It’s finally time to welcome someone new into our mission. We’re hiring a Community Manager to help shape and support the growing scverse ecosystem. This is a position we’ve been looking forward to and I couldn’t be more excited to pass this opportunity on to someone new.

Excited to share new preprint led by Sergio Salas on “unassigned RNAs” in imaging-based spatial transcriptomics. Across technologies, 30-40% of transcripts fall outside segmentation, & many show structured, biologically meaningful extrasomatic patterns. 📄 www.biorxiv.org/content/10.6...

Proud to close out an incredible year with an update on where scverse is today and where we’re heading. I’d love for you to join me, share your ideas, challenge us, and help shape what comes next. It’s time! 💪

As more single-cell perturbation data become available, it is crucial to establish a consensus on measures of success for perturbation prediction models. I reviewed recent literature and collected some thoughts on the current state of affairs. open.substack.com/pub/giovanni...

We wrapped up an inspiring week with a visit to NVIDIA headquarters right after the scverse conference. Huge thanks to the NVIDIA Healthcare team and @severin7.bsky.social for hosting us and for the great discussions on scaling single-cell analysis and accelerating open science ⚡️

We will have our next community meeting on Tuesday, 2025-11-25 at 11:00 CST! Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI! More information and Zoom registration link in 🧵

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 😄

It’s rare to have the core of innovation in one place, but the scverse conference 2025 made it happen. @biohub.org x NVIDIA x @scverse.bsky.social : three forces, one room, endless acceleration.

What a suitable moment to have a community meeting by @maltekuehl.com and @biocontext.ai! Since we didn’t manage to have him on the conference, join us next Tuesday! 💪❤️

John Marioni at the @scverse.bsky.social conference 2025! “Make sure you understand first when complex methods are valuable” 💪

🤖🧬 New biomedical MCP server added to the registry: anndata-mcp Check it out at https://biocontext.ai/registry/biocontext-ai/anndata-mcp

We will have our next community meeting on Tuesday, 2025-11-11 at 11:00 CST! Eric Armingol will be presenting on scCellFie! More information and Zoom registration link in 🧵

You asked, we delivered! Online participation is now live.

We will have our next community meeting on Tuesday, 2025-11-11 at 11:00 CST! Eric Armingol will be presenting on scCellFie! More information and Zoom registration link in 🧵

We will have our next community meeting on Tuesday, 2025-10-28 at 18:00 CEST! @kexinhuang.bsky.social will be presenting on Biomni: Building a Virtual Biomedical Scientist. (Zoom registration link and more information in thread!) 🧵

How amazing that Genentech supports us and will have such a strong representation at the @scverse.bsky.social conference! 🙏

How amazing that Genentech supports us and will have such a strong representation at the @scverse.bsky.social conference! 🙏

🌟 Thank You to Our Silver Sponsor: Proteintech! 🌟 We're excited to recognize Proteintech as a Silver Sponsor of scverse conference 2025! 🥈 @proteintech.bsky.social #scverse2025 #Proteintech #ComputationalBiology #SingleCell #Antibodies #ProteomicsTools #SpatialOmics #Bioinformatics

👉 and make sure not to miss the one-and-only Romain Lopez's talk about PhenoBridge, our joint work on ML approaches to integrate perturb-seq and genetic association data (Wed 10.45am) Come find me or just reach out if you'd like to chat! [2/2]

En route to Boston for #ASHG25 #ASHG2025! 👉 I'll be presenting a poster on our new work on genome-wide perturb-seq screens in primary human T cells (5049W, Wed 2.30pm) 👉 you can hear me talk about it at the Industry Education session presented by Ultima Genomics (Thu 3pm) [1/2]

While the conference is underway, business as usual! 💪

Last chance for the early-bird 🐣 Join us!

🌟 Thank You to Our Gold Sponsor: Stellaromics! 🌟 We're proud to recognize Stellaromics as a Gold Sponsor of scverse conference 2025! 🥇 @stellaromics.bsky.social #scverse2025 #SpatialBiology #3DSpatial #ComputationalBiology #SingleCell #Stellaromics #SpatialOmics #Bioinformatics

We will have our next community meeting on Tuesday, 2025-10-14 at 18:00 CEST! Yimin Zheng will be presenting on LazySlide, a Python framework for whole slide image (WSI) analysis. (Zoom registration link and more information in thread!) 🧵

ICYMI! 🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀 We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025! More information in 🧵 #scverse2025 #Bioinformatics #AgenticAI #Conference

🤖🧬 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