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Hoyin Chu

@hoyinchu.bsky.social
57 followers 169 following 0 posts

PhD student at MSKCC Lareau Lab interested in computational protein design for cancer therapies

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Reposted by Hoyin Chu
Rita Strack @ritastrack.bsky.social · 09/09/2026
Here is a link to the main paper. The link embedded goes to the Research Briefing. www.nature.com/articles/s41...
nature.com
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...
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Reposted by Hoyin Chu
Caleb Lareau @caleblareau.bsky.social · 09/09/2026
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-
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17/03/2026
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
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Reposted by Hoyin Chu
Kieran Didi @kdidi.bsky.social · 17/03/2026
📢 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
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EMBL-EBI @ebi.embl.org · 17/02/2026
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...
ebi.ac.uk
AlphaFold Database welcomes community datasets
Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities
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Sherry Nyeo @sherrynyeo.bsky.social · 28/01/2026
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 🧬
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Reposted by Hoyin Chu
Caleb Lareau @caleblareau.bsky.social · 28/01/2026
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...
nature.com
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...
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Reposted by Hoyin Chu
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 03/01/2026
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...
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Reposted by Hoyin Chu
Caleb Lareau @caleblareau.bsky.social · 14/12/2025
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—
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Reposted by Hoyin Chu
Martin Pacesa @martinpacesa.bsky.social · 27/08/2025
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...
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Caleb Lareau @caleblareau.bsky.social · 22/07/2025
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/
the treasure trove of all sequencing datasets
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taykhoomdalal.bsky.social @taykhoomdalal.bsky.social · 15/07/2025
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 🧵
doi.org
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...
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Reposted by Hoyin Chu
Damon Runyon Cancer Research Foundation @damonrunyon.org · 04/06/2025
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!
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Reposted by Hoyin Chu
Nature Methods @natmethods.nature.com · 27/05/2025
And read the News & Views highlighting this work, here: www.nature.com/articles/s41...
nature.com
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.
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Reposted by Hoyin Chu
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 27/04/2025
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...
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Caleb Lareau @caleblareau.bsky.social · 14/03/2025
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
media.tenor.com
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 .
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Reposted by Hoyin Chu
Caleb Lareau @caleblareau.bsky.social · 08/03/2025
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!
Lareau Lab at Cycle for Survival 2025
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Diego del Alamo @delalamo.xyz · 27/11/2024
Chai-1, the open source AF3 clone, is now available with an Apache 2 license github.com/chaidiscover...
Chai-1 is released under an Apache 2.0 License, which means it can be used for both academic and commerical purposes, including for drug discovery.
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Reposted by Hoyin Chu
Simon Mathis @simonmathis.bsky.social · 25/11/2024
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`
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