Hoyin Chu
@hoyinchu.bsky.social
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PhD student at MSKCC Lareau Lab interested in computational protein design for cancer therapies
reposted by
Hoyin Chu
Sherry Nyeo
17 days ago
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 🧬
add a skeleton here at some point
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Hoyin Chu
Caleb Lareau
17 days 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...
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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...
https://www.nature.com/articles/s41586-025-10020-2#citeas
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Hoyin Chu
Roland Dunbrack 🏳️🌈
about 1 month ago
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
2 months ago
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—
add a skeleton here at some point
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reposted by
Hoyin Chu
Martin Pacesa
6 months ago
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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reposted by
Hoyin Chu
Caleb Lareau
7 months ago
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/
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reposted by
Hoyin Chu
7 months ago
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 🧵
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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...
https://doi.org/10.1101/2025.07.05.662870
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Hoyin Chu
Damon Runyon Cancer Research Foundation
9 months ago
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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Hoyin Chu
Nature Methods
9 months ago
And read the News & Views highlighting this work, here:
www.nature.com/articles/s41...
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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.
https://www.nature.com/articles/s41592-025-02657-8
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reposted by
Hoyin Chu
Martin Steinegger 🇺🇦
10 months ago
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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reposted by
Hoyin Chu
Caleb Lareau
11 months ago
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
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reposted by
Hoyin Chu
Caleb Lareau
11 months ago
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!
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Hoyin Chu
Diego del Alamo
about 1 year ago
Chai-1, the open source AF3 clone, is now available with an Apache 2 license
github.com/chaidiscover...
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Hoyin Chu
Simon Mathis
about 1 year ago
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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