Vikram Agarwal
@vagar.bsky.social
Head of mRNA Platform Design Data Science @Sanofi. R&D in mRNA therapeutics using ML/DL. Formerly @ UTAustin, MIT, MSFTResearch, UW, & Calico. Latest work: gScholar (https://tinyurl.com/3xdfksy6)
Pinned
Vikram Agarwal
@vagar.bsky.social
· Jul 25
Predicting the translation efficiency of messenger RNA in mammalian cells
Nature Biotechnology - A deep convolutional neural network model predicts the influence of the full-length mRNA sequence on translation efficiency.
url.de.m.mimecastprotect.com
Very excited that our most significant work, a collaboration w/ Dr. Can Cenik at UT Austin on translational gene regulation, was finally published in Nature Biotechnology in a dual set of studies:
Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l
Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l
Reposted by Vikram Agarwal
Halting mRNA vaccine development in the US has broader implications beyond infectious diseases, impeding innovative cancer and rare disease treatments. Science is interconnected; each step forward contributes to collective knowledge and new breakthroughs.
www.sciencenews.org/article/mrna...
www.sciencenews.org/article/mrna...
mRNA vaccines hold promise for many diseases. Now the tech is under fire
Researchers warn that halting federal contracts for mRNA vaccine research could weaken pandemic preparedness and slow medical advances.
www.sciencenews.org
August 21, 2025 at 11:44 PM
Halting mRNA vaccine development in the US has broader implications beyond infectious diseases, impeding innovative cancer and rare disease treatments. Science is interconnected; each step forward contributes to collective knowledge and new breakthroughs.
www.sciencenews.org/article/mrna...
www.sciencenews.org/article/mrna...
One sane article in a sea of endless misinformation: www.nytimes.com/2025/08/18/o...
Opinion | America Is Abandoning One of the Greatest Medical Breakthroughs
www.nytimes.com
August 18, 2025 at 8:06 PM
One sane article in a sea of endless misinformation: www.nytimes.com/2025/08/18/o...
Reposted by Vikram Agarwal
RFK Jr. should resign. Any healthy Democratic Party would demand it right now. Any public health apparatus of value would demand it right now. We are leaderless in government and academia. America is a fucking death cult
August 10, 2025 at 1:40 AM
RFK Jr. should resign. Any healthy Democratic Party would demand it right now. Any public health apparatus of value would demand it right now. We are leaderless in government and academia. America is a fucking death cult
Reposted by Vikram Agarwal
Pseudobabble.
There is deliberate confusion here.
1) The first claim is made concerning infections.
Fact: No vaccine is or can be effective in stopping infections.
Why? Because antibodies are our only pathogen-specific protection against infection ,and they wane.
1/4
There is deliberate confusion here.
1) The first claim is made concerning infections.
Fact: No vaccine is or can be effective in stopping infections.
Why? Because antibodies are our only pathogen-specific protection against infection ,and they wane.
1/4
August 7, 2025 at 10:19 AM
Pseudobabble.
There is deliberate confusion here.
1) The first claim is made concerning infections.
Fact: No vaccine is or can be effective in stopping infections.
Why? Because antibodies are our only pathogen-specific protection against infection ,and they wane.
1/4
There is deliberate confusion here.
1) The first claim is made concerning infections.
Fact: No vaccine is or can be effective in stopping infections.
Why? Because antibodies are our only pathogen-specific protection against infection ,and they wane.
1/4
Reposted by Vikram Agarwal
At his confirmation hearing, RFK Jr claimed he wouldn’t take away vaccines. So far he has:
Removed COVID vaccine recommendations
Fired the CDC’s vaccine committee
Replaced scientists with antivaxxers
Cancelled vaccine hesitancy research
Pulled $500m in mRNA vaccine research
Removed COVID vaccine recommendations
Fired the CDC’s vaccine committee
Replaced scientists with antivaxxers
Cancelled vaccine hesitancy research
Pulled $500m in mRNA vaccine research
August 6, 2025 at 2:41 AM
At his confirmation hearing, RFK Jr claimed he wouldn’t take away vaccines. So far he has:
Removed COVID vaccine recommendations
Fired the CDC’s vaccine committee
Replaced scientists with antivaxxers
Cancelled vaccine hesitancy research
Pulled $500m in mRNA vaccine research
Removed COVID vaccine recommendations
Fired the CDC’s vaccine committee
Replaced scientists with antivaxxers
Cancelled vaccine hesitancy research
Pulled $500m in mRNA vaccine research
Reposted by Vikram Agarwal
mRNA vaccines are so close to magic as to be basically indistinguishable, and the administration is stopping them because they worship death.
