C2Bio

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ Human genetics across levels of biological organization — Genetic variation influences human physiology across biological scales from molecules to cells, tissues, organs and the whole organism. ★ From static structures to dynamic landscapes: cryo-EM redefines RNA biology — Recent advances in cryoEM are now transforming this landscape by enabling the visualization of RNA molecules across a broad spectrum of functionally relevant conformations at near atomic resolution (arxiv-digest, 2026-09-01) ★ Operationalizing open-ended biological discovery across single-cell representations — Projection into unseen datasets then evaluates their generalizability and phenotype association, providing a scalable screen for candidates that warrant prospective validation (arxiv-digest, 2026-09-01) ★ Learning Task-Specific Anti...

It have been quite a busy time since a recent family visiting trip. I only get a chance to read a few articles in the past week. Here is one that seems interesting. ★ Megalodon: Efficient LLM Pretraining and Inference with Unlimited Context Length — The quadratic complexity and weak length extrapolation of Transformers limits their ability to scale to long sequences, and while sub-quadratic solutions like linear attention and state space models exist, they empirically underperform Transformers in pretraining efficiency and downstream task accuracy. Another interesting article on synthetic biology, where researchers created a synthetic cell that puts user closer to building life from scratch. Here is a comment article from Science .

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ ViMax: Agentic Video Generation — Long-form video generation requires systematic narrative planning and visual consistency that current short-clip methods cannot provide. ★ Decoding intercellular activities for more than 1,000 secreted proteins ★ A light-controlled tetanus neurotoxin enables rapid and reversible synaptic inhibition in vivo ★ Alignment with experimental data improves protein generative modeling ★ Efficient evidence-based genome annotation with EviAnn — Machine-learning-based ab initio gene finders have long been central to eukaryotic genome annotation, largely because gene expression data were historically expensive and limited. ★ ClairS: a deep-learning method for long-read tumor–normal pair somatic small variant calling — Somatic variant discovery in tumors is crucial for clinical ana...

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ CAFE: A Co-folding Approach for Fragment Exploration of Allosteric and Cryptic Binding Sites — Co-folding models hold immense potential for allosteric drug discovery, but have been severely hampered by their systematic bias toward orthosteric ligand binding. ★ Decoding cancer circulating transcriptomic signatures with language models — Current liquid biopsy methods for multi-cancer detection using plasma cell-free RNA (cfRNA, short RNA fragments circulating in blood that can reflect disease states) typically rely on gene annotations, which can overlook signals from unannotated or repetitive genomic regions. ★ An expanded codebook of human transcription factor DNA-binding specificity — Abstract Gene expression is regulated by transcription factors (TFs), which recognize specific DNA sequence motifs. ★ Generat...

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation ★ Miniaturizing and modifying natural proteins with Raygun ★ Cellular and signalling mechanisms that regulate the blood–brain barrier — The blood-brain barrier (BBB) is a unique specialization of central nervous system (CNS) capillary endothelial cells that controls molecular traffic between the blood and the brain. ★ Structure-free, site-resolved contrastive learningextends small-molecule discovery beyond the reachof structure-based modeling — Virtual screening asks which molecules, among an enormous space of drug-like chemistry, are worth synthesizing and testing against a protein target. ★ Structure and evolution-guided design of minimal RNA-guided nucleases — The design of RNA-guid...

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ AI-redesigned starting points and outcomes enhance protein evolution — Abstract Engineered or laboratory-evolved proteins often have suboptimal stability, activity or specificity. ★ Distributional regression using generalized additive models for location, scale and shape ★ High-throughput machine learning-aided antibody discovery for cell surface antigens — Machine learning (ML) has the potential to revolutionize antibody design and selection, but its success depends on access to well-curated datasets of antibody-antigen interactions.

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ Biotech's digital twin dilemma — Nature Biotechnology explores how digital twins — from virtual patients to simulated cells and organs-on-chips — are forecasting disease and guiding drug development. ★ Universal cell embedding provides a foundation model for cell biology — A self-supervised single-cell foundation model (>650M-parameter, 33-layer transformer) trained on 36M cells across eight species, producing a 1,280-dimensional universal embedding that enables zero-shot cross-species cell-type mapping without fine-tuning or annotation. ★ De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging — Fluorescent proteins and small-molecule dyes offer complementary advantages for biological imaging: proteins are amenable to genetic tagging, whereas dyes pr...