Soham Sankaran
@soh.am
I run @popvax.com (https://popvax.com). We develop mRNA vaccines using computational protein design, including a broadly-protective COVID-19 vax to preempt new variants. I write at https://infinitesunrise.com, and I used to build robots (https://soh.am).
I've finally published a long-gestating piece about why India has largely failed at research & development, and inventing novel products downstream of R&D, over the past few decades, as well as what we can do about it.
www.infinitesunrise.com/p/overcoming...
www.infinitesunrise.com/p/overcoming...
Overcoming India's technological cowardice
How can we learn to invent tomorrow?
www.infinitesunrise.com
May 28, 2025 at 9:12 PM
I've finally published a long-gestating piece about why India has largely failed at research & development, and inventing novel products downstream of R&D, over the past few decades, as well as what we can do about it.
www.infinitesunrise.com/p/overcoming...
www.infinitesunrise.com/p/overcoming...
Reposted by Soham Sankaran
It is indeed striking how much AF3-based methods struggle to generalize to novel protein-ligand interfaces. It is also interesting that there remains a meaningful delta between AF3 and other reproductions at the most difficult generalization task (~25% vs ~13% success rate, so roughly double).
In this work, we explored how training data similarity impacts protein-ligand prediction accuracy—an overlooked aspect in recent benchmarks. Our analysis shows that the current co-folding methods struggle to generalize beyond ligand poses in their training data.(2/n)
February 8, 2025 at 2:08 PM
It is indeed striking how much AF3-based methods struggle to generalize to novel protein-ligand interfaces. It is also interesting that there remains a meaningful delta between AF3 and other reproductions at the most difficult generalization task (~25% vs ~13% success rate, so roughly double).
Reposted by Soham Sankaran
It's long seemed that molecular biology is a natural home for ML interpretability research, given the maturity of human-constructed models of biological mechanisms—permitting direct comparison with their ML-derived counterparts—unlike vision and NLP. Our first foray below👇.
Can we learn protein biology from a language model?
In new work led by @liambai.bsky.social and me, we explore how sparse autoencoders can help us understand biology—going from mechanistic interpretability to mechanistic biology.
In new work led by @liambai.bsky.social and me, we explore how sparse autoencoders can help us understand biology—going from mechanistic interpretability to mechanistic biology.
February 10, 2025 at 4:15 PM
It's long seemed that molecular biology is a natural home for ML interpretability research, given the maturity of human-constructed models of biological mechanisms—permitting direct comparison with their ML-derived counterparts—unlike vision and NLP. Our first foray below👇.
I presented on PopVax’s ongoing efforts to develop broadly-protective mRNA vaccines against influenza and other pathogens at the BARDA Vaccine Innovation Forum held on January 13 in San Francisco. Here’s BARDA’s press release about the prize: (11/12)
www.medicalcountermeasures.gov/newsroom/202...
www.medicalcountermeasures.gov/newsroom/202...
BARDA announced four Concept Stage winners of the Patch Forward Prize
BARDA announces $8 million in awards to advance patch-based RNA vaccine development as part of the Patch Forward Prize
www.medicalcountermeasures.gov
February 10, 2025 at 1:03 PM
I presented on PopVax’s ongoing efforts to develop broadly-protective mRNA vaccines against influenza and other pathogens at the BARDA Vaccine Innovation Forum held on January 13 in San Francisco. Here’s BARDA’s press release about the prize: (11/12)
www.medicalcountermeasures.gov/newsroom/202...
www.medicalcountermeasures.gov/newsroom/202...
