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Reposted by Emma Dann

scverse @scverse.bsky.social · 5d

🚀 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

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Reposted by Emma Dann

scverse @scverse.bsky.social · Sep 2

🧬 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

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Reposted by Emma Dann

scverse @scverse.bsky.social · Sep 1

🎉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

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Reposted by Emma Dann

scverse @scverse.bsky.social · Aug 28

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

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Reposted by Emma Dann

scverse @scverse.bsky.social · Aug 26

🧫 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

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Emma Dann @emmamarydann.bsky.social · Aug 25

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 · Aug 25

💰 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

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Reposted by Emma Dann

scverse @scverse.bsky.social · Aug 19

🧠 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

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Reposted by Emma Dann

scverse @scverse.bsky.social · Aug 2

🎉 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

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Reposted by Emma Dann

Jonathan Pritchard @jkpritch.bsky.social · Jun 1

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.

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Emma Dann @emmamarydann.bsky.social · May 12

It's happening! 🙌

scverse @scverse.bsky.social · May 12

📣 Mark your calendars! The 2025 edition of the scverse conference will take place on 17-19 November at Stanford University (US) scverse.org/conference20...

Call for abstracts and registrations coming soon!

scverse conference 2025

Follow us on our channels to learn more details in the coming weeks

scverse.org

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Reposted by Emma Dann

scverse @scverse.bsky.social · Feb 14

🎉 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

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Reposted by Emma Dann

Sophie Belman @sophiebelman.bsky.social · Feb 9

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

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Reposted by Emma Dann

scverse @scverse.bsky.social · Feb 5

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

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Reposted by Emma Dann

Wolfgang Huber @wkhuber.bsky.social · Jan 31

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...

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Reposted by Emma Dann

Florian Jug @florianjug.bsky.social · Jan 29

🚨🚨 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

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Reposted by Emma Dann

Jonathan Pritchard @jkpritch.bsky.social · Jan 27

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 · Jan 26

GWAS 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...

Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq

Genetic association studies provide a unique tool for identifying causal links from genes to human traits and diseases. However, it is challenging to determine the biological mechanisms underlying mos...

www.biorxiv.org

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Emma Dann @emmamarydann.bsky.social · Jan 26

@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 · Jan 26

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 🧵

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Reposted by Emma Dann

Jonathan Pritchard @jkpritch.bsky.social · Jan 24

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

bioRxiv Genetics @biorxiv-genetic.bsky.social · Jan 24

Causal 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

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Reposted by Emma Dann

Giacomo Bartolucci (he) @gbart.bsky.social · Jan 4

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

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Reposted by Emma Dann

Constantin Ahlmann-Eltze @const-ae.bsky.social · Jan 3

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⬇️

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

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Reposted by Emma Dann

Jeff Spence @jeffspence.github.io · Dec 17

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...

www.biorxiv.org

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Reposted by Emma Dann

bioRxiv Genomics @biorxiv-genomic.bsky.social · Dec 16

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

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Reposted by Emma Dann

Jonathan Pritchard @jkpritch.bsky.social · Dec 11

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...

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.

www.nature.com

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Reposted by Emma Dann

Gregor Sturm @grst.bsky.social · Dec 7

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/

# 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")
)

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Reposted by Emma Dann

Mr. Chau @srirachachau.bsky.social · Nov 16

Seeing all my old friends on here again

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