"The U.S. Department of Health and Human Services (HHS) today announced the beginning of a coordinated wind-down of its mRNA vaccine development activities...."
cc: Sen. Bill Cassidy
cc: Sen. Bill Cassidy
August 5, 2025 at 10:10 PM
mRNA vaccines are so close to magic as to be basically indistinguishable, and the administration is stopping them because they worship death.
Reposted by Vikram Agarwal
Hey congrats to everyone who took the soft anti-vaccine stance of “mRNA vaccines aren’t 100% effective and aren’t useful against future variants so the mRNA vaccines aren’t good, we need to mask forever”, your stance has been noted by RFK Jr. to kill mRNA technology in America.
"The U.S. Department of Health and Human Services (HHS) today announced the beginning of a coordinated wind-down of its mRNA vaccine development activities...."
cc: Sen. Bill Cassidy
cc: Sen. Bill Cassidy
August 5, 2025 at 10:40 PM
Hey congrats to everyone who took the soft anti-vaccine stance of “mRNA vaccines aren’t 100% effective and aren’t useful against future variants so the mRNA vaccines aren’t good, we need to mask forever”, your stance has been noted by RFK Jr. to kill mRNA technology in America.
Reposted by Vikram Agarwal
Every reputable expert I know considers mRNA vaccine technology to be one of the most revolutionary advances in medicine in our lifetimes. Its inventors won the Nobel Prize in 2023. Shutting it down now is pointless self-harm to humanity.
Release from HHS: HHS will wind down its development of the mRNA vaccine development activities under the Biomedical Advanced Research and Development Authority (BARDA).
August 5, 2025 at 10:54 PM
Every reputable expert I know considers mRNA vaccine technology to be one of the most revolutionary advances in medicine in our lifetimes. Its inventors won the Nobel Prize in 2023. Shutting it down now is pointless self-harm to humanity.
Reposted by Vikram Agarwal
Check out the latest study from our lab, led by Coffee Xiang (@coffeebond007.bsky.social) www.nature.com/articles/s41... (1/2)
PAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation, with relevance to human fertility - Nature Communications
Gene regulation in oocytes relies heavily on poly(A) tail-length changes. Here, the authors develop PAL-AI, a neural network model that predicts tail-length changes, identifies regulatory motifs, and ...
www.nature.com
August 2, 2025 at 3:00 PM
Check out the latest study from our lab, led by Coffee Xiang (@coffeebond007.bsky.social) www.nature.com/articles/s41... (1/2)
Reposted by Vikram Agarwal
🧬 A new AI tool from @utaustin.bsky.social & Sanofi could speed the development of mRNA-based therapies for viruses, cancers and genetic disorders. RiboNN predicts which mRNA sequences will be most efficiently translated into proteins. cns.utexas.edu/news/researc... @taccutexas.bsky.social
New AI Tool Accelerates mRNA-Based Treatments for Viruses, Cancers, Genetic Disorders
UT Austin and Sanofi partner to build tool that predicts translation efficiency of mRNA sequences.
cns.utexas.edu
July 25, 2025 at 4:03 PM
🧬 A new AI tool from @utaustin.bsky.social & Sanofi could speed the development of mRNA-based therapies for viruses, cancers and genetic disorders. RiboNN predicts which mRNA sequences will be most efficiently translated into proteins. cns.utexas.edu/news/researc... @taccutexas.bsky.social
Reposted by Vikram Agarwal
Predicting the translation efficiency of messenger RNA in mammalian cells go.nature.com/4mgXR0C
Predicting the translation efficiency of messenger RNA in mammalian cells - Nature Biotechnology
A deep convolutional neural network model predicts the influence of the full-length mRNA sequence on translation efficiency.
go.nature.com
July 25, 2025 at 3:37 PM
Predicting the translation efficiency of messenger RNA in mammalian cells go.nature.com/4mgXR0C
Reposted by Vikram Agarwal
Translation efficiency covariation identifies conserved coordination patterns across cell types go.nature.com/3TXvmZy
Translation efficiency covariation identifies conserved coordination patterns across cell types - Nature Biotechnology
Matched ribosome profiling and RNA sequencing data quantify translation efficiency patterns across 140 human and mouse cell lines.
