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Jingyou Rao

@jingyour.bsky.social
168 followers 135 following 27 posts

Incoming Postdoc @UCSF wcoyotelab.com | PhD in Computer Science @UCLA protein epistasis and mutational scanning

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Reposted by Jingyou Rao
Atlas of Variant Effects Alliance @varianteffect.bsky.social · 06/04/2026
🧬 Join the VESS Organizing Committee! We are looking for early-career scientists to help shape our global, community-driven seminar program. 📅 Deadline to apply: April 30, 2026 ℹ️ Learn more and apply👇 forms.gle/vdLh3mu9Fuid... #VESS #VariantEffects #Seminar #Genomics #EarlyCareer
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albertsxue.bsky.social @albertsxue.bsky.social · 02/03/2026
My preprint on keju, a statistical tool for Massively Parallel Reporter Assay (MPRA) data, is out! keju improves sensitivity, calibration, and reliability over previous methods by closely modeling important uncertainty sources in MPRAs. Check it out: www.biorxiv.org/content/10.6... (1/n)
biorxiv.org
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Willow Coyote-Maestas @willowcoyote.bsky.social · 20/02/2026
A wonderful first for me at the upcoming @biophysicalsoc.bsky.social meeting in SF is having many lab members present! See 6 brilliant graduate students postdocs from the lab present talks and posters on how they are pushing the boundaries of technology and mechanistic membrane protein biology
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Atlas of Variant Effects Alliance @varianteffect.bsky.social · 28/01/2026
Two #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...
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Jeff Spence @jeffspence.github.io · 07/11/2025
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...
nature.com
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
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Jingyou Rao @jingyour.bsky.social · 04/11/2025
🎙️ 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
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Atlas of Variant Effects Alliance @varianteffect.bsky.social · 10/10/2025
🌏 🧬 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
mss2026.org
MSS26
Mutational Scanning Symposium 2026, 25-27 March, Melbourne
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Jingyou Rao @jingyour.bsky.social · 10/10/2025
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
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Rob Patro @robp.bsky.social · 08/10/2025
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
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 ...
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Jingyou Rao @jingyour.bsky.social · 06/10/2025
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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The Wells Lab of UCLA @wellslab.bsky.social · 30/09/2025
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.
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Harold Pimentel @hjp.bsky.social · 22/09/2025
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...
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Yun S. Song @yun-s-song.bsky.social · 22/09/2025
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)
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Sasha Gusev @sashagusevposts.bsky.social · 10/08/2025
I wrote about how genetic risk works in the context of embryo selection and how people often think about it all wrong. A short 🧵:
open.substack.com
What we talk about when we talk about risk
How embryo selection exploits our flawed intuitions about risk
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Anshul Kundaje @anshulkundaje.bsky.social · 19/08/2025
@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
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Atlas of Variant Effects Alliance @varianteffect.bsky.social · 19/08/2025
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
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Harold Pimentel @hjp.bsky.social · 15/08/2025
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...
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Roshni Patel @roshnipatel.bsky.social · 06/08/2025
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.
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Jingyou Rao @jingyour.bsky.social · 04/08/2025
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]
biorxiv.org
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...
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Alicia Izquierdo @aliciaizquierdo.bsky.social · 01/08/2025
Suspension of all grants to UCLA www.latimes.com/california/s...
latimes.com
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...
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Yun S. Song @yun-s-song.bsky.social · 06/06/2025
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
Home - ProbGen 2026
Your Site Description
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Jingyou Rao @jingyour.bsky.social · 31/07/2025
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
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Harold Pimentel @hjp.bsky.social · 22/07/2025
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...
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Jingyou Rao @jingyour.bsky.social · 21/07/2025
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
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Doug Fowler @dougfowler.bsky.social · 21/07/2025
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
nature.com
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...
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Harold Pimentel @hjp.bsky.social · 02/07/2025
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...
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Jerome @jeromics.bsky.social · 30/06/2025
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)
biorxiv.org
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...
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 28/06/2025
Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace www.biorxiv.org/content/10.1101/202…
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Wolfgang Huber @wkhuber.bsky.social · 13/06/2025
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)
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Brunilda Balliu @brunildaballiu.bsky.social · 10/06/2025
🚨 Applications are open for the UCLA Postdoct Training Program in Neurobehavioral Genetics 🧠🧬 Deadline: 6/30 👉 neurogen.semel.ucla.edu/curriculum/ Contact me if you're interested to write a proposal together combining genetics + functional genomics + digital phenotypes from wearables/smartphones!
neurogen.semel.ucla.edu
Curriculum – UCLA Center for Neurobehavioral GeneticsAccessibility ToolsIncrease TextDecrease TextGrayscaleHigh ContrastNegative ContrastLight BackgroundLinks UnderlineReadable FontReset
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Alex Holehouse @alexholehouse.bsky.social · 23/05/2025
