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Reposted by Jan Mathony

Michael Jendrusch @mjendrusch.bsky.social · 14d

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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EMBL @embl.org · 15d

‘Salad’ – a new AI model from EMBL scientists – offers major improvements in synthetic protein design.

Salad is significantly faster than comparable methods, and designing proteins that don't exist in nature can have applications in many scientific fields.

www.nature.com/articles/s42...

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Jan Mathony @jmathony.bsky.social · 14d

🎉🎉 congrats Michael!!

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Jan Mathony @jmathony.bsky.social · Aug 22

Happy to hear that, thank you!

Jan Mathony @jmathony.bsky.social · Aug 5

Thanks Julian!

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Reposted by Jan Mathony

Nature Methods @natmethods.nature.com · Aug 4

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

Nature Methods @natmethods.nature.com · Aug 4

ProDomino is a machine learning-based method that predicts domain insertion sites and helps guide the engineering of functional multi-domain proteins.

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

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Jan Mathony @jmathony.bsky.social · Aug 4

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...

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.

rdcu.be

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Reposted by Jan Mathony

Nils Trost @trostnils.bsky.social · Jun 20

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.

Kaessmann Lab @kaessmannlab.bsky.social · Jun 20

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...

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Reposted by Jan Mathony

Kaessmann Lab @kaessmannlab.bsky.social · Jun 20

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...

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Jan Mathony @jmathony.bsky.social · Jun 20

Congrats Michael, great work as always!

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Reposted by Jan Mathony

Michael Jendrusch @mjendrusch.bsky.social · Jun 19

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/🧵

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Reposted by Jan Mathony

Niopek Lab @niopeklab.bsky.social · Jun 13

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...

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...

doi.org

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Jan Mathony @jmathony.bsky.social · Jun 13

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

Niopek Lab @niopeklab.bsky.social · Jun 13

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...

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...

doi.org

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Jan Mathony @jmathony.bsky.social · Jun 13

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!

Dominik Niopek @dominikniopek.bsky.social · Jun 13

Check out the new pre-print from our lab on phage-assisted evolution of light-switchable, allosteric proteins. Congrats to first author @neuroscinikolai.bsky.social, co-corresponding author @jmathony.bsky.social and everyone from the @niopeklab.bsky.social involved!

www.biorxiv.org/content/10.1...

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...

www.biorxiv.org

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Jan Mathony @jmathony.bsky.social · May 3

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

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...

www.biorxiv.org

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Jan Mathony @jmathony.bsky.social · May 3

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

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Jan Mathony @jmathony.bsky.social · May 3

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.

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...

www.nature.com

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Jan Mathony @jmathony.bsky.social · May 3

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.

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Jan Mathony @jmathony.bsky.social · May 3

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.

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Jan Mathony @jmathony.bsky.social · May 3

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...

doi.org

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Jan Mathony @jmathony.bsky.social · Apr 22

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

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Reposted by Jan Mathony

Kerstin Göpfrich @kgoepfrich.bsky.social · Apr 20

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!

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...

www.biorxiv.org

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Reposted by Jan Mathony

Bastienne Zaremba @bassi-z.bsky.social · Apr 7

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

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.

shorturl.at

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Jan Mathony @jmathony.bsky.social · Apr 1

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.

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Reposted by Jan Mathony

Bastienne Zaremba @bassi-z.bsky.social · Feb 14

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 💛

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Reposted by Jan Mathony

Kaessmann Lab @kaessmannlab.bsky.social · Feb 13

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/...

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...

www.science.org

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