iiinova — where your digital self keeps evolving

Keasling Lab 🏳️‍🌈 @keaslinglab.bsky.social · 25/08/2026

The Keasling Lab is now on Bluesky! 🧬🌏🏳️‍🌈 We engineer the chemistry inside microbial cells to produce life-saving therapies, clean-burning fuels, and new materials. Follow along for cool science, lab news, and to celebrate the people behind our work. Repost to help us find our community! 🔁

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Keasling Lab 🏳️‍🌈 @keaslinglab.bsky.social · 02/12/2025

Our latest manuscript, led by @peterwinegar.bsky.social et al., highlights key advances in microbial terpenoid biosynthesis and how emerging technologies will drive the next generation of designed, new-to-nature molecules. Read it now: www.sciencedirect.com/science/arti...

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Keasling Lab 🏳️‍🌈 @keaslinglab.bsky.social · 12/11/2025

Excited to share the work of our PhD candidate, Leah Keiser. Leah engineered polyketide synthases (PKSs) to control stereochemistry. By systematically exchanging domains, her work provides insights into the biosynthesis of complex molecules with tunable stereocenters 👩‍🔬🧪 pubs.acs.org/doi/full/10....

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Reposted by Keasling Lab 🏳️‍🌈

cathy ji @crji.bsky.social · 01/11/2025

If you want to do single or multi-mutant protein optimization with a (very) small amount of data and a laptop, check out our recent work FolDE (github.com/JBEI/foldy)! Open platform with a super nice, intuitive UI! Led by @jacoberts.bsky.social at @keaslinglab.bsky.social.

github.com

GitHub - JBEI/foldy: Foldy: a web-based platform for interactive protein structure analysis

Foldy: a web-based platform for interactive protein structure analysis - JBEI/foldy

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Keasling Lab 🏳️‍🌈 @keaslinglab.bsky.social · 30/10/2025

This work was led by @jacoberts.bsky.social in collaboration with @ben-eysenbach.bsky.social and @crji.bsky.social. It would not have been possible without funding from the United States federal government, via the NIH, NSF, DOE, and AFOSR.

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Keasling Lab 🏳️‍🌈 @keaslinglab.bsky.social · 30/10/2025

This method is now built into Foldy, our lab's open-source protein engineering platform. Other updates: Foldy uses Boltz-2x for structure prediction, runs ESM family models, and is deployable with a single command. Setup instructions: github.com/JBEI/foldy

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Keasling Lab 🏳️‍🌈 @keaslinglab.bsky.social · 30/10/2025

Where did the improvements come from? We show that the biggest factor is a new policy called naturalness warm-start, a way to pretrain the activity predictions with the outputs of the ESM family of protein language models.

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Keasling Lab 🏳️‍🌈 @keaslinglab.bsky.social · 30/10/2025

We present FolDE, an ALDE method designed to maximize end-of-campaign success. Across 20 ProteinGym datasets, FolDE discovers 23% more top 10% mutants than the random forest-based ALDE baseline (p=0.005) and is 55% more likely to find top 1% mutants.

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Keasling Lab 🏳️‍🌈 @keaslinglab.bsky.social · 30/10/2025

We've observed that existing zero-shot and few-shot protein activity prediction methods often select batches of very similar mutants. We found that selecting closely related mutations narrows the data used to train subsequent models, thereby weakening predictions in later rounds.

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Keasling Lab 🏳️‍🌈 @keaslinglab.bsky.social · 30/10/2025

We're excited to share FolDE, a low-N protein optimization method. In simulation, we found that FolDE is 55% more likely to identify top-1% hits than current baseline methods. FolDE is open and can be set up on a personal computer with a single command. arxiv.org/abs/2510.24053

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