Happy to announce the release of IggyTop, a metadatabase for immune receptor–epitope interactions. It's integrated with scirpy v0.24 so you can readily use it to annotate your single-cell TCR datasets. iggytop.readthedocs.io/en/latest/

This started as a collaboration with biocypher (@slobentanzer.bsky.social) at a @scverse.bsky.social hackathon, was then advanced by @valeriiadragan.bsky.social as a master thesis project and finally pushed over the finish line by Raphael De Gottardi

scverse conference 2026 will take place in Copenhagen, October 12–14. ✨ Three days of all-things-single-cell and open-source tooling and community in real life. More details soon but for now, mark your calendars. scverse.org/conference20... See you in Copenhagen 🇩🇰

scverse conference 2026

scverse.org

Last week I attended a SpatialData hackathon with members of the @scverse.bsky.social, @bioconductor.bsky.social and @openmicroscopy.org communities in Padua, Italy. Here is a short blog post about the experience www.data-intuitive.com/insights/blo....

2nd SpatialData Hackathon – Data Intuitive

Frameworks, formats and Interoperability

data-intuitive.com

The main challenge was extending pandera-based schema validation to the complicated structure of SpatialData; Parquet and AnnData are easier! Blog: blog.lamin.ai/spatialdata Code: github.com/laminlabs/la... With @lukasheumos.bsky.social and many others!

Excited to share new preprint with NVIDIA on GPU-accelerated single-cell analysis 🚀 rapids-singlecell brings native GPU support to scverse/AnnData: hours → seconds (1M cells: ~52m → ~25s), scaling to 100M cells. Huge thanks to Severin Dicks 🙌 📄 arxiv.org/abs/2603.02402

We're excited to announce that registration for our upcoming Spatial Omics workshop has opened! Details in 🧵

Nice blog post from @thomas-sandmann.genomic.social.ap.brid.gy testing out {anndataR} 📦 tomsing1.github.io/blog/posts/a... 🎉! Cool to see people trying it out, find it on @bioconductor.bsky.social if you want to give it a go bioconductor.org/packages//re...

It's kind of insane that I need a firefox addon for every LLM chat interface to enforce usage of the (full) width of my screen

🚀 Interested in a postdoc in computational biology & AI for neuroscience? The NOMIS Synergy Fellowship offers a great opportunity to develop such a position in my lab within the interdisciplinary Synergy excellence cluster. 🔗 www.synergy-munich.de/news-events/...

NOMIS–SyNergy Fellowship Program in Systems Neurology (Munich, Germany) | SyNergy - Munich Cluster for Systems Neurology

The NOMIS Foundation, in collaboration with the DFG-funded Munich Cluster for Systems Neurology (SyNergy), invites exceptional early-career scientists from around the world to apply for elite…

synergy-munich.de

Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Scientific Workflows Developer

The European Molecular Biology Laboratory (EMBL) is Europe’s life sciences laboratory – an intergovernmental organisation with more than 110 independent research groups and service teams covering the ...

embl.wd103.myworkdayjobs.com

Pertpy: a one-stop and performant framework for single-cell perturbation analysis. @lukasheumos.bsky.social @fabiantheis.bsky.social www.nature.com/articles/s41...

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

While we've been somewhat successful in spurring adoption of alevin-fry/simpleaf for scRNAseq processing, an impediment Dongze brought to our attention (now working directly w/ many experimentalists) was the need for a nice QC report for it's output; hence QCatch www.biorxiv.org/content/10.1... 1/x

QCatch: A framework for quality control assessment and analysis of single-cell sequencing data

Motivation: Single-cell sequencing data analysis requires robust quality control (QC) to mitigate technical artifacts and ensure reliable downstream results. While tools like alevin-fry and simpleaf (...

biorxiv.org

We are looking for a Research Engineer (E13 TV-L) to work at the intersection of #ML and #compneuro! 🤖🧠 Help us build large-scale bio-inspired neural networks, write high-quality research code, and contribute to open-source tools like jaxley, sbi, and flyvis 🪰. More info: www.mackelab.org/jobs/

scverse conference 2025 done ✅ Really engaging week at Stanford with scPerturb-seq work, agentic models in biology, and strong interest in scaling software to millions of cells. Organizing alongside the rest of the @scverse.bsky.social team was a blast! Hope attendees found it productive 😄