Now 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/...
science.org
Sequence-based prediction of intermolecular interactions driven by disordered regions
Intrinsically disordered regions (IDRs) in proteins play essential roles in cellular function. A growing body of work has shown that IDRs often interact with partners in a manner that does not depend ...
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Isabelle Zane @isabellease.bsky.social · 23/05/2025
That’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.
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Matteo Cagiada @mcagiada.bsky.social · 18/04/2025
Backbone 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!
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Nature Chemical Biology @natchembio.nature.com · 25/04/2025
A 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...
nature.com
Advances in uncovering the mechanisms of macromolecular conformational entropy - Nature Chemical Biology
Protein conformational entropy plays a vital role in functions like binding and catalysis. This Perspective discusses three ways macromolecules use conformational entropy: prepaying entropic costs, re...
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Justin English @justingenglish.bsky.social · 08/04/2025
Want to Nanopore sequence complex nucleotide populations accurately, at low cost, with QC standards, using a plug-and-play informatics GUI, where you can PCR observed sequences out from your sample and not synthesize them? See our new pre-print! www.biorxiv.org/content/10.1...
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Matt Howard @matthewkhoward.bsky.social · 06/01/2025
Happy New Year! (and first post here 😀) Excited to share the final version of our work where we combine deep mutational scanning, cryo-EM, and molecular dynamics to further resolve the mechanisms of pH sensing in GPCRs. 🧵(1/n) www.cell.com/cell/fulltex...
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Diego del Alamo @delalamo.xyz · 11/12/2024
The more I think about it, the more convinced I am that the holy grail here is if this can go beyond predicting ratio of folded to unfolded, to also predicting ratio of folded state A to folded states B, C, D, etc. Example from doi.org/10.1016/j.molcel.2024.04.008 w/ changes in the transporter OCT1
1D projection of free energy landscapes of Apo and liganded OCT1 WT, D149R, D303G, either Apo (blue) or MPP-bound (red). x axis indicates the path collective variable and y axis is free energy in kJ/mol.
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Jim Woodgett @jwoodgett.bsky.social · 08/12/2024
A 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...
danielnettle.org.uk
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Harold Pimentel @hjp.bsky.social · 09/12/2024
Friends, 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
recruit.apo.ucla.edu
Faculty Member in Computational Medicine
University of California, Los Angeles is hiring. Apply now!
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Jingyou Rao @jingyour.bsky.social · 07/12/2024
Bye SF. Guess it's time to stop pretending I’m a biologist.
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Jingyou Rao @jingyour.bsky.social · 06/12/2024
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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Pascal Falter-Braun @interactome.bsky.social · 05/12/2024
Hey #networkbiology bubble and affinionados. Don't miss the CSHL Meeting: Network Biology in spring 2025. Great panel of speakers lined up by the organizers @fritzroth.bsky.social @pedrobeltrao.bsky.social, Roded Sharan, and @jsvanleeuwen.bsky.social. meetings.cshl.edu/meetings.asp...
meetings.cshl.edu
Network Biology
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
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Rob Patro @robp.bsky.social · 04/12/2024
Very cool work from Yang Lu et al. demonstrating miscalibration of BLASTP’s E-values and generating well-calibrated values via a knockoff-based approach (cc @mikelove.bsky.social) - academic.oup.com/bioinformati...! More analyses could benefit from knockoff-based approaches.
academic.oup.com
A BLAST from the past: revisiting blastp’s E-value
AbstractMotivation. The Basic Local Alignment Search Tool, BLAST, is an indispensable tool for genomic research. BLAST established itself as the canonical
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Diego del Alamo @delalamo.xyz · 05/12/2024
Been a while since I read a paper like this: • "What [DiffDock] appears to be doing cannot be considered" docking • "Results are ... contaminated with near neighbors to test cases" • "Results for DiffDock were artifactual" • "Results for other methods were incorrectly done" arxiv.org/abs/2412.02889
arxiv.org
Deep-Learning Based Docking Methods: Fair Comparisons to Conventional Docking Workflows
The diffusion learning method, DiffDock, for docking small-molecule ligands into protein binding sites was recently introduced. Results included comparisons to more conventional docking approaches, wi...
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CEGS-CMAP @cegs-cmap.bsky.social · 04/12/2024
CONGRATS CMAP PIs Nasa Sinnott-Armstrong, Stanley Fields, @fritzroth.bsky.social , @leastarita.bsky.social, Cole Trapnell, Judit Villen, @dougfowler.bsky.social & Christine Queitsch for their new publication, up on eLife: "Understanding genetic variants in context" 🎉 elifesciences.org/articles/88231
elifesciences.org
Understanding genetic variants in context
Multiplexed assays of variant effect are an increasingly important tool in genetic research and including more context specificity in their design would aid interpretation and discovery.
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Jingyou Rao @jingyour.bsky.social · 04/12/2024
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 🌎.
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 03/12/2024
Biology 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...
meetings.cshl.edu
Biology of Genomes
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
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Ben Lehner @benlehner.bsky.social · 03/12/2024
Can a single small molecule rescue the stability of nearly all mutations in a protein? Our new preprint by Taylor Mighell www.biorxiv.org/content/10.1... thread on the other place: x.com/taylor_mighe...
biorxiv.org
A pharmacological chaperone stabilizer rescues the expression of the vast majority of pathogenic variants in a G protein-coupled receptor
Reduced protein stability is the most frequent mechanism by which rare missense variants cause disease. A promising therapeutic avenue for treating destabilizing variants is pharmacological chaperones...
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Leigh Senderowicz @lsenderowicz.bsky.social · 02/12/2024
The 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...
Purple and white flyer that contains the the following information:

One of the only opportunities of its kind, the Wittig Postdoctoral Fellows Program in Feminist Science offers a fellowship at the intersection of biological/biomedical sciences and feminist science studies. We aim to train the next generation of feminist scientists/feminist science scholars and cultivate an interdisciplinary community of thinkers, practitioners, and advocates. UW Madison has a distinguished history of excellence in these areas and continues to be a dynamic site of research and teaching in feminist science scholarship.

Applicants with a new or recent PhD are invited to apply for this two year, fully funded position. We welcome scholars working at the intersection of feminist scholarship and the sciences, including the life sciences, public health, history of science, science and technology studies, or medicine. Fellows will conduct original research mentored by a UW faculty member.

This research can be feminist topics within existing research programs in the life sciences (e.g., studies of sex and the variability of sex), implementing feminist methodologies in life science research, or historical, philosophical, artistic, and feminist engagements in life science research. Successful applicants will be paired with a mentor among the UW faculty who has agreed to provide guidance during the fellowship period. For a range of examples of stellar candidates, we’ve included some sample profiles below. The postdoc will also take primary responsibility for planning and executing a feminist science one-day conference. 

The Wittig postdoc is administered through the Center for Research on Gender & Women (CRGW). For further information, contact the Director of the Center for Research on Gender and Women (CRGW), Christine Garlough, clgarlough@wisc.edu.
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Nikolai Slavov @slavov-n.bsky.social · 01/12/2024
Timescales in Cell Biology
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