RNA BENASQUE July 05-17 2026

Registration to the next RNA BENASQUE meeting July 05-17 2026 is open. benasque.org/2026rna/ Yes, Benasque is my profile pic. This #RNA meeting puts together for 2 weeks researchers in computational methods for structural RNA. 9th edition already! #RNAsky

Please join us for our next seminar, featuring Danny IncaRNAto, PhD: “Discovery of RNA regulatory structural switches via ensemble mapping” @incarnatolab.bsky.social #rna #casprnasig #rnastructure

RNA3DB 2025-10-01 release github.com/marcellszi/r... #RNA #RNAsky The database of all RNA chains in PDB arranged in structurally disimilar components, including Rfam annotation. More chains (25,666), more independent components (144), more Rfam families represented (853).

RNA Structure beyond Canonical Base Pairs Guided by Evolution 🧪🧬 #AcademicSky #higherEd www.mcb.harvard.edu/department/n... @rivaselenarivas.bsky.social @rachellegaudet.bsky.social @cryptogenomicon.bsky.social @dulaclab.bsky.social @neurovenki.bsky.social @naoshigeuchida.bsky.social

@aakaran31.bsky.social @rivaselenarivas.bsky.social

Laser ablation of imaged surface layers under adaptive control enables volumetric imaging of heterogeneous tissue like skull and brain. www.nature.com/articles/s41...

Integrated prediction of RNA secondary structure jointly with 3D motifs and pseudoknots guided by evolutionary information. @aakaran31.bsky.social and @rivaselenarivas.bsky.social link.springer.com/article/10.1...

Vaccines have one of the highest reward to risk ratios of any medical intervention in human history. This sociopathic conspiracy theorist is literally killing people, causing the deaths by vaccine-preventable diseases of people who could have lived.

New York Times story with profiles of researchers whose grants were terminated. [Gift Link] www.nytimes.com/2025/08/24/o...

we asked a simple question: What does it take to learn the rules of RNA base pairing? using standard deep-learning technics, got a simple answer: don't need structures, nor alignments or many parameters only a few RNA sequences and 21 parameters; doi.org/10.1101/2025...

The neighborhood is getting ready for tomorrow

Kseniia Petrova walked out of the Boston federal courthouse this afternoon on pre-trial release. My writeup for @cambridgeday.com www.cambridgeday.com/2025/06/12/p...

Reminder: Nobel-prize winning PCR (1983), used in basically all genetic tech today, was only possible because of extremophile bacterium discovered in 1964 in Yellowstone funded by a small ~$80k NSF grant with no obvious application at the time. #science 🧪 www.richmondscientific.com/how-a-discov...

Important validation of our covariation-based screens for conserved structural RNAs. academic.oup.com/nar/article/... work lead (both computational and experimental) by then undergraduate, William Gao

Another fantastic explanation of how basic science helps people and society.

This NYT analysis is incomplete, because the underlying data provided by HHS is inaccurate. It does not include the mass termination of all federal funding to Harvard. www.nytimes.com/interactive/...

The lab is at the RNA Society meeting #RNA25 #RNA2025 They have terminated ALL our funding, but we keep going. Here is Dr Agata Kilar @amkilar.bsky.social presenting her work on conserved structural RNAs in nematodes.

The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.

The $700M/year of federal funding to Harvard (not $3B or other fictional numbers) is for research labs, not for the college. Trade schools are great, but taking science funding and giving it to trade schools shows a misunderstanding of how the US has funded scientific research since WWII.

(1/7) Very excited to share my first PhD preprint on the interactions of two of my favorite mobile genetic elements: phages and group II introns! www.biorxiv.org/content/10.1...

On a day when all research grants at Harvard were terminated, and in a context where Congress seems to broadly accept the notion that destroying science and health research in the US is fine, it’s worth noting that this is not what the public wants.

All funding that supports my lab including myself terminated, just now.

rnahub.org paper now published. academic.oup.com/nar/advance-...

correct RNAhub webserver address rnahub.org

Almost every line of this story would have been simply unbelievable a few months ago: —Pioneering cancer researcher; —*Arrested* at airport in Boston; —Now indefinite ICE detention in Louisiana; —"Crime": not declaring some frog-embryo samples for research. Read it. www.nbcnews.com/news/us-news...

A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods? Our paper in @naturemethods.bsky.social answers this: use evolutionary history to guide compression and search. rdcu.be/eg4OA w/ @baym.lol, @zaminiqbal.bsky.social et al. 🧵1/

The Americans are doing to Kseniia what the Russians did to Brittney Griner for having 0.7 grams of cannabis oil. Except no one is coming to negotiate her freedom and Harvard is sitting on their hands. I am so ashamed. Please share this story. www.nytimes.com/2025/04/11/s...

Kseniia Petrova took my course mcb111 "mathematics in biology" two years ago. Great scientist and scholar. As Hillary Clinton says: it is just plain dumb www.nytimes.com/2025/03/28/o... www.bostonglobe.com/2025/03/27/m...

rnahub.og A webserver to generate RNA alignments with secondary structure assessment www.biorxiv.org/content/10.1...

Tom Maniatis coming in hot in @CellCellPress to spell out in no uncertain terms what cutting indirect cost rates to 15% will cost science. And a call to action: "A united front...is essential to preventing this devastating policy from taking effect." 💯 www.cell.com/cell/fulltex...

We present Rfam-based RNA structural alignments and other structure-based inputs for RNA 3D structure prediction by deep learning. www.biorxiv.org/content/10.1...

🚨Exciting news! We're partnering with @naturemethods.bsky.social 🧬High-quality submissions to the AI4NA workshop on @iclr-conf.bsky.social can also be considered for publication in the journal! 🌟 👉More details on our web page (link in comments) #AI4NA #ICLR2025

The Trump administration, moving quickly to clamp down on health and science agencies, has canceled a string of scientific meetings and instructed federal health officials to refrain from all public communications. www.nytimes.com/2025/01/22/h...

I wrote a similar sentence more than three years ago and was skewered for it. Good to see others coming around to the same conclusion (albeit @rafalab.bsky.social fails to critique many of the issues, e.g. the use of UMAPs for RNA velocity etc.) x.com/lpachter/sta...

Hi Bluesky, just in time for the holidays I am excited to share the latest pre-print from my group! We solved the 3D structure of a mysterious viral RNA that resists degradation by host nucleases. A short 🧵 &link below – please also check out the full video! #RNA #RNAbiology #RNASky #lovevirology

Inaugural post "All-at-one RNA folding with 3D motif prediction framed by evolutionary information" www.biorxiv.org/content/10.1... Introducing CaCoFold-R3D by @aakaran31.bsky.social and myself @rivaselenarivas.bsky.social

🚀Thrilled to be part of ICLR 2025! Join our workshop AI for Nucleic Acids (AI4NA) to explore cutting-edge research and connect with field leaders. Thanks to our organizers and @iclr-conf.bsky.social for making this possible. Find the link to the website in our bio! More info below👇

Where RNA Science Meets AI, May 4–8, 2025, Ascona. Invited speakers: @evamarianovoa.bsky.social @fabiantheis.bsky.social @rivaselenarivas.bsky.social, Sterling Churchman, Barbara Treutlein, Rahul Satijia, Registration open www.rna-ai.org @hagentilgner.bsky.social @quaidmorris.bsky.social