Elena Rivas

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

Coming up for the 2025-11 November release:

New annotations:

-base pairs (canonical and non-canonical)

-modifications (more than 50k already observed)

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 - Harvard University - Department of Molecular & Cellular Biology In addition to messenger RNA (mRNA) that provide the code for proteins, there are other RNAs that exert their function just as RNA, usually referred to as non-coding […]

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...

All-at-once RNA folding with 3D motif prediction framed by evolutionary information - Nature Methods Structural RNAs exhibit a vast array of recurrent short three-dimensional (3D) elements found in loop regions involving non-Watson–Crick interactions that help arrange canonical double helices into tertiary structures. Here we present CaCoFold-R3D, a probabilistic grammar that predicts these RNA 3D motifs (also termed modules) jointly with RNA secondary structure over a sequence or alignment. CaCoFold-R3D uses evolutionary information present in an RNA alignment to reliably identify canonical helices (including pseudoknots) by covariation. Here we further introduce the R3D grammars, which also exploit helix covariation that constrains the positioning of the mostly noncovarying RNA 3D motifs. Our method runs predictions over an almost-exhaustive list of over 50 known RNA motifs (‘everything’). Motifs can appear in any nonhelical loop region (including three-way, four-way and higher junctions) (‘everywhere’). All structural motifs as well as the canonical helices are arranged into one single structure predicted by one single joint probabilistic grammar (‘all-at-once’). Our results demonstrate that CaCoFold-R3D is a valid alternative for predicting the all-residue interactions present in a RNA 3D structure. CaCoFold-R3D is fast and easily customizable for novel motif discovery and shows promising value both as a strong input for deep learning approaches to all-atom structure prediction as well as toward guiding RNA design as drug targets for therapeutic small molecules.

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.

Here

Opinion | America First? Not When It Comes to Your Health.

New York Times story with profiles of researchers whose grants were terminated.

[Gift Link]

www.nytimes.com/2025/08/24/o...

What does it take to learn the rules of RNA base pairing? A lot less than you may think Amidst the fast-developing trend of RNA large language models with millions of parameters, we asked what would be the minimum required to rediscover the rules of RNA canonical base pairing, mainly the...

www.biorxiv.org/content/10.1...

What does it take to learn the rules of RNA base pairing? A lot less than you may think Amidst the fast-developing trend of RNA large language models with millions of parameters, we asked what would be the minimum required to rediscover the rules of RNA canonical base pairing, mainly the...

www.biorxiv.org/content/10.1...

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

Petrova released on bail from federal detention, walks out of courthouse; indictment still possible - Cambridge Day Harvard researcher Kseniia Petrova was released on bail after a 10-minute hearing in her criminal smuggling case – of frog embryos meant for scientific use.

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...

How a discovery in Yellowstone National Park led to the development of PCR - Richmond Scientific A discovery in Yellowstone National Park led to the development of PCR, the gold-standard COVID-19 tests used to fight the global pandemic.

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...

RNAhub—an automated pipeline to search and align RNA homologs with secondary structure assessment Abstract. The complexity in the generation of RNA multiple sequence alignments and assessment of the accuracy of such alignments contributes to the challen

Now provided as a web server

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.

Here Are the Nearly 2,500 Medical Research Grants Canceled or Delayed by Trump Some cuts have been starkly visible, but the country’s medical grant-making machinery has also radically transformed outside the public eye.

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/...

All-at-once RNA folding with 3D motif prediction framed by evolutionary information Structural RNAs exhibit a vast array of recurrent short 3D elements found in loop regions involving non-Watson-Crick interactions that help arrange canonical double helices into tertiary structures. W...

good eye! We haven't checked yet. But now we have the tool to do so. doi.org/10.1101/2024...

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.

Prevalence of Group II Introns in Phage Genomes Although bacteriophage genomes are under strong selective pressure for high coding density, they are still frequently invaded by mobile genetic elements (MGEs). Group II introns are MGEs that reduce h...

(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.