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Stefan Holderbach

@sholderbach.bsky.social
68 followers 68 following 23 posts

Playing with programming languages, proteins, and photography. Nerding out about Nushell and niche applications of synthetic biology.

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Reposted by Stefan Holderbach
Jonas Koeppel @jonaskoeppel.bsky.social · 04/06/2026
1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...
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Nicholas Southern @neuroscinikolai.bsky.social · 15/04/2026
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🧵
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Michael Jendrusch @mjendrusch.bsky.social · 02/03/2026
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!
jobs.dkfz.de
Technical Assistant
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Diego del Alamo @delalamo.xyz · 19/12/2025
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?
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Tim Krief @timkrief.com · 16/09/2025
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Reposted by Stefan Holderbach
Rob Patro @robp.bsky.social · 18/09/2025
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
blog.rust-lang.org
Announcing Rust 1.90.0 | Rust Blog
Empowering everyone to build reliable and efficient software.
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Martin Pacesa @martinpacesa.bsky.social · 27/08/2025
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...
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Andy Gayton @ndyg.ca · 26/08/2025
overheard, with regards to nushell "That is pretty cool that you can just do that kind of stuff with the shell scripting. " 🩵
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Reposted by Stefan Holderbach
Jan Mathony @jmathony.bsky.social · 04/08/2025
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...
rdcu.be
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.
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Yo Akiyama @yoakiyama.bsky.social · 05/08/2025
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🧵
biorxiv.org
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 05/08/2025
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... & 🐍
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 04/08/2025
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! 🧵
Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.
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Dominik Niopek @dominikniopek.bsky.social · 04/08/2025
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...
nature.com
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.
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Rob Patro @robp.bsky.social · 03/08/2025
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!🧬🖥️
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Stefan Holderbach @sholderbach.bsky.social · 09/07/2025
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)
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Reposted by Stefan Holderbach
Rob Patro @robp.bsky.social · 08/07/2025
#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!
docs.astral.sh
uv
uv is an extremely fast Python package and project manager, written in Rust.
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Rust Language @rust-lang.org · 27/06/2025
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...
blog.rust-lang.org
Announcing Rust 1.88.0 | Rust Blog
Empowering everyone to build reliable and efficient software.
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Nicholas Southern @neuroscinikolai.bsky.social · 13/06/2025
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 🌚🌞
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Zeqian Li @zeqianli.bsky.social · 28/05/2025
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
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Jan Mathony @jmathony.bsky.social · 03/05/2025
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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Andy Gayton @ndyg.ca · 30/04/2025
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
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 27/04/2025
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...
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Julia Evans @b0rk.jvns.ca · 29/04/2025
terminal escape codes wizardzines.com/comics/escap...
Panel 1: a program's input and outputs are streams of bytes

everything you type goes into standard input

all the output you see comes from either 
standard output or standard error

your terminal emulator can only communicate with programs by reading/writing bytes

panel 2: some inputs/outputs are text and some are special instructions

in: mouse position, ctrl+left arrow
out: make text green, make cursor invisible

panel 3: these special instructions are called "escape codes"

they're called "escape codes" because they all start with the ESC character

panel 4: example: how colours get set

program: “^[[31m”

Terminal emulator: “ok, I'll make text red from now on!!”

(there are also codes for bold, underline, background colour)

panel 5: programs can easily "break" your terminal by printing escape codes

program: “oops I made your cursor disappear”

It's easy to fix though, run reset to print a special escape code that resets everything

It's easy to fix though, run reset to print a special escape code that resets everything
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Diego del Alamo @delalamo.xyz · 21/04/2025
"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)
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Jan Mathony @jmathony.bsky.social · 01/04/2025
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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Stefan Holderbach @sholderbach.bsky.social · 01/04/2025
The state of academic funding in 2025!!!
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Reposted by Stefan Holderbach
Arjun Raj @arjunraj.bsky.social · 12/03/2025
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.
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Stefan Holderbach @sholderbach.bsky.social · 06/03/2025
Using Rust for Bioinformatics tackling the complexity of VCF with a common scripting language (lua) Color me intrigued! github.com/brentp/vcfex...
github.com
GitHub - brentp/vcfexpress: expressions on VCFs
expressions on VCFs. Contribute to brentp/vcfexpress development by creating an account on GitHub.
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Reposted by Stefan Holderbach
Scott Coyle @cellraiser.bsky.social · 04/03/2025
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 🧵
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Randall Munroe @xkcd.com · 26/02/2025
RNA xkcd.com/3056
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Stefan Holderbach @sholderbach.bsky.social · 14/02/2025
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.
Red colored protein model of the Avena sativa LOV2 domain (PDBID: 7PGY)
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Stefan Holderbach @sholderbach.bsky.social · 07/02/2025
Drake - Hotline Bling image template:
rejecting face: Performance advances for LLM AI chatbots
appreciating face: Performance advances for protein design models
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Oskar Staufer @ostaufer.bsky.social · 22/01/2025
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
sciencedirect.com
Synthetic cells in tissue engineering
Tissue functions rely on complex structural, biochemical, and biomechanical cues that guide cellular behavior and organization. Synthetic cells, a pro…
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Clay Kosonocky @kosonocky.bsky.social · 04/02/2025
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 🧵
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Michael Jendrusch @mjendrusch.bsky.social · 06/02/2025
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)
Five generated protein structures coloured with a gradient from purple to teal. The structures are shaped and positioned to spell out the word "salad" – the name of the software described in the mentioned preprint – in all-capital letters.
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Rob Patro @robp.bsky.social · 07/01/2025
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 🤯!
play.rust-lang.org
Rust Playground
A browser interface to the Rust compiler to experiment with the language
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Stefan Holderbach @sholderbach.bsky.social · 22/12/2024
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!
nushell.sh
Upcoming Configuration Enhancements | Nushell
A new type of shell.
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nushell @nushell.bsky.social · 07/12/2024
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...
screenshot of new config format
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Frank Noe @franknoe.bsky.social · 06/12/2024
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...
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Niopek Lab @niopeklab.bsky.social · 05/12/2024
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...
biorxiv.org
Rational engineering of allosteric protein switches by in silico prediction of domain insertion sites
Domain insertion engineering is a powerful approach to juxtapose otherwise separate biological functions, resulting in proteins with new-to-nature activities. A prominent example are switchable protei...
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Stefan Holderbach @sholderbach.bsky.social · 05/12/2024
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!
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Reilly Wood @reillywood.com · 02/12/2024
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.
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nushell @nushell.bsky.social · 30/11/2024
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...
screenshot of linked changelog
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 27/11/2024
Lazysky time: has anybody actually shown that structural self consistency correlates with successful expression on either a per design or per model basis?
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Stefan Holderbach @sholderbach.bsky.social · 28/11/2024
Under appreciated value of (functioning) social media: sharing those tacit social norms obvious to the in-group
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Nicholas Southern @neuroscinikolai.bsky.social · 26/11/2024
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 😄)
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Niopek Lab @niopeklab.bsky.social · 26/11/2024
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)
doi.org
A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins
Abstract. Deep mutational scanning is a powerful method for exploring the mutational fitness landscape of proteins. Its adaptation to anti-CRISPR proteins,
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Stefan Holderbach @sholderbach.bsky.social · 26/11/2024
Tried to touch grass, looked into the blue sky instead
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