Lukas Heumos
@lukasheumos.bsky.social
Research software engineer at Lamin Labs | Steering council at scverse | Postdoc at Fabian Theis lab
Reposted by Lukas Heumos
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...
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...
anndataR: converting single-cell data, from R to python and back – Thomas Sandmann’s blog
tomsing1.github.io
February 17, 2026 at 3:08 PM
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...
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
February 5, 2026 at 2:00 PM
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
Reposted by Lukas Heumos
🚀 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/...
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…
www.synergy-munich.de
February 3, 2026 at 5:52 PM
🚀 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/...
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/...
Reposted by Lukas Heumos
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
January 14, 2026 at 9:37 AM
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...
Reposted by Lukas Heumos
Pertpy: a one-stop and performant framework for single-cell perturbation analysis. @lukasheumos.bsky.social @fabiantheis.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 14, 2026 at 4:20 PM
Pertpy: a one-stop and performant framework for single-cell perturbation analysis. @lukasheumos.bsky.social @fabiantheis.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Lukas Heumos
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
January 5, 2026 at 6:42 PM
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
Reposted by Lukas Heumos
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 (...
www.biorxiv.org
January 3, 2026 at 6:18 PM
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
Reposted by Lukas Heumos
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/
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/
Jobs - mackelab
The MackeLab is a research group at the Excellence Cluster Machine Learning at Tübingen University!
www.mackelab.org
November 28, 2025 at 1:54 PM
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/
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/
Reposted by Lukas Heumos
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 😄
November 21, 2025 at 5:37 PM
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
BioContextAI is a community hub for agentic biomedical systems - @puellesv.bsky.social @biocontext.ai go.nature.com/3JmqKux
BioContextAI is a community hub for agentic biomedical systems - Nature Biotechnology
Nature Biotechnology - BioContextAI is a community hub for agentic biomedical systems
go.nature.com
November 6, 2025 at 7:28 PM
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
Reposted by Lukas Heumos
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
Erika Alden DeBenedictis, Co-founder of The Align Foundation 🧵
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
November 4, 2025 at 4:38 PM
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
Erika Alden DeBenedictis, Co-founder of The Align Foundation 🧵
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
Reposted by Lukas Heumos
🌟 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
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
October 16, 2025 at 3:11 PM
🌟 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
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
Reposted by Lukas Heumos
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! 🖥️🧬
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!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
October 10, 2025 at 1:02 PM
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! 🖥️🧬
Reposted by Lukas Heumos
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
Submissions and travel grant applications close in 3 days. Find out more and apply at scverse.org/conference2025
@scverse.bsky.social
September 12, 2025 at 8:11 PM
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
Submissions and travel grant applications close in 3 days. Find out more and apply at scverse.org/conference2025
@scverse.bsky.social
Reposted by Lukas Heumos
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!
August 26, 2025 at 6:50 PM
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 .
August 18, 2025 at 8:31 PM
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 .
Reposted by Lukas Heumos
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
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
August 13, 2025 at 5:51 AM
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
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.
August 8, 2025 at 5:56 PM
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.
Reposted by Lukas Heumos
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...
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...
July 29, 2025 at 12:41 PM
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...
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...
Reposted by Lukas Heumos
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!)
(Zoom registration link and more information in thread!)
June 23, 2025 at 4:00 PM
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!)
(Zoom registration link and more information in thread!)
Reposted by Lukas Heumos
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 😉👇
🔧 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/
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/
June 12, 2025 at 11:32 AM
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 😉👇
Reposted by Lukas Heumos
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.
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
March 28, 2025 at 4:53 PM
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.
Inspired by ideas in www.nature.com/articles/s41... and github.com/VPetukhov/GP..., implemented as an scVerse ecosystem package with docs and tutorials.
Reposted by Lukas Heumos
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...
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
April 14, 2025 at 10:41 PM
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...
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...
Reposted by Lukas Heumos
We are back 🔥
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...
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
April 14, 2025 at 10:45 PM
We are back 🔥
Reposted by Lukas Heumos
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
Free to read here: rdcu.be/eabUB
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...
go.nature.com
February 17, 2025 at 12:15 PM
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
Free to read here: rdcu.be/eabUB