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Noah Holzleitner

@noahholzleitner.bsky.social
337 followers 146 following 15 posts

PhD Student at Grünewald Lab (TUM) 🧬Protein Design for CRISPR proteins🧑🏽‍💻👨🏽‍🎨

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Reposted by Noah Holzleitner
Kate Michie @kmichie.bsky.social · 23h
This is deeply embarrassing. A simple run through Amber and it’s gone. That should have been obvious before they started. How is it a Nature paper? How is this big news and how does it offer anything in the way of security? #structural biology glonce.com/google-deepm...
glonce.com
Google DeepMind introduces SynthID Bio to watermark AI-designed proteins
Google DeepMind's SynthID Bio is a proof of concept for embedding an imperceptible watermark in AI-generated protein sequences and predicted 3D structures. In wet-lab tests on three targets, watermark...
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Reposted by Noah Holzleitner
Julian Grünewald @grunewald.bsky.social · 03/09/2026
In 2025, one child got a CRISPR therapy made for him. Gene therapy's "moon landing". My #ERCStG ONE2MANY asks how editing scales from n=1 to many, in the heart: one edit for a group of mutations, AI-guided protein engineering & delivery. Thanks @erc.europa.eu & my fantastic team in the lab!
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 20/08/2026
Binder design is nice and all, but here we have three agents sharing data and autonomously controlling a lab to design enzymes with shifted substrate scopes and high activity! @cobanbrooks.bsky.social @pascalnotin.bsky.social @philromero.bsky.social www.biorxiv.org/content/10.6...
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Adam Phillippy @aphillippy.bsky.social · 06/08/2026
For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 01/08/2026
Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek
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Nature Biotechnology @natbiotech.nature.com · 23/07/2026
AI model using AlphaFold3-predicted contact probabilities maps and reduces genome editor off-targets, enabling highly precise DNA base editing with improved specificity. #NBThighlight www.nature.com/articles/s41...
nature.com
Precise DNA base editing using AlphaFold3-based contact modelling - Nature
ContactSeek is an AlphaFold3-driven model that can improve the precision of genome-editing tools.
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Doudna Lab @doudna-lab.bsky.social · 16/07/2026
Our AI-guided design of RNA-guided nucleases is now out in @science.org 💻🧬 We used structure and evolutionary data to generate minimal, active and divergent gene editors! www.science.org/doi/10.1126/... Congrats to @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social & team!
science.org
Structure and evolution-guided design of minimal RNA-guided nucleases
The design of RNA-guided nucleases with properties not limited by evolution can expand programmable genome-editing capabilities. However, generating diverse multidomain proteins with robust enzymatic ...
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Reposted by Noah Holzleitner
Nicholas Southern @neuroscinikolai.bsky.social · 05/07/2026
New preprint! We used protein domain insertion to tighten the editing window of the TadA8e adenine base editor. Bulky domain insertions concentrated editing around position A5, maintained robust on-target activity, and reduced Cas-independent off-target editing. 🧬 doi.org/10.64898/202...
biorxiv.org
Domain Insertion Improves the Precision of a CRISPR Adenine Base Editor
Adenine base editors (ABEs) enable efficient A:T to G:C conversion, but their broad activity windows frequently cause unintended bystander edits. We hypothesized that insertion of a bulky, inert prote...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 25/06/2026
Great. Goes well with this paper on how to write bad papers: doi.org/10.1111/j.00...
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Itai Yanai @itaiyanai.bsky.social · 24/06/2026
🔥 Published today, and just in time for summer conferences, here are your guidelines for presenting badly www.nature.com/articles/s41... rdcu.be/fqa92
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 15/06/2026
Aggregating many experiments into one zero-shot protein language model score obscures that current models cannot meaningfully rank a set of fit mutations or prioritize new-to-nature functions @clauswilke.com www.biorxiv.org/content/10.6...
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Erik Poppleton @poppleton.phd · 11/06/2026
RNA imaging 👀🧬👀🧬
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Matthew Taliaferro @jmtali.bsky.social · 11/06/2026
New paper! How do RNAs "know" where to go inside a cell? We dug into the sequence elements that route RNAs to the right place. It turns out that, in mammals, they're surprisingly massive (>200 nt), multipartite, and wonderfully complicated. 🧵
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AI x Bio Discovery @aixbiobot.bsky.social · 12/06/2026
HalluDesign-NA: Extending HalluDesign for De Novo Nucleic Acid Design [new] by integrating NA-MPNN for iterative sequence-structure co-optimization, enabling constrained de novo design of nucleic acids.
