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...

🎙️ 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...

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.

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...

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 🧵:

@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...

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]

Suspension of all grants to UCLA www.latimes.com/california/s...

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...

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

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...

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 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!

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/...

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.

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!

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...

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...

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...

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

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...

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

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.

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...

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.

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

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

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 🌎.

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...

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...

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...

Timescales in Cell Biology

⚠️ 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...

Yet more evidence that transfer learning of sequence-only PLMs does not benefit from scale beyond 650M params 🧵

Maintain a public archive of your old tweets that's independent of X, as a self-hosted static webpage. An R/Quarto script that reads your tweet archive (downloaded from X) & creates an HTML page. Example (w/ my own tweets 2015-24): wolfganghuber.github.io/tweets/index... github.com/wolfganghube...

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. 🦃✨