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Vikram Agarwal

@vagar.bsky.social
1.9K followers 383 following 82 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 (tinyurl.com/3xdfksy6)

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Reposted by Vikram Agarwal
Jay Shendure @jshendure.bsky.social · 31/07/2026
Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote 1/n
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Vikram Agarwal @vagar.bsky.social · 18/04/2026
Haley Stevens, you got my vote!! youtu.be/MJd0rcfX-DI?...
youtu.be
Watch: Congresswoman tells RFK Jr. he "should be ashamed" and resign as HHS secretary
YouTube video by CBS News
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Reposted by Vikram Agarwal
Xuebing Wu @xuebingwu.bsky.social · 31/01/2026
Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...
biorxiv.org
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Reposted by Vikram Agarwal
Angie Rasmussen @angierasmussen.bsky.social · 14/12/2025
Take a moment to meet FDA Commissioner Marty Makary. He is the guy who is leading the agency that is working overtime to enrich his MAHA patrons by taking away your kids’ access to vaccines & essential medicines. He’s replacing evidence-based regulation with corruption.
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Vikram Agarwal @vagar.bsky.social · 26/08/2025
The post is about sliding window attention not convolutional, right?
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Reposted by Vikram Agarwal
Jeff Coller @jmcoller.bsky.social · 22/08/2025
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...
sciencenews.org
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.
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Vikram Agarwal @vagar.bsky.social · 18/08/2025
One sane article in a sea of endless misinformation: www.nytimes.com/2025/08/18/o...
nytimes.com
Opinion | America Is Abandoning One of the Greatest Medical Breakthroughs
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Vikram Agarwal @vagar.bsky.social · 13/08/2025
Looking forward to MINI ME in your next paper
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Reposted by Vikram Agarwal
Colin Carlson @colincarlson.bsky.social · 10/08/2025
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 · 07/08/2025
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 · 06/08/2025
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 · 05/08/2025
mRNA vaccines are so close to magic as to be basically indistinguishable, and the administration is stopping them because they worship death.
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Reposted by Vikram Agarwal
Boo!-per Lund @cooperlund.online · 05/08/2025
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.
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Reposted by Vikram Agarwal
Katie Mack @astrokatie.com · 05/08/2025
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.
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Reposted by Vikram Agarwal
David Bartel's Lab @bartellab.bsky.social · 02/08/2025
Check out the latest study from our lab, led by Coffee Xiang (@coffeebond007.bsky.social) www.nature.com/articles/s41... (1/2)
nature.com
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 ...
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Reposted by Vikram Agarwal
Texas Science @texasscience.bsky.social · 25/07/2025
🧬 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
cns.utexas.edu
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.
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Reposted by Vikram Agarwal
Nature Biotechnology @natbiotech.nature.com · 25/07/2025
Predicting the translation efficiency of messenger RNA in mammalian cells go.nature.com/4mgXR0C
go.nature.com
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.
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Reposted by Vikram Agarwal
Nature Biotechnology @natbiotech.nature.com · 25/07/2025
Translation efficiency covariation identifies conserved coordination patterns across cell types go.nature.com/3TXvmZy
go.nature.com
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.
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Vikram Agarwal @vagar.bsky.social · 25/07/2025
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!
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Vikram Agarwal @vagar.bsky.social · 25/07/2025
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/...
nature.com
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.
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Vikram Agarwal @vagar.bsky.social · 25/07/2025
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
url.de.m.mimecastprotect.com
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.
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Reposted by Vikram Agarwal
Elizabeth Warren @warren.senate.gov · 07/07/2025
RFK Jr.’s war on vaccines is hurting America's kids.
washingtonpost.com
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.
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Reposted by Vikram Agarwal
Elizabeth Jacobs, PhD @elizabethjacobs.bsky.social · 05/07/2025
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.
amp.cnn.com
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.
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Reposted by Vikram Agarwal
Han Yuan @hy395.bsky.social · 02/06/2025
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...
biorxiv.org
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...
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Reposted by Vikram Agarwal
Katie Mack @astrokatie.com · 03/06/2025
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
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Vikram Agarwal @vagar.bsky.social · 31/05/2025
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
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Vikram Agarwal @vagar.bsky.social · 29/05/2025
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
GitHub - Sanofi-Public/RiboNN: RiboNN: predicting translation efficiencies from mRNA sequences
RiboNN: predicting translation efficiencies from mRNA sequences - Sanofi-Public/RiboNN
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Dr. Lucky Tran @luckytran.com · 28/04/2025
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 · 02/05/2025
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 😢
nytimes.com
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.
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Reposted by Vikram Agarwal
Colin Carlson @colincarlson.bsky.social · 02/05/2025
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...
nature.com
Exclusive: NSF stops awarding new grants and funding existing ones
US science funder also plans to screen grant applications for compliance with ‘agency priorities’.
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Reposted by Vikram Agarwal
Saganism @sagan.bsky.social · 02/05/2025
Dr. Anthony Fauci urges Americans not to accept "Normalization of Untruths".
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Reposted by Vikram Agarwal
David Ho @davidho.bsky.social · 02/05/2025
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.
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Reposted by Vikram Agarwal
Sean Carroll @seanmcarroll.bsky.social · 02/05/2025
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.
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Carl Zimmer @carlzimmer.com · 02/05/2025
Time to catch up on the past week’s news about science and medicine in the US. Whew. 1/10
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Dan Garisto @dangaristo.bsky.social · 01/05/2025
BREAKING: NSF has frozen all grant funding, as of yesterday. It's unclear when they will resume funding awards, or why the pause has been put in place. www.nature.com/articles/d41...
nature.com
Exclusive: NSF stops awarding new grants and funding existing ones
US science funder also plans to screen grant applications for compliance with ‘agency priorities’.
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Reposted by Vikram Agarwal
Elizabeth Jacobs, PhD @elizabethjacobs.bsky.social · 02/05/2025
The possibility that RFK Jr. is going to undermine herd immunity in the United States grows increasingly likely. This would mean that US will be responsible for starting numerous pandemics and potentially destroying the effectiveness of the entire globe’s vaccine arsenal. This is bioterrorism.
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Reposted by Vikram Agarwal
Alex Merz 🇺🇸🇨🇦🇺🇦 @merz.bsky.social · 23/04/2025
In what proportions is our new NIH Director a flaming ignoramus vs. a brazen liar?
Jonny Paradise 🌱
@plantparadise7
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NIH Director Jay Bhattacharya on mRNA tech: 