Figure 1Figure 2Figure 3Figure 4
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 06/06/2026
Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe. 📄 www.nature.com/articles/s41... 💾 folddisco.foldseek.com​​​​​​​​​​​​​​​​ 🌐 search.foldseek.com/folddisco
nature.com
Structural motif search across the protein universe with Folddisco - Nature Biotechnology
Folddisco enables protein structural motif search in million scale databases.
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Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 02/06/2026
Phages invented sgRNAs before humans!! 🧬 Obviously, for mischief… 😈 Loved seeing this story unfold!
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Michael Lin, MD PhD @michaelzlin.bsky.social · 19/05/2026
Happy to reveal our latest work, Microbe-Independent Deep Assembly and Screening (MIDAS), a method for engineering proteins >10x more cheaply and quickly than before. MIDAS addresses the slowest step in protein engineering — construction and expression of variants — by skipping cloning entirely
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 21/05/2026
Another banger
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William DeWitt @wsdewitt.github.io · 29/04/2026
Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis. Preprint (w/ Gian Marco Visani and Aayush Verma): www.biorxiv.org/content/10.6... Blog: dewitt-lab.github.io/posts/2026-0...
dewitt-lab.github.io
Additivity is all you need?
Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis.
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Reposted by Noah Holzleitner
Yeqing Lin @yeqinglin.bsky.social · 08/05/2026
Introducing Genie 3, a generative protein model that substantially advances the state-of-the-art for binder design, increasing in silico success rates by up to 20x on hard multimeric targets. It also debuts a form of inference-time scaling unobserved in other design models. 🧵1/8
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Erik Sontheimer 🇺🇸💙🇺🇦 @eriksontheimer.bsky.social · 29/04/2026
Site-specific, multi-kilobase insertions and over-writes in mammalian cells, without DSBs, HDR, recombinases, integrases, transposases, or active cell cycling? Using fully or predominantly single-stranded DNA donors? 1/15
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Martin Pacesa @martinpacesa.bsky.social · 27/04/2026
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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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Karl Carlström @carlstrom.bsky.social · 27/03/2026
🚨🚨🚨Job alert We are looking for postdoc joining our lab. If you are interested in subcellular distribution of proteins using iPSC and animal models in combination with leading genome engineering tools, check this add out!! 🧠🧬🔬🧫💊 www.linkedin.com/posts/karl-c...
linkedin.com
Postdoctoral position (scholarship) in metabolic-epigenetic interplay | Karl Carlström
📣 📣 📣 Job alert!!! Join us at Karolinska Institutet We are looking for a postdoc to the Carlström lab curious to dissect metabolic and epigenetic interplay using iPSCs and animal models coupled with...
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Reposted by Noah Holzleitner
AI x Bio Discovery @aixbiobot.bsky.social · 26/03/2026
ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural Embeddings [new] Leverages pre-structural embeddings that capture RNA flexibility for direct, sequence-based affinity prediction via cross-modal attention, bypassing structural data.
ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural EmbeddingsFigure 1Figure 2Figure 3
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Reposted by Noah Holzleitner
Mohammed AlQuraishi @moalquraishi.bsky.social · 13/03/2026
New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9
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Ben Kleinstiver @bkleinstiver.bsky.social · 10/03/2026
Interested in gaining research experience, and curious about genome editing tool development and their application to treat human diseases? 🧬 🧫 We are hiring!! Join us at Mass General Hospital in Boston! 📣 massgeneralbrigham.wd1.myworkdayjobs.com/MGBExternal/...
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Joe Greener @jgreener64.bsky.social · 15/10/2025
I wrote a blog post about the future of structural bioinformatics. Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs? Let me know what you think. jgreener64.github.io/posts/struct...
jgreener64.github.io
Where next for structural bioinformatics?
