Here is a link to the main paper. The link embedded goes to the Research Briefing. www.nature.com/articles/s41...

Sequence and structural determinants of efficacious de novo chimaeric antigen receptors - Nature Biomedical Engineering

A generative protein design workflow addresses important challenges with de novo protein engineering of chimaeric antigen receptors (CARs) to improve targeting of proteins important in cancer and crea...

nature.com

Rita Strack@ritastrack.bsky.social · last mo.

Even though CAR T therapies are already successful, there is still a LOT that can be done in CAR design for safer, more effective therapies.

Out today! I could not be more proud of @arthurwchow.bsky.social @hoyinchu.bsky.social and Betty Li for their fearless efforts to understand how to use diffusion models to enable a new generation of cell therapies! read more here-

Nature Biomedical Engineering@natbiomedeng.nature.com · last mo.

Sequence and structural determinants of efficacious de novo chimaeric antigen receptors

AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk

📢 We’re launching Proteina-Complexa — and after the Jensen keynote mention, we definitely had to post this thread now ;) Atomistic binder design with generative pretraining + test-time compute, plus large-scale wet-lab validation. Project page: research.nvidia.com/labs/genair/... 🧵 1/n

The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities. This includes rich datasets for microbes, viruses & parasites associated with tropical diseases. Explore the new datasets in the AlphaFold Database. www.ebi.ac.uk/about/news/u...

AlphaFold Database welcomes community datasets

Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities

ebi.ac.uk

First paper from grad school & first first-author! It's been a huge team effort, and it was lovely working with everyone. Check out Caleb’s thread summarizing how we used discarded WGS reads from biobanks to study EBV at population scale 🧬

Caleb Lareau@caleblareau.bsky.social · 9mo ago

Today in @nature.com, we describe how discarded reads in biobank-scale WGS can help resolve the genetic predictors and consequences of Epstein-Barr Virus (EBV) infection. Wonderful working with @ryandhindsa.bsky.social @sherrynyeo.bsky.social @erinmayc.bsky.social www.nature.com/articles/s41...

Today in @nature.com, we describe how discarded reads in biobank-scale WGS can help resolve the genetic predictors and consequences of Epstein-Barr Virus (EBV) infection. Wonderful working with @ryandhindsa.bsky.social @sherrynyeo.bsky.social @erinmayc.bsky.social www.nature.com/articles/s41...

Population-scale sequencing resolves determinants of persistent EBV DNA - Nature

Population-scale WGS reveals genetic determinants of persistent EBV DNA, linking immune regulation—especially antigen processing and MHC class II variation—to EBV persistence and heterogeneous di...

nature.com

I updated ipSAE code to handle Boltz2 files properly -- non-standard chainIDs/order, PDB input as well as mmCIF; other pull requests. github.com/DunbrackLab/.... Also updated preprint--fixed Latin grammar error in title - very embarrassing and added new figure. www.biorxiv.org/content/10.1...

Roland Dunbrack 🏳️‍🌈@rolanddunbrack.bsky.social · last yr.

pip install ipsae from www.linkedin.com/in/ullah-sam... www.youtube.com/watch?v=A5ph... PyPI pypi.org/project/ipsae/ His github fork github.com/ullahsamee/I... My github github.com/DunbrackLab/... Paper www.biorxiv.org/content/10.1... For designed protein binders www.biorxiv.org/content/10.1...

We are very excited to share the first preprint of a new direction for our group. Led by the fearless duo of @arthurwchow.bsky.social and @hoyinchu.bsky.social, our foray into computational protein design—

bioRxiv Bioengineering@biorxiv-bioeng.bsky.social · 10mo ago

Sequence and structural determinants of efficacious de novo chimeric antigen receptors https://www.biorxiv.org/content/10.64898/2025.12.12.694033v1

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1... Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/

We are excited to introduce mRNABench, a comprehensive benchmarking suite that we used to evaluate the representational capabilities of 18 families of nucleotide foundation models on mature mRNA specific tasks. Paper: doi.org/10.1101/2025... Code: github.com/morrislab/mR... A 🧵

mRNABench: A curated benchmark for mature mRNA property and function prediction

Messenger RNA (mRNA) is central in gene expression, and its half-life, localization, and translation efficiency drive phenotypic diversity in eukaryotic cells. While supervised learning has widely bee...

doi.org

Congratulations to the newest Damon Runyon Quantitative Biology Fellows, five exceptional early-career scientists who are using state-of-the-art computational tools to bring cancer biology into high resolution!

And read the News & Views highlighting this work, here: www.nature.com/articles/s41...

Methods for multiplexing single-cell multi-omics - Nature Methods

Advances in single-cell multi-omics assays that co-detect two or more modalities enable a new frontier in resolving cellular heterogeneity and gene regulation.

nature.com

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...

Trying a slightly new model (for us at least) of #openscience. With @ronanchaligne.bsky.social and @karolisk.bsky.social, we pitted 10x Genomics Chromium GEM-X against Illumina PIPseq V head-to-head to understand these two platforms for single-cell genomics. Some thoughts off the bleeding edge: /1

a baby is eating a piece of food while sitting on the ground .

ALT: a baby is eating a piece of food while sitting on the ground .

media.tenor.com

Feeling invigorated after hearing from patients and their families while riding with @cycleforsurvival.bsky.social. I am SO grateful to work with this talented and motivating team at @mskcancercenter.bsky.social! Thank you to everyone who participated in and donated to this outstanding cause!

Chai-1, the open source AF3 clone, is now available with an Apache 2 license github.com/chaidiscover...

A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely. I use it a lot for my protein design workflows together with @biotite.bsky.social. Just `pip install pymol-remote`