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Antoine Koehl

@antoinekoehl.bsky.social
234 followers 192 following 2 posts

Structural Biologist turned computational biologist @UCBerkeley. Former Miller Fellow

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Reposted by Antoine Koehl
Yun S. Song @yun-s-song.bsky.social · 09/09/2026
We are thrilled to share that our GPN-Star manuscript is now published and freely available: doi.org/10.1038/s415... (1/n)
doi.org
Predicting genome-wide functional constraints with GPN-Star - Nature
GPN-Star, a genomic language model with a phylogeny-aware architecture for whole-genome alignment data, is shown to be a scalable and flexible tool for genetic variant effect prediction across species...
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Reposted by Antoine Koehl
marialukarska.bsky.social @marialukarska.bsky.social · 30/07/2026
Our ProteinGuide paper is finally out! Thanks to all the co-authors @junhaobearxiong.bsky.social, @ishangaur.bsky.social, @hnisonoff.bsky.social, @loltrogge.bsky.social, @jlistgarten.bsky.social, @savagecatsonly.bsky.social! @innovativegenomics.bsky.social www.nature.com/articles/s41...
nature.com
Property guidance for protein sequence generative models with ProteinGuide - Nature Biotechnology
On-the-fly conditioning of pretrained protein generative models guides protein generation toward specific properties.
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Reposted by Antoine Koehl
marialukarska.bsky.social @marialukarska.bsky.social · 24/07/2026
I’m happy to share our pre-print exploring the activity and specificity trade-offs in adenine base editors. Thanks to my amazing co-authors Luke Oltrogge, @hnisonoff.bsky.social, and all the other contributors @jlistgarten.bsky.social @savagecatsonly.bsky.social @innovativegenomics.bsky.social 🧵1/7
biorxiv.org
Activity and specificity trade-offs in adenine base editors
Adenine base editors (ABEs) are CRISPR effectors that introduce A-T to G-C transitions in the genome using a nucleotide deaminase fused to a Cas protein. ABEs have been evolved to have very high editi...
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Reposted by Antoine Koehl
bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 03/05/2026
Structural Insights into the Coupling Mechanism of Vectorial CO2 Uptake by DAB1 www.biorxiv.org/content/10.64898/20…
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Reposted by Antoine Koehl
Nature Biotechnology @natbiotech.nature.com · 11/03/2026
Engineered TnpB genome editors for plants and human cells identified by ribonucleoprotein mutational scanning - @savagecatsonly.bsky.social go.nature.com/4loaOGn
go.nature.com
Engineered TnpB genome editors for plants and human cells identified by ribonucleoprotein mutational scanning - Nature Biotechnology
TnpB endonucleases are engineered for improved genome editing.
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Reposted by Antoine Koehl
Yun S. Song @yun-s-song.bsky.social · 21/02/2026
Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n doi.org/10.64898/202...
doi.org
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Reposted by Antoine Koehl
Yun S. Song @yun-s-song.bsky.social · 22/09/2025
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)
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Reposted by Antoine Koehl
Junhao (Bear) Xiong @junhaobearxiong.bsky.social · 31/05/2025
Guide your favorite protein generative model with experimental data? Meet ProteinGuide - a method to condition pre-trained models on properties without retraining. We validated it both in silico by guiding ProteinMPNN and ESM3 on 3 tasks and in vitro by engineering base editors.
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Reposted by Antoine Koehl
Savage Lab @savagecatsonly.bsky.social · 26/02/2025
What's better than 1 deep mutational scanning (DMS) library? 2! In a new pre-print @brittneywthornton.bsky.social and @rfw.bsky.social et al. map the mutational landscape of ISDra2 TnpB protein and reRNA and leverage these datasets to engineer highly active variants (1/9)
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