We believe broadly-protective flu vaccines are vital to save lives each flu season and prevent potential future pandemics. This work would not have been possible without generous support for our vaccine platform and open-source COVID-19 vaccine from Vitalik Buterin (@vitalik.ca) & Balvi. (10/12)
February 10, 2025 at 1:03 PM
We believe broadly-protective flu vaccines are vital to save lives each flu season and prevent potential future pandemics. This work would not have been possible without generous support for our vaccine platform and open-source COVID-19 vaccine from Vitalik Buterin (@vitalik.ca) & Balvi. (10/12)
We are also developing vaccines that cover potential pandemic strains such as H5N1, which appears to already be undergoing mutations that may allow it to replicate more easily in mammalian cells, creating an increased risk of transmission to and between humans. (9/12)
February 10, 2025 at 1:03 PM
We are also developing vaccines that cover potential pandemic strains such as H5N1, which appears to already be undergoing mutations that may allow it to replicate more easily in mammalian cells, creating an increased risk of transmission to and between humans. (9/12)
Current seasonal flu vaccines can often be ineffective – in the past decade, their efficacy in a given flu season has fallen to as low as 6% due to strain mutation. PopVax is developing broadly-protective flu vaccines intended to reliably provide 80%+ efficacy. (8/12)
February 10, 2025 at 1:03 PM
Current seasonal flu vaccines can often be ineffective – in the past decade, their efficacy in a given flu season has fallen to as low as 6% due to strain mutation. PopVax is developing broadly-protective flu vaccines intended to reliably provide 80%+ efficacy. (8/12)
Formulation into a microarray patch also enhances mRNA vaccine thermostability, broadening global accessibility. PopVax & LTS are working to advance the self-administered patch-delivered seasonal influenza vaccine into preclinical studies in the coming months. (7/12)
February 10, 2025 at 1:03 PM
Formulation into a microarray patch also enhances mRNA vaccine thermostability, broadening global accessibility. PopVax & LTS are working to advance the self-administered patch-delivered seasonal influenza vaccine into preclinical studies in the coming months. (7/12)
Imagine getting a vaccine delivered to your home on demand via DoorDash or Zomato, and administering it yourself by applying a small patch to your upper arm that can be discarded in 15 minutes – no need to go to a pharmacy or clinic and wait in line to be injected. (6/12)
February 10, 2025 at 1:03 PM
Imagine getting a vaccine delivered to your home on demand via DoorDash or Zomato, and administering it yourself by applying a small patch to your upper arm that can be discarded in 15 minutes – no need to go to a pharmacy or clinic and wait in line to be injected. (6/12)
We are working with Germany’s LTS Lohmann Therapie-Systeme AG, a leading player in transdermal drug delivery, to deliver our flu vaccine using their self-administrable microarray patch delivery system. (5/12)
February 10, 2025 at 1:03 PM
We are working with Germany’s LTS Lohmann Therapie-Systeme AG, a leading player in transdermal drug delivery, to deliver our flu vaccine using their self-administrable microarray patch delivery system. (5/12)
The vaccine is built on our mRNA-encoded immunogen display architecture that boosts the magnitude and breadth of the elicited strain-specific antibody response, and our lipid nanoparticle (LNP) platform built on PopVax-designed novel ionizable lipids. (4/12)
February 10, 2025 at 1:03 PM
The vaccine is built on our mRNA-encoded immunogen display architecture that boosts the magnitude and breadth of the elicited strain-specific antibody response, and our lipid nanoparticle (LNP) platform built on PopVax-designed novel ionizable lipids. (4/12)
Our influenza vaccine candidate shows as much as 250x greater strain-specific antibody response in mice in comparison with a leading approved influenza vaccine. It also elicits a broader antibody response, including against pandemic H5N1 influenza, a rising threat. (3/12)
February 10, 2025 at 1:03 PM
Our influenza vaccine candidate shows as much as 250x greater strain-specific antibody response in mice in comparison with a leading approved influenza vaccine. It also elicits a broader antibody response, including against pandemic H5N1 influenza, a rising threat. (3/12)
The Patch Forward Prize is a multi-stage $50M competition launched by BARDA to accelerate the development of microneedle patch-based RNA vaccines for COVID-19, seasonal influenza, and pandemic influenza. (2/12)
February 10, 2025 at 1:03 PM
The Patch Forward Prize is a multi-stage $50M competition launched by BARDA to accelerate the development of microneedle patch-based RNA vaccines for COVID-19, seasonal influenza, and pandemic influenza. (2/12)
I'm delighted to announce that PopVax (@popvax.com) has been awarded $2M by the US Biomedical Advanced Research and Development Authority (@bardagov.bsky.social) as a winner of the first stage of BARDA’s Patch Forward Prize for our seasonal influenza vaccine, along with our partner LTS. (1/12)
February 10, 2025 at 1:03 PM
I'm delighted to announce that PopVax (@popvax.com) has been awarded $2M by the US Biomedical Advanced Research and Development Authority (@bardagov.bsky.social) as a winner of the first stage of BARDA’s Patch Forward Prize for our seasonal influenza vaccine, along with our partner LTS. (1/12)
Reposted by Soham Sankaran
Rare bird flu strain #H5N9 found in California flock infected with #H5N1, reports @washingtonpost.com.
