C2Bio

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. The most interesting article from the past week is the " Function-preserving watermarking of AI-generated proteins" from Stutz et al. Their approach integrates watermarking into ProteinMPNN in the sequence design step on top of a backbone structure. Although I haven't tested it, this approach suggests generating specific patterns in amino acids used to fit specific backbone structure requirements. In other words, the sequence one can get through SynthIDBio (their methods reported in this paper) is a subset of all the possible sequences that can likely fold into the targeted structure. The sequence itself can be checked for patterns that suggests its origin. Similar methods have been used to watermark LLM generated texts. The ML realization part is simple and effective. Figure 1 in this paper showed in the Sampling phase the ...

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ SurfGraphPro: Integrating Protein Language Models with Geometric Deep Learning On Coarse Protein Surfaces for Binding Site Prediction — This work from my team introduced a new protein representation algorithm that bridges proteins structure model and language model. Our algorithm does not compute amino acid features computationally. Instead, it utilizes PLM embeddings plus protien surface contour coarse-grained graph model to replace the feature engineering. In test application focusing on protein binding interface prediction, we achieved state-of-the-art performance at a much faster (~18x-28x) speed. ★ GitHub - PacesaLab/BindCraft2: Easy to use suite for designing a wide range of protein binder modalities. — Easy to use suite for designing a wide range of protein binder modalities. ★ The Virtual Biotech: A mult...

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ QO‑BRA: A Quantum Operator-Based Autoencoder for De Novo Molecular Design — We introduce a variational quantum autoencoder tailored for de novo molecular design, named QO-BRA (Quantum Operator-Based Real Amplitude autoencoder). QO-BRA leverages quantum circuits for real-amplitude encoding and the SWAP test to estimate reconstruction and latent-space regularization errors during back-propagation. Adjoint encoder and decoder operators enable unitary transformations and a generative process that ensures accurate reconstruction, as well as the novelty, uniqueness, and validity of the generated samples. We showcase the capabilities of QO-BRA as applied to the de novo design of Ca2+-, Mg2+-, and Zn2+-binding metalloproteins after training the generative model with a modest data set. ★ The quantum ensemble variational opti...

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-enhanced adaptive virtual screening of large libraries for ligand discovery — Ultralarge virtual screenings (ULVSs) evaluate billions of molecules for drug discovery but face cost, flexibility and scalability limits. ★ AlphaGenome Atlas: in silico mutagenesis of the entire human genome improves prioritization and interpretation of non-coding variants — This is a very interesting work from AlphaGenome Atlas Team/Google, where the authors generated all possible single nucleotide variations (in silico saturation mutagenesis (ISM)) and many indels. They then demonstrated potential application of their model in rare diseases related to non-coding mutations. ★ A landscape of sequence variants in 51 commercial antibody therapeutics — Sequence variants (SVs), unintended amino acid substitutions, represent a quality ...

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ Roche pens $2.5 billion pact for Hanmi's muscle-conserving obesity drug — Roche has entered a $2.5 billion deal to license Hanmi's early-stage muscle-conserving obesity asset, betting on a novel approach to weight loss that preserves muscle mass. (morning-news-biotech, 2026-08-26) ★ CRISPR Therapeutics reports Durability of Effects of CTX310 gene therapy at ESC Congress — CRISPR Therapeutics presented late-breaking abstract on CTX310, a CRISPR-Cas9 gene therapy targeting ANGPTL3 for familial hypercholesterolemia, with clinical update planned for August. (morning-news-biotech, 2026-08-26) ★ Ultrafast and reference-free sequence discovery in single-cell data — Abstract Knowledge of RNA sequences, expression, splicing, isoforms, structure and modifications is central for understanding and targeting cellu...

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...