I will probably be hiring either a PhD or a Postdoc in the near future. If you are interested in deep biochemical history or molecular mechanisms of evolution please get in touch.

Light-directed evolution of dynamic, multi-state, and computational protein functionalities Optovolution leverages optogenetics and the yeast cell cycle to impose rapid, tunable selection, enabling the continuous evolution of light-responsive regulators, logic gates, and other complex protei...

Check out this incredible new method for the directed evolution of protein ON/OFF switches!!!
www.cell.com/cell/fulltex...

Spread the word!

Looking for a truly unique PhD programme on RNA drugs and therapeutics? We have just opened the call for the second cohort of RNAmed-Future leaders in RNA-based medicine. More details under www.rnamed.de Please spread the word.

This is easily the most exciting ribozyme selection since the discovery of the Class I ligase! Must read!

Graphical abstract on the evolution of DNA polymerases to an RNA polymerase

Engineering polymerases to synthesize alternative genetic polymers remains a challenge. Using DNA shuffling and droplet microfluidics, this study provides a short evolutionary path from a DNA polymerase to one with robust RNA-synthesizing activity

www.nature.com/articles/s41...

Inspired by 2025 Stanford #RNA 3D folding
@kaggle
challenge outcome, we’ve collected cryo-EM of new-to-Nature RNA folds, RNA complexes with small molecules and proteins, and assemblies up to 6000 nts - and launched PART 2! Deadline: March 2026. www.kaggle.com/c/stanford-r...

Template-based RNA structure prediction advanced through a blind code competition Automatically predicting RNA 3D structure from sequence remains an unsolved challenge in biology and biotechnology. Here, we describe a Kaggle code competition engaging over 1700 teams and 43 previous...

Preprint on the Stanford #RNA 3D folding Kaggle challenge is out. My scientific new year’s resolution is to brush up on template-based modeling. #gofai
www.biorxiv.org/content/10.6...

Metabolite-responsive scaffold RNAs for dynamic CRISPR transcriptional regulation Abstract. CRISPR activation is a powerful tool to upregulate a vast array of genes in many different contexts. However, there are few dynamic CRISPR transc

RNA switches designed by @eternagame.org players not only are highly efficient in vitro, they also work in cells! This is so cool! 🧪
@narjournal.bsky.social @markblenner.bsky.social

Metabolite-responsive scaffold RNAs for dynamic CRISPR transcriptional regulation: academic.oup.com/nar/article/...

Maybe a dumb question (not my field of expertise): what would negative data even look like in this case? Every sequence should fold into something, unless intrinsically unstructured. Would negative data just be structures of proteins mutated to misfold? Or unstructured proteins? Or something else?

✨New preprint!

🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬

🔗👇

This is incredible!

Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy - Nature Communications How RNA folds into functional structures is still largely uncharacterized. Here, using cryo-EM, SAXS, and molecular dynamics (MD) simulations, the authors create a movie of a medically relevant ribozy...

Really cool paper on the mechanism of group II intron folding. Will be very useful for RNA design in the future.
www.nature.com/articles/s41...

The Eterna puzzle interface displaying the three states of the RNA polymerase ribozyme using RibonanzaNet in state 1 and Eternafold in states 2 and 3.

A new 3-state Replicase challenge has been launched on Eterna and will only be open for two weeks before sequences are collected for experimental testing at the Das Lab. Will Eterna players be able to improve the catalytic activity of the RNA polymerase?

eternagame.org/labs/14183416

loci encoding lncRNA aren't genes? How would you define a gene? Notoriously tricky problem.

🪱 Selfish genes are everywhere and drive some of biology’s biggest innovations (CRISPR, antibody recombination, epigenetics). Yet almost no one asks the obvious question: how does a selfish gene begin? Our new manuscript uncovers how selfishness can emerge directly from the host genome.

So happy to see this work out! Was such a pleasure to co-lead this effort with Erin. Do you like viral immune evasion, and using protein structure to study immune antagonists? Give it a read!

End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio

Antiviral reverse transcriptases reveal the evolutionary origin of telomerase Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...

1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?

Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

RNAcanvas: interactive drawing and exploration of nucleic acid structures Abstract. Two-dimensional drawing of nucleic acid structures, particularly RNA structures, is fundamental to the communication of nucleic acids research. H

🧪 #RNAsky

If you aren’t using RNAcanvas to draw your RNA structures and explore alternative structures, you are missing out! 56 citations in a year, with multiple ones in top journals like Nature, Science & Cell. Easy to use and packed with unique features! Try it!

academic.oup.com/nar/article/...

Happy to share our paper in Nano Letters!🧬 We developed programmable RNA nanostructures for detecting cotranscriptionally introduced RNA modifications using nanopores. Big congrats to first authors Iva &
Gerardo and thanks to all collaborators! 🔗https://pubs.acs.org/doi/10.1021/acs.nanolett.5c02391

Employing "a much larger ribozyme" is always the solution to any problem, in my opinion.

Thank you so much for sharing! I'm glad you like it!

Thank you! Yes, absolutely! We wouldn't know what to do without it. I strongly recommend people check it out! www.rnacanvas.app

Yes, that's correct, and honestly I was surprised with how well it worked, too. I believe the trick was paying close attention to sequence/structure motif conservation which seems to hold sufficient information to reconstruct the whole ribozyme class.

I'm grateful to my student Lukas, who did a lot of the early characterization of Arq.I2, and of course @mutschlerlab.bsky.social for his mentorship and making this project possible! And ofc @crc392molevo.bsky.social!

I will be answering any questions, so feel free to ask if you have any! (11/11)

This project was my brainchild and I'm overjoyed to finally see it published!

I want to thank my co-1st author: @noemi-n.bsky.social for all her hard work in seeing the project through until the end! I expect a lot of cool upcoming work from her, so follow her if you like group II introns! (10/11)

This work serves as a proof of concept for the viability of complex ncRNA design through inverse folding, and we hope it paves the way for the computational design of bespoke G2Is and possibly other complex ncRNAs with traits that are favorable for biotech or therapeutic applications. (9/11)