Emma Dann
@emmamarydann.bsky.social
Postdoc fellow @ Stanford & Gladstone Institutes Core team @scverse-team.bsky.social Bringing the single-cell genomics in human complex trait genetics https://emdann.github.io/
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
🧬 2026 Internship: Marioni Group @genentech.bsky.social Seeking PhD intern for Deep Learning on large-scale genetic screens (Perturb-seq/Optical). Focus: ML for single-cell + imaging to decode phenotypes. 📍 SSF (On-site) | 12-wk paid ⚠️ Apply via portal only: 🔗 bit.ly/45P7TQB #CompBio #AI #Genetics
2026 Summer Intern (Computational Sciences - Cluster of Excellence)
2026 Summer Intern (Computational Sciences - Cluster of Excellence) The Marioni group in the Computational Sciences (CS) department studies the molecular mechanisms of cell fate decisions in early dev...
roche.wd3.myworkdayjobs.com
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time! doi.org/10.64898/202... 1/n
High false sign rates in transcriptome-wide association studies
Transcriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it r...
doi.org
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...
tinyurl.com
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult. Our latest work on causal models for this is out yesterday: www.nature.com/articles/s41... A short🧵:
Causal modelling of gene effects from regulators to programs to traits - Nature
Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
nature.com
Thank you Alex! Excited to see our paper published in @nature.com ! Huge thanks to @jeffspence.github.io , @tkyzeng.bsky.social , @emmamarydann.bsky.social, @nikhilmilind.dev, @marsonlab.bsky.social, @jkpritch.bsky.social, and all the members of the Pritchard and Marson labs for your enormous help!
Causal modelling of gene effects from regulators to programs to traits
Nature - Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
rdcu.be
Marson Lab@marsonlab.bsky.social · 8mo agoOur latest collaboration with @jkpritch.bsky.social – led by joint post-doc Mineto Ota – is in @nature.com today: www.nature.com/articles/s41...
@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪 www.nature.com/articles/d41...
How do genetic association studies rank genes?
Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.
nature.com
Excited to see a home for MCP servers in bioinformatics emerge! The community needs a central hub for developing MCP servers for key bioinfo tools. At @scverse.bsky.social we're contributing to this effort - can't wait to share what we're building
Nature Biotechnology@natbiotech.nature.com · 9mo agoBioContextAI is a community hub for agentic biomedical systems - @puellesv.bsky.social @biocontext.ai go.nature.com/3JmqKux
I'm recruiting a postdoc for my group (based in beautiful Eugene, OR). Please get in touch if you're interested, esp if you'd like to chat at #ASHG25!
Roshni Patel@roshnipatel.bsky.social · last yr.We'll primarily work at the intersection of statistical and population genetics, and we also have active projects related to the ethical and social implications of human genetics (ELSI). Please get in touch if that's a combination that sounds interesting to you!
Last call, scverse community! 🐦 Early-bird closes October 17 for the scverse Conference 2025. Single-cell, open science, and the people behind it — all in one place. 📝 Register here: www.eventbrite.com/e/scverse-co... 2 days of talks + 1 day of workshops ℹ️ Info: scverse.org/conference2025
🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀 We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025! More information in 🧵 #scverse2025 #Bioinformatics #AgenticAI #Conference
🧬 Tahoe Workshop at scverse conference 2025 🧬 Disease Biology and Therapeutics in the Age of Frontier Datasets 🧵 @tahoetherapeutics.bsky.social #scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
🎉scverse conference 2025 Call for Abstracts DEADLINE EXTENDED! 🎉 We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025! 🧵 #scverse #scverse2025 #SingleCell #Conference
Meet the keynote speakers for the 2025 scverse conference! Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University 🧵 @elhamazizi.bsky.social @columbiauniversity.bsky.social #scverse #scverse2025 #machinelearning #genomics #cancerimmunology
🧫 Meet the keynote speakers for the 2025 scverse conference! Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs @erika-alden.bsky.social @alignbio.bsky.social @pioneerlabs.bsky.social #scverse #scverse2025 #StructuralBiology #Biotech #Stanford
We're committed to support as many attendees as possible join us at #scverse2025 - feel free to reach out if you have questions!
