Lukas Heumos
@lukasheumos.bsky.social
Research software engineer at Lamin Labs | Steering council at scverse | Postdoc at Fabian Theis lab
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!
🎉 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
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
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
Reposted by Lukas Heumos
🎉 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:
- 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
February 14, 2025 at 12:08 PM
🎉 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:
- sc.pp.sample replaces subsample with many new features
- Sparse Dask support pca
- session-info2 package for more reproducible notebooks
See the release notes:
We have additional available spots. Please consider joining! It will be a blast.
I am Stoked about our upcoming @scverse.bsky.social
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: 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
January 30, 2025 at 4:24 PM
We have additional available spots. Please consider joining! It will be a blast.
I keep being astonished at how terrible @microsoft.com Teams works on Firefox and I certainly don't blame Mozilla for it.
January 22, 2025 at 9:46 AM
I keep being astonished at how terrible @microsoft.com Teams works on Firefox and I certainly don't blame Mozilla for it.
Ahhh finally I can use @nextflow.io to run doom! github.com/nextflow-io/...
GitHub - nextflow-io/doom: A Nextflow pipeline to play Doom
A Nextflow pipeline to play Doom. Contribute to nextflow-io/doom development by creating an account on GitHub.
github.com
January 21, 2025 at 9:55 AM
Ahhh finally I can use @nextflow.io to run doom! github.com/nextflow-io/...
I am Stoked about our upcoming @scverse.bsky.social
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: 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
January 17, 2025 at 10:34 AM
I am Stoked about our upcoming @scverse.bsky.social
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
Why is there still no proper "thank you" emoji on @github.com ? I am grateful for other peoples time and feel like a thumbs up is kind of like a drive by reaction and a heart isn't always perfectly appropriate
January 14, 2025 at 12:51 PM
Why is there still no proper "thank you" emoji on @github.com ? I am grateful for other peoples time and feel like a thumbs up is kind of like a drive by reaction and a heart isn't always perfectly appropriate
I actually think that it' awesome that even fundamental packages like numpy, pandas, scipy, and others still develop rapidly and aren't afraid of making big API changes but it's quite time consuming to keep up when one maintains many packages. I can't imagine what e.g. the numba devs go through
January 10, 2025 at 4:57 PM
I actually think that it' awesome that even fundamental packages like numpy, pandas, scipy, and others still develop rapidly and aren't afraid of making big API changes but it's quite time consuming to keep up when one maintains many packages. I can't imagine what e.g. the numba devs go through
I was just looking at our @scverse.bsky.social zulip chat statistics and am super happy about our steady and healthy growth. The two bursts are our official launch in May 2022 and the inaugural scverse conference in September of 2024. Please join us! scverse.zulipchat.com
December 15, 2024 at 3:52 PM
I was just looking at our @scverse.bsky.social zulip chat statistics and am super happy about our steady and healthy growth. The two bursts are our official launch in May 2022 and the inaugural scverse conference in September of 2024. Please join us! scverse.zulipchat.com
Reposted by Lukas Heumos
Reminder!Today at 18:00 CET will be the last community meeting of the year! @lukasheumos.bsky.social will talk about about pertpy, a Python-based modular framework for the analysis of large-scale perturbation single-cell experiments. Zoom link can be found here: scverse.zulipchat.com#narrow/chann...
December 10, 2024 at 12:24 PM
Reminder!Today at 18:00 CET will be the last community meeting of the year! @lukasheumos.bsky.social will talk about about pertpy, a Python-based modular framework for the analysis of large-scale perturbation single-cell experiments. Zoom link can be found here: scverse.zulipchat.com#narrow/chann...