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Christopher Snow @cdsnow.bsky.social · 10/03/2026
We built DNA scaffold crystals that can be reprogrammed to host different guest proteins for X-ray structure determination — no new crystallization screen required. This animation shows a guest protein (glowing) seeking its designed binding site inside the crystal lattice. shorturl.at/DANdc
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matt-dejong.bsky.social @matt-dejong.bsky.social · 27/02/2026
First preprint of the @pollyfordyce.bsky.social and @dunnlab.bsky.social collaboration! We used high-throughput microfluidics for sequence-strength mapping at the single-molecule level. Our new tech allowed us to discover a fundamental nonequilibrium property of multivalent systems. 1/13
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RNAmed @rnamed.bsky.social · 26/02/2026
🧬 RNAMed is hiring! Apply for one of 11 fully funded PhD positions in RNA medicine and work with leading RNA experts in an international, interdisciplinary environment. 📅 Deadline: 24 March 2026 More info & apply: lnkd.in/eX7fQcJi
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Nicholas Southern @neuroscinikolai.bsky.social · 24/02/2026
Wow congrats to the authors this is truly impressive
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Jörg Vogel @jorg-vogel-lab.bsky.social · 23/02/2026
Looking for a truly unique PhD programme on RNA drugs and therapeutics? We have just opened the call for the second cohort of RNAmed-Future leaders in RNA-based medicine. More details under www.rnamed.de Please spread the word.
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Diego del Alamo @delalamo.xyz · 20/02/2026
A detailed comparison of de novo designed proteins by NMR finally puts to rest the idea that structure prediction confidence metrics have any correlation with local flexibility
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AI x Bio Discovery @aixbiobot.bsky.social · 18/02/2026
AlphaFast: High-throughput AlphaFold 3 via GPU-accelerated MSA construction [new] ...is a drop-in framework integrating GPU-accelerated MMseqs2 to overcome the CPU-bound MSA generation bottleneck in AlphaFold 3.
Figure 2
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Diego del Alamo @delalamo.xyz · 16/02/2026
The fitness landscapes of binders targeting protein surfaces that are evolutionarily predisposed to engage in PPIs is much narrower and deeper than those that target surfaces with no known interacting proteins. This might be b/c random binding events is bad, and selected against
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Jan Mathony @jmathony.bsky.social · 12/02/2026
🎉🎉 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.
nature.com
Modular engineering of thermoresponsive allosteric proteins - Nature Chemical Biology
Thermogenetics enables spatiotemporal control of protein activity using temperature. Now, engineering of a compact, insertable thermoresponsive protein module diversifies the classes of proteins amena...
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Edoardo Gianni @edogia.bsky.social · 13/02/2026
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller? Excited to share our latest work in @science.org on a new small polymerase. 1/n
science.org
A small polymerase ribozyme that can synthesize itself and its complementary strand
The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...
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Theo Sanderson @theo.io · 08/02/2026
I made a map of 3.4 million Bluesky users - see if you can find yourself! bluesky-map.theo.io I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
bluesky-map.theo.io
Bluesky Map
Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.
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Patrick Bryant @patrickbryant1.bsky.social · 07/02/2026
Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure. We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
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Di Jiang @dijiang319.bsky.social · 06/02/2026
🧬🌉Online @science.org Programmable genome editing in human cells using RNA-guided bridge recombinases | Science www.science.org/doi/10.1126/...
science.org
Programmable genome editing in human cells using RNA-guided bridge recombinases
Site-specific insertion of gene-sized DNA fragments remains an unmet need in the genome editing field. IS110-family serine recombinases have recently been shown to mediate programmable DNA recombinati...
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Khmelinskaia Lab @akhmelinlab.bsky.social · 03/02/2026
🗓️ Save the Date! The 5th European RosettaCon – Crossing Boundaries with Protein Design will take place in Lisbon, Portugal 🇵🇹 🗓️ October 28–30, 2026 Join the protein design community for an inspiring scientific meeting at the intersection of innovation and design.
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Xuebing Wu @xuebingwu.bsky.social · 31/01/2026
Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...
biorxiv.org
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 30/01/2026
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...
science.org
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
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Nature Biotechnology @natbiotech.nature.com · 27/01/2026
China’s innovation in translational medicine: rethinking early-stage clinical development - @caidyacro.bsky.social go.nature.com/4agbEkG
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Erik Poppleton @poppleton.phd · 22/01/2026
Neat paper! Boosting to the MP feed 🧬
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 13/01/2026
EDEN: a family of genomic language models trained on up to 9.7 trillion nucleotides from @basecamp-research.bsky.social's BaseData can design large serine recombinases, bridge recombinases, and antimicrobial peptides. www.biorxiv.org/content/10.6... Happy to have played a small part in this!
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