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/🧵

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

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...

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/🧵

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...

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!

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...

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!

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 💛

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/...

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...

Interested in allosteric protein switches? Check our ProDomino - our new model for the prediction of domain insertion sites. With ProDomino we engineered several potent inducible proteins including Cas9 and Cas12a variants.

Multi-modal control of gene editing with inducible anti-CRISPR proteins! Congrats to first authors @lucabrenker.bsky.social, Sabine and Felix.

Now out in Nucleic Acids Research: A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins: doi.org/10.1093/nar/... (1/4)

New pre-print from our group reporting engineered, broad-spectrum anti-CRISPR proteins based on AcrIIA5, a type II inhibitor, and AcrVA1, a type V inhibitor, for opto- and chemogenetic control of CRISPR-Cas9 and -Cas12a: www.biorxiv.org/content/10.1... (1/3)

A Versatile Anti-CRISPR Platform for Opto- and Chemogenetic Control of CRISPR-Cas9 and Cas12 across a Wide Range of Orthologs https://www.biorxiv.org/content/10.1101/2024.11.25.625186v1

Our paper on DMS of anti-CRISPR proteins is out in it's final form Nucleic Acids Research! Many congrats to first authors Tobias and Michael! It was lots of fun to see the story develop. academic.oup.com/nar/advance-...