We built a joint experimental and computational platform for scalable multi-modal single-cell chemical screens — profiling RNA, protein (including phospho-signaling), and chromatin accessibility responses to thousands of small molecule perturbations in parallel. www.biorxiv.org/content/10.6...

I'm excited to share that our work studying gene dosage response curves (GDRCs) is now out in Cell Genomics (@cellpress.bsky.social). www.cell.com/cell-genomic... [1/n]

Buffering of gene dosage response curves for human complex traits

Milind et al. explore why loss-of-function variants and duplications tend to have average effects in the same direction on 94 complex traits. Using gene dosage response curves (GDRCs), they gather evi...

cell.com

Happy to share that this is now out in Cell Genomics and a featured paper for Multi-Journal Submission from @cellpress.bsky.social — many thanks to the editorial team + our reviewers! Short recap + some further thoughts on the paper ⬇️ [1/7] www.cell.com/cell-genomic...

Matthew Aguirre@aguirre404.bsky.social · 12mo ago

Thrilled to share the second half of my PhD work here! We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/) doi.org/10.1101/2025...

Today is the last day to apply‼️ Thank you everyone for the incredible interest so far! We are especially looking for more folks with experience or willingness to learn and support trainees in metagenomics, microbiome, and/or bacterial/viral genetics 🧬. Spread the word!

Tami Gjorgjieva@tamigj.bsky.social · 3mo ago

Hi Genetics/Comp-Bio community 👋 Interested in mentoring a comp-bio research student in East Africa over the summer? Do you have any experience in bioinformatics, biostats, genome/RNA-seq analyses, ML, or metagenomics? We'd love to have you as a mentor in our new program! 🧵 (1/n)

Hi Genetics/Comp-Bio community 👋 Interested in mentoring a comp-bio research student in East Africa over the summer? Do you have any experience in bioinformatics, biostats, genome/RNA-seq analyses, ML, or metagenomics? We'd love to have you as a mentor in our new program! 🧵 (1/n)

Why do schizophrenia GWAS signals look so flat across the genome? In our recent preprint, we explored why psychiatric disorders — and, more broadly, brain-related traits involving the central nervous system — appear to have unusual genetic architectures. 🧵1/n

New paper alert 🚨 w/ @NoahRosenberg, out in EJHG (www.nature.com/articles/s41...) 🧵

Toward minimal SNP sets for record-matching with CODIS STR profiles - European Journal of Human Genetics

European Journal of Human Genetics - Toward minimal SNP sets for record-matching with CODIS STR profiles

nature.com

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)

Staff scientist position (computational): I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record. #sciencejobs

What a joy to work on exciting science AND do it with a great friend like @itskatelawrence.bsky.social! Check out her 🧵 on our recent preprint with @sbmontgom.bsky.social:

Kate (Kathryn) Lawrence@itskatelawrence.bsky.social · last yr.

Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️

Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease? I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵

Thrilled to share the first paper of my PhD! It was so much fun working on this collaborative project from day one as a rotation student! Huge thanks @khoulahan.bsky.social, @lisemangiante.bsky.social, @crissotomayor.bsky.social, @cncurtis.bsky.social, Jennifer Caswell-Jin & the Curtis lab!

Katie Houlahan@khoulahan.bsky.social · 2y ago

The Curtis Lab’s latest study on the genomic architecture of breast cancer from the pre-invasive to metastatic setting is now out in Nature! www.nature.com/articles/s41...

What do GWAS and rare variant burden tests discover, and why? Do these studies find the most IMPORTANT genes? If not, how DO they rank genes? Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬) www.biorxiv.org/content/10.1...

Specificity, length, and luck: How genes are prioritized by rare and common variant association studies

Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...

biorxiv.org

In a new preprint led by @TheNikhilMilind, we explored a fascinating paradox: For many traits the number of duplications or loss-of-function (LoF) mutations is correlated with phenotype. Curiously, for most traits, the AVERAGE direction of LoFs and Dups is the SAME. Why?

Just posting this to #popgen Here's a link to my notes on population & quantitative genetics: github.com/cooplab/popg... Hoping to extend it more after the winter holidays, as I'm just finishing up teaching the undergrad version of class.

Releases · cooplab/popgen-notes

Population genetics notes. Contribute to cooplab/popgen-notes development by creating an account on GitHub.

github.com

🧬 What are protein language models (PLMs) actually learning about biology? Our paper introduces InterPLM - a framework that reveals interpretable features in PLMs using sparse autoencoders, giving us a window into how these models represent protein structure and function. 🧵(1/8)

I’ve decided to leave Scientific American after an exciting 4.5 years as editor in chief. I’m going to take some time to think about what comes next (and go birdwatching), but for now I’d like to share a very small sample of the work I’ve been so proud to support (thread)