🧬 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

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)

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

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...

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...

Specificity, length and luck drive gene rankings in association studies - Nature

Genetic association tests prioritize candidate genes based on different criteria.

nature.com

🎙️ 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

🌏 🧬 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

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...

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

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...

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.

bioRxiv Genetics@biorxiv-genetic.bsky.social · 10mo ago

Cell villages and Dirichlet modeling map human cell fitness genetics https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1

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...

Bioinformatics Advances@bioinfoadv.bsky.social · 11mo ago

🧩 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

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)

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

@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

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

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...

Jingyou Rao@jingyour.bsky.social · last yr.

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]

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]

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...

biorxiv.org

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...

latimes.com

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.

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

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...

Jingyou Rao@jingyour.bsky.social · last yr.

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

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...

nature.com

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...

Jerome@jeromics.bsky.social · last yr.

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)

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...

biorxiv.org

Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace https://www.biorxiv.org/content/10.1101/2025.06.24.661380v1

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)

🚨 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!