Mikaela Koutrouli
@mkoutrouli.bsky.social
Computing all things single-cell | Postdoc at Genentech @MarioniLab | Steering council at scverse.org
Pinned
Mikaela Koutrouli
@mkoutrouli.bsky.social
· May 12
📣 Mark your calendars! The 2025 edition of the scverse conference will take place on 17-19 November at Stanford University (US) scverse.org/conference20...
Call for abstracts and registrations coming soon!
Call for abstracts and registrations coming soon!
scverse conference 2025
Follow us on our channels to learn more details in the coming weeks
scverse.org
It’s happening 💪
Reposted by Mikaela Koutrouli
🤖🧬 New biomedical MCP server added to the registry:
anndata-mcp
Check it out at https://biocontext.ai/registry/biocontext-ai/anndata-mcp
anndata-mcp
Check it out at https://biocontext.ai/registry/biocontext-ai/anndata-mcp
November 13, 2025 at 12:46 PM
🤖🧬 New biomedical MCP server added to the registry:
anndata-mcp
Check it out at https://biocontext.ai/registry/biocontext-ai/anndata-mcp
anndata-mcp
Check it out at https://biocontext.ai/registry/biocontext-ai/anndata-mcp
Reposted by Mikaela Koutrouli
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 🧵
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in 🧵
November 10, 2025 at 3:16 PM
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 🧵
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in 🧵
You asked, we delivered!
Online participation is now live.
Online participation is now live.
We're pleased to announce that we are now offering online attendance via Zoom.
Remote attendance is available for 30 USD, and you can secure your spot by registering at www.eventbrite.com/e/scverse-co....
We hope to see you online at the conference!
Remote attendance is available for 30 USD, and you can secure your spot by registering at www.eventbrite.com/e/scverse-co....
We hope to see you online at the conference!
Scverse Conference 2025
From the foundational open-source software in the life sciences — to its large community coming together
www.eventbrite.com
November 6, 2025 at 4:18 AM
You asked, we delivered!
Online participation is now live.
Online participation is now live.
Reposted by Mikaela Koutrouli
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 🧵
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in 🧵
November 5, 2025 at 4:39 PM
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 🧵
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in 🧵
Reposted by Mikaela Koutrouli
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!)
🧵
(Zoom registration link and more information in thread!)
🧵
October 24, 2025 at 3:55 PM
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!)
🧵
(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! 🙏
🌟 Thank You to Our Gold Sponsor: Genentech! 🌟
We're delighted to recognize Genentech as a Gold Sponsor of scverse conference 2025! 🏆
#scverse2025 #ComputationalBiology #SingleCell #DrugDiscovery #Genentech #SpatialOmics #Bioinformatics #Biotechnology
We're delighted to recognize Genentech as a Gold Sponsor of scverse conference 2025! 🏆
#scverse2025 #ComputationalBiology #SingleCell #DrugDiscovery #Genentech #SpatialOmics #Bioinformatics #Biotechnology
October 22, 2025 at 12:58 AM
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! 🙏
October 21, 2025 at 4:48 PM
How amazing that Genentech supports us and will have such a strong representation at the @scverse.bsky.social conference! 🙏
Reposted by Mikaela Koutrouli
🌟 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
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
October 14, 2025 at 2:30 PM
🌟 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
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
Reposted by Mikaela Koutrouli
👉 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]
Come find me or just reach out if you'd like to chat! [2/2]
October 13, 2025 at 11:19 PM
👉 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]
Come find me or just reach out if you'd like to chat! [2/2]
Reposted by Mikaela Koutrouli
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]
👉 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]
October 13, 2025 at 11:19 PM
While the conference is underway, business as usual! 💪
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!)
🧵
(Zoom registration link and more information in thread!)
🧵
October 13, 2025 at 5:03 PM
While the conference is underway, business as usual! 💪
Last chance for the early-bird 🐣 Join us!
Last call, scverse community!
🐦 Early-bird closes October 17 for the scverse Conference 2025.
Single-cell, open science, and the people behind it — all in one place.
📝 Register here: www.eventbrite.com/e/scverse-co...
2 days of talks + 1 day of workshops
ℹ️ Info: scverse.org/conference2025
🐦 Early-bird closes October 17 for the scverse Conference 2025.
Single-cell, open science, and the people behind it — all in one place.
