Jan Mathony

With this, the last bit of my PhD at @embl.org is finally out!
We developed salad (sparse all-atom denoising), a family of blazing fast protein structure diffusion models.
Paper: nature.com/articles/s42256-…
Code: github.com/mjendrusch/salad
Data: zenodo.org/records/14711580
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🎉🎉 congrats Michael!!

Happy to hear that, thank you!

Thanks Julian!

Work by @bene837.bsky.social @jmathony.bsky.social @dominikniopek.bsky.social @uniheidelberg.bsky.social

Rational engineering of allosteric protein switches by in silico prediction of domain insertion sites Nature Methods - ProDomino is a machine leaning-based method, trained on a semisynthetic domain insertion dataset, to guide the engineering of protein domain recombination.

Publication alert: Our paper on domain insertion predictions in proteins is now out in @natmethods.nature.com in its final form: rdcu.be/ey7w3
Also check out the nice perspective by @noahholzleitner.bsky.social and @grunewald.bsky.social : www.nature.com/articles/s41...

I'm very excited to finally share the main work of my PhD!
We explored the evolutionary dynamics of gene regulation and expression during gonad development in primates. We cover among others: X chromosome dynamics (incl. in a developing XXY testis), gene regulatory networks and cell type evolution.

We are delighted to share our new preprint “The evolution of gene regulatory programs controlling gonadal development in primates” www.biorxiv.org/content/10.1...

Congrats Michael, great work as always!

Happy to announce the first paper from my PhD at Korbel group at @embl.org has finally been published:
embopress.org/doi/full/10.1038…
Collaborating with @typaslab.bsky.social, @hennig-lab.bsky.social and the EMBL PEPCF, we designed de novo inhibitors to a bacterial phage defense system 1/🧵

Phage-Assisted Evolution of Allosteric Protein Switches Allostery, the transmission of locally induced conformational changes to distant functional sites, is a key mechanism for protein regulation. Artificial allosteric effectors enable remote manipulation...

Inspired by how nature evolves trigger responsiveness through alternating pressures, we are excited to present POGO-PANCE and RAMPhaGE:

Phage-assisted evolution platforms for engineering allosteric protein switches under dynamic selection.

Preprint: doi.org/10.1101/2025...

Find a longer thread about our work here:
bsky.app/profile/niop...

New Preprint on phage-assisted evolution and retron-mediated mutagenesis for protein optimization.
Many congrats to @neuroscinikolai.bsky.social for this heroic effort and all other lab members involved!

Modular Engineering of Thermo-Responsive Allosteric Proteins Thermogenetics enables non-invasive spatiotemporal control over protein activity in living cells and tissues, yet its applications have largely been restricted to transcriptional regulation and membra...

The link above seems to be broken, so here is the actual link to the paper: www.biorxiv.org/content/10.1...

Huge congrats to all authors, especially to co-first authors @ann-sophiekroell.bsky.social and Kira Hoffmann, who did an outstanding job!

Precision control of cellular functions with a temperature-sensitive protein - Nature Methods Temperature-sensitive proteins would enable the remote control of cellular functions deep within tissues, although few such proteins have been characterized. Melt is a protein that reversibly clusters...

In line with recent work by Bugaj and colleagues, who pioneered the thermal programming of protein localization and signaling using BcLOV4 (www.nature.com/articles/s41...), our result highlight LOV domains as versatile thermoreceptors.

Finally, we also show efficient thermal protein control using another (chemo-)receptor domain as insert. Our work expands thermogenetics to the allostreric control of proteins.

The insertion of our LOV2 variants into transcription factors, Cas9 and an RNA-binding protein enables the thermogenetic control of various cellular processes. We expect the approach to be easily tranferrable to the various AsLOV2-based tools out there.

New paper alert! We introduce the modular allosteric thermo-control of protein activity. Employing the AsLOV2 domain and mutants thereof as thermoreceptors, we engineered diverse hybrid proteins, whose activity can be controlled by small temperature changes (37-40/41 °C).

doi.org/10.1101/2025...

It was a pleasure to meet all of you and discuss science! Many thanks again for the invitation.

PyFuRNAce: An integrated design engine for RNA origami To realize the full potential of RNA nanotechnology and RNA origami, user-friendly design tools are needed. Here, we present pyFuRNAce, an open-source, Python-based software package with a graphical u...

Hey #RNA world, we are excited to share our RNA design engine #pyFuRNAce - an integrated tool for RNA origami experts and novices alike. Kudos to @monari-luca.bsky.social @floppleton.bsky.social et al! Preprint: www.biorxiv.org/content/10.1... Try it out at pyfurnace.de Feedback welcome!

Intelligence Evolved at Least Twice in Vertebrate Animals | Quanta Magazine Complex neural circuits likely arose independently in birds and mammals, suggesting that vertebrates evolved intelligence multiple times.

Thank you to @yaseminsaplakoglu.bsky.social, who wrote a fantastic article for @quantamagazine.bsky.social about our studies on the evolution of the avian pallium. Love it! shorturl.at/vmTLq

We have an exciting new PhD opportunity!

If you are fsacinated by proteins and their dynamics and want to engineer them to develop new molecular tools: apply now!
We are a young and dynamic team combining state-of-the-art laboratory and bioinformatics approaches.
Please share.

What a week! I defended my PhD on Monday, and now my first first-author paper was published in @science.org.
shorturl.at/fvIGZ
I am so incredibly grateful to everyone who made this possible! Especially @kaessmannlab.bsky.social and the García-Moreno lab 💛

Developmental origins and evolution of pallial cell types and structures in birds Innovations in the pallium likely facilitated the evolution of advanced cognitive abilities in birds. We therefore scrutinized its cellular composition and evolution using cell type atlases from chick...

So excited to announce that our study on the development and evolution of pallial cell types and structures in birds, led by @bassi-z.bsky.social, is now out in @science.org!
www.science.org/doi/10.1126/...

Congrats Michael! Impressive work!

Thanks Nick! It was a lot of fun to work with you and all others :)

A modular toolbox for the optogenetic deactivation of transcription Abstract. Light-controlled transcriptional activation is a commonly used optogenetic strategy that allows researchers to regulate gene expression with high

Excited to announce our optogenetic transcriptional deactivation toolbox is now out in its final form at Nucleic Acids research: academic.oup.com/nar/advance-....

I am super excited and grateful to be funded by the BW-Stiftung within the Postdoc Elite Program. Looking forward to bringing exciting new research from the drawing board into the lab. Many thanks to all my amazing colleagues for all the continued collaboration and support!

We updated our BindCraft preprint with lots of new exciting results! We release all our binder sequences and models, include more in silico analysis, novel design targets, and present AAV retargeting to specific cell types using de novo binders!
www.biorxiv.org/content/10.1...