Emma Dann

🎉 scverse conference 2025 Registration & Call for Abstracts NOW OPEN! 🎉
We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025!
Details in thread!
🧵 1/3

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.

It's happening! 🙌

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...

🎉 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:

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

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

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...

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...

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...

@minetoota.bsky.social set the groundwork for many ongoing projects in @jkpritch.bsky.social and Marson lab. Great to see this out!

Very excited about this new work from our lab! Explainer thread coming soon
@minetoota.bsky.social

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

Overview of the LEMUR steps: (1) subspace alignment, (2) differential expression, (3) DE neighborhoods, (4) pseudobulking.

After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳

www.nature.com/articles/s41...

LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.

Some highlights⬇️

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...

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 https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1

Central control of dynamic gene circuits governs T cell rest and activation - Nature Resting and activated T cell states are established by context-specific regulators and dynamic gene circuits.

Beautiful work led by Maya Arce from Marson lab reveals a fascinating story about rewiring of a critical gene regulatory circuit in different T cell types: T effectors and Tregs
www.nature.com/articles/s41...

# Define model with interaction term model = MyModel(data, "~ treatment * timepoint") # compare timepoints contrast = model.cond(timepoint="on_treatment") - model.cond(timepoint="baseline") # compare timepoints within drugA only contrast = ( model.cond(treatment="drugA", timepoint="on_treatment") - model.cond(treatment="drugA", timepoint="baseline") ) # compare interaction of timepoint with treatment # (= difference of changes between both treatments) contrast = ( mod.cond(treatment="drugB", timepoint="on_treatment") - mod.cond(treatment="drugB", timepoint="baseline") ) - ( mod.cond(treatment="drugA", timepoint="on_treatment") - mod.cond(treatment="drugA", timepoint="baseline") )

Formulaic is the go-to way to specify design formulas in Python, e.g. ~treatment + timepoint.

To compare sth, one needs to specify a contrast, e.g "on treatment vs baseline".

To make this easier, we developed "formulaic-contrasts":
formulaic-contrasts.readthedocs.io/en/latest/

Seeing all my old friends on here again

Explore the scverse Starter Pack!

Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d

For many traits there is a correlation between the number of duplications or loss-of-function (LoF) mutations someone carries, and their phenotype. Curiously, for most traits, these effects are aligned in the SAME direction. Why?