"Culling flocks is costly," says @jennifernuzzo.bsky.social . "We see that in the price of eggs, and the continued infection of cows will only add to the economic burden."
Read more ⤵️
"Culling flocks is costly," says @jennifernuzzo.bsky.social . "We see that in the price of eggs, and the continued infection of cows will only add to the economic burden."
Read more ⤵️
Rare bird flu strain found in California raises potential of wider spread
First U.S. detection of virulent H5N9 strain, at a California duck farm, draws scrutiny as evidence of genetic reassortment that could trigger human outbreaks.
www.washingtonpost.com
January 29, 2025 at 2:02 PM
Rare bird flu strain #H5N9 found in California flock infected with #H5N1, reports @washingtonpost.com.
"Culling flocks is costly," says @jennifernuzzo.bsky.social . "We see that in the price of eggs, and the continued infection of cows will only add to the economic burden."
Read more ⤵️
"Culling flocks is costly," says @jennifernuzzo.bsky.social . "We see that in the price of eggs, and the continued infection of cows will only add to the economic burden."
Read more ⤵️
Reposted by Soham Sankaran
So here's an interesting development...
It's been observed that shingles vaccination with the live attenuated vaccine Zostavax:
www.medrxiv.org/content/10.1...
and also with the (much more effective) recombinant vaccine:
www.nature.com/articles/s41...
But, though the study designs are strong...
It's been observed that shingles vaccination with the live attenuated vaccine Zostavax:
www.medrxiv.org/content/10.1...
and also with the (much more effective) recombinant vaccine:
www.nature.com/articles/s41...
But, though the study designs are strong...
The recombinant shingles vaccine is associated with lower risk of dementia - Nature Medicine
A natural experiment including more than 200,000 people who received a shingles vaccine reveals that, within 6 years of vaccination, the recombinant vaccine is associated with lower risk of dementia t...
www.nature.com
January 7, 2025 at 9:54 PM
So here's an interesting development...
It's been observed that shingles vaccination with the live attenuated vaccine Zostavax:
www.medrxiv.org/content/10.1...
and also with the (much more effective) recombinant vaccine:
www.nature.com/articles/s41...
But, though the study designs are strong...
It's been observed that shingles vaccination with the live attenuated vaccine Zostavax:
www.medrxiv.org/content/10.1...
and also with the (much more effective) recombinant vaccine:
www.nature.com/articles/s41...
But, though the study designs are strong...
You can read more of what I’ve written about the emergence of H5N1 and the utility of vaccines that elicit a broader immune response here:
chronicles.popvax.com/p/potent-bro...
chronicles.popvax.com/p/potent-bro...
Potent, broadly-protective flu vaccines to protect against potential pandemic influenza viruses such as H5N1
PopVax’s influenza vaccine designs elicit as much as 250x greater antibody titer against seasonal strains than existing approved flu vaccines, as well as robust antibody titer against H5N1
chronicles.popvax.com
January 3, 2025 at 2:50 PM
You can read more of what I’ve written about the emergence of H5N1 and the utility of vaccines that elicit a broader immune response here:
chronicles.popvax.com/p/potent-bro...
chronicles.popvax.com/p/potent-bro...
