Lightnews — Scholar-powered news

Reposted by The Align Foundation

scverse @scverse.bsky.social · Aug 26

🧫 Meet the keynote speakers for the 2025 scverse conference!
Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs

@erika-alden.bsky.social ‪
@alignbio.bsky.social
@pioneerlabs.bsky.social

#scverse #scverse2025 #StructuralBiology #Biotech #Stanford

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The Align Foundation @alignbio.bsky.social · Aug 21

Register before Oct. 17 👉 alignbio.org/get-involved...
More about EvolutionaryScale’s API (Forge) 👉 forge.evolutionaryscale.ai

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The Align Foundation @alignbio.bsky.social · Aug 21

📣 Evolutionary Scale is supporting the 2025 Protein Engineering Tournament!

Teams get sponsored ESM inference through
@evolutionaryscale.bsky.social's API (Forge), bringing frontier protein AI models into the competition.

Level playing field, real experiments, open results. Register now 👇

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The Align Foundation @alignbio.bsky.social · Aug 19

Thrilled to welcome Amanda Reider Apel to The Align Foundation as Director of Protein Projects! 🚀 A biotech leader who builds high-impact science and thriving teams, she’ll drive protein engineering strategy while fostering a culture of innovation and collaboration.

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The Align Foundation @alignbio.bsky.social · Aug 13

Why PETase for our tournament? In 2024, the world made about 30 million tonnes of PET plastic, most from fossil fuels.

PETase can degrade PET, but isn’t ready for industrial-scale waste. The challenge: design an improved variant that can change that.

Register by Oct 17 alignbio.org/protein-engi...

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The Align Foundation @alignbio.bsky.social · Jul 21

4/4
What’s coming:
→ More protein functions
→ Sharper ML strategies
→ Public data access portal
→ And yes—we’re hiring.
🔗 alignbio.org/careers
#openbiology #machinelearning #proteinfunction #bioengineering

Careers — Align to Innovate

alignbio.org

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The Align Foundation @alignbio.bsky.social · Jul 21

3/4
GROQ-seq is designed for reproducibility.
Standardized assays + distributed data collection = a foundation for robust, ML-ready protein function data.

Next: scale up function types, refine ML pipelines, expand access.

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The Align Foundation @alignbio.bsky.social · Jul 21

2/4
🧪 Year One in brief:
Started onboarding 6 protein function types
Launched multi-site runs at NIST + DAMP Lab
Achieved 100K–500K variant throughput per run
Standardized, modular, reproducible, open-source
📘 Full report: doi.org/10.5281/zeno...

Year One Report: Growth-based Quantitative Sequencing (GROQ-Seq) Platform

This report summarizes the first year of development and deployment of the Growth-based Quantitative Sequencing (GROQ-seq) platform, a pooled functional assay pipeline for large-scale, reproducible me...

doi.org

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The Align Foundation @alignbio.bsky.social · Jul 21

1/4 We just published the 1st-year update on GROQ-seq: an open access, high-throughput experimental platform capable of testing hundreds of thousands of protein variants per run, running @ NIST and the DAMP Lab. Here’s what we built, learned, and what’s next:

#GROQseq #syntheticbiology

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The Align Foundation @alignbio.bsky.social · Jul 8

🔗 Sign up by Oct 17 → bit.ly/Tournament25
🔗 Want to read more? Last year’s amalyase engineering competition was recently published in PROTEINS: onlinelibrary.wiley.com/doi/10.1002/...
#AIforBiology #ProteinDesign #ClimateTech

2025 Tournament — Align to Innovate

bit.ly

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The Align Foundation @alignbio.bsky.social · Jul 8

4/4
🏆 Why join?:
• $30K in cash prizes
• Free DNA synthesis + wet lab testing
• Leaderboard visibility
• Publication in a special issue of Proteins
• Sponsored conference presentations

2025 Tournament — Align to Innovate

bit.ly

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The Align Foundation @alignbio.bsky.social · Jul 8

3/4
The tournament has two phases:

🔹 *Predictive* (Nov 3 – Dec 23):
Predict PETase sequence properties
🔹 *Generative* (Jan 5 – Apr 10): Design novel sequences to maximize enzyme activity.

