iiinova — where your digital self keeps evolving

Reposted by Mikaela Koutrouli

Nature Biotechnology @natbiotech.nature.com · 27/03/2026

Unpaired data as a first-order challenge in single-cell and spatial proteomics - @mkoutrouli.bsky.social @panosroussos.bsky.social @scverse.bsky.social go.nature.com/3NHDkGP

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 31/03/2026

Two inspiring days in Berlin just wrapped up with our scverse hackathon on single-cell and spatial proteomics and it’s hard not to feel energized by what this community can do together.

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Mikaela Koutrouli @mkoutrouli.bsky.social · 12/12/2025

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.

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Reposted by Mikaela Koutrouli

Fabian Theis @fabiantheis.bsky.social · 10/12/2025

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...

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Mikaela Koutrouli @mkoutrouli.bsky.social · 03/12/2025

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! 💪

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Reposted by Mikaela Koutrouli

Giovanni Palla @giopll.bsky.social · 27/11/2025

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...

open.substack.com

Virtual Cell Perturbation Metrics Reloaded

Thoughts on metrics for perturbation prediction models

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 26/11/2025

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 ⚡️

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 24/11/2025

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 🧵

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Reposted by Mikaela Koutrouli

Pau Badia i Mompel @paubadiam.bsky.social · 21/11/2025

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 😄

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Mikaela Koutrouli @mkoutrouli.bsky.social · 19/11/2025

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.

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Mikaela Koutrouli @mkoutrouli.bsky.social · 19/11/2025

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! 💪❤️

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Mikaela Koutrouli @mkoutrouli.bsky.social · 17/11/2025

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

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Reposted by Mikaela Koutrouli

BioContextAI @biocontext.ai · 13/11/2025

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

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 10/11/2025

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 🧵

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Mikaela Koutrouli @mkoutrouli.bsky.social · 06/11/2025

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

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 05/11/2025

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 🧵

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 24/10/2025

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!) 🧵

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Mikaela Koutrouli @mkoutrouli.bsky.social · 22/10/2025

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

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Mikaela Koutrouli @mkoutrouli.bsky.social · 21/10/2025

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

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 14/10/2025

🌟 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

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Reposted by Mikaela Koutrouli

Emma Dann @emmamarydann.bsky.social · 14/10/2025

👉 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]

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Reposted by Mikaela Koutrouli

Emma Dann @emmamarydann.bsky.social · 14/10/2025

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]

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Mikaela Koutrouli @mkoutrouli.bsky.social · 13/10/2025

While the conference is underway, business as usual! 💪

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Mikaela Koutrouli @mkoutrouli.bsky.social · 10/10/2025

Last chance for the early-bird 🐣 Join us!

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 09/10/2025

🌟 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

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 08/10/2025

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!) 🧵

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 06/10/2025

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

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Reposted by Mikaela Koutrouli

BioContextAI @biocontext.ai · 03/10/2025

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

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Reposted by Mikaela Koutrouli

Giovanni Palla @giopll.bsky.social · 03/10/2025

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

eventbrite.com

Scverse Conference 2025

From the foundational open-source software in the life sciences — to its large community coming together

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 30/09/2025

🌟 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

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Reposted by Mikaela Koutrouli

Fabian Theis @fabiantheis.bsky.social · 28/09/2025

🚀 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...

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 04/09/2025

🔬 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

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 02/09/2025

🧬 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

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 01/09/2025

🎉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

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Reposted by Mikaela Koutrouli

Lars Juhl Jensen @larsjuhljensen.bsky.social · 01/09/2025

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

youtu.be

Choosing research projects: the risk–reward–work triangle

YouTube video by Lars Juhl Jensen

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 28/08/2025

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

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 27/08/2025

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". 🧵

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 26/08/2025

🧫 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

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Reposted by Mikaela Koutrouli

Anshul Kundaje @anshulkundaje.bsky.social · 26/08/2025

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!

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Mikaela Koutrouli @mkoutrouli.bsky.social · 22/08/2025

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.

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Mikaela Koutrouli @mkoutrouli.bsky.social · 19/08/2025

@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.

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Mikaela Koutrouli @mkoutrouli.bsky.social · 02/08/2025

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. 💪

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Reposted by Mikaela Koutrouli

Malte Kuehl @maltekuehl.com · 29/07/2025

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...

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).

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Reposted by Mikaela Koutrouli

Saez-Rodriguez Group @saezlab.bsky.social · 27/06/2025

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

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 24/06/2025

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

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Reposted by Mikaela Koutrouli

scverse @scverse.bsky.social · 03/06/2025

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!)

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Mikaela Koutrouli @mkoutrouli.bsky.social · 17/05/2025

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.

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Reposted by Mikaela Koutrouli

Rob Patro @robp.bsky.social · 12/05/2025

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!

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