"The next step is [to halt] the mRNA platform itself... the manufacturer has no idea what dose they're giving, no idea where it goes in the body, and whether they are producing off-target antigens"
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Vikram Agarwal @vagar.bsky.social · 22/04/2025
One of the toughest parts of the field of massively parallel reporter assays to measure >~thousands of elements is that there are hundreds of pubs using them, but no central repo to easily locate the results....until now! Great collab w/ Jingjing Zhao, Ilias G-S, and @nadavahituv.bsky.social!!
genome.cshlp.org
MPRAbase a Massively Parallel Reporter Assay database
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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Vikram Agarwal @vagar.bsky.social · 17/04/2025
Glad I'm not the only one observing the irony of tech billionaires handing out science prizes while backing an admin that has dismantled American science. New level of #respect for Seth Rogan
pcgamer.com
Seth Rogen goes rogue at science awards show to slam tech billionaires for backing Trump: 'It's amazing how much good science you can destroy with $320 million and RFK Jr'
You invite Seth Rogen on stage, you take your chances, as the scientific community recently discovered.
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Vikram Agarwal @vagar.bsky.social · 06/04/2025
Pretty cool study... But to me it also highlights simply how releasing more historical medical records could lead to powerful scientific findings that would impact public health policy. Not fully sure the reasons the medical community isn't doing that despite being able to anonymize them...
nature.com
A natural experiment on the effect of herpes zoster vaccination on dementia - Nature
Using a natural experiment that avoids common bias concerns, this study finds that the live-attenuated shingles vaccine reduced the probability of a new dementia diagnosis within a follow-up period of...
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Reposted by Vikram Agarwal
David Corn @davidcorn.bsky.social · 02/04/2025
It’s stunning to me that the New York Times did not put the story on the bloodbath at the NIH, CDC, and FDA on its front page this morning.
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Vikram Agarwal @vagar.bsky.social · 28/03/2025
Hmm, I just went to an Indian restaurant today and got 3/5 spice, and it was almost bland. Then there are parts of India where spices are eye watering with green/red chili on everything. But it's been a while I've been back there to know what the average is like
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Vikram Agarwal @vagar.bsky.social · 26/03/2025
Dear America: if your daughter or son or mother or father or YOU have cancer, and there is or could be an mRNA vaccine that would treat it, are you prepared to destroy the research/tech that would save their lives? Because doing so would take your self-sabotage to unprecedented levels of stupidity..
kffhealthnews.org
Scientists Say NIH Officials Told Them To Scrub mRNA References on Grants - KFF Health News
Two senior scientists say National Institutes of Health officials advised them to remove references to mRNA vaccines in grant applications, and they fear the Trump administration will abandon a promis...
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Vikram Agarwal @vagar.bsky.social · 20/03/2025
Most bizarre article I've read in quite some time...of course, Florida is no stranger to bizarre
floridaphoenix.com
Proposal to ban mRNA vaccines in fruits & vegetables advances in Florida Senate • Florida Phoenix
The Florida Legislature for the first time Wednesday heard testimony about a measure that would prevent vaccines from being incorporated into food products. The bill (SB 196) sponsored by Sarasota Sen...
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Reposted by Vikram Agarwal
Jake Wintermute @synbio1.bsky.social · 03/03/2025
I know that the mRNA is larger than the protein it codes for but I don't believe it
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Vikram Agarwal @vagar.bsky.social · 14/03/2025
Your publisher correction inspired my whole career man
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Vikram Agarwal @vagar.bsky.social · 13/03/2025
Published in today's issue! OPEN ACCESS article, FREE massive dataset, FREE code, FREE pre-trained AI/ML model. #OpenScience was a mountain of work to make this happen: check it out if you haven't already 😉
nature.com
Massively parallel characterization of transcriptional regulatory elements - Nature
Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.
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Ardem Patapoutian @ardemp.bskyverified.social · 08/03/2025
Interesting! @nytimes.com still hasn’t covered any of the Stand Up for Science protests today, but they made sure to put this important news front and center online. Powerful reporting…
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Vikram Agarwal @vagar.bsky.social · 08/03/2025
Lol love the Elon hair growth reference...he also benefitted a lot from weight loss meds like Ozempic...weird that the people using these research-derived products are now waging war against science
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Vikram Agarwal @vagar.bsky.social · 04/03/2025
media.tenor.com
a group of women in red robes are walking down a street with the words under his eye above them
ALT: a group of women in red robes are walking down a street with the words under his eye above them
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