Augustine Duffy
@augustineduffy.bsky.social
GT BioEngineering Ph.D. student - Kane Lab | CMU alum | Granite Stater at heart
Interests: F1, Yankees, Penguins, vaccines, protein design
he/him
Interests: F1, Yankees, Penguins, vaccines, protein design
he/him
Reposted by Augustine Duffy
How I will remember April Fools' Day 2025.
Reckless.
My heart is out for these dedicated folks at NIH, FDA and CDC
www.statnews.com/2025/04/01/h...
Reckless.
My heart is out for these dedicated folks at NIH, FDA and CDC
www.statnews.com/2025/04/01/h...
HHS starts layoffs of thousands of workers across its agencies
Layoff notices began arriving early Tuesday for thousands of employees of HHS and its subsidiary agencies, with as many 10,000 workers potentially expected to be hit by the cuts.
www.statnews.com
April 1, 2025 at 2:44 PM
How I will remember April Fools' Day 2025.
Reckless.
My heart is out for these dedicated folks at NIH, FDA and CDC
www.statnews.com/2025/04/01/h...
Reckless.
My heart is out for these dedicated folks at NIH, FDA and CDC
www.statnews.com/2025/04/01/h...
Reposted by Augustine Duffy
From Harold Varmus (Former NIH and NCI Director and Nobel laureate)
Why Would We Undermine the Marvel of American Science?
www.nytimes.com/2025/02/14/o...
Why Would We Undermine the Marvel of American Science?
www.nytimes.com/2025/02/14/o...
Opinion | American Science is Under Attack (Gift Article)
The Trump administration hobbles research and endangers the public health.
www.nytimes.com
February 14, 2025 at 3:48 PM
From Harold Varmus (Former NIH and NCI Director and Nobel laureate)
Why Would We Undermine the Marvel of American Science?
www.nytimes.com/2025/02/14/o...
Why Would We Undermine the Marvel of American Science?
www.nytimes.com/2025/02/14/o...
Reposted by Augustine Duffy
Fantastic review on chronic SARS-CoV-2 infections by virological superstars @neher.io & Alex Sigal in Nature Microbiology. I’ll do a short overview, outline a couple minor quibbles, & defend the honor of ORF9b w/some stats & 3 striking sequences from the past week. 1/64
December 23, 2024 at 6:08 PM
Fantastic review on chronic SARS-CoV-2 infections by virological superstars @neher.io & Alex Sigal in Nature Microbiology. I’ll do a short overview, outline a couple minor quibbles, & defend the honor of ORF9b w/some stats & 3 striking sequences from the past week. 1/64
Reposted by Augustine Duffy
In new study, we measure how all mutations to rabies G affect cell entry & antibody neutralization
Sheds light on constraints on type III fusion proteins, suggests ways to stabilize G vaccine antigens, and quantifies antibody robustness to rabies variation
www.biorxiv.org/content/10.1...
Sheds light on constraints on type III fusion proteins, suggests ways to stabilize G vaccine antigens, and quantifies antibody robustness to rabies variation
www.biorxiv.org/content/10.1...
Deep mutational scanning of rabies glycoprotein defines mutational constraint and antibody-escape mutations
Rabies virus causes nearly 60,000 human deaths annually. Antibodies that target the rabies glycoprotein (G) are being developed as post-exposure prophylactics, but mutations in G can render such antib...
www.biorxiv.org
December 18, 2024 at 8:39 PM
In new study, we measure how all mutations to rabies G affect cell entry & antibody neutralization
Sheds light on constraints on type III fusion proteins, suggests ways to stabilize G vaccine antigens, and quantifies antibody robustness to rabies variation
www.biorxiv.org/content/10.1...
Sheds light on constraints on type III fusion proteins, suggests ways to stabilize G vaccine antigens, and quantifies antibody robustness to rabies variation
www.biorxiv.org/content/10.1...
Reposted by Augustine Duffy
Anne Gagneux, Ségolène Martin, @quentinbertrand.bsky.social Remi Emonet and I wrote a tutorial blog post on flow matching: dl.heeere.com/conditional-... with lots of illustrations and intuition!
