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)

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

The Sudmant lab at UC Berkeley is seeking a postdoc to work on a fully funded NIH project to understand differences in DNA repair and somatic mutation across the primate tree of life. Please spread widely to those who may be interested aprecruit.berkeley.edu/JPF05052

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.

‘Genetic Risk Effects on Psychiatric Disorders Act in Sets’, the title of our new preprint on @medrxivpreprint.bsky.social! This huge collaborative effort advances our understanding of psychiatric genetic architecture and emphasizes the importance of looking beyond additive effects. 🧵1/n; 🧪👩🏽‍🔬🧬

Very happy to share our new paper now on @medrxivpreprint: “Genetic risk effects on psychiatric disorders act in sets”, a great effort led my PhD student @jolienrietkerk.bsky.social, and performed together with collaborators Andy Dahl, Jonathan Flint, Andrew Schork etc. Thread 1/n

Today, our two new faculty members held their inaugural lectures @ethzurich.bsky.social. Basile Wicky | Biomedical Design Lab, presented on designing proteins that interface with life; Michael Moor @michaelmoor.bsky.social | Medical AI Lab, spoke about AI in medicine. Recordings > u.ethz.ch/hQdQl

I just had the most wonderful time at the Quantgen GRC in Italy with these lovely and brilliant people :) hope to see everyone again in Ventura for the next Quantgen GRC in 2 years time, and sooner on other occasions!

New year new start! My group has moved to the Dept of Biosystems Science and Engineering in ETH Zurich - very excited to work with new colleagues here! We’re also hiring soon, if interested in a PhD/postdoc in quantitative genetics and genomics, esp with focus in psych disorders, pls get in touch!

How population stratification makes environments look like genes. A short 🧵:

Unsure how recent changes in U.S. policy regarding the NIH will impact the psychiatric genetics world? You're not alone. Join ISPG for a Member’s Meetup for community discussion and support: 📅 Wednesday, January 29 🕗 3 PM EST 📍 Pre-Register: us06web.zoom.us/meeting/regi...

📢 Quantgen friends: We will continue to accept applications for the GRC on Quantgen in Feb 2025 till 26 Jan or when we are full, so there is still time to put in an application and join us! 😁 Check out our latest program and apply now! www.grc.org/quantitative...

🚨 RECOMB-Genetics Deadline 🚨 The RECOMB-Genetics 2025 workshop is in Seoul 🌏 on April 25, 2025, just before the main RECOMB conference (April 26–29). 📅 Submission deadline: Feb 14, 2025 (AoE) 👉recomb.org/recomb2025/rec… Submit your work and join us for this exciting event!

I wrote about the ongoing debates over genomic data sharing and the use of such data for "abhorrent science", including some perspective papers that came out last month. A few key points: 🧵

Quantgen GRC (16-21 Feb 2025) in Lucca, Italy: we are still accepting applications and poster abstracts! Deadline: 19 Jan 2025 Apply now - we have a great selection of invited speakers and the posters abstracts are amazing. It’s going to be a blast 💥 www.grc.org/quantitative...

How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3) doi.org/10.1038/s415...

Come join us as a group leader: www.jobs.cam.ac.uk/job/49356/ Happy to answer queries.

Great to see this out. From @caina89.bsky.social and @pgcgenetics.bsky.social Cross-disorder group rdcu.be/d4ZF0

Last work tweet of 2024 (maybe 😉): I, Ken Kendler, Brad Verhulst, @jorsmo.bsky.social and @andrewgrotzinger.bsky.social et al in the Psychiatric Genomics Consortium Cross Disorder Group (PGC-CDG) wrote a review on challenges studying cross disorder (psych) genetics: www.nature.com/articles/s41...

Very happy to share *two* new projects from my group now on @biorxivpreprint.bsky.social on mtDNA variation effects on tissue-specific gene expression conducted using RNAseq data in 49 tissues in the GTEx project! 🧵 1/n

After 4 fantastic years of research, together with @caina89.bsky.social & Matthias Heinig, I’m thrilled to share the first tissue specific map of apparent mtDNA heteroplasmy in humans and their relationships with donor age and mtDNA gene expr across 49 tissues! www.biorxiv.org/content/10.1...

