Jan Mathony

Thermogenetics: How Proteins Are Controllable by Heat – Modular design strategy makes it possible to precisely control cellular functions through minimal temperature changes www.uni-heidelberg.de/en/newsroom/...

Technical Assistant

Are you interested in working with a fresh team on cutting edge protein design?
We're hiring a Technical Assistant for our protein design team at DKFZ Heidelberg: jobs.dkfz.de/en/jobs/1683...

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Congrats and many thanks to co-first authors @ann-sophiekroell.bsky.social & Kira Hoffmann and all people involved for their amazing effort!

🎉🎉 Our paper on temperature-dependent protein control using AsLOV2 variants is now published at @natchembio.nature.com: www.nature.com/articles/s41... including some new insights from extend variant characterizations.

Check out the open positions in the new Mari Sepp lab. She is a great scientist and mentor!

Join us for a 📢 #CIBSS / SFB 1381 Joint Seminar

🗓 13 Jan 2026 | 12:00–13:00
👉 @jmathony.bsky.social (#uniheidelberg)
🎙 Engineering stimulus-controlled proteins through modular domain recombination
📍 Lecture Hall, Institute of Biology I, Hauptstr. 1

🔗 kurzlinks.de/4mlv

#SynBio #ProteinEngineering

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
1/🧵

🎉🎉 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 💛