Anton Petrov
@antonipetrov.bsky.social
RNA bioinformatician | Building http://riboscope.com and http://r2dt.bio | Previously led RNAcentral, Rfam, and RNA 3D Hub
Pinned
Anton Petrov
@antonipetrov.bsky.social
· Feb 10
🚀 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 🧵👇
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 🧵👇
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 🤔
www.sciencedirect.com/science/arti...
Really liked the paper but I found it interesting that the word "alignment" only appeared once, in references 🤔
September 27, 2025 at 10:04 AM
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 🤔
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/...
September 12, 2025 at 6:29 PM
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! 👀
Cross-talk between RNA secondary and three-dimensional structure prediction: a comprehensive study https://www.biorxiv.org/content/10.1101/2025.06.23.661015v1
July 2, 2025 at 8:42 AM
Bad RNA 2D → bad 3D — unless the software knows when to say “no thanks.” Can’t wait to read more! 👀
Reposted by Anton Petrov
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.
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
June 6, 2025 at 7:30 AM
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.
The only downside is you have to live near Cambridge in the UK.
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...
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
June 6, 2025 at 10:01 AM
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...
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...
Reposted by Anton Petrov
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.
May 22, 2025 at 12:42 PM
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...
May 23, 2025 at 8:21 PM
🤯 Implications for OLE RNA as a natural integral membrane RNA from Ron Breaker's lab rnajournal.cshlp.org/content/earl...
Reposted by Anton Petrov
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
More details on our blog (tinyurl.com/3v7cz2sm)%22
#Genomes #bioinformatics
https://tinyurl.com/3v7cz2sm)"
May 7, 2025 at 2:58 PM
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
More details on our blog (tinyurl.com/3v7cz2sm)%22
#Genomes #bioinformatics
Reposted by Anton Petrov
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.
RNA struct. analysis via QC; encodes base interact. for motifs & drug targets.
April 29, 2025 at 2:30 PM
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.
RNA struct. analysis via QC; encodes base interact. for motifs & drug targets.
Reposted by Anton Petrov
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
March 20, 2025 at 2:19 AM
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
Reposted by Anton Petrov
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!
May 6, 2025 at 5:24 AM
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!
Reposted by Anton Petrov
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....
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....
March 13, 2025 at 2:03 PM
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....
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
Long-read transcriptome-wide RNA structure maps using DMS-FIRST-seq https://www.biorxiv.org/content/10.1101/2025.04.22.649934v1
April 28, 2025 at 12:47 PM
Cool stuff: DMS-FIRST-seq generates high-resolution, accurate RNA structures by coupling chemical probing with nanopore direct RNA sequencing
Increasing probe concentration causes some base-paired nucleotides to become unexpectedly reactive, often alongside changes in their complementary partners
academic.oup.com/nar/article/...
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
April 20, 2025 at 10:17 AM
Increasing probe concentration causes some base-paired nucleotides to become unexpectedly reactive, often alongside changes in their complementary partners
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
Reposted by Anton Petrov
🚨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
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...
www.medrxiv.org
April 11, 2025 at 10:00 AM
🚨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
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
Reposted by Anton Petrov
Embed-Search-Align: DNA Sequence Alignment using Transformer models. #DNAalignment #TransformerModels #LLMs #LargeLanguageModels #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
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
February 10, 2025 at 10:02 PM
Embed-Search-Align: DNA Sequence Alignment using Transformer models. #DNAalignment #TransformerModels #LLMs #LargeLanguageModels #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
A synthetic tetracycline aptamer linked to a hammerhead ribozyme was engineered to regulate PD-1 expression
academic.oup.com/nar/article/...
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
March 17, 2025 at 12:10 PM
A synthetic tetracycline aptamer linked to a hammerhead ribozyme was engineered to regulate PD-1 expression
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
Reposted by Anton Petrov
rnahub.og
A webserver to generate RNA alignments with secondary structure assessment
www.biorxiv.org/content/10.1...
A webserver to generate RNA alignments with secondary structure assessment
www.biorxiv.org/content/10.1...
March 16, 2025 at 12:24 PM
rnahub.og
A webserver to generate RNA alignments with secondary structure assessment
www.biorxiv.org/content/10.1...
A webserver to generate RNA alignments with secondary structure assessment
www.biorxiv.org/content/10.1...
Reposted by Anton Petrov
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
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
March 11, 2025 at 1:18 PM
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
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
Reposted by Anton Petrov
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.
Automated Ab design using iterative ML, property prediction, & lab experiments, yielding improved binders against key targets.
February 25, 2025 at 1:28 AM
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.
Automated Ab design using iterative ML, property prediction, & lab experiments, yielding improved binders against key targets.
Reposted by Anton Petrov
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 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
February 19, 2025 at 9:36 AM
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 doi.org/10.1093/giga...
Reposted by Anton Petrov
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...
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...
www.nature.com
February 25, 2025 at 10:13 AM
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...
www.nature.com/articles/s41...
Reposted by Anton Petrov
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...
www.biorxiv.org
January 28, 2025 at 1:12 PM
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! 🙌 🧬
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
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
r2d2 from star wars is excited and beeps
ALT: r2d2 from star wars is excited and beeps
media.tenor.com
February 10, 2025 at 2:43 PM
Many @ebi.embl.org resources rely on R2DT for RNA visualisation - huge thanks to everyone for their amazing work! 🙌 🧬