Upcoming seminar: 🎓Dr Masahiro Ono @monotockylab.bsky.social, @imperialcollegeldn.bsky.social 📢‘Measuring Biological Time in T Cells: Integrated Experimental and Computational Approaches to Decoding Dynamic Immune Responses’ 📅4-5 PM, Thu 2 Jul 📍JCBC @cambridgebiocampus.bsky.social #CITIID

Thank you for highlighting our work. It has been a pleasure to develop this research through the Centre’s support for Imperial–ICR collaboration.

We’ve also released the mCanonicalTockySeq R package! 📦💻 monotockylab.github.io/mCanonicalTo... It reconstructs temporally resolved developmental state spaces by integrating Tocky signalling history into scRNA-seq workflows.

Delighted to share our new bioRxiv preprint: biorxiv.org/content/10.6... We present mCanonicalTockySeq, which uses the Nr4a3-Tocky system to anchor single-cell transcriptomes in experimental time, allowing resolution of time-dependent thymic development in both mice and humans.

Delighted to share our new bioRxiv preprint: biorxiv.org/content/10.6... We present mCanonicalTockySeq, which uses the Nr4a3-Tocky system to anchor single-cell transcriptomes in experimental time, allowing resolution of time-dependent thymic development in both mice and humans.

I am pleased to share the release of CanonicalTockySeq: Canonical Tocky Analysis for Temporal Gradient on a Transcriptomic Manifold. This package provides tools for analysing temporal gradients on transcriptomic manifolds within the Tocky framework. monotockylab.github.io/CanonicalToc...

Delighted to share our new bioRxiv preprint: www.biorxiv.org/content/10.6... We present a new approach to resolve T cell temporal states at single-cell resolution in cancer immunotherapy. My thanks to all co-authors and collaborators. #Immunology #CancerResearch

@biorxivpreprint.bsky.social @masahirono.bsky.social @monotockylab.bsky.social @imperialcollegeldn.bsky.social Temporal Mechanisms of T-Cell Fate Decisions under Immune Checkpoint Blockade Resolved by CanonicalTockySeq www.biorxiv.org/content/10.6...

I am pleased to share the release of CanonicalTockySeq: Canonical Tocky Analysis for Temporal Gradient on a Transcriptomic Manifold. This package provides tools for analysing temporal gradients on transcriptