Lukas Heumos

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

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…

🚀 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/...

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 ...

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...

Pertpy: a one-stop and performant framework for single-cell perturbation analysis. @lukasheumos.bsky.social @fabiantheis.bsky.social

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

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, ...

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

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 (...

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

How many hours is the whole WOT series? It must be a lot

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/

All scverse attendees

scverse conference organizers

First session

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

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

"Usability besides performance is also key."

Cannot stress this enough. There's a ton of methods out there that might not even be the best but are used because a substantial amount of time was invested into making it fast, accessible, and documented. Such methods are benchmarked in real use cases

🌟 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! 🖥️🧬

I see where you're coming from but what is your opinion on scientific-python.org/specs/spec-0... then? I find it valuable that the pydata ecosystem moves together.

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.

Diagram showing MCP-enabled research architecture. Part A illustrates the flow between MCP servers (including BioContextAI Knowledgebase MCP and Community-developed MCP servers), Agentic systems connected via Model Context Protocol, and researchers asking research questions. MCP servers connect to knowledgebases and specialized software. Part B details the BioContextAI project components, divided into Registry (Schema.org ontology, Web interface, Open source licensing, MCP-enabled chatbot, Continuous integration) and Community (Documentation, Community forums, MCP server reviews, Shareable collections, Interoperability with tools like BioChatter).

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 😉👇

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

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 - 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

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...

We are back 🔥

Best practices for single-cell analysis across modalities - Nature Reviews Genetics Practitioners in the field of single-cell omics are now faced with diverse options for analytical tools to process and integrate data from various molecular modalities. In an Expert Recommendation art...

Best practices for single-cell analysis across modalities go.nature.com/4gJkk3c #ExpertRecommendation by @lukasheumos.bsky.social et al. (from the @fabiantheis.bsky.social lab) - now nearing 250k accesses!
Free to read here: rdcu.be/eabUB

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: