Vikram Agarwal

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...

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.

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

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.

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...

Opinion | America Is Abandoning One of the Greatest Medical Breakthroughs

One sane article in a sea of endless misinformation: www.nytimes.com/2025/08/18/o...

Looking forward to MINI ME in your next paper

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

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

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

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

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.

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.

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 ...

Check out the latest study from our lab, led by Coffee Xiang (@coffeebond007.bsky.social) www.nature.com/articles/s41... (1/2)

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.

🧬 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

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.

Predicting the translation efficiency of messenger RNA in mammalian cells go.nature.com/4mgXR0C

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.

Translation efficiency covariation identifies conserved coordination patterns across cell types go.nature.com/3TXvmZy

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!

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.

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/...

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.

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

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.

RFK Jr.’s war on vaccines is hurting America's kids.

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.

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.

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...

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...

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

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

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

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...

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.

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.

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 😢

Exclusive: NSF stops awarding new grants and funding existing ones US science funder also plans to screen grant applications for compliance with ‘agency priorities’.

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...

Dr. Anthony Fauci urges Americans not to accept "Normalization of Untruths".

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.