Yufeng Shen
@yshen.bsky.social
Computational genomics and human genetics. Associate Professor @ Columbia University
Lab: http://www.columbia.edu/~ys2411/
Lab: http://www.columbia.edu/~ys2411/
Reposted by Yufeng Shen
📢 Our Dept. of Systems Biology at Columbia University has an open tenure-track Assistant Professor position in the broad area of quantitative biology. Come join our awesome department in NYC! Please circulate.
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social
November 15, 2025 at 4:02 AM
📢 Our Dept. of Systems Biology at Columbia University has an open tenure-track Assistant Professor position in the broad area of quantitative biology. Come join our awesome department in NYC! Please circulate.
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social
Reposted by Yufeng Shen
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
Reposted by Yufeng Shen
How can we better understand pathogenic variants in intrinsically disordered regions (IDRs)? How do models such as AlphaMissense and ESM1b predict pathogenicity, when these regions typically exhibit lower genomic conservation than ordered regions? Read more:
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Molecular dynamics simulations of intrinsically disordered protein regions enable biophysical interpretation of variant effect predictors
Predictive models for missense variant pathogenicity offer little functional interpretation for intrinsically disordered regions, since they rely on conservation and coevolution across homologous sequ...
doi.org
May 13, 2025 at 2:15 PM
How can we better understand pathogenic variants in intrinsically disordered regions (IDRs)? How do models such as AlphaMissense and ESM1b predict pathogenicity, when these regions typically exhibit lower genomic conservation than ordered regions? Read more:
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Reposted by Yufeng Shen
Why do large protein language models like ESM2-15B underperform compared to medium-sized ones like ESM2-650M in predicting mutation effects? 🤔
We dive into this issue in our new preprint—bringing insights into model scaling on mutation effect prediction. 🧬📉
We dive into this issue in our new preprint—bringing insights into model scaling on mutation effect prediction. 🧬📉
April 29, 2025 at 5:54 PM
Why do large protein language models like ESM2-15B underperform compared to medium-sized ones like ESM2-650M in predicting mutation effects? 🤔
We dive into this issue in our new preprint—bringing insights into model scaling on mutation effect prediction. 🧬📉
We dive into this issue in our new preprint—bringing insights into model scaling on mutation effect prediction. 🧬📉
Reposted by Yufeng Shen
We have updated our protein lanuage model trained on structure dynamics. Our new models show significant better zero-shot performance on mutation effects of designed and viral proteins compared to ESM2. check the new preprint here: www.biorxiv.org/content/10.1...
April 17, 2025 at 2:40 PM
We have updated our protein lanuage model trained on structure dynamics. Our new models show significant better zero-shot performance on mutation effects of designed and viral proteins compared to ESM2. check the new preprint here: www.biorxiv.org/content/10.1...
Reposted by Yufeng Shen
Why do association studies prioritize trait-specific variants???
A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
December 17, 2024 at 7:04 AM
Why do association studies prioritize trait-specific variants???
A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
A quick thread about the importance of thinking about all traits at once 👇 1/6 (🧪🧬)
Reposted by Yufeng Shen
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 6, 2024 at 8:39 AM
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Yufeng Shen
Most of the talks from our Oct meeting are now online, with a few more to come: www.precisionmedicine.columbia.edu/videos
December 5, 2024 at 3:47 PM
Most of the talks from our Oct meeting are now online, with a few more to come: www.precisionmedicine.columbia.edu/videos
Reposted by Yufeng Shen
The final program for the conference is now up: events.columbia.edu/cal/event/ev...
September 28, 2024 at 6:30 PM
The final program for the conference is now up: events.columbia.edu/cal/event/ev...
Open rank faculty search in the Program for Mathematical Genomics at Columbia University:
www.nature.com/naturecareer...
www.nature.com/naturecareer...
December 5, 2023 at 1:06 AM
Open rank faculty search in the Program for Mathematical Genomics at Columbia University:
www.nature.com/naturecareer...
www.nature.com/naturecareer...
Reposted by Yufeng Shen
I'm delighted to release the first half of my new textbook in human genetics:
web.stanford.edu/group/pritch...
"An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"
web.stanford.edu/group/pritch...
"An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"
An Owner's Guide to the Human Genome
An Owner's Guide to the Human Genome
web.stanford.edu
October 1, 2023 at 10:53 PM
I'm delighted to release the first half of my new textbook in human genetics:
web.stanford.edu/group/pritch...
"An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"
web.stanford.edu/group/pritch...
"An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"
Reposted by Yufeng Shen
2nd Bluesky post … faculty search! Genomics and Comp Bio dept @ UMass Chan Med School academicjobsonline.org/ajo/jobs/25641 pop genomics, imaging, stat. genetics, machine learning aka cool science w big data.
Collab & supportive environment where you can innovate & make discoveries. Join us!
Collab & supportive environment where you can innovate & make discoveries. Join us!
University of Massachusetts Chan Medical School, Program in Bioinformatics and Integrative Biology
Full service online faculty recruitment and application management system for academic institutions worldwide. We offer unique solutions tailored for academic communities.
academicjobsonline.org
September 13, 2023 at 8:50 PM
2nd Bluesky post … faculty search! Genomics and Comp Bio dept @ UMass Chan Med School academicjobsonline.org/ajo/jobs/25641 pop genomics, imaging, stat. genetics, machine learning aka cool science w big data.
Collab & supportive environment where you can innovate & make discoveries. Join us!
Collab & supportive environment where you can innovate & make discoveries. Join us!