Jingyou Rao
Incoming Postdoc @UCSF wcoyotelab.com | PhD in Computer Science @UCLA protein epistasis and mutational scanning
- Reposted by Jingyou RaoTwo #CRISPR talks on Feb3! 1️⃣ Stephan Riesenberg (Group Leader, Max Planck Leipzig): CRISPR-mediated generation of genetic variants for functional analysis. 2️⃣ Yuriy Baglaenko @baglaenkolab.bsky.social: Causal variants with CRISPR editing in primary human cells www.varianteffect.org/seminar-seri...
- Reposted by Jingyou RaoHow 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...
- 🎙️ 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
- 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
- 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
- Reposted by Jingyou RaoHave 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...
- 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...
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- Reposted by Jingyou RaoWe 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)
- Reposted by Jingyou RaoI 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
- Reposted by Jingyou RaoWhy 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
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- Reposted by Jingyou RaoBittersweet 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]
- Multi-phenotype DMS experiments are revealing how mutations impact different protein functions. But these phenotypes are often causally linked—e.g., when measuring activity, we may also capture effects propagated from abundance. So how do we tell what’s direct vs indirect? [2/n]
- Reposted by Jingyou RaoSuspension of all grants to UCLA www.latimes.com/california/s...
- Reposted by Jingyou RaoThe 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.
- 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 RaoSuper 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
- 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 RaoInterested 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 RaoVery 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...
- Reposted by Jingyou RaoCheck 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)
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- Reposted by Jingyou RaoNow published! Big congrats to first author @gginell.bsky.social We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions. www.science.org/doi/10.1126/...
- Excited to share new work from Garrett Ginell et al where we present an approach for predicting intermolecular interaction driven by disordered regions. We focus on how chemical complementarity can contribute to and even dictate intermolecular interactions www.biorxiv.org/content/10.1...
- Reposted by Jingyou RaoThat’s all for #VariantEffect25! This was my first time live sketching a conference, it was a really fun and interesting experience. The science was fantastic, i learnt so much!! Big thanks to everyone who shared any of my sketches or spoke to me about them, i really appreciate it.
- Reposted by Jingyou RaoBackbone predictions are great - but what about side chains? Me and @emilthomasen.bsky.social are happy to present AF2χ, a tool for predicting side-chain heterogeneity in protein structures!. If you want to read more about it, check out our preprint and localColabFold implementation!
- AlphaFold is amazing but gives you static structures 🧊 In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃 Code: github.com/KULL-Centre/... Colab: github.com/matteo-cagia...
- Reposted by Jingyou RaoA Perspective by @stephanieaw.bsky.social and @fraserlab.com discusses ways macromolecules use conformational entropy to control binding, catalysis, and allostery www.nature.com/articles/s41...
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- Reposted by Jingyou RaoA long read from 2017 but well worth the time for any scientist who both loves their job and and often finds themselves questioning their life decisions. www.danielnettle.org.uk/wp-content/u...
- Reposted by Jingyou RaoFriends, We are hiring! My department (Computational Medicine) has an open rank faculty position search this year! I know we are late to the party, but please consider applying! Feel free to ask question here. recruit.apo.ucla.edu/JPF09935
- Bye SF. Guess it's time to stop pretending I’m a biologist.
- Why is it so hard to include an actual data file in the paper? Attaching one in a pdf is not the “nature” way.
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- Night emo talk: UCSF holds such a special place in my heart—a life saver for my career. The science is fascinating, and the people here are unbelievably kind and welcoming. It’s hard to say goodbye. Next week I’ll start floating around again 🌎.
- Reposted by Jingyou RaoBiology of Genomes 2025 is coming up: - meeting dates: May 6 - 10, 2025 - abstract deadline: Feb 14, 2025 We hope to see you there for another great meeting with a fantastic speaker lineup! meetings.cshl.edu/meetings.asp...
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- Reposted by Jingyou RaoThe coolest postdoc I know is now accepting applications: 🧪🔬THE WITTIG POSTDOC IN FEMINIST BIOLOGY🧪🔬 Our interdisciplinary program @ UW Madison seeks to train the next generation of feminist scientists/scholars of science Please share widely and read more here: crgw.gws.wisc.edu/scholarships...
- Reposted by Jingyou RaoTimescales in Cell Biology
- Reposted by Jingyou Rao⚠️ Tag with Caution ⚠️ New preprint led by Kerstin Dörner in Maria Hondele’s lab with contributions from Fan Cao on our side on the effects of tagging with FPs and peptides on condensation and phase separation 🧪 TL/DR: It’s complicated See more: doi.org/10.1101/2024...
- Reposted by Jingyou RaoYet more evidence that transfer learning of sequence-only PLMs does not benefit from scale beyond 650M params 🧵
- The complete guide for transfer learning with the protein language model ESM-2. (In brief: Use ESM-2 650M and calculate mean embeddings across sites.) www.biorxiv.org/content/10.1...
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- Thanksgiving week mood: surrounded by incredible people in academia, soaking in the good vibes, and ditching the negativity. Gonna focus on the bright side and let the bad stuff roll off. 🦃✨
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- Reposted by Jingyou RaoFollowing the news that eLife will not receive an Impact Factor in 2025, we’ve shared an update on how our model is doing since we were first placed “on hold” by Web of Science, and what we’re up to now. Find out more. buff.ly/3ATRAFT
- One thing I love about SF is the ballet studio. Every night, my teacher shouts at me, 'Look more arrogant!' He reminds me, whether I'm having a bad or good day in the lab, that when the music starts, I should lift my chest, look beautiful, and turn it into a great day. This seriously keeps me sane.
- I'm new to AI in biology, so I've started reading papers. I've noticed that people often generate benchmarking datasets using LLMs and then test their models on those same LLMs. Is this similar to how, in my field, people use the same model to simulate functional genetic datasets and evaluate them?
- Reposted by Jingyou Rao🚨NEW PREPRINT! Interested in Mendelian randomization and proteomics? 🧬 We created a comprehensive multi-ancestry proteome-phenome-wide atlas of protein-disease associations in European, African, and East Asian ancestries! Preprint: www.medrxiv.org/content/10.1... Website: broad.io/protein_mr_a...
- Reposted by Jingyou RaoWe will be hosting 3rd Full Circle Symposium for Native Biologists hosted at UCSF in April 2025! We aim to build community and provide meaningful opportunities for Native scientists. If you are a Native biologist who is interested plz fill this out to stay up to date: forms.gle/AN7nfkhdB3Fv...
- Reposted by Jingyou Rao🧵 Bioinformatics faces a critical challenge: despite its importance, software quality often falls short due to the lack of proper development practices. In our latest paper, we advocate for improving software quality in bioinformatics through teamwork. academic.oup.com/bioinformati...
- Reposted by Jingyou RaoI made one for stats papers
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