N2 influenza HA (C3). We're consistently getting better than 4Å and we don't even have the newer camera.
www.ebi.ac.uk/emdb/EMD-74650
3.55Å for Croatia 2023 H3N2 influenza HA (C3). We're consistently getting better than 4Å and we don't even have the newer camera.
www.ebi.ac.uk/emdb/EMD-74650
Reposted by Dr J
First high-resolution structure of key herpes virus protein opens path to new antivirals
phys.org/news/2025-1...
phys.org/news/2025-1...
December 27, 2025 at 10:41 PM
First high-resolution structure of key herpes virus protein opens path to new antivirals
phys.org/news/2025-1...
phys.org/news/2025-1...
Reposted by Dr J
The National Center User Offices at NYSBC/SEMC wish you a wonderful holiday season - December 2025.
As we head into 2026 I thank our team and center staff’s efforts to offer cryoEM resources at no cost to biomedical researchers across the nation.
Find out about our network: cryoemcenters.org
As we head into 2026 I thank our team and center staff’s efforts to offer cryoEM resources at no cost to biomedical researchers across the nation.
Find out about our network: cryoemcenters.org
December 26, 2025 at 12:56 AM
The National Center User Offices at NYSBC/SEMC wish you a wonderful holiday season - December 2025.
As we head into 2026 I thank our team and center staff’s efforts to offer cryoEM resources at no cost to biomedical researchers across the nation.
Find out about our network: cryoemcenters.org
As we head into 2026 I thank our team and center staff’s efforts to offer cryoEM resources at no cost to biomedical researchers across the nation.
Find out about our network: cryoemcenters.org
Seems more of an observation than a recommendation 😜
Recommendation #4: The PDB and structural models are weird and biased
Recommendation #4: The PDB and structural models are weird and biased
Ten rules for a structural bioinformatic analysis
PLOS Comp Bio offers a roadmap for users to leverage the Protein Data Bank’s vast collection of protein structural models into reliable and valuable insights.
PLOS Comp Bio offers a roadmap for users to leverage the Protein Data Bank’s vast collection of protein structural models into reliable and valuable insights.
Ten rules for a structural bioinformatic analysis | PLOS Computational Biology
Author summary Here, we provide a roadmap for users to leverage the Protein Data Bank’s vast collection of protein structural models into reliable and valuable insights. It lays out 10 clear rules that help readers quality control their data, choose fair comparison sets, and judge model quality so results aren’t led astray by noise, bias, or overconfidence. The guide also shows how to connect structures to other databases. By highlighting best practices, such as utilizing re-refined models and being aware of common pitfalls, we guide users to leverage this rich data for enhanced biological insights. These guidelines will enable stronger, more reproducible structural analyses that accelerate drug discovery, illuminate disease mechanisms, and make open data broadly useful across the life sciences.
journals.plos.org
December 22, 2025 at 6:35 PM
Seems more of an observation than a recommendation 😜
Recommendation #4: The PDB and structural models are weird and biased
Recommendation #4: The PDB and structural models are weird and biased
Let's see if we can get one more deposit released before the end of the year -because setting arbitrary, make-believe deadlines for myself is key to productivity :)
December 21, 2025 at 11:49 PM
Let's see if we can get one more deposit released before the end of the year -because setting arbitrary, make-believe deadlines for myself is key to productivity :)
Reposted by Dr J
people who are new to academia tend to find its obsession with sources and citations a brake on their "i'm just trying to be CREATIVE, man" mindset. but it turns out the relentless obsession with accuracy, citation, and *provenance* is a load-bearing pillar of the whole enterprise
December 21, 2025 at 6:59 PM
people who are new to academia tend to find its obsession with sources and citations a brake on their "i'm just trying to be CREATIVE, man" mindset. but it turns out the relentless obsession with accuracy, citation, and *provenance* is a load-bearing pillar of the whole enterprise
Ya, it’s basically this. For writing, LLMs are fine for wordsmithing but beyond that more trouble than they’re worth.
suspect a big reason why many academics and others who work in areas where getting facts RIGHT is key are disinterested in using LLMs for research:
they’ve tried it, they keep noticing major errors in output, and they conclude that having to verify all that doesn’t actually save them time.
they’ve tried it, they keep noticing major errors in output, and they conclude that having to verify all that doesn’t actually save them time.
December 21, 2025 at 7:59 PM
Ya, it’s basically this. For writing, LLMs are fine for wordsmithing but beyond that more trouble than they’re worth.