📝 Register here: www.eventbrite.com/e/scverse-co...
2 days of talks + 1 day of workshops
ℹ️ Info: scverse.org/conference2025
October 10, 2025 at 2:51 AM
Last chance for the early-bird 🐣 Join us!
Reposted by Mikaela Koutrouli
🌟 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're proud to recognize Stellaromics as a Gold Sponsor of scverse conference 2025! 🥇
@stellaromics.bsky.social
#scverse2025 #SpatialBiology #3DSpatial #ComputationalBiology #SingleCell #Stellaromics #SpatialOmics #Bioinformatics
October 9, 2025 at 3:25 PM
🌟 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're proud to recognize Stellaromics as a Gold Sponsor of scverse conference 2025! 🥇
@stellaromics.bsky.social
#scverse2025 #SpatialBiology #3DSpatial #ComputationalBiology #SingleCell #Stellaromics #SpatialOmics #Bioinformatics
Reposted by Mikaela Koutrouli
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!)
🧵
Yimin Zheng will be presenting on LazySlide, a Python framework for whole slide image (WSI) analysis.
(Zoom registration link and more information in thread!)
🧵
October 8, 2025 at 3:19 PM
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!)
🧵
Yimin Zheng will be presenting on LazySlide, a Python framework for whole slide image (WSI) analysis.
(Zoom registration link and more information in thread!)
🧵
Reposted by Mikaela Koutrouli
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 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
October 6, 2025 at 3:26 PM
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 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
Reposted by Mikaela Koutrouli
🤖🧬 New biomedical MCP server added to the registry:
OMOP MCP Server
Check it out at https://biocontext.ai/registry/OHNLP/omop_mcp
OMOP MCP Server
Check it out at https://biocontext.ai/registry/OHNLP/omop_mcp
October 3, 2025 at 4:55 PM
🤖🧬 New biomedical MCP server added to the registry:
OMOP MCP Server
Check it out at https://biocontext.ai/registry/OHNLP/omop_mcp
OMOP MCP Server
Check it out at https://biocontext.ai/registry/OHNLP/omop_mcp
Reposted by Mikaela Koutrouli
Fantastic lineup of panelists to discuss everything agentic coding in bioinformatics, still time to register here:
www.eventbrite.com/e/scverse-co...
www.eventbrite.com/e/scverse-co...
October 3, 2025 at 8:34 PM
Fantastic lineup of panelists to discuss everything agentic coding in bioinformatics, still time to register here:
www.eventbrite.com/e/scverse-co...
www.eventbrite.com/e/scverse-co...
Can’t wait 😱
🚀 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
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
October 4, 2025 at 2:51 AM
Can’t wait 😱
Reposted by Mikaela Koutrouli
🌟 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
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
September 30, 2025 at 4:25 PM
🌟 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
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
Reposted by Mikaela Koutrouli
🚀 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...
🔗 www.biorxiv.org/content/10.1...
September 28, 2025 at 5:50 PM
🚀 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...
🔗 www.biorxiv.org/content/10.1...
Reposted by Mikaela Koutrouli
🔬 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
Multimodal And Spatial Single Cell Data: From Data APIs to AI-driven Biological Discovery
🧵
@chanzuckerberg.bsky.social
#scverse2025 #SingleCell #SpatialOmics #CELLxGENE #VirtualCells #AIBiology
September 4, 2025 at 3:03 PM
🔬 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
Multimodal And Spatial Single Cell Data: From Data APIs to AI-driven Biological Discovery
🧵
@chanzuckerberg.bsky.social
#scverse2025 #SingleCell #SpatialOmics #CELLxGENE #VirtualCells #AIBiology
Reposted by Mikaela Koutrouli
🧬 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
Disease Biology and Therapeutics in the Age of Frontier Datasets
🧵
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
September 2, 2025 at 4:03 PM
🧬 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
Disease Biology and Therapeutics in the Age of Frontier Datasets
🧵
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
Reposted by Mikaela Koutrouli
🎉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
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
September 1, 2025 at 4:18 PM
🎉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
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
Reposted by Mikaela Koutrouli
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
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
Choosing research projects: the risk–reward–work triangle
YouTube video by Lars Juhl Jensen
youtu.be
September 1, 2025 at 9:58 AM
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
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
Reposted by Mikaela Koutrouli
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
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
August 28, 2025 at 3:04 PM
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
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