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
November 27, 2024 at 9:00 AM
Anne Gagneux, Ségolène Martin, @quentinbertrand.bsky.social Remi Emonet and I wrote a tutorial blog post on flow matching: dl.heeere.com/conditional-... with lots of illustrations and intuition!
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
Reposted by Augustine Duffy
Interesting follow-up on this. We're running automated analyses on H5N1 data on the SRA to look for potentially important mutations in the virus.
Following the study 👇, we looked to see if we could find *any* evidence of the HA Q226L mutation.
We did. In a mouse from June of this year.
Short 🧵
Following the study 👇, we looked to see if we could find *any* evidence of the HA Q226L mutation.
We did. In a mouse from June of this year.
Short 🧵
If an #H5N1 pandemic starts tomorrow or in three months, there will be little mystery as to how it happened. The conditions are all there. They have been for a while.
So in some ways the more interesting question to me at the moment is: Why aren’t we in a pandemic yet?
Story here, 🧵 to come:
🧪#IDSky
So in some ways the more interesting question to me at the moment is: Why aren’t we in a pandemic yet?
Story here, 🧵 to come:
🧪#IDSky
Why hasn’t the bird flu pandemic started?
Some scientists examining mutations found in H5N1 viruses fear major outbreak is imminent but others says pathogen remains unpredictable
www.science.org
December 6, 2024 at 8:02 PM
Interesting follow-up on this. We're running automated analyses on H5N1 data on the SRA to look for potentially important mutations in the virus.
Following the study 👇, we looked to see if we could find *any* evidence of the HA Q226L mutation.
We did. In a mouse from June of this year.
Short 🧵
Following the study 👇, we looked to see if we could find *any* evidence of the HA Q226L mutation.
We did. In a mouse from June of this year.
Short 🧵
Reposted by Augustine Duffy
Excellent study by my Penn-CEIRR colleagues showing that a single HA substitution in H5 (at same exact residue that changed in the British Columbia case!) enables efficient H5N1 binding to receptors in the human upper airway.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
A single mutation in bovine influenza H5N1 hemagglutinin switches specificity to human receptors
In 2024, several human infections with highly pathogenic clade 2.3.4.4b bovine influenza H5N1 viruses in the United States raised concerns about their capability for bovine-to-human or even human-to-h...
www.science.org
December 5, 2024 at 7:49 PM
Excellent study by my Penn-CEIRR colleagues showing that a single HA substitution in H5 (at same exact residue that changed in the British Columbia case!) enables efficient H5N1 binding to receptors in the human upper airway.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Augustine Duffy
The preliminary sequence from the H5N1 human case in British Columbia has been posted and it is not good news. The virus potentially has a quasispecies at HA residue 226 (H3 numbering). This is bad news because we know that mutations at residue 226 can increase binding to human receptors. 1/
November 16, 2024 at 3:19 PM
The preliminary sequence from the H5N1 human case in British Columbia has been posted and it is not good news. The virus potentially has a quasispecies at HA residue 226 (H3 numbering). This is bad news because we know that mutations at residue 226 can increase binding to human receptors. 1/
Reposted by Augustine Duffy
Ok, this is actually concerning. The sequence of the hospitalized teen with H5N1 has been released. Both of these mutation sites are known to impact α2,6 binding that is needed for human to human transmissibility.
Need top experts on H5N1 to immediately to look into this.
Need top experts on H5N1 to immediately to look into this.
Excellent summary thread here by @scottehensley.bsky.social. To add a few more important notes, the sequence (GISAID EPI_ISL_19548836) is ambiguous at *both* site Q226 (as Scott mentions above) and site E190 (H3 numbering)
Both these sites play an important role in sialic acid binding specificity
Both these sites play an important role in sialic acid binding specificity
November 16, 2024 at 5:01 PM
Ok, this is actually concerning. The sequence of the hospitalized teen with H5N1 has been released. Both of these mutation sites are known to impact α2,6 binding that is needed for human to human transmissibility.
Need top experts on H5N1 to immediately to look into this.
Need top experts on H5N1 to immediately to look into this.