The Align Foundation

Designed to be scalable and with closed-loop experimentation, Tesseract will power AI to map sequence → function, predict gene transfer success, and assign function to unknown genes from rich phenotypic signatures.

Big thanks to all the collaborators and reviewers who helped shape this proposal!

In partnership with @pioneerlabs.bsky.social, we’re proposing Tesseract: a large-scale, open microbial phenomics dataset to functionally annotate microbial genomes at scale. 🧬🤖
✅5M diverse genes x 50 host strains × 100 conditions
🔗 Read the proposal:https://zenodo.org/records/17990299

5/5
We understand this may cause inconvenience, and we appreciate your patience and continued support as we work to deliver a high-quality, impactful Tournament. For any questions or concerns, please contact us at tournament@alignbio.org

4/5
The new timeline is as follows:

-Registration deadline: Nov. 14th 2025

Predictive phase:
-Zero-shot track: Dec. 1st 2025 to Jan. 16th 2026
-Supervised track: Jan. 26th to Feb. 20th 2026

Generative phase:
-Round-1: Mar. 9th to Apr. 3rd 2026
-Round-2: Jul. 20th to Aug. 14th 2026

3/5
The Tournament will establish the first-of-its-kind benchmark for predictive and generative AI/ML models in engineering PETases. We remain committed to enabling real-world, transparent, and accessible benchmarking competitions, and this adjustment is to uphold that commitment.

2/5
This additional time will allow us to:
•Complete the generation of a high-quality training dataset 🧬🧪
•Secure the best sponsorships to expand access to the Tournament 🖥️💪
•Register more participants 👥🚀

1/5
To ensure the highest impact and participation, we are adjusting the timeline of the Protein Engineering Tournament. The Tournament will now begin on December 1st, 2025.

🧫 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

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

📣 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 👇

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.

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...

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

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.

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...

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

🔗 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

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

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.

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

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

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

🧬 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...

🚨 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.

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

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!

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

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.

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...

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

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.