go.nature.com
July 25, 2025 at 7:10 PM
Translation efficiency covariation identifies conserved coordination patterns across cell types go.nature.com/3TXvmZy
Very excited that our most significant work, a collaboration w/ Dr. Can Cenik at UT Austin on translational gene regulation, was finally published in Nature Biotechnology in a dual set of studies:
Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l
Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l
Predicting the translation efficiency of messenger RNA in mammalian cells
Nature Biotechnology - A deep convolutional neural network model predicts the influence of the full-length mRNA sequence on translation efficiency.
url.de.m.mimecastprotect.com
July 25, 2025 at 1:37 PM
Very excited that our most significant work, a collaboration w/ Dr. Can Cenik at UT Austin on translational gene regulation, was finally published in Nature Biotechnology in a dual set of studies:
Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l
Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l
Reposted by Vikram Agarwal
RFK Jr.’s war on vaccines is hurting America's kids.
U.S. measles cases reach 33-year record high as outbreaks spread
Johns Hopkins University data reflects the public health reversal in defeating the vaccine-preventable disease since measles was officially eliminated from the U.S. in 2000.
www.washingtonpost.com
July 7, 2025 at 9:17 PM
RFK Jr.’s war on vaccines is hurting America's kids.
Reposted by Vikram Agarwal
Vaccine refusal, encouraged by Robert F. Kennedy Jr., has now led to the worst U.S. measles outbreak since the disease was classified as eliminated in 2000.
This was preventable. Vaccines save lives and prevent hospitalizations that are physically, mentally, and financially draining.
This was preventable. Vaccines save lives and prevent hospitalizations that are physically, mentally, and financially draining.
Measles cases surge to record high since disease was declared eliminated in the US | CNN
There have been more measles cases in the US this year than any other since the disease was declared eliminated a quarter-century ago.
amp.cnn.com
July 5, 2025 at 5:07 PM
Vaccine refusal, encouraged by Robert F. Kennedy Jr., has now led to the worst U.S. measles outbreak since the disease was classified as eliminated in 2000.
This was preventable. Vaccines save lives and prevent hospitalizations that are physically, mentally, and financially draining.
This was preventable. Vaccines save lives and prevent hospitalizations that are physically, mentally, and financially draining.
Reposted by Vikram Agarwal
1/ DNA sequence models like Borzoi predict gene expression and variant effects across tissues — but how can someone adapt the model to a custom experiment? @drkbio.bsky.social, Johannes Linder and I propose a solution via parameter-efficient fine-tuning (PEFT).
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Parameter-Efficient Fine-Tuning of a Supervised Regulatory Sequence Model
DNA sequence deep learning models accurately predict epigenetic and transcriptional profiles, enabling analysis of gene regulation and genetic variant effects. While large-scale training models like E...
www.biorxiv.org
June 2, 2025 at 8:09 PM
1/ DNA sequence models like Borzoi predict gene expression and variant effects across tissues — but how can someone adapt the model to a custom experiment? @drkbio.bsky.social, Johannes Linder and I propose a solution via parameter-efficient fine-tuning (PEFT).
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Vikram Agarwal
I've seen folks talk about how "in four years" they'll be able to get back to their planned projects and I really don't think that's going to work out. People & projects losing funding now will not be able to hit pause and come back once funding is restored. Hard-won progress & capacity will be lost
I worry that not enough of a big deal is being made about how long-term the devastation of these budget cuts to our scientific and health agencies will be, beyond the absolute ruin they will cause in the acute period.
June 3, 2025 at 8:51 PM
I've seen folks talk about how "in four years" they'll be able to get back to their planned projects and I really don't think that's going to work out. People & projects losing funding now will not be able to hit pause and come back once funding is restored. Hard-won progress & capacity will be lost
Some exciting news! 🥳👍 finally dropped our open-source AI model to predict translation rates from mRNA sequences online for free academic use! Hope it's widely used among RNA scientists! Code:
github.com/Sanofi-Publi...; Model: zenodo.org/records/1537...; Preprint: www.biorxiv.org/content/10.1...
github.com/Sanofi-Publi...; Model: zenodo.org/records/1537...; Preprint: www.biorxiv.org/content/10.1...
