Hoyin Chu
@hoyinchu.bsky.social
PhD student at MSKCC Lareau Lab interested in computational protein design for cancer therapies
Reposted by Hoyin Chu
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—
Sequence and structural determinants of efficacious de novo chimeric antigen receptors https://www.biorxiv.org/content/10.64898/2025.12.12.694033v1
December 14, 2025 at 10:38 AM
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—
Reposted by Hoyin Chu
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...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
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...
www.nature.com/articles/s41...
Reposted by Hoyin Chu
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/
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/
July 22, 2025 at 9:59 PM
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/
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/
Reposted by Hoyin Chu
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 🧵
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
July 15, 2025 at 7:09 PM
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 🧵
Paper: doi.org/10.1101/2025...
Code: github.com/morrislab/mR...
A 🧵
Reposted by Hoyin Chu
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!
June 4, 2025 at 7:57 PM
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!
Reposted by Hoyin Chu
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...
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
April 27, 2025 at 12:13 AM
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...
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
Reposted by Hoyin Chu
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
March 14, 2025 at 1:29 PM
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
Reposted by Hoyin Chu
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!
March 8, 2025 at 4:49 PM
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!
Reposted by Hoyin Chu
Chai-1, the open source AF3 clone, is now available with an Apache 2 license github.com/chaidiscover...
November 27, 2024 at 4:58 PM
Chai-1, the open source AF3 clone, is now available with an Apache 2 license github.com/chaidiscover...
Reposted by Hoyin Chu
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`
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
November 25, 2024 at 2:50 PM
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`
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`