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Vikram Agarwal

@vagar.bsky.social

1.9K followers 380 following 81 posts

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)

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Vikram Agarwal @vagar.bsky.social · Jul 25

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

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

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Vikram Agarwal @vagar.bsky.social · Aug 26

The post is about sliding window attention not convolutional, right?

Reposted by Vikram Agarwal

Jeff Coller @jmcoller.bsky.social · Aug 21

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...

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

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Vikram Agarwal @vagar.bsky.social · Aug 18

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

Vikram Agarwal @vagar.bsky.social · Aug 13

Looking forward to MINI ME in your next paper

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Reposted by Vikram Agarwal

Colin Carlson @colincarlson.bsky.social · Aug 10

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

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Reposted by Vikram Agarwal

Marc Veldhoen @marcveld.bsky.social · Aug 7

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

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Reposted by Vikram Agarwal

Dr. Lucky Tran @luckytran.com · Aug 6

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

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Reposted by Vikram Agarwal

The Fig Economy @figgityfigs.bsky.social · Aug 5

mRNA vaccines are so close to magic as to be basically indistinguishable, and the administration is stopping them because they worship death.

Jen Bendery @jbendery.bsky.social · Aug 5

"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

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Reposted by Vikram Agarwal

Boo!-per Lund @cooperlund.online · Aug 5

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.

Jen Bendery @jbendery.bsky.social · Aug 5

"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

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Reposted by Vikram Agarwal

Katie Mack @astrokatie.com · Aug 5

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.

Eric Michael Garcia @ericmgarcia.bsky.social · Aug 5

Release from HHS: HHS will wind down its development of the mRNA vaccine development activities under the Biomedical Advanced Research and Development Authority (BARDA).

HHS Winds Down mRNA Vaccine Development Under BARDA

WASHINGTON, DC—AUGUST 5, 2025—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 under the Biomedical Advanced Research and Development Authority (BARDA), including the cancellation and de-scoping of various contracts and solicitations. The decision follows a comprehensive review of mRNA-related investments initiated during the COVID-19 public health emergency.

“We reviewed the science, listened to the experts, and acted,” said HHS Secretary Robert F. Kennedy, Jr. “BARDA is terminating 22 mRNA vaccine development investments because the data show these vaccines fail to protect effectively against upper respiratory infections like COVID and flu. We’re shifting that funding toward safer, broader vaccine platforms that remain effective even as viruses mutate.”

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Reposted by Vikram Agarwal

David Bartel's Lab @bartellab.bsky.social · Aug 2

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

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Reposted by Vikram Agarwal

Texas Science @texasscience.bsky.social · Jul 25

🧬 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

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Reposted by Vikram Agarwal

Nature Biotechnology @natbiotech.nature.com · Jul 25

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

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Reposted by Vikram Agarwal

Nature Biotechnology @natbiotech.nature.com · Jul 25

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

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Vikram Agarwal @vagar.bsky.social · Jul 25

Much appreciated! It was a long and tough slog (as usual) to get to the finish line...very proud of the team on this milestone! Time for a 🍺 to celebrate!

Vikram Agarwal @vagar.bsky.social · Jul 25

Paper 2 -- Translational co-regulation detected in mammalian cells www.nature.com/articles/s41...

A deeper explanation of the human story, scientific conclusions, and Github/Zenodo links to use the pre-trained models: www.linkedin.com/feed/update/...

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.

www.nature.com

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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

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Reposted by Vikram Agarwal

Elizabeth Warren @warren.senate.gov · Jul 7

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

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Reposted by Vikram Agarwal

Elizabeth Jacobs, PhD @elizabethjacobs.bsky.social · Jul 5

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.

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

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Reposted by Vikram Agarwal

Han Yuan @hy395.bsky.social · Jun 2

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...

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

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Reposted by Vikram Agarwal

Katie Mack @astrokatie.com · Jun 3

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

Edward Nirenberg @enirenberg.bsky.social · Jun 3

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.

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Vikram Agarwal @vagar.bsky.social · May 31

One would need data from each species and retrain a new model with the code, but out of the box I don't expect our model would work well in species so distant to ours

Vikram Agarwal @vagar.bsky.social · May 29

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 - Sanofi-Public/RiboNN: RiboNN: predicting translation efficiencies from mRNA sequences

RiboNN: predicting translation efficiencies from mRNA sequences - Sanofi-Public/RiboNN

github.com

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Reposted by Vikram Agarwal

Dr. Lucky Tran @luckytran.com · Apr 28

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.

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Vikram Agarwal @vagar.bsky.social · May 2

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

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