Reposted by Dr J
Here is why friends don't let friends calculate FSC on denoised half-maps. I took EMD-17961, denoised the maps using Warp's Noise2Map, and calculated the FSC between various things. With noise gone from the half-maps, their consistency is no longer related to SSNR. Denoised map vs. model still works
December 15, 2025 at 1:53 AM
Here is why friends don't let friends calculate FSC on denoised half-maps. I took EMD-17961, denoised the maps using Warp's Noise2Map, and calculated the FSC between various things. With noise gone from the half-maps, their consistency is no longer related to SSNR. Denoised map vs. model still works
I've never used isonet but the images in this paper are amazing
Love the caption of Fig. 3 in this impressive preprint:
"A Goodsell-esque 3D orthogonal rendering of an IsoNet2-processed FIB-milled tomogram of C. reinhardtii"
doi.org/10.64898/202...
Since I am no expert, what does the cryoET community think of IsoNet? @cellarchlab.com
doi.org/10.1038/s414...
"A Goodsell-esque 3D orthogonal rendering of an IsoNet2-processed FIB-milled tomogram of C. reinhardtii"
doi.org/10.64898/202...
Since I am no expert, what does the cryoET community think of IsoNet? @cellarchlab.com
doi.org/10.1038/s414...
December 12, 2025 at 3:00 PM
I've never used isonet but the images in this paper are amazing
Reposted by Dr J
Reposted by Dr J
Researchers use AI and Reverse Vaccinology 2.0 on human blood samples to identify a potential new mpox target, and use the target in a vaccine that elicited mpox-neutralizing antibodies in mice. #ScienceTranslationalMedicine https://scim.ag/48Huqzj
Antigen-agnostic identification of poxvirus broadly neutralizing antibodies targeting OPG153
Antigen-agnostic isolation of B cells enabled the AI-assisted identification of broadly neutralizing antibodies targeting OPG153.
scim.ag
December 11, 2025 at 4:00 PM
Researchers use AI and Reverse Vaccinology 2.0 on human blood samples to identify a potential new mpox target, and use the target in a vaccine that elicited mpox-neutralizing antibodies in mice. #ScienceTranslationalMedicine https://scim.ag/48Huqzj
Reposted by Dr J
#onthisday Dec 9, 1979 the WHO certified that smallpox had been eradicated—the first human disease eliminated by coordinated global vaccination and surveillance, a landmark that transformed public health strategy worldwide #ScienceHistory
December 9, 2025 at 12:13 PM
#onthisday Dec 9, 1979 the WHO certified that smallpox had been eradicated—the first human disease eliminated by coordinated global vaccination and surveillance, a landmark that transformed public health strategy worldwide #ScienceHistory
A lot of the conversations yesterday were some version of -HepB used to be a problem so it made sense to vaccinate but now I don’t know anybody who’s gotten HepB so why are we still vaccinating?
And then the 2 reasonable people in the room flustered not knowing where to even begin.
And then the 2 reasonable people in the room flustered not knowing where to even begin.
December 6, 2025 at 5:01 PM
A lot of the conversations yesterday were some version of -HepB used to be a problem so it made sense to vaccinate but now I don’t know anybody who’s gotten HepB so why are we still vaccinating?
And then the 2 reasonable people in the room flustered not knowing where to even begin.
And then the 2 reasonable people in the room flustered not knowing where to even begin.
Paraphrasing:
-I think we should vote NO on the motion.
>We are not voting now, we are just discussing any proposed changes to the wording of the motion.
-I propose we remove all words from the motion.
-I think we should vote NO on the motion.
>We are not voting now, we are just discussing any proposed changes to the wording of the motion.
-I propose we remove all words from the motion.
December 6, 2025 at 4:57 PM
Paraphrasing:
-I think we should vote NO on the motion.
>We are not voting now, we are just discussing any proposed changes to the wording of the motion.
-I propose we remove all words from the motion.
-I think we should vote NO on the motion.
>We are not voting now, we are just discussing any proposed changes to the wording of the motion.
-I propose we remove all words from the motion.
Something that gets overlooked by a lot of bad takes on covid like the lab-leak theory or the current dismantling of the CDC is the we know at least 3 coronaviruses cross over in a 17 year period. There will likely be more and the next may be closer than we expect.
France is reporting two cases of MERS in two individuals who recently returned from the middle east. Both remain i hospital. MERS is caused by another coronavirus with spillover events occurring from usually from contact with camels.
www.cidrap.umn.edu/mers-cov/fra...
www.cidrap.umn.edu/mers-cov/fra...
France reports MERS in 2 travelers who had been to Middle East
No secondary transmission chains have been identified in France.
www.cidrap.umn.edu
December 5, 2025 at 7:27 PM
Something that gets overlooked by a lot of bad takes on covid like the lab-leak theory or the current dismantling of the CDC is the we know at least 3 coronaviruses cross over in a 17 year period. There will likely be more and the next may be closer than we expect.
