Reposted by Vikram AgarwalJay Shendure @jshendure.bsky.social · 31/07/2026Thrilled 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 313458
Vikram Agarwal @vagar.bsky.social · 18/04/2026Haley Stevens, you got my vote!! youtu.be/MJd0rcfX-DI?...youtu.beWatch: Congresswoman tells RFK Jr. he "should be ashamed" and resign as HHS secretaryYouTube video by CBS News 010
Reposted by Vikram AgarwalXuebing Wu @xuebingwu.bsky.social · 31/01/2026Does 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 412846
Reposted by Vikram AgarwalAngie Rasmussen @angierasmussen.bsky.social · 14/12/2025Take 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. 8228123
Reposted by Vikram AgarwalJeff Coller @jmcoller.bsky.social · 22/08/2025Halting 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.orgmRNA vaccines hold promise for many diseases. Now the tech is under fireResearchers warn that halting federal contracts for mRNA vaccine research could weaken pandemic preparedness and slow medical advances. 185
Vikram Agarwal @vagar.bsky.social · 18/08/2025One sane article in a sea of endless misinformation: www.nytimes.com/2025/08/18/o...nytimes.comOpinion | America Is Abandoning One of the Greatest Medical Breakthroughs 030
Reposted by Vikram AgarwalColin Carlson @colincarlson.bsky.social · 10/08/2025RFK 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 111138280
Reposted by Vikram AgarwalMarc Veldhoen @marcveld.bsky.social · 07/08/2025Pseudobabble. 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 54119
Reposted by Vikram AgarwalDr. Lucky Tran @luckytran.com · 06/08/2025At 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 471316584
Reposted by Vikram AgarwalThe Fig Economy @figgityfigs.bsky.social · 05/08/2025mRNA vaccines are so close to magic as to be basically indistinguishable, and the administration is stopping them because they worship death. 291190329
Reposted by Vikram AgarwalBoo!-per Lund @cooperlund.online · 05/08/2025Hey 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. 141118185
Reposted by Vikram AgarwalKatie Mack @astrokatie.com · 05/08/2025Every 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. 539179726696
Reposted by Vikram AgarwalDavid Bartel's Lab @bartellab.bsky.social · 02/08/2025Check out the latest study from our lab, led by Coffee Xiang (@coffeebond007.bsky.social) www.nature.com/articles/s41... (1/2)nature.comPAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation, with relevance to human fertility - Nature CommunicationsGene 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 ... 13214
Reposted by Vikram AgarwalTexas 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.socialcns.utexas.eduNew AI Tool Accelerates mRNA-Based Treatments for Viruses, Cancers, Genetic DisordersUT Austin and Sanofi partner to build tool that predicts translation efficiency of mRNA sequences. 098
Reposted by Vikram AgarwalNature Biotechnology @natbiotech.nature.com · 25/07/2025Predicting the translation efficiency of messenger RNA in mammalian cells go.nature.com/4mgXR0Cgo.nature.comPredicting the translation efficiency of messenger RNA in mammalian cells - Nature BiotechnologyA deep convolutional neural network model predicts the influence of the full-length mRNA sequence on translation efficiency. 14212
Reposted by Vikram AgarwalNature Biotechnology @natbiotech.nature.com · 25/07/2025Translation efficiency covariation identifies conserved coordination patterns across cell types go.nature.com/3TXvmZygo.nature.comTranslation efficiency covariation identifies conserved coordination patterns across cell types - Nature BiotechnologyMatched ribosome profiling and RNA sequencing data quantify translation efficiency patterns across 140 human and mouse cell lines. 0155
Vikram Agarwal @vagar.bsky.social · 25/07/2025Very 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/exN1lurl.de.m.mimecastprotect.comPredicting the translation efficiency of messenger RNA in mammalian cellsNature Biotechnology - A deep convolutional neural network model predicts the influence of the full-length mRNA sequence on translation efficiency. 35021
Reposted by Vikram AgarwalElizabeth Warren @warren.senate.gov · 07/07/2025RFK Jr.’s war on vaccines is hurting America's kids.washingtonpost.comU.S. measles cases reach 33-year record high as outbreaks spreadJohns 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. 821574427
Reposted by Vikram AgarwalElizabeth Jacobs, PhD @elizabethjacobs.bsky.social · 05/07/2025Vaccine 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.comMeasles cases surge to record high since disease was declared eliminated in the US | CNNThere have been more measles cases in the US this year than any other since the disease was declared eliminated a quarter-century ago. 48887350
Reposted by Vikram AgarwalHan Yuan @hy395.bsky.social · 02/06/20251/ 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.orgParameter-Efficient Fine-Tuning of a Supervised Regulatory Sequence ModelDNA 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... 13312
Reposted by Vikram AgarwalKatie Mack @astrokatie.com · 03/06/2025I'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 310119862929
Vikram Agarwal @vagar.bsky.social · 29/05/2025Some 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.comGitHub - Sanofi-Public/RiboNN: RiboNN: predicting translation efficiencies from mRNA sequencesRiboNN: predicting translation efficiencies from mRNA sequences - Sanofi-Public/RiboNN 1246
Reposted by Vikram AgarwalDr. Lucky Tran @luckytran.com · 28/04/2025Deaths 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. 5650332379
Vikram Agarwal @vagar.bsky.social · 02/05/2025At 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.comTrump’s Budget Calls for Deep Cuts to NIH and CDCA 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. 072
Reposted by Vikram AgarwalColin Carlson @colincarlson.bsky.social · 02/05/2025I 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.comExclusive: NSF stops awarding new grants and funding existing onesUS science funder also plans to screen grant applications for compliance with ‘agency priorities’. 3269154
