Structural architecture of the human long non-coding RNA-PAAN, as a potential target for anti-influenza drug development www.sciencedirect.com/science/arti... Really liked the paper but I found it interesting that the word "alignment" only appeared once, in references 🤔

High-throughput competitive binding assay for targeting RNA tertiary structures with small molecules: application to pseudoknots and G-quadruplexes academic.oup.com/nar/article/...

Bad RNA 2D → bad 3D — unless the software knows when to say “no thanks.” Can’t wait to read more! 👀

bioRxiv Biophysics@biorxiv-biophys.bsky.social · last yr.

Cross-talk between RNA secondary and three-dimensional structure prediction: a comprehensive study https://www.biorxiv.org/content/10.1101/2025.06.23.661015v1

An opportunity to run the greatest little RNA Databases that can, Rfam & RNAcentral: embl.wd103.myworkdayjobs.com/en-US/EMBL/j... The only downside is you have to live near Cambridge in the UK.

RNA Resources Project Leader

About the team/job We are recruiting a Project Leader to spearhead the development of the RNAcentral and Rfam databases. Rfam and RNAcentral are key resources for RNA Biology that serve tens of thousa...

embl.wd103.myworkdayjobs.com

I used to lead this team and genuinely loved it: @rnacentral.bsky.social & @rfamdb.bsky.social are hiring a new Project Leader If you care about RNA, open data, and the future of RNA therapeutics + AI, this is a rare and impactful role in bioinformatics embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

RNA Resources Project Leader

About the team/job We are recruiting a Project Leader to spearhead the development of the RNAcentral and Rfam databases. Rfam and RNAcentral are key resources for RNA Biology that serve tens of thousa...

embl.wd103.myworkdayjobs.com

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

🤯 Implications for OLE RNA as a natural integral membrane RNA from Ron Breaker's lab rnajournal.cshlp.org/content/earl...

Ensembl release 114 is now out! We have now updated human data to MANE v1.4, new and exciting rodents, livestock, plants and insect genome 🐀 🐈‍⬛ 🪲, lots of species with variation data (@evarchive) and much more! More details on our blog (tinyurl.com/3v7cz2sm)%22 #Genomes #bioinformatics

Quantum algorithm for identifying RNA 3D motifs by processing RNA secondary structure graphs [new] RNA struct. analysis via QC; encodes base interact. for motifs & drug targets.

MAFin: Motif Detection in Multiple Alignment Files | Bioinformatics | Oxford Academic https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaf125/8086993?rss=1&login=false

MAFin: Motif Detection in Multiple Alignment Files

AbstractMotivation. Whole Genome and Proteome Alignments, represented by the Multiple Alignment File (MAF) format, have become a standard approach in compa

dx.doi.org

It's difficult to counter the basic challenges of RNA 3D -- more torsion angles, magnitudes fewer (unique) PDB structures & I'd add, it's more difficult to build good alignments!

Arne Elofsson@handle.invalid · last yr.

In this evaluation of AlphaFold3 (and other methods), we show that (i) accurate predictions are limited to RNA structures/complexes with structural similarity to PDB and (ii) that current methods are bad at estimating the accuracy of the predictions. www.biorxiv.org/content/10.1...

The crux of rigorously characterizing #IRES: Kathrin Leppek @katleppek.bsky.social, Maria Barna and colleagues compile a toolbox of approaches to study internal #ribosome entry sites in mammalian cells and embryonic tissues www.embopress.org/doi/full/10....

Cool stuff: DMS-FIRST-seq generates high-resolution, accurate RNA structures by coupling chemical probing with nanopore direct RNA sequencing

bioRxiv Molecular Biology@biorxiv-molbio.bsky.social · last yr.

Long-read transcriptome-wide RNA structure maps using DMS-FIRST-seq https://www.biorxiv.org/content/10.1101/2025.04.22.649934v1

Increasing probe concentration causes some base-paired nucleotides to become unexpectedly reactive, often alongside changes in their complementary partners academic.oup.com/nar/article/...

Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments

Abstract. Small molecule chemical probes that covalently bond atoms of flexible nucleotides are widely employed in RNA structure determination. Atomistic m

academic.oup.com

🚨I could not be more excited to share our new preprint on saturation genome editing of the small nuclear RNA (snRNA) RNU4-2: www.medrxiv.org/content/10.1... A super fun collaboration with incredible duo @gregfindlay.bsky.social @joachimdejonghe.bsky.social from @crick.ac.uk 🧬🖥️🩺 🧵1/12

Saturation genome editing of RNU4-2 reveals distinct dominant and recessive neurodevelopmental disorders

Recently, de novo variants in an 18 nucleotide region in the centre of RNU4-2 were shown to cause ReNU syndrome, a syndromic neurodevelopmental disorder (NDD) that is predicted to affect tens of thous...

medrxiv.org

Embed-Search-Align: DNA Sequence Alignment using Transformer models. #DNAalignment #TransformerModels #LLMs #LargeLanguageModels #Bioinformatics 🧬 🖥️ academic.oup.com/bioinformati...

