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The Align Foundation

@alignbio.bsky.social
139 followers 94 following 59 posts

Improving life science with programmable experiments. 🧬 🤖 Home of the Protein Engineering Tournament & Open Datasets Initiative.

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The Align Foundation @alignbio.bsky.social · 31/03/2026
This release was made possible by a strong cross-team effort, with key contributions from @erika-alden.bsky.social, Anjali Chadha, Dave Ross’s team at National Institute of Standards and Technology (NIST) and the DAMP Lab at @bostonu.bsky.social. 🔗 Access the dataset: data.alignbio.org
data.alignbio.org
Accelerate scientific discovery with reproducible, shareable, and scalable biological datasets. Access cutting-edge research data or compete in our tournaments.
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The Align Foundation @alignbio.bsky.social · 31/03/2026
TEV protease is a cornerstone tool in biotechnology, known for its high substrate specificity, and this dataset provides a rich resource for enzyme engineering and ML-driven protein design.
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The Align Foundation @alignbio.bsky.social · 31/03/2026
To our knowledge, this is the largest mutational dataset on TEV protease to date. Notably, no comprehensive deep mutational scanning study across the full protein has been reported in over three decades, leaving key aspects of its functional landscape unexplored.
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The Align Foundation @alignbio.bsky.social · 31/03/2026
📢 Data Release Tuesday: Align TEV Protease Dataset 📊 We’re expanding the The Align Foundation data ecosystem again with ~30,000 high-quality GROQ-seq data points capturing TEV protease sequence–function relationships at scale.
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The Align Foundation @alignbio.bsky.social · 24/03/2026
To our knowledge, this is the largest mutational dataset on T7 RNA polymerase to date! 🔗 Access the dataset on the Align Data Portal: hubs.la/Q04802KK0 #OpenScience #SyntheticBiology #ProteinEngineering #BioAI #MachineLearning #AlignData #GROQSEQ #RNApolymerase
hubs.la
Accelerate scientific discovery with reproducible, shareable, and scalable biological datasets. Access cutting-edge research data or compete in our tournaments.
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The Align Foundation @alignbio.bsky.social · 24/03/2026
📢 Public Data Release: Align T7 RNA Polymerase Dataset. 📊The data keeps coming at Align! We’re excited to release our T7 RNA polymerase dataset, adding ~35,000 unique GROQ-seq data points to the growing Align data ecosystem, capturing sequence–function relationships across variants at scale.
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The Align Foundation @alignbio.bsky.social · 17/03/2026
🔗 Access the dataset on the Align Data Portal: hubs.la/Q0470NBn0 👏 Huge thanks to our collaborators and everyone involved in making this dataset possible.
hubs.la
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The Align Foundation @alignbio.bsky.social · 17/03/2026
This is the result of a fantastic collaboration with David Ross's Lab at NIST, @doelsnitz.bsky.social at @harvard.edu and the DAMP Lab. We’re thrilled to make the data publicly accessible to support the broader research community.
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The Align Foundation @alignbio.bsky.social · 17/03/2026
This dataset was generated using the GROQ-seq platform, enabling large-scale quantitative mapping of TF binding landscapes. This dataset demonstrates strong cross-site reproducibility, with highly consistent measurements generated independently at NIST and the DAMP Lab at @bostonu.bsky.social.
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The Align Foundation @alignbio.bsky.social · 17/03/2026
📊 100,000+ data points measuring transcription factor–DNA interactions across three regulators (LacI, RamR, VanR).
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The Align Foundation @alignbio.bsky.social · 17/03/2026
🚀 Public Data Release: GROQ-seq Transcription Factor Dataset We’re excited to announce the public release of The Align Foundation's first GROQ-seq dataset, one of the largest high-resolution transcription factor datasets of its kind.
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The Align Foundation @alignbio.bsky.social · 24/02/2026
See our press release here: www.businesswire.com/news/home/20...
businesswire.com
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The Align Foundation @alignbio.bsky.social · 24/02/2026
Align and Google DeepMind are partnering to build AI-ready datasets & evaluations for the future of predictive #AMR biology. Researchers worldwide can submit concepts through March 31 with roadmapping workshops coming to North America + APAC this spring. 🔗 docs.google.com/forms/d/e/1F...
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The Align Foundation @alignbio.bsky.social · 15/01/2026
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!
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The Align Foundation @alignbio.bsky.social · 15/01/2026
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
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The Align Foundation @alignbio.bsky.social · 15/10/2025
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
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The Align Foundation @alignbio.bsky.social · 15/10/2025
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
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The Align Foundation @alignbio.bsky.social · 15/10/2025