Reposted by Vikram AgarwalSaganism @sagan.bsky.social · 02/05/2025Dr. Anthony Fauci urges Americans not to accept "Normalization of Untruths". 10594528612443
Reposted by Vikram AgarwalDavid Ho @davidho.bsky.social · 02/05/2025Well, 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. 22399131
Reposted by Vikram AgarwalSean Carroll @seanmcarroll.bsky.social · 02/05/2025Short 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. 1021144
Reposted by Vikram AgarwalCarl Zimmer @carlzimmer.com · 02/05/2025Time to catch up on the past week’s news about science and medicine in the US. Whew. 1/10 26646351
Reposted by Vikram AgarwalDan Garisto @dangaristo.bsky.social · 01/05/2025BREAKING: 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.comExclusive: NSF stops awarding new grants and funding existing onesUS science funder also plans to screen grant applications for compliance with ‘agency priorities’. 381309963
Reposted by Vikram AgarwalElizabeth Jacobs, PhD @elizabethjacobs.bsky.social · 02/05/2025The 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. 29385442754
Reposted by Vikram AgarwalAlex Merz 🇺🇸🇨🇦🇺🇦 @merz.bsky.social · 23/04/2025In what proportions is our new NIH Director a flaming ignoramus vs. a brazen liar? 71827214
Vikram Agarwal @vagar.bsky.social · 22/04/2025One 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.orgMPRAbase 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 0249
Vikram Agarwal @vagar.bsky.social · 17/04/2025Glad 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 Roganpcgamer.comSeth 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. 072
Vikram Agarwal @vagar.bsky.social · 06/04/2025Pretty 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.comA natural experiment on the effect of herpes zoster vaccination on dementia - NatureUsing 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... 040
Reposted by Vikram AgarwalDavid Corn @davidcorn.bsky.social · 02/04/2025It’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. 1221248005740
Vikram Agarwal @vagar.bsky.social · 26/03/2025Dear 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.orgScientists Say NIH Officials Told Them To Scrub mRNA References on Grants - KFF Health NewsTwo 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... 040
Vikram Agarwal @vagar.bsky.social · 20/03/2025Most bizarre article I've read in quite some time...of course, Florida is no stranger to bizarrefloridaphoenix.comProposal to ban mRNA vaccines in fruits & vegetables advances in Florida Senate • Florida PhoenixThe 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... 040
Reposted by Vikram AgarwalJake Wintermute @synbio1.bsky.social · 03/03/2025I know that the mRNA is larger than the protein it codes for but I don't believe it 917041
Vikram Agarwal @vagar.bsky.social · 13/03/2025Published 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.comMassively parallel characterization of transcriptional regulatory elements - NatureLentivirus-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. 0187
Reposted by Vikram AgarwalArdem Patapoutian @ardemp.bskyverified.social · 08/03/2025Interesting! @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… 814324
Vikram Agarwal @vagar.bsky.social · 03/03/2025Life achievement unlocked: our first cover art accepted alongside our new review on computational techniques to model lipid nanocarriers for drug delivery! 0100
Vikram Agarwal @vagar.bsky.social · 01/03/2025Waiting for someone to download the 80M papers on sci-hub and train an agentic AI reasoning system to query it...would be illegal but simultaneously synthesize all of scientific knowledge as we know it into one oracle of knowledge...😈 040
Reposted by Vikram AgarwalHarmit Singh Malik @harmitmalik.bsky.social · 01/03/2025Heartbreaking chats this week with students thinking of giving up on their dreams of getting a PhD. They worry about getting in PhD programs and careers post PhD. My suggestions: don’t be hasty, think broadly incl EU & Canada, & careers beyond traditional academia. What’re you telling your students? 1926852
Vikram Agarwal @vagar.bsky.social · 27/02/2025#Vibes I'm feeling these days in USA...Incubus was way ahead of their time 🫣youtube.comIncubus - Megalomaniac (Video Version)YouTube video by IncubusVEVO 000
Reposted by Vikram AgarwalStephen Floor @snf.bsky.social · 27/02/2025Shot: first measles death in the US in a decade Chaser: March FDA meeting on flu vaccine design cancelled www.nbcnews.com/health/healt... 067
Reposted by Vikram AgarwalOffice of Mayor Michelle Wu 吳弭 @mayorwu.boston.gov · 20/02/2025The City of Boston is leading 40+ mayors, cities, and counties in an amicus brief against the Trump Administration's drastic and illegal cuts to federal research funding—cuts that will lead to immediate job losses nationwide. 331471425
Vikram Agarwal @vagar.bsky.social · 21/02/2025Very interesting work, congrats @anshulkundaje.bsky.social and team!!! 050
Reposted by Vikram AgarwalAdam Bonica @adambonica.bsky.social · 20/02/2025The DOGE firings have nothing to do with “efficiency” or “cutting waste.” They’re a direct push to weaken federal agencies perceived as liberal. This was evident from the start, and now the data confirms it: targeted agencies overwhelmingly those seen as more left-leaning. 🧵⬇️ 251106234758
Reposted by Vikram AgarwalScience Magazine @science.org · 19/02/2025Scientists are now organizing events, called Stand Up for Science, on 7 March in Washington, D.C., and state capitals. So far, they have attracted more than 100 volunteers from some 30 states who are hoping to rally support for research as a public good. scim.ag/4328LADscim.ag‘I really wanted something to happen.’ The students behind the Stand Up for Science protestsNew group hopes to turn out researchers for 7 March demonstrations against Trump administration policies 2723360