Embed-Search-Align: DNA Sequence Alignment using Transformer models

AbstractMotivation. DNA sequence alignment, an important genomic task, involves assigning short DNA reads to the most probable locations on an extensive re

academic.oup.com

A synthetic tetracycline aptamer linked to a hammerhead ribozyme was engineered to regulate PD-1 expression academic.oup.com/nar/article/...

Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells

Abstract. Synthetic RNA devices are engineered to control gene expression and offer great potential in both biotechnology and clinical applications. Here,

academic.oup.com

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

openRxiv has arrived! We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences. openrxiv.org/introducing-... #openRxiv #OpenScience #Preprints #bioRxiv #medRxiv

Lab-in-the-loop therapeutic antibody design with deep learning [new] Automated Ab design using iterative ML, property prediction, & lab experiments, yielding improved binders against key targets.

Presenting a new flexible web platform for sharing and integrating microbial omics data, including RNA-seq and transposon-insertion sequencing. Micromix: web infrastructure for visualizing and remixing microbial ‘omics data doi.org/10.1093/giga...

Micromix: web infrastructure for visualizing and remixing microbial ‘omics data

Abstract. Micromix is a flexible web platform for sharing and integrating microbial omics data, including RNA sequencing and transposon-insertion sequencin

doi.org

#RNA rules

Insightful review on the ‘blind spots’ in current RNA modification detection methods, suggesting that the existing transcriptome-wide maps of modified nucleosides ‘should be considered as first drafts.’ A great read! 🧬📝 www.nature.com/articles/s41...

All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies - Nature Reviews Molecular Cell Biology

Specialized RNA modification sequencing techniques are helping to uncover how dysregulation of RNA modification leads to disease. This Review discusses how technical artefacts can cause false negative...

nature.com

This year, miRNAs won the Nobel Prize—small non-coding RNAs (smRNAs) have arrived! But the biology of many smRNAs remains a mystery. With Decoy-seq, we’re bringing smRNA genetics into the new decade. @hsnajafabadi.bsky.social www.biorxiv.org/content/10.1...

Decoy-seq unlocks scalable genetic screening for regulatory small noncoding RNAs

Small noncoding RNAs (smRNAs) play critical roles in regulating various cellular processes, including development, stress response, and disease pathogenesis. However, functional characterization of sm...

biorxiv.org

Many @ebi.embl.org resources rely on R2DT for RNA visualisation - huge thanks to everyone for their amazing work! 🙌 🧬

EMBL-EBI@ebi.embl.org · last yr.

Move over R2D2, this is about R2DT. The latest R2DT updates include template-free mode, faster performance, and interactive editors, enough to make any #RNA enthusiast jump to lightspeed. Isn’t that right R2? #RNAsky

🚀 New Paper Alert! 🚀 𝐑𝟐𝐃𝐓: a comprehensive platform for visualising RNA secondary structure Check it out in @narjournal.bsky.social: academic.oup.com/nar/article/... Here’s why you should give it a try 🧵👇

8/12 Want to try it yourself? Search for RNAs with summaries at: rnacentral.org/search?q=has...

1/12 Excited to share our new paper in DATABASE on LitSumm - our system that uses large language models to automatically generate high-quality literature summaries for non-coding RNAs! 🧬📚

Here are my slides from today's talk on R2DT at the Cambridge RNA Club: docs.google.com/presentation...

R2DT - Cambridge RNA Club 2025

R2DT: A comprehensive platform for visualising RNA secondary structure Anton I. Petrov Riboscope Ltd Jan 23rd, 2025 · Cambridge RNA Club 1 1

docs.google.com

Cambridge RNA@cambridgerna.bsky.social · 2y ago

Hello RNA people! Our first RNA Club of the year is taking place online this Thursday (5-6 pm)! We welcome @antonipetrov.bsky.social and @oguzhanbegik.bsky.social for some interesting talks! Thank you to our sponsors RNASociety and Lexogen! 🤩🧬

Hello RNA people! Our first RNA Club of the year is taking place online this Thursday (5-6 pm)! We welcome @antonipetrov.bsky.social and @oguzhanbegik.bsky.social for some interesting talks! Thank you to our sponsors RNASociety and Lexogen! 🤩🧬