Hoyin Chu
@hoyinchu.bsky.social
PhD student at MSKCC Lareau Lab interested in computational protein design for cancer therapies
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`