GitHub - Sanofi-Public/RiboNN: RiboNN: predicting translation efficiencies from mRNA sequences
RiboNN: predicting translation efficiencies from mRNA sequences - Sanofi-Public/RiboNN
github.com
May 29, 2025 at 2:37 PM
Some exciting news! 🥳👍 finally dropped our open-source AI model to predict translation rates from mRNA sequences online for free academic use! Hope it's widely used among RNA scientists! Code:
github.com/Sanofi-Publi...; Model: zenodo.org/records/1537...; Preprint: www.biorxiv.org/content/10.1...
github.com/Sanofi-Publi...; Model: zenodo.org/records/1537...; Preprint: www.biorxiv.org/content/10.1...
Reposted by Vikram Agarwal
Deaths from heart disease down 75%, that’s NIH.
Deaths from stroke down 75%, that’s NIH.
HIV/AIDS no longer a death sentence, that’s NIH.
99% of FDA approved drugs in the last decade, that’s NIH.
Please show this video to anyone who doesn’t understand why the NIH is so important.
Deaths from stroke down 75%, that’s NIH.
HIV/AIDS no longer a death sentence, that’s NIH.
99% of FDA approved drugs in the last decade, that’s NIH.
Please show this video to anyone who doesn’t understand why the NIH is so important.
April 28, 2025 at 5:20 PM
Deaths from heart disease down 75%, that’s NIH.
Deaths from stroke down 75%, that’s NIH.
HIV/AIDS no longer a death sentence, that’s NIH.
99% of FDA approved drugs in the last decade, that’s NIH.
Please show this video to anyone who doesn’t understand why the NIH is so important.
Deaths from stroke down 75%, that’s NIH.
HIV/AIDS no longer a death sentence, that’s NIH.
99% of FDA approved drugs in the last decade, that’s NIH.
Please show this video to anyone who doesn’t understand why the NIH is so important.
At what point in history did science become partisan? Didn't we all agree that innovations help all of us? If our brother/mother/father or YOU are stricken with cancer, do you really think you have "owned the libs" by destroying NIH/NSF funding? The amount of self-inflicted destruction is dizzying 😢
Trump’s Budget Calls for Deep Cuts to NIH and CDC
A budget blueprint released on Friday advances, in hard numbers and biting words, President Trump’s assault on the nation’s universities and scientific research enterprise.
www.nytimes.com
May 2, 2025 at 4:50 PM
At what point in history did science become partisan? Didn't we all agree that innovations help all of us? If our brother/mother/father or YOU are stricken with cancer, do you really think you have "owned the libs" by destroying NIH/NSF funding? The amount of self-inflicted destruction is dizzying 😢
Reposted by Vikram Agarwal
I talked to Nature about the latest development at NSF, which is a five-alarm fire for American science. The scale of immediate impact is massive. We narrowly escaped this affecting @viralemergence.org for now, but will have to shut down in a few months if this stays.
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Exclusive: NSF stops awarding new grants and funding existing ones
US science funder also plans to screen grant applications for compliance with ‘agency priorities’.
www.nature.com
May 1, 2025 at 11:06 PM
I talked to Nature about the latest development at NSF, which is a five-alarm fire for American science. The scale of immediate impact is massive. We narrowly escaped this affecting @viralemergence.org for now, but will have to shut down in a few months if this stays.
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Vikram Agarwal
Dr. Anthony Fauci urges Americans not to accept "Normalization of Untruths".
May 2, 2025 at 2:27 AM
Dr. Anthony Fauci urges Americans not to accept "Normalization of Untruths".
Reposted by Vikram Agarwal
Well, fuck! Just got a message from my university that we can no longer spend money on our NSF-funded grants. This is as good as having the grants taken away from us.
Welp…NSF will now suspend the awarding of new and existing research grants until further notice.
Exclusive: NSF stops awarding new grants and funding existing ones
US science funder also plans to screen grant applications for compliance with ‘agency priorities’.
www.nature.com
May 2, 2025 at 7:51 AM
Well, fuck! Just got a message from my university that we can no longer spend money on our NSF-funded grants. This is as good as having the grants taken away from us.
Reposted by Vikram Agarwal
Short of literally launching a war, it’s hard to imagine how a foreign adversary could do more lasting damage to the US than the Trump administration is doing.
May 2, 2025 at 11:22 AM
Short of literally launching a war, it’s hard to imagine how a foreign adversary could do more lasting damage to the US than the Trump administration is doing.
Reposted by Vikram Agarwal
Time to catch up on the past week’s news about science and medicine in the US. Whew. 1/10
May 1, 2025 at 11:50 PM
Time to catch up on the past week’s news about science and medicine in the US. Whew. 1/10