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Quantifying uncertainty in Protein Representations Across Models and Task 1. This work introduces the Random Neighbor Score (RNS), a model-agnostic metric to quantify the uncertainty of protein embeddings produced by language models, enabling users to assess the biological

🌞 Take Your Lenses Off—Seriously You don’t need them to check your phone or stir eggs. Overuse weakens your eyes. Let them adapt. Wear glasses for distance if you must—but up close? Go RAW. And stop wearing plastic contacts soaked in PFAS. I did for 10 years. Never again.

Predicting gene expression from DNA sequence using deep learning models nature.com/articles/s4157… (read free: rdcu.be/elSrE) 🧬🖥️🧪

How can we align protein language models with functional objectives to generate proteins with enhanced properties beyond what natural evolution has explored?bioRxiv "Functional alignment of protein language models via reinforcement learning" 1. RLXF (Reinforcement

How can we efficiently design biological sequences that optimize multiple competing objectives simultaneously?arXiv.org Duke University "Multi-Objective-Guided Discrete Flow Matching for Controllable Biological Sequence Design" • The paper introduces Multi-Objective-Guided Discrete Flow

End to end differentiable protein structure alignment! Jeanne Trinquier Sergey Ovchinnikov

biorxiv.org/content/10.110…

Steered generation for protein optimization: On datasets with ~10^2 measurements, steering a discrete diffusion model outperforms RL on a protein language model for generating improved variants. Jason Yang Wenda Chu Frances Arnold Yisong Yue

Combinatorial mutagenesis of N-terminal sequences reveals unexpected and expanded stability determinants of the Escherichia coli ... biorxiv.org/content/10.110… #biorxiv_synbio

Cable bacteria were discovered more than a decade ago, but I haven't seen a deep article on them yet. Last year, I visited Aarhus University in Denmark (where they were discovered) to learn more about them. So let me break down why I think these microbes are so fascinating...

Young scientists: Hang in there. The world needs you. I'm working on a solution

PhDs make up 37% of R&D personnel and contribute to 10–30% of U.S. GDP. For over half a century, 85% of U.S. economic growth has stemmed from advances in science and technology. The U.S. risks a decline in living standards as anti-intellectualism takes hold Source: ChatGPT4o

🧪🪐 Big week for ancient nitrogen! Checkout these three papers from our lab: 1️⃣ Rucker et al.: Engineered ancient nitrogenases to trace 2 billion years of biosignature reliability ➡️biorxiv.org/content/10.110…

1/ This graph from Jon Bruner tells an important story: America's current dominance in science only began after the mid-1930s, when persecuted scientists began fleeing universities in Germany and then elsewhere in occupied Europe.

Full study here: nature.com/articles/s4159…

"We aim to understand & reverse the underlying mechanisms of aging to treat a range of diseases & injuries...The loss of funding halts ongoing experiments that cannot simply be restarted," geneticist David Sinclair told BBC News (UK) 🧵 bbc.com/news/articles/…

Most proteins are left-handed, but scientists have found an ancient molecule that works in both mirror-image forms go.nature.com/3Hfax8W

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.

Artificial Intelligence And First Principle Methods In Protein Redesign: A Marriage Of Convenience? biorxiv.org/content/10.110…

Making deep mutational scanning accessible: a cost-efficient approach to construct barcoded libraries for genes of any length biorxiv.org/content/10.110… #biorxiv_synbio