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 ago

BioContextAI is a community hub for agentic biomedical systems - @puellesv.bsky.social @biocontext.ai go.nature.com/3JmqKux

Meet the keynote speakers for the 2025 scverse conference! Erika Alden DeBenedictis, Co-founder of The Align Foundation 🧵 @erika-alden.bsky.social @alignbio.bsky.social @pioneerlabs.bsky.social #scverse #scverse2025 #StructuralBiology #Biotech #Stanford

🌟 Thank You to Our Platinum Sponsor: 10x Genomics! 🌟 We're delighted to recognize 10x Genomics as a Platinum Sponsor of scverse conference 2025! 🏆 @10xgenomics.bsky.social #scverse2025 #ComputationalBiology #SingleCell #SpatialOmics #10xGenomics #Bioinformatics #Biotechnology

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

Rob Patro@robp.bsky.social · 10mo ago

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j.... If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

My favorite part of last-year #scverse conference was to finally meet in-person many developers that I only knew from their GitHub username! Submissions and travel grant applications close in 3 days. Find out more and apply at scverse.org/conference2025 @scverse.bsky.social

scVerse conference is at Stanford this year! Encourage folks (especially Bay Area/West coast folks) to sign up and attend. Cool workshops/talks and other events + great community of developers for one of the most widely used open source software for single cell data analysis!

It is pretty heart warming to see people start their really good pull request with "this is my first open source contribution. I hope that this is good.". Everyone starts somewhere and we're always happy to guide at @scverse.bsky.social .

Our benchmark + guidelines for atlas-level differential gene expression of single cells is online: academic.oup.com/bib/article/... Bottom line: Use pseudobulk + DESeq2 in simple and pseudobulk + DREAM in more complex settings. Collab w/ @leonhafner.bsky.social @itisalist.bsky.social

I hate reference limits of journals so much. I'm sitting here trying to find a few more references to remove despite me knowing that I'll either remove context & evidence for scientific conclusions or not mention tools that very much deserve to be mentioned and cited.

Preprint alert 🚨 Do you use chatbots in your work or even build MCP servers and agentic systems yourself? Or would you like to find a way to use biomedical tools using natural language? Then check out biocontext.ai, now out on bioRxiv: www.biorxiv.org/content/10.1...

We will have our next community meeting on Tuesday, 2025-06-24 at 18:00 CEST! Sneha Mitra (@snehamitra.bsky.social) will speak about SCARlink. (Zoom registration link and more information in thread!)

Happy to have this finally out! Check out the updated vignettes and if something is broken please open a GitHub issue and I'll have a look 😉👇

Saez-Rodriguez Group@saezlab.bsky.social · last yr.

🔧 decoupler 2.0.6 is out thanks to @paubadiam.bsky.social‬, now as a core @scverse.bsky.social package scverse.org This release includes a streamlined API aligned with scverse standards, updated vignettes, and a new one on pseudotime enrichment analysis 👇 decoupler.readthedocs.io/en/latest/

Happy to share CellAnnotator, a lightweight Python package to query OpenAI models for initial cell type annotations: github.com/quadbio/cell... Inspired by ideas in www.nature.com/articles/s41... and github.com/VPetukhov/GP..., implemented as an scVerse ecosystem package with docs and tutorials.

GitHub - quadbio/cell-annotator: Automatically annotate cell types, consistently across samples.

Automatically annotate cell types, consistently across samples. - quadbio/cell-annotator

github.com

Tomorrow at 2025-04-15 18:00 CEST, we’ll have our next community meeting! Anastasia Litinetskaya will present “Multimodal integration and identification of disease-specific changes in single-cell atlases”. Check out the GitHub repo here: github.com/theislab/mul...

GitHub - theislab/multimil: Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases

Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases - theislab/multimil

github.com