🤖🧬 New biomedical MCP server added to the registry: OMOP MCP Server Check it out at https://biocontext.ai/registry/OHNLP/omop_mcp

Fantastic lineup of panelists to discuss everything agentic coding in bioinformatics, still time to register here: www.eventbrite.com/e/scverse-co...

Can’t wait 😱

🌟 Thank You to Our Diamond Sponsor: Tahoe Therapeutics! 🌟 We're thrilled to announce that Tahoe Therapeutics is supporting scverse conference 2025 as a Diamond Sponsor! 💎 Details in thread! 🧵 @tahoetherapeutics.bsky.social #ComputationalBiology #SingleCell #DrugDiscovery #TahoeTherapeutics

🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights. 🔗 www.biorxiv.org/content/10.1...

🔬 CZI Workshop at scverse 2025 🔬 Multimodal And Spatial Single Cell Data: From Data APIs to AI-driven Biological Discovery 🧵 @chanzuckerberg.bsky.social #scverse2025 #SingleCell #SpatialOmics #CELLxGENE #VirtualCells #AIBiology

🧬 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

🎉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

Simple advice on choosing research projects This video has been a long time coming. It reflects my thoughts on how to wisely choose which projects to work on, balancing the risk, reward, and work required. youtu.be/D5FBB7OPrLw

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

We will have our next community meeting on Tuesday, 2025-09-02 at 18:00 CEST! Emma Dann will be presenting on "Mapping genetic effects on complex traits with single-cell perturbation data". 🧵

🧫 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

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!

My supervisor, John Marioni, will be giving a keynote at the scverse conference. His contributions to single-cell and spatial transcriptomics have shaped much of the field, and I’m looking forward to hearing his perspective on where computational biology is headed.

@panosroussos.bsky.social will be one of the keynote speakers at the @scverse.bsky.social conference. Looking forward to his talk and the rare chance to have him on the West Coast.

We’re doing this. Come hang with us at Stanford in November. scverse people, real talks, and all things single-cell. Don’t miss it. 💪

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...

The final version of our multi-omics study on kidney fibrosis is out now (tinyurl.com/kidneyfibMSB). Together w/ Pepperkok + Savitski labs @embl.org, we present a time-resolved #multiomics + computational network modeling approach in combination w/ phenotypic assays to study #kidneyfibrosis

Great open-source QC reporting tool from @robp.bsky.social Rob Patro’s group, member of our management committee!

We are hiring! Together with Ana Carolina de Sousa Leote, I am looking for two Computational Biology interns to join us at Genentech in South San Francisco. Deadline June 26. Apply here: roche.wd3.myworkdayjobs.com/ROG-A2O-GENE...

We will have our next community meeting on Tuesday, 2025-06-10 at 18:00 CEST! @Sergei will speak about MappedCollection. (Zoom registration link and more information in thread!)

Honored to be part of the @scverse.bsky.social journey. Past, present, and future. All things single-cell and spatial. All open. Let’s keep going.

The scverse conference is new (last year was the first one), but it was a blast! If you work in single-cell omics, this is a great meeting; especially if you care about methods, community, and open science!

It’s happening 💪

Just released a new version of the @scverse.bsky.social cookiecutter template: github.com/scverse/cook... Some highlights: 🔃 improved template sync (merge conflicts now show up as such) 🚀 use hatch as project manager 🔧 lots of fixes and documentation updates

Our 3D study of the tumor microenvironment is finally out! Play around with the data yourself at lung-3d-browser.mdc-berlin.de (Kudos to @danilexn.bsky.social👏 ) Many thanks to Nikolaus Rajewsky lab at @mdc-bimsb.bsky.social and everyone involved, it takes a village to raise a multimodal paper!

The @chanzuckerberg.bsky.social Cell Science Meeting in Chicago just concluded. I had the opportunity to present the latest advancements in spatial omics within the #scverse ecosystem, highlighting our efforts to scale our infrastructure in preparation for the datasets of tomorrow.

We are back 🔥

We just released v0.7.1 of our long-read RNA-seq quantification tool `oarfish` (github.com/COMBINE-lab/...)! The main new feature in this release is silent to the user, but kind of cool, so I thought I'd describe it briefly :). So ...

A pre-trained SCVI model of our Tahoe-100M cell atlas is now available as a HubModel! It can be used for gene expression visualization, differential expression, or cell clustering. Available at Hugging Face with instructions on how to load it (see thread)

Should scientists leave Twitter? Pros: It's a form of protest against an ecosystem that may no longer be a safe or inclusive space, under Elon Musk. Cons: It may not serve the best interests of science communication because it cedes an influential space to misinformation. @ivanoamelio.bsky.social

Join us Tuesday at 2025-03-04 18:00 CET! @berombau.bsky.social from @saeyslab.bsky.social will speak about Harpy, a tool to analyze spatial proteomics data . For more information, check out the GitHub:buff.ly/MUT81ar & lab website : buff.ly/RJUDHJZ - Zoom link can be found here: buff.ly/y0MmT65

This Tuesday at 2025-03-04 18:00 CET, Benjamin Rombaut @berombau.bsky.social will speak about Harpy, a spatial proteomics tool, as well as other tools from the Saeys lab @saeyslab.bsky.social ! For more information, check out the Github: buff.ly/3XnViQl , and lab website: buff.ly/3XlL6HX !

The first version of NetworkCommons is now published in Bioinformatics. Next, we’ll focus on involving more of the network biology community. academic.oup.com/bioinformati... In parallel, we’ll continue expanding benchmarks and developing new applications. Interested in contributing? Reach out! ⬇️

Join us Tuesday at 2025-02-18 18:00 CET! Marius Lange will speak about Moslin, a new algorithm to map cells across time and lineage. For more information, check out the GitHub: https://buff.ly/4hTO522 & publication: https://buff.ly/41gcQzZ

🎉 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:

On Tuesday at 2025-02-04 18:00 CET, @jkobject will talk about scPrint, a transformer model that infers gene networks from scRNA-seq data, at our 2nd community meeting of 2025! For more information, check out the GitHub: https://buff.ly/40RJ3gT & pre-print https://buff.ly/4hwK4Av

Recently, we held the first #scverse SpatialData 3-day hackathon in Basel (Switzerland), where we brought together 20 developers from the Python, R, and web communities to work on interoperability, performance, and ergonomics for spatial omics data. Here is what we worked on!

Two years after publication of our single-cell lung cancer atlas, a user found a mistake in the annotation of the EGFR-status of some patients. We fixed the issue and the atlas is now updated on cell-x-gene: cellxgene.cziscience.com/collections/... What are the takeaways from that? (1/3)

We are back! 🎉 See you all soon!

Last YouTube presentation made while at UCPH (didn't get it recorded and edited till now due to Christmas and computer issues). This time it is a deeper dive into how STRING uses text mining. youtu.be/A_AZC5nVKbk

The final chapter of my PhD thesis is now out! 🎉 We compared the latest gene regulatory network (#GRN) inference methods for #single-cell multimodal datasets and evaluated their performance across various tasks. Hard to believe this journey started in March 2021 and has finally reached this point 😅🥳

Being part of something greater than the sum of its parts has been a revelation. Another year with the scverse core team has been an incredible journey. Grateful to everyone who contributed – your dedication makes it all possible. Excited for what we will achieve in 2025!

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

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...

Next Tuesday at 2024-12-10 18:00 CET, we will hold the last community meeting of the year! @lukasheumos.bsky.social will talk about pertpy, a Python-based modular framework for the analysis of large-scale perturbation single-cell experiments. The GitHub repo: github.com/scverse/pertpy

Noor (@noorpratap.bsky.social) has been working on this for quite some time! It took a bit of work to figure out, but now you can map your scATAC-seq reads directly to the genome and sort and dedup them with alevin-fry-atac. You get a BED file with counts ready for downstream analysis! 1/

Reminder! Today at 18:00 CET will be another community meeting! Malte Lücken will talk about about Open Problems in Single-Cell Analysis. Zoom link can be found here:

🚀 We're #Hiring #PhD students at #MLBio Lab at @EPFL through the #EDIC Program! 📅 Deadline: Dec 15 💥 We're part of School of Computer Science and School of Life Sciences at EPFL which gives access to excellent collaborators, network, and resources! 👉 Learn more at brbiclab.epfl.ch!

To expedite the development of a network focussed on single-cell and spatial genomics on this platform, I started to collect accounts of scientists & groups that are broadly active in these fields. This is work in progress, DM if you want to be added or have suggestions! go.bsky.app/HZTJxbZ