scverse@scverse.bsky.social · 12mo ago💰 Travel Grants Available for scverse conference 2025! 💰 Did you know we are offering grants to help anyone in financial need attend our annual conference? 🌍 🧵 #scverse #scverse2025 #SingleCell #Conference #StanfordUniversity #TravelGrant
🧠 Meet the keynote speakers for the 2025 scverse conference! Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai 🧵 @panosroussos.bsky.social #scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required. Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
🎉 Scanpy 1.11.0 is out! 🎉 just after reaching 2000 stars on GitHub! - sc.pp.sample replaces subsample with many new features - Sparse Dask support pca - session-info2 package for more reproducible notebooks See the release notes:
Release notes
Version 1.11: 1.11.0 2025-02-14: Release candidates: rc2 2025-01-24, rc1 2024-12-20. Features: rc1 sample() supports both upsampling and downsampling of observations and variables. subsample() is n...
buff.ly
I’m racing a Half Ironman triathlon this June. 2km swim, 90km cycle, 20km run and raising money for the Meningitis Research Foundation. Meningitis has ~2.5 million cases and 250,000 deaths annually predominantly among children. Any donation would be great! gofund.me/a958252f
Donate to Half Iron(wo)man for Meningitis Research, organized by Sophie Belman
I will be racing my first Half Ironman triathlon in Zurich this June. It includ… Sophie Belman needs your support for Half Iron(wo)man for Meningitis Research
gofund.me
Don't forget to apply to the upcoming @scverse.bsky.social x @owkin.bsky.social hackathon - applications due this Friday, February 7th! 📆March 17-19, 2025 📍Owkin Office, Paris docs.google.com/forms/d/e/1F...
Scverse x Owkin Hackathon in Paris
We're pleased to announce the next Scverse Hackathon will take place in the Owkin offices in Paris from 17/03/2025 9am to 19/03/2025 1:30pm. This hackathon is a joint initiative between the scverse c...
docs.google.com
Come work at the European Molecular Biology Laboratory in the beautiful science & university city Heidelberg as a Research Software Engineer on R/Bioconductor tools for biological data science and AI ! embl.wd103.myworkdayjobs.com/EMBL/job/Hei...
🚨🚨 MEGA JOB ALERT 🚨🚨 Independent Group Leader Positions in Computational Biology @humantechnopole.bsky.social! Are you ready to start your own lab? Do you know someone who is? Repost this + share with everyone who might want to know about it. Thanks!!! 🙏 More details below... check it out! 🧵 1/3
I posted a couple days ago about our new paper on building causal graphs from genetic associations + Perturb-seq. Here I want to expand on the value of using DIRECTIONAL information contained in LoF burden tests.🧵 [work led by @minetoota.bsky.social ] bsky.app/profile/jkpr...
Jonathan Pritchard@jkpritch.bsky.social · 2y agoGWAS provides a unique tool in human biology as it can establish causal links from variants to trait. But interpretation is difficult as most effects flow through (unobserved) gene regulatory networks. Can we gain insight by linking to modern Perturb-seq data? www.biorxiv.org/content/10.1...
@minetoota.bsky.social set the groundwork for many ongoing projects in @jkpritch.bsky.social and Marson lab. Great to see this out!
Jonathan Pritchard@jkpritch.bsky.social · 2y agoModern 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 🧵
Very excited about this new work from our lab! Explainer thread coming soon @minetoota.bsky.social
bioRxiv Genetics@biorxiv-genetic.bsky.social · 2y agoCausal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq https://www.biorxiv.org/content/10.1101/2025.01.22.634424v1
1/n Some time ago my colleague, excellent cook, and friend Ivan told me: "Cacio e pepe is the recipe that I screw up more often. Let's make a project studying systematically the physics of that sauce". Prepare to get cheesy, I'm glad to share the Cacio e paper preprint: arxiv.org/abs/2501.00536