Every submission is synthesized and tested.

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The Align Foundation @alignbio.bsky.social · Jul 8

2/4
This is a *lab-validated* benchmark competition for real protein function.

The winner will be determined by experiment. We’ll test:

🔥 Enzymatic activity at high temperatures
🧬 Protein expression
Results go straight to the leaderboard.

🔗 Register by Oct. 17: bit.ly/Tournament25

2025 Tournament — Align to Innovate

bit.ly

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The Align Foundation @alignbio.bsky.social · Jul 8

1/4
🚀 Announcing the 2025 Protein Engineering Tournament.

This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️

#AIforBiology #ClimateTech #ProteinEngineering #OpenScience

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The Align Foundation @alignbio.bsky.social · Jun 18

Read the news release here: alignbio.org/pressrelease...

The Align Foundation @alignbio.bsky.social · Jun 18

🧬 Growth + morphology data across diverse conditions
🔗 Linked to genome references with robust metadata
📊 Built for ML training, benchmarking, reproducibility

🙌 Thx to Jensen Lab for their foundational work that helped enable this platform. Lean more here: alignbio.org/datasets-mic...

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The Align Foundation @alignbio.bsky.social · Jun 18

🚨 Align × ATCC are partnering to build the world’s largest public microbial phenotyping dataset.
✅ 1K strains
✅ 1K conditions
✅ 1M reproducible experiments
✅ Open access
This experimental platform will use high-throughput automation, linked to ATCC’s authenticated genomes.

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The Align Foundation @alignbio.bsky.social · May 16

Align's GROQ-seq platform just turned 1 🎂 it now supports 7 protein function projects across 6 labs worldwide. 300k variants measured per run @ <$0.05 each, and it works. Not theory. Real infrastructure. Open to the world. 🔗 1-year technical report → hubs.la/Q03mSrW_0

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The Align Foundation @alignbio.bsky.social · Apr 28

7/7 🧵Once operational, the method will be openly available through Align’s Data Portal. The community will be able to request new enzyme measurements – and explore our findings. Stay tuned!

The Align Foundation @alignbio.bsky.social · Apr 28

6/7 🧵Read the full, peer-reviewed proposal here—work is already underway! zenodo.org/records/1527...

GROQ-seq Platform Expansion: Design of growth-coupled measurements of Dihydrofolate Reductase in vivo Biochemistry

This proposal details the development of a high-throughput, growth-based assay for measuring enzyme kinetics of Escherichia coli dihydrofolate reductase (DHFR) in vivo using the GROQ-seq platform. By ...

zenodo.org

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The Align Foundation @alignbio.bsky.social · Apr 28

5/7 🧵Align is excited to support expanding this method using our GROQ-seq platform! We’ll generate comprehensive kinetic datasets for thousands of DHFR enzyme variants–measured in vivo.

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The Align Foundation @alignbio.bsky.social · Apr 28

4/7 🧵This builds on her previous work with the metabolic enzyme dihydrofolate reductase (DHFR) in @eLife, showing how growth rates can map enzyme activities inside cells: elifesciences.org/articles/53476

Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme

Changes to cellular protein homeostasis reveal widespread advantageous effects of destabilizing mutations, opening the possibility to switch mutational landscapes back-and-forth from permissive to res...

elifesciences.org

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The Align Foundation @alignbio.bsky.social · Apr 28

3/7 🧵Kimberly Reynolds at UT Southwestern has an exciting new idea: measuring kinetic parameters (kcat, Km) at scale inside living cells using a pooled, growth-based assay.

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The Align Foundation @alignbio.bsky.social · Apr 28

2/7 🧵👇 Plus, enzymes behave differently inside cells than in test tubes. To truly engineer enzymes for real-world applications, we need measurements in the cellular context.

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The Align Foundation @alignbio.bsky.social · Apr 28

Measuring precise enzyme kinetics (like kcat and Km) is key to understanding enzyme function. But these measurements are most often conducted in singleplex in vitro assays - expensive and tough to scale. 1/7 🧵👇

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