Jingyou Rao
@jingyour.bsky.social
Incoming Postdoc @UCSF wcoyotelab.com | PhD in Computer Science @UCLA protein epistasis and mutational scanning
Reposted by Jingyou Rao
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
🎙️ Next up Dec 2 in VESS!
Thea Schulze (Lindorff-Larsen Lab): Predicting mutated protein abundance @tkschulze.bsky.social
Taylor Mighell (Lehner Lab): Massive mutagenesis to understand GPCRs @taylor-mighell.bsky.social
🔗 More info at varianteffect.org/seminar-series
@varianteffect.bsky.social
Thea Schulze (Lindorff-Larsen Lab): Predicting mutated protein abundance @tkschulze.bsky.social
Taylor Mighell (Lehner Lab): Massive mutagenesis to understand GPCRs @taylor-mighell.bsky.social
🔗 More info at varianteffect.org/seminar-series
@varianteffect.bsky.social
November 4, 2025 at 6:31 PM
🎙️ Next up Dec 2 in VESS!
Thea Schulze (Lindorff-Larsen Lab): Predicting mutated protein abundance @tkschulze.bsky.social
Taylor Mighell (Lehner Lab): Massive mutagenesis to understand GPCRs @taylor-mighell.bsky.social
🔗 More info at varianteffect.org/seminar-series
@varianteffect.bsky.social
Thea Schulze (Lindorff-Larsen Lab): Predicting mutated protein abundance @tkschulze.bsky.social
Taylor Mighell (Lehner Lab): Massive mutagenesis to understand GPCRs @taylor-mighell.bsky.social
🔗 More info at varianteffect.org/seminar-series
@varianteffect.bsky.social
Reposted by Jingyou Rao
🌏 🧬 Join the global functional genomics community in Melbourne this March for MSS26! The 9th Annual Mutational Scanning Symposium #VariantEffect26 runs March 25–27, 2026 at the Aikenhead Centre for Medical Discovery.
🗓️ Early bird registration & abstract submissions close Nov 2, 2025.
www.mss2026.org
🗓️ Early bird registration & abstract submissions close Nov 2, 2025.
www.mss2026.org
MSS26
Mutational Scanning Symposium 2026, 25-27 March, Melbourne
www.mss2026.org
October 10, 2025 at 2:40 PM
🌏 🧬 Join the global functional genomics community in Melbourne this March for MSS26! The 9th Annual Mutational Scanning Symposium #VariantEffect26 runs March 25–27, 2026 at the Aikenhead Centre for Medical Discovery.
🗓️ Early bird registration & abstract submissions close Nov 2, 2025.
www.mss2026.org
🗓️ Early bird registration & abstract submissions close Nov 2, 2025.
www.mss2026.org
Coming up next in the VESS (Nov 4):
Population genetics × variant effects:
🧬 Nikhil Milind (Stanford) on gene dosage and complex traits @nikhilmilind.dev
🧬 Leslie Smith (U Florida) on equitable ML in cancer genomics
www.varianteffect.org/seminar-seri...
@varianteffect.bsky.social
Population genetics × variant effects:
🧬 Nikhil Milind (Stanford) on gene dosage and complex traits @nikhilmilind.dev
🧬 Leslie Smith (U Florida) on equitable ML in cancer genomics
www.varianteffect.org/seminar-seri...
@varianteffect.bsky.social
October 10, 2025 at 2:43 PM
Coming up next in the VESS (Nov 4):
Population genetics × variant effects:
🧬 Nikhil Milind (Stanford) on gene dosage and complex traits @nikhilmilind.dev
🧬 Leslie Smith (U Florida) on equitable ML in cancer genomics
www.varianteffect.org/seminar-seri...
@varianteffect.bsky.social
Population genetics × variant effects:
🧬 Nikhil Milind (Stanford) on gene dosage and complex traits @nikhilmilind.dev
🧬 Leslie Smith (U Florida) on equitable ML in cancer genomics
www.varianteffect.org/seminar-seri...
@varianteffect.bsky.social
Reposted by Jingyou Rao
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
docs.google.com/document/d/1...
