1/28 How do you optimize a dynamic protein property that emerges from multiple states? Our finally published paper in @NatureComms takes on one of the hardest problems in protein engineering with phage assisted evolution: evolving allosteric switches🧵

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... Please share!

Not sure how to reconcile A) bindcraft consistently outperforming RFDiffusion, but B) AF3-gen diffusion-based design outperforming AF3-gen hallucination-based design. My best guess is that there's something about AF2 but not AF3-gen methods that makes them amenable to backprop?

Rust 1.90.0 is out! blog.rust-lang.org/2025/09/18/R... Major features: * lld as the default linker on x86_64-unknown-linux-gnu * cargo workspace publishing support built into cargo * more const context APIs, and stabilization of new useful APIs

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

overheard, with regards to nushell "That is pretty cool that you can just do that kind of stuff with the shell scripting. " 🩵

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...

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

MMseqs2 v18 is out - SIMD FW/BW alignment (preprint soon!) - Sub. Mat. λ calculator by Eric Dawson - Faster ARM SW by Alexander Nesterovskiy - MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API) 💾 github.com/soedinglab/M... & 🐍

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵

Our work on rationally engineering allosteric protein switches is now out in Nature Methods: www.nature.com/articles/s41... Thanks a lot to @grunewald.bsky.social and @noahholzleitner.bsky.social for the comprehensive news and views: www.nature.com/articles/s41...

I talk a lot about Rust for building high-perf (& even non-perf critical) software, & scientific software in particular. I often discuss what's interesting to me, but wanted to offer the chance to those interested for me to answer their questions about Rust in science. Fire away with questions!🧬🖥️

Absolutely spoiled by match and if/else being expressions in Rust and Nushell. Really feels pedestrian trying to achieve the same in Typescript or Python. (No the ternary operator is not "control flow as expressions" we have at home)

#AwesomeTools 1: uv docs.astral.sh/uv/ has transformed how I work with Python projects locally and for development and distribution. No more pip, venv, poetry, etc. seamless package management, virtual environments, development and deployment deliverer FAST & without hassle!

Rust 1.88.0 has been released! ✨🎊 🦀 This release brings you let chains, naked functions, automatic Cargo cache cleaning, Cell::update, proc_macro span locations, as_chunks methods on slices, and more! Check out the blog post and release notes for all the details: blog.rust-lang.org/2025/06/26/R...

Excited to share my main PhD work is finally out! 🥳 We built a phage-assisted evolution platform to evolve allosteric protein switches (POGO-PANCE) and introduce cumulative, targeted mutations/Indels (RAMPhaGE)! See how we evolved ultra-strong, light-switchable AraC variants 🌚🌞

I started tgv to learn Rust and building it has been unbelievably fun! If you wanna pick up a super fast and fun programming language, tgv is open for contribution! There aren't many bioinformatics tools built entirely by the community. If tgv can become one, I'll be so psyched

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...

Nushell 0.104 is out: www.nushell.sh/blog/2025-04... gh's @cosineblast continues to iterate on job support, with experimental support for message passing between jobs

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...

terminal escape codes wizardzines.com/comics/escap...

"If you're used to being able to sit down and bang out code, any time, anywhere, with all kinds of tools (libraries, compilers, virtual machines, what have you) at your fingertips, then yeah, working up a new assay protocol in a cell line is going to seem agonizingly slow" (from 2015)

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.

The state of academic funding in 2025!!!

Labeling your axes and then explaining them slowly is perhaps the biggest bang for the buck you can get for making your slides more understandable.

Using Rust for Bioinformatics tackling the complexity of VCF with a common scripting language (lua) Color me intrigued! github.com/brentp/vcfex...

Excited to share a new preprint! Wireless devices use FM modulation to transmit multiplexed noise-resistant data. Led by @born2raisecell.bsky.social, we create a biochemical analogue of this paradigm using genetically encoded oscillators (GEOs) for single-cell FM streaming tinyurl.com/nbs8rw42 🧵

RNA xkcd.com/3056

This Valentine's day I want to share the LOV2 with you! ❤️ Roses are red, the light is blue, stimuli are read by the domain LOV2.

Hello BlueSky 👋 Happy to start here by sharing our lastest review on synthetic cells in tissue engineering. Great concepts presented by the amazing PhD students Anna Burgstaller and Sara Madureira www.sciencedirect.com/science/arti... #SynCells #tissueengineering #biomimetics #biomaterials #SynBio

PSA: Digging into Chai-1 and found out that it gives different protein-ligand structures & confidences depending on the SMILES canonicalization used May also be the case with AF3 & Boltz-1, but haven't verified As to what this means... see the rest of the thread 🧵

New protein ML preprint from my PhD project. We describe salad (sparse all-atom denoising), a family of efficient protein structure diffusion models and show that it works well on a bunch of protein design task previously described in the literature. Preprint: www.biorxiv.org/content/10.1... (1/N)

I just learned this amazing trick --- H/T /u/CocktailPerson on the rust subreddit: play.rust-lang.org?version=stab... you get fast dyn compile times in debug builds, but monomorphization and static dispatch in release builds 🤯!

Our last Nushell release of 2024 is a holiday special! You can now set up a much simpler config thanks to changes to how we load it and provide defaults. More at www.nushell.sh/blog/2024-12.... And for folks eager to contribute, we have cool new introspection tools to peek under the hood of Nu!

Heads up: Nushell configuration will be changing (for the better!) in the upcoming v0.101 release. Instead of specifying *everything* in config.nu and env.nu, you can specify only the settings you care about. Details: www.nushell.sh/blog/2024-12...

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...

We are thrilled to share ProDomino a model for the prediction of domain insertion sites in proteins. Our approach enables the simple and rapid engineering of highly potent switchable proteins, as we exemplify by creating novel inducible variants of Cas9 and Cas12a. www.biorxiv.org/content/10.1...

Hot new tech from the @niopeklab.bsky.social: we apply @bene837.bsky.social's ProDomino model to predict sites in proteins where domains can be inserted to create allosterically switchable enzymes. From light-switchable antibiotic resistance to a glucocorticoid-dependent Cas12a!

This is an underacknowledged strength of Rust; the stdlib and wider ecosystem has the best, most comprehensive+thoughtful support for both *nix and Windows of any programming language I've used.

This week in Nu: big progress on WebAssembly support, a new `term query` command for terminal info, config improvements, and more github.com/nushell/this...

Lazysky time: has anybody actually shown that structural self consistency correlates with successful expression on either a per design or per model basis?

Under appreciated value of (functioning) social media: sharing those tacit social norms obvious to the in-group

Interested in regulating CRISPR-Cas systems for your experiments? Go check out these awesome chemical and optogenetic tools from our lab 👇 (made by some pretty cool people 😄)

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)

Tried to touch grass, looked into the blue sky instead