My first PhD student Lianyun Huang has now successfully defended her PhD and is now Dr Huang! 🎉🎉🎉 Thank you for 4 years of hard work, it’s an honor to be part of your academic journey!

Quantgen GRC (16-21 Feb 2025) updates: we are now 75% subscribed! Deadline: 19 Jan 2025 BUT: We will pick talks from submitted abstracts 16 Dec and aim to send decisions before Xmas. So submit your abstracts now (even if not perfect - editable after submission)! www.grc.org/quantitative...

New work by Andy Dahl and Michal Sadowski on using GxE to study genetics of drug response now out in Cell Genomics www.cell.com/cell-genomic...

New paper by Andy Dahl and I on phenotype integration improving GWAS power while preserving specificity is now out in Nature Genetics 🧬🎉 thank you all collaborators and reviewers! www.nature.com/articles/s41...

Dear statgen friends at #ASHG2023 #ASHG23, my lab is #hiring #phds #postdocs to work on heterogeneity and trajectories of psychiatric disorders using EHR/cohorts across US/Europe/Asia (incl. data from PGC), lots of cool stuff to be done! Please reach out by email! Ad link: tinyurl.com/7tae8k

Feeling FOMO big time seeing all the #ASHG2023 posts, sadly I’m not there this year! 🥲 My PhD student Jolien Rietkerk is there though and she has a poster (PB4102), go say hi to her and she can tell you about how PRS can be used to find pathways (using method by Andy Dahl, David Tang)✨

On the problem of inflation in TWAS Does TWAS yield inflated p-values?

Hi #WCPG2023, it’s been a great few days! But more today 😉: I’m talking about my work with Andy Dahl on phenotype integration and PRS specificity in the symposium on GWAS phenotyping, 3pm in Rm 510, with Travis Mallard, Justin Tubbs, Jeanne Savage and Abe Palmer. Come join us!! Preprint linked:

Hi #wcpg2023! Today: my student Lianyun Huang is gonna talk about MDD symptoms assessed in the UKBiobank in the PGC session on mental health research using UKB data! ✨ Where/When: 4pm in Rm 510, with Ben Lacey, Ana Lucia Espinosa Dice and Cathryn Lewis 🤩 Come hear her out!

The "we did a lot of stuff" talk is always so tempting as a speaker. It's fun for you, but not for your audience. Cut those slides - just do it. Less data, more drama.

Good morning #wcpg2023! Today: My student Jolien Rietkerk is giving a talk at 1pm in the Stats Methods session (Rm 510) on use of PRS in pathway interaction test + method considerations; Lianyun Huang is giving a poster (no 74) on MDD symptom genetics. Come hear them out, feedback welcome! 🤩

One week left to apply for junior faculty positions in the Data Driven Life Science program in Sweden! Competitive startup, big program with a strong peer+mentorship networks, great country with strong science, international vibe and nice quality of life. www.scilifelab.se/data-driven/...

On our way to #wcpg2023! This is a big year for Cai lab, all of us have talks! 🤩 Lianyun Huang is in the UKB session, Jolien Rietkerk is in the stats methods session, and I’m in a symposium on GWAS phenotyping. I’ll remind everyone on the morning of. 😉 See you all in Montreal!

I'm recruiting PhD students for Oct 24 start at University of Bath. Fully funded for UK students only. If interested in developing data structures/algorithms for bacterial genomics, or exploring plasmid epidemiology, or ML/AI on bacterial/phage geno/pheno data, give me a call!

Less than a week to #wcpg2023, looking forward to seeing everyone there! My lab is hiring postdocs to work on quantgen methods, EHR utilisation, disease heterogeneity and trajectories, if interested please email me, also happy to chat during the conference! www.nacailab.com

I'm delighted to release the first half of my new textbook in human genetics: web.stanford.edu/group/pritch... "An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"

bioRxiv goes big on Bluesky: accounts for all subject categories now available (Please Reskeet) connect.biorxiv.org/news/2023/09...