We are eager to work with investors, industry partners, governments, and regulators to accelerate the development and clinical testing of our influenza vaccines. If this is of interest to you, please reach out to us via email at [email protected].
January 3, 2025 at 2:50 PM
We are eager to work with investors, industry partners, governments, and regulators to accelerate the development and clinical testing of our influenza vaccines. If this is of interest to you, please reach out to us via email at [email protected].
We also have an H5N1 influenza vaccine candidate that elicits robust antibody responses against both the same strain of H5N1 that it is based on as well as other distinct H5N1 strains in mice.
January 3, 2025 at 2:50 PM
We also have an H5N1 influenza vaccine candidate that elicits robust antibody responses against both the same strain of H5N1 that it is based on as well as other distinct H5N1 strains in mice.
A vaccine such as ours could be used primarily as a seasonal influenza vaccine of the kind that hundreds of millions of people take each year, but has the potential to additionally provide some protection against H5N1 and other emerging strains which current influenza vaccines do not.
January 3, 2025 at 2:50 PM
A vaccine such as ours could be used primarily as a seasonal influenza vaccine of the kind that hundreds of millions of people take each year, but has the potential to additionally provide some protection against H5N1 and other emerging strains which current influenza vaccines do not.
Our vaccine candidate also elicits as much as 250x greater antibody response in mice against seasonal strains compared with a seasonal influenza vaccine from the global market leader.
January 3, 2025 at 2:50 PM
Our vaccine candidate also elicits as much as 250x greater antibody response in mice against seasonal strains compared with a seasonal influenza vaccine from the global market leader.
At PopVax (@popvax.com) we’ve been developing broadly-protective vaccines against influenza, and are already seeing signs of potential utility against H5N1. Our seasonal influenza candidate elicits a potent antibody response against H5N1 despite not containing an H5N1 antigen.
January 3, 2025 at 2:50 PM
At PopVax (@popvax.com) we’ve been developing broadly-protective vaccines against influenza, and are already seeing signs of potential utility against H5N1. Our seasonal influenza candidate elicits a potent antibody response against H5N1 despite not containing an H5N1 antigen.
While we all certainly hope that H5N1 influenza doesn’t mutate into a strain that causes a pandemic in humans, there is a distinct and unnerving possibility that it does, as Alex Tabarrok (marginalrevolution.com/marginalrevo...) and commentary in @nejm.org have recently noted.
The Cows in the Coal Mine - Marginal REVOLUTION
I remain stunned at how poorly we are responding to the threat from H5N1. Our poor response to COVID was regrettable but perhaps understandable given the US hadn’t faced a major pandemic in decades. H...
marginalrevolution.com
January 3, 2025 at 2:50 PM
While we all certainly hope that H5N1 influenza doesn’t mutate into a strain that causes a pandemic in humans, there is a distinct and unnerving possibility that it does, as Alex Tabarrok (marginalrevolution.com/marginalrevo...) and commentary in @nejm.org have recently noted.
I've written a short piece about the potent, broadly-protective flu vaccines we're developing at PopVax to protect against both seasonal influenza strains and potential pandemic influenza such as the H5N1 strains currently circulating in cows
chronicles.popvax.com/p/potent-bro...
(thread below)
chronicles.popvax.com/p/potent-bro...
(thread below)
Potent, broadly-protective flu vaccines to protect against potential pandemic influenza viruses such as H5N1
PopVax’s influenza vaccine designs elicit as much as 250x greater antibody titer against seasonal strains than existing approved flu vaccines, as well as robust antibody titer against H5N1
chronicles.popvax.com
January 3, 2025 at 2:50 PM
I've written a short piece about the potent, broadly-protective flu vaccines we're developing at PopVax to protect against both seasonal influenza strains and potential pandemic influenza such as the H5N1 strains currently circulating in cows
chronicles.popvax.com/p/potent-bro...
(thread below)
chronicles.popvax.com/p/potent-bro...
(thread below)