Thread of vaccine studies with placebo controls
1/ Aaron Siri is presenting to ACIP right now. He's not a vaccine scientist. He's a plaintiff's attorney whose firm profits from vaccine-injury litigation, RFK Jr.'s personal lawyer, and someone who helped vet HHS leadership. He's now advising the committee that sets U.S. vaccine policy.
December 5, 2025 at 7:21 PM
Thread of vaccine studies with placebo controls
Reposted by Dr J
Molecular insights into species-specific ACE2 recognition of coronavirus HKU5
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Molecular insights into species-specific ACE2 recognition of coronavirus HKU5 - Nature Communications
This study reveals how the bat coronavirus HKU5 recognizes ACE2 receptors across mammals and birds, uncovering a cross-class receptor usage in coronaviruses and highlighting its potential for interspe...
www.nature.com
December 4, 2025 at 6:54 PM
Molecular insights into species-specific ACE2 recognition of coronavirus HKU5
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Pretty impressive to get 12 commissioners together...
12 former commissioners of the FDA came together to write a Perspectives piece for the New England Journal of Medicine; raising our concerns about recent changes to vaccine approval policy at the FDA and its implications for patients and public health.
December 4, 2025 at 5:12 PM
Pretty impressive to get 12 commissioners together...
Reposted by Dr J
If you'd like to celebrate the biology of viruses - or the fight against viral diseases - this winter, try out our free and updated #VirusSnowflake designs.
Please share, and if you have any photos of Virus Snowflakes in your area it would be lovely to see them!
cvr-engagement.co.uk/virus-snowfl...
Please share, and if you have any photos of Virus Snowflakes in your area it would be lovely to see them!
cvr-engagement.co.uk/virus-snowfl...
November 17, 2025 at 5:39 PM
If you'd like to celebrate the biology of viruses - or the fight against viral diseases - this winter, try out our free and updated #VirusSnowflake designs.
Please share, and if you have any photos of Virus Snowflakes in your area it would be lovely to see them!
cvr-engagement.co.uk/virus-snowfl...
Please share, and if you have any photos of Virus Snowflakes in your area it would be lovely to see them!
cvr-engagement.co.uk/virus-snowfl...
Reposted by Dr J
To welcome our new friends, first spoonful of sugar 🥄🍬
Glycan structures can be very complex and deceivingly similar, yet they have unique GlyTouCan IDs[1] that you can find by drawing the glycan you need in gb.glytoucan.org or in the glycoshape.org sugar drawer 1/3 🧵
Glycan structures can be very complex and deceivingly similar, yet they have unique GlyTouCan IDs[1] that you can find by drawing the glycan you need in gb.glytoucan.org or in the glycoshape.org sugar drawer 1/3 🧵
November 25, 2025 at 9:02 AM
To welcome our new friends, first spoonful of sugar 🥄🍬
Glycan structures can be very complex and deceivingly similar, yet they have unique GlyTouCan IDs[1] that you can find by drawing the glycan you need in gb.glytoucan.org or in the glycoshape.org sugar drawer 1/3 🧵
Glycan structures can be very complex and deceivingly similar, yet they have unique GlyTouCan IDs[1] that you can find by drawing the glycan you need in gb.glytoucan.org or in the glycoshape.org sugar drawer 1/3 🧵
Reposted by Dr J
It’s been a while since I put together the Structural Virology starter pack, and I’m sure some new folks have joined Bluesky since then. There’s still plenty of space to fill, so if you’d like to be added to the list just let me know.
#virology #cryoEM
go.bsky.app/Qxv95BL
#virology #cryoEM
go.bsky.app/Qxv95BL
November 25, 2025 at 9:46 AM
It’s been a while since I put together the Structural Virology starter pack, and I’m sure some new folks have joined Bluesky since then. There’s still plenty of space to fill, so if you’d like to be added to the list just let me know.
#virology #cryoEM
go.bsky.app/Qxv95BL
#virology #cryoEM
go.bsky.app/Qxv95BL
Reposted by Dr J
Exclusive: Scientists at the U.S. Centers for Disease Control and Prevention have been told to phase out all of their monkey research, Science has learned. https://scim.ag/48foQEk
Exclusive: CDC to end all monkey research
Studies related to HIV and other infectious diseases will be phased out, sources say; fate of the agency's animals remains unclear
www.science.org
November 21, 2025 at 3:08 PM
Exclusive: Scientists at the U.S. Centers for Disease Control and Prevention have been told to phase out all of their monkey research, Science has learned. https://scim.ag/48foQEk