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.
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The Align Foundation @alignbio.bsky.social · 15/10/2025
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 👥🚀
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The Align Foundation @alignbio.bsky.social · 15/10/2025
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.
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Reposted by The Align Foundation
scverse @scverse.bsky.social · 26/08/2025
🧫 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
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The Align Foundation @alignbio.bsky.social · 21/08/2025
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 · 21/08/2025
📣 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 · 19/08/2025
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 · 13/08/2025
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 · 21/07/2025
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
alignbio.org
Careers — Align to Innovate
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The Align Foundation @alignbio.bsky.social · 21/07/2025
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 · 21/07/2025
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...
doi.org
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...
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The Align Foundation @alignbio.bsky.social · 21/07/2025
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 · 08/07/2025
🔗 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
bit.ly
2025 Tournament — Align to Innovate
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The Align Foundation @alignbio.bsky.social · 08/07/2025
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
bit.ly
2025 Tournament — Align to Innovate
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The Align Foundation @alignbio.bsky.social · 08/07/2025
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 · 08/07/2025
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
bit.ly
2025 Tournament — Align to Innovate
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The Align Foundation @alignbio.bsky.social · 08/07/2025
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 · 18/06/2025
Read the news release here: alignbio.org/pressrelease...
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The Align Foundation @alignbio.bsky.social · 18/06/2025
🧬 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 · 18/06/2025
🚨 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 · 16/05/2025
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 · 28/04/2025
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!
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The Align Foundation @alignbio.bsky.social · 28/04/2025
6/7 🧵Read the full, peer-reviewed proposal here—work is already underway! zenodo.org/records/1527...
zenodo.org
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 ...
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The Align Foundation @alignbio.bsky.social · 28/04/2025
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 · 28/04/2025
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
elifesciences.org
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...
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The Align Foundation @alignbio.bsky.social · 28/04/2025
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 · 28/04/2025
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 · 28/04/2025
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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The Align Foundation @alignbio.bsky.social · 17/04/2025
Q1 at Align = ✅ Team doubled ✅ 65k GROQ-seq datapoints ✅ Genotype-by-Phenotype platform ✅ Global conf. circuit ✅ Tournament prep underway Get the full download → hubs.la/Q03hT_V60 #ProteinEngineering #AIxBiology #SynBio #OpenScience
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The Align Foundation @alignbio.bsky.social · 13/03/2025
🚀 New proposal from Align! The experimental platform aims to standardize #microbial #phenotyping & support predictive modeling. 🦠 Capturing data across 1k strains & 1k conditions; using BacterAI; generating high-quality datasets for ML @jensen_lab
zenodo.org
Genotype to Phenotype: Design of an Extensible Experimental Platform for Characterizing Microbes
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The Align Foundation @alignbio.bsky.social · 19/02/2025
We are gearing up for our 2025 Protein Engineering Tournament! 🧬 🏆 Have ideas on what the next community benchmarking competition for protein design and engineering should look like? 💡 💪 Join our organizing committee here: buff.ly/3ELqfrb
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The Align Foundation @alignbio.bsky.social · 09/01/2025
🚀 Collaborative, AI-Ready datasets would revolutionize life sciences and catalyze progress. Government funding plays a critical role in making this a reality. 📖 Read our policy memo here:
buff.ly
Kickstarting Collaborative, AI-Ready Datasets in the Life Sciences
The government should fund collaborative roadmapping, certification, collection, and sharing of large, high-quality datasets in life science.
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The Align Foundation @alignbio.bsky.social · 03/12/2024
💻 Curious? Want to help? Want to advocate for data in YOUR favorite organism? 😜 Let’s connect. We’re building the future of protein expression—one dataset at a time. Reach out via social or contact@alignbio.org
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