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 💪
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.
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.
We’re looking for a Community Manager to help shape and support the growing scverse ecosystem.
Deadline January 10, 2026!
More details here: jobs.helmholtz-muenchen.de/jobposting/d...
Deadline January 10, 2026!
More details here: jobs.helmholtz-muenchen.de/jobposting/d...
December 12, 2025 at 11:10 PM
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.
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.
Reposted by Mikaela Koutrouli
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...
📄 www.biorxiv.org/content/10.6...
December 10, 2025 at 3:21 PM
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...
📄 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! 💪
I’d love for you to join me, share your ideas, challenge us, and help shape what comes next. It’s time! 💪
We will have our final community meeting of 2026 on Tuesday, 2025-12-09 at 11:00 CST/ 9:00 PST!
Mikaela Koutrouli (@mkoutrouli.bsky.social) will wrap up a great year of meetings by giving an update on the state of scverse!
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
Mikaela Koutrouli (@mkoutrouli.bsky.social) will wrap up a great year of meetings by giving an update on the state of scverse!
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
December 3, 2025 at 6:13 PM
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! 💪
I’d love for you to join me, share your ideas, challenge us, and help shape what comes next. It’s time! 💪
Reposted by Mikaela Koutrouli
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...
I reviewed recent literature and collected some thoughts on the current state of affairs.
open.substack.com/pub/giovanni...
Virtual Cell Perturbation Metrics Reloaded
Thoughts on metrics for perturbation prediction models
open.substack.com
November 27, 2025 at 1:15 AM
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...
I reviewed recent literature and collected some thoughts on the current state of affairs.
open.substack.com/pub/giovanni...
Reposted by Mikaela Koutrouli
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 ⚡️
November 26, 2025 at 4:53 PM
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 ⚡️
Reposted by Mikaela Koutrouli
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 🧵
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in 🧵
November 24, 2025 at 4:39 PM
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 🧵
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in 🧵
Reposted by Mikaela Koutrouli
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 😄
November 21, 2025 at 5:37 PM
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.
@biohub.org x NVIDIA x @scverse.bsky.social : three forces, one room, endless acceleration.
November 19, 2025 at 7:49 PM
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.
@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! 💪❤️
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 🧵
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in 🧵
November 19, 2025 at 5:26 PM
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” 💪
November 17, 2025 at 6:03 PM
John Marioni at the @scverse.bsky.social conference 2025! “Make sure you understand first when complex methods are valuable” 💪
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