Anton Petrov

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! 👀

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...

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...

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...

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

Figure 1

Figure 2

Figure 3

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

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

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!

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

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

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

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...

🚨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

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

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

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,

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

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

Figure 1

Figure 2

Figure 3

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.

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

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...

#RNA rules

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...

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...

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...

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...

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

Last but not least, a huge thanks to the amazing R2DT team! Shoutout to teams at @ebi.embl.org, @pdbeurope.bsky.social, @rnacentral.bsky.social, @rfamdb.bsky.social and many more for their great contributions! 🌟

R2DT · Visualise RNA secondary structure R2DT is a tool for visualising RNA secondary structure.

R2DT can be used on the web, through an API, in Jupyter notebooks, or locally with #Docker 🚀

Get started at r2dt.bio and reach out with any questions!
#RNA #Bioinformatics #dataviz

🤖 Simply type, ‘Straighten nucleotides 123 to 135’ – RNAcanvas Code converts your commands to instructions using a custom ChatGPT ✨

The R2DT diagrams can be edited online using 𝐑𝐍𝐀-𝐬𝐩𝐞𝐜𝐢𝐟𝐢𝐜 editors and the tweaked layouts can be imported back into R2DT 🎨🔄

R2DT can also visualise 𝐚𝐧𝐲 𝐝𝐚𝐭𝐚 overlaid on top of RNA structures. Think reactivities, conservation, SNPs, 3D distances, or anything else! 🧬✨