Postdoc Description.docx
Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...
docs.google.com
October 8, 2025 at 4:03 PM
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
docs.google.com/document/d/1...
VESS is happening tomorrow (Oct 7). See you there!
First speaker: Shelby Hemker (Dr. Jacob Kitzman Lab, University of Michigan)
Second speaker: Karl Romanowicz (Dr. Calin Plesa Lab, University of Oregon) @kroman.bsky.social
Link: www.varianteffect.org/seminar-seri...
First speaker: Shelby Hemker (Dr. Jacob Kitzman Lab, University of Michigan)
Second speaker: Karl Romanowicz (Dr. Calin Plesa Lab, University of Oregon) @kroman.bsky.social
Link: www.varianteffect.org/seminar-seri...
October 6, 2025 at 5:05 PM
VESS is happening tomorrow (Oct 7). See you there!
First speaker: Shelby Hemker (Dr. Jacob Kitzman Lab, University of Michigan)
Second speaker: Karl Romanowicz (Dr. Calin Plesa Lab, University of Oregon) @kroman.bsky.social
Link: www.varianteffect.org/seminar-seri...
First speaker: Shelby Hemker (Dr. Jacob Kitzman Lab, University of Michigan)
Second speaker: Karl Romanowicz (Dr. Calin Plesa Lab, University of Oregon) @kroman.bsky.social
Link: www.varianteffect.org/seminar-seri...
Reposted by Jingyou Rao
The first (of hopefully many) reports to come from our collaboration with @hjp.bsky.social
We present a new type of cell fitness assay that allows you to both quantify and explain differences across human donors in cell proliferation and sensitivity to environmental toxicants.
We present a new type of cell fitness assay that allows you to both quantify and explain differences across human donors in cell proliferation and sensitivity to environmental toxicants.
Cell villages and Dirichlet modeling map human cell fitness genetics https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1
September 30, 2025 at 7:17 PM
The first (of hopefully many) reports to come from our collaboration with @hjp.bsky.social
We present a new type of cell fitness assay that allows you to both quantify and explain differences across human donors in cell proliferation and sensitivity to environmental toxicants.
We present a new type of cell fitness assay that allows you to both quantify and explain differences across human donors in cell proliferation and sensitivity to environmental toxicants.
Reposted by Jingyou Rao
Super excited to have this out. Thanks very much to the reviewers who helped improve this manuscript. Congrats to @jingyour.bsky.social!
bsky.app/profile/bioi...
bsky.app/profile/bioi...
🧩 Recently published in Bioinformatics Advances: “Rosace-AA: Enhancing interpretation of deep mutational scanning data with amino acid substitution and position-specific insights”
Full article available: https://doi.org/10.1093/bioadv/vbaf218
Full article available: https://doi.org/10.1093/bioadv/vbaf218
September 22, 2025 at 5:35 PM
Super excited to have this out. Thanks very much to the reviewers who helped improve this manuscript. Congrats to @jingyour.bsky.social!
bsky.app/profile/bioi...
bsky.app/profile/bioi...
Reposted by Jingyou Rao
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by Jingyou Rao
I wrote about how genetic risk works in the context of embryo selection and how people often think about it all wrong. A short 🧵:
What we talk about when we talk about risk
How embryo selection exploits our flawed intuitions about risk
open.substack.com
August 10, 2025 at 7:08 PM
I wrote about how genetic risk works in the context of embryo selection and how people often think about it all wrong. A short 🧵:
Reposted by Jingyou Rao
@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease.
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
August 19, 2025 at 12:29 AM
@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease.
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Reposted by Jingyou Rao
Why yes! You can watch previous Variant Effects Seminar Series talks on our YouTube channel!
ℹ️ www.varianteffect.org/previous-sem... 📺 www.youtube.com/playlist?lis...
#Genomics #Seminar #EarlyCareerResearchers #ScientificSeminar #PrecisionMedicine
ℹ️ www.varianteffect.org/previous-sem... 📺 www.youtube.com/playlist?lis...
#Genomics #Seminar #EarlyCareerResearchers #ScientificSeminar #PrecisionMedicine
August 19, 2025 at 1:34 AM
Why yes! You can watch previous Variant Effects Seminar Series talks on our YouTube channel!
ℹ️ www.varianteffect.org/previous-sem... 📺 www.youtube.com/playlist?lis...
#Genomics #Seminar #EarlyCareerResearchers #ScientificSeminar #PrecisionMedicine
ℹ️ www.varianteffect.org/previous-sem... 📺 www.youtube.com/playlist?lis...
#Genomics #Seminar #EarlyCareerResearchers #ScientificSeminar #PrecisionMedicine
Reposted by Jingyou Rao
Very excited to have this out! Here, we take inspiration from model selection MR to decouple direct and indirect effects in DMS experiments. Check out Jingyou's explainer and paper below:
bsky.app/profile/jing...
bsky.app/profile/jing...
How do we decouple the effects of two functional phenotypes in protein deep mutational scanning (DMS)?
Meet Cosmos, our new statistical framework for causal inference in multi-phenotype DMS.
www.biorxiv.org/content/10.1...
[1/n]
Meet Cosmos, our new statistical framework for causal inference in multi-phenotype DMS.
www.biorxiv.org/content/10.1...
[1/n]
Cosmos: A Position-Resolution Causal Model for Direct and Indirect Effects in Protein Functions
Multi-phenotype deep mutational scanning (DMS) experiments provide a powerful means to dissect how protein variants affect different layers of molecular function, such as abundance, surface expression...
www.biorxiv.org
August 15, 2025 at 4:22 PM
Very excited to have this out! Here, we take inspiration from model selection MR to decouple direct and indirect effects in DMS experiments. Check out Jingyou's explainer and paper below:
bsky.app/profile/jing...
bsky.app/profile/jing...
Reposted by Jingyou Rao
Bittersweet to be leaving @docedge.bsky.social after a wonderful postdoc, but excited to share that I'm joining @uoregon.bsky.social next month as an Assistant Professor in the Department of Data Science.
August 6, 2025 at 5:18 PM
Bittersweet to be leaving @docedge.bsky.social after a wonderful postdoc, but excited to share that I'm joining @uoregon.bsky.social next month as an Assistant Professor in the Department of Data Science.
How do we decouple the effects of two functional phenotypes in protein deep mutational scanning (DMS)?
Meet Cosmos, our new statistical framework for causal inference in multi-phenotype DMS.
www.biorxiv.org/content/10.1...
[1/n]
Meet Cosmos, our new statistical framework for causal inference in multi-phenotype DMS.
www.biorxiv.org/content/10.1...
[1/n]
Cosmos: A Position-Resolution Causal Model for Direct and Indirect Effects in Protein Functions
Multi-phenotype deep mutational scanning (DMS) experiments provide a powerful means to dissect how protein variants affect different layers of molecular function, such as abundance, surface expression...
www.biorxiv.org
August 4, 2025 at 3:08 PM
How do we decouple the effects of two functional phenotypes in protein deep mutational scanning (DMS)?
Meet Cosmos, our new statistical framework for causal inference in multi-phenotype DMS.
www.biorxiv.org/content/10.1...
[1/n]
Meet Cosmos, our new statistical framework for causal inference in multi-phenotype DMS.
www.biorxiv.org/content/10.1...
[1/n]
Reposted by Jingyou Rao
Suspension of all grants to UCLA www.latimes.com/california/s...
Trump freezes $200 million in UCLA science and medical research funding, citing antisemitism
The Trump administration has frozen roughly $200 million in National Science Foundation, National Institutes of Health and other federal agency-funded research at UCLA, citing allegations the school d...
www.latimes.com
August 1, 2025 at 4:27 AM
Suspension of all grants to UCLA www.latimes.com/california/s...
Reposted by Jingyou Rao
The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs:
probgen2026.github.io
Please help spread the news.
probgen2026.github.io
Please help spread the news.
Home - ProbGen 2026
Your Site Description
probgen2026.github.io
June 6, 2025 at 5:52 PM
The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs:
probgen2026.github.io
Please help spread the news.
probgen2026.github.io
Please help spread the news.
Perfect first day: receiving a set of new pipettes! Can’t wait to do more cool experiments with the lab for the next few years. @willowcoyote.bsky.social
July 31, 2025 at 10:57 PM
Perfect first day: receiving a set of new pipettes! Can’t wait to do more cool experiments with the lab for the next few years. @willowcoyote.bsky.social
Reposted by Jingyou Rao
Super proud of my first student, @jingyour.bsky.social! Well done! Looking forward to the amazing work you will do in the future 🥲 bsky.app/profile/jing...
Thrilled to share that I just successfully defended my PhD! Thanks to my committee, collaborators, and everyone who’d supported me throughout my seven years at UCLA. A special thank you to my PI Harold for his incredible mentorship! @hjp.bsky.social
July 21, 2025 at 11:15 PM
Super proud of my first student, @jingyour.bsky.social! Well done! Looking forward to the amazing work you will do in the future 🥲 bsky.app/profile/jing...
Thrilled to share that I just successfully defended my PhD! Thanks to my committee, collaborators, and everyone who’d supported me throughout my seven years at UCLA. A special thank you to my PI Harold for his incredible mentorship! @hjp.bsky.social
July 21, 2025 at 9:35 PM
Thrilled to share that I just successfully defended my PhD! Thanks to my committee, collaborators, and everyone who’d supported me throughout my seven years at UCLA. A special thank you to my PI Harold for his incredible mentorship! @hjp.bsky.social
Reposted by Jingyou Rao
Interested in using functional data to understand clinical variants? Been hunting for a good review of the topic? We just wrote one! rdcu.be/exaEU
Multiplexed assays of variant effect for clinical variant interpretation
Nature Reviews Genetics - Multiplexed assays of variant effect (MAVEs) are highly scalable experimental approaches used to generate functional data for genetic variants. In this Review, McEwen et...
www.nature.com
July 21, 2025 at 7:34 PM
Interested in using functional data to understand clinical variants? Been hunting for a good review of the topic? We just wrote one! rdcu.be/exaEU
Reposted by Jingyou Rao
Very excited to have this work out by @jeromics.bsky.social ! Please check it out.
I think my favorite story from the supplement is how impactful normalization can be in this context.
bsky.app/profile/jero...
I think my favorite story from the supplement is how impactful normalization can be in this context.
bsky.app/profile/jero...
July 2, 2025 at 3:56 PM
Very excited to have this work out by @jeromics.bsky.social ! Please check it out.
I think my favorite story from the supplement is how impactful normalization can be in this context.
bsky.app/profile/jero...
I think my favorite story from the supplement is how impactful normalization can be in this context.
bsky.app/profile/jero...
Reposted by Jingyou Rao
Check out our new preprint on Lilace, a statistical tool for scoring FACS-based deep mutational scanning experiments! Lilace directly models the shift between variant fluorescence distributions and provides score uncertainty estimates to better assess reliability and reproducibility. (1/3)
Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace
Deep mutational scanning (DMS) experiments interrogate the effect of genetic variants on protein function, often using fluorescence-activated cell sorting (FACS) to quantitatively measure molecular ph...
www.biorxiv.org
June 30, 2025 at 4:03 PM
Check out our new preprint on Lilace, a statistical tool for scoring FACS-based deep mutational scanning experiments! Lilace directly models the shift between variant fluorescence distributions and provides score uncertainty estimates to better assess reliability and reproducibility. (1/3)
Reposted by Jingyou Rao
Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace https://www.biorxiv.org/content/10.1101/2025.06.24.661380v1
June 28, 2025 at 12:46 AM
Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace https://www.biorxiv.org/content/10.1101/2025.06.24.661380v1
Reposted by Jingyou Rao
I sometimes overhear conversations about tool choice in bioinformatics, where implementation language is stated as the primary criterion. Such thinking stands in the way of scientific quality and productivity. It is a form of self-harm.
What should one really care about?
(1/5)
What should one really care about?
(1/5)
June 13, 2025 at 5:23 PM
I sometimes overhear conversations about tool choice in bioinformatics, where implementation language is stated as the primary criterion. Such thinking stands in the way of scientific quality and productivity. It is a form of self-harm.
What should one really care about?
(1/5)
What should one really care about?
(1/5)