@youngsuko9.bsky.social
PhD student at UCSD, biochemistry and molecular biophysics, working on bio+ml
Reposted
We’re getting more and more papers on de novo protein design, but I still don’t really know what it means
What’s your definition of de novo design?
What’s your definition of de novo design?
January 4, 2025 at 10:50 PM
We’re getting more and more papers on de novo protein design, but I still don’t really know what it means
What’s your definition of de novo design?
What’s your definition of de novo design?
Reposted
We've updated the Raygun preprint with additional validations (more fluorescence assays, biotin ligase reengineering, EGF optimization etc.) Take a look!
Here's the preprint: www.biorxiv.org/content/10.1...
Here's the preprint: www.biorxiv.org/content/10.1...
Miniaturizing, Modifying, and Magnifying Nature's Proteins with Raygun
Proteins have evolved over billions of years through extensive and coordinated substitutions, insertions and deletions (indels). Computational protein design cannot yet fully mimic nature's ability to...
www.biorxiv.org
March 19, 2025 at 4:17 PM
We've updated the Raygun preprint with additional validations (more fluorescence assays, biotin ligase reengineering, EGF optimization etc.) Take a look!
Here's the preprint: www.biorxiv.org/content/10.1...
Here's the preprint: www.biorxiv.org/content/10.1...
Reposted
Congratulations to @youngsuko9.bsky.social on their top-10 placement in Adaptyv Bio's EGFR-binder competition!
It's an elegant pipeline-- using our protein-design method Raygun to expand and modify the template (EGF), then filtering with ProTrek.
foundry.adaptyvbio.com/competition
1/
It's an elegant pipeline-- using our protein-design method Raygun to expand and modify the template (EGF), then filtering with ProTrek.
foundry.adaptyvbio.com/competition
1/
Adaptyv Foundry
foundry.adaptyvbio.com
December 8, 2024 at 2:46 PM
Congratulations to @youngsuko9.bsky.social on their top-10 placement in Adaptyv Bio's EGFR-binder competition!
It's an elegant pipeline-- using our protein-design method Raygun to expand and modify the template (EGF), then filtering with ProTrek.
foundry.adaptyvbio.com/competition
1/
It's an elegant pipeline-- using our protein-design method Raygun to expand and modify the template (EGF), then filtering with ProTrek.
foundry.adaptyvbio.com/competition
1/
Reposted
This is really horrific. These single cell reference atlases are widely used as is to train all kinds of models! This is one of the reasons I've constantly harping about uniform reprocessing & extremely careful QC of large atlases. 1/
scRNA-seq has revolutionized biology, but it’s not without challenges. We uncovered significant quality issues in widely used reference cell atlases like the Human Cell Atlas and Tabula Sapiens. Up to 85% of cells in some datasets are low-quality or misidentified!
2/8
2/8
December 4, 2024 at 7:06 AM
This is really horrific. These single cell reference atlases are widely used as is to train all kinds of models! This is one of the reasons I've constantly harping about uniform reprocessing & extremely careful QC of large atlases. 1/
Reposted
Super excited to share our review on genomic deep learning models for non-coding variant effect prediction, with Ayesha Bajwa and Nilah Ioannidis. We’d like this review to be a useful resource, and welcome any feedback, comments, or questions! 1/4
arxiv.org/abs/2411.11158
arxiv.org/abs/2411.11158
Leveraging genomic deep learning models for non-coding variant effect prediction
The majority of genetic variants identified in genome-wide association studies of complex traits are non-coding, and characterizing their function remains an important challenge in human genetics. Gen...
arxiv.org
November 20, 2024 at 1:31 AM
Super excited to share our review on genomic deep learning models for non-coding variant effect prediction, with Ayesha Bajwa and Nilah Ioannidis. We’d like this review to be a useful resource, and welcome any feedback, comments, or questions! 1/4
arxiv.org/abs/2411.11158
arxiv.org/abs/2411.11158
Reposted
Hello 🦋 #protein / #microbio / #BioML community! We are excited to release Gaia🌎, a context-aware protein search tool, extending protein search and discovery capabilities beyond sequence and structure, to include *genomic context*. Search your favorite protein sequences with on gaia.tatta.bio
November 19, 2024 at 3:07 PM
Hello 🦋 #protein / #microbio / #BioML community! We are excited to release Gaia🌎, a context-aware protein search tool, extending protein search and discovery capabilities beyond sequence and structure, to include *genomic context*. Search your favorite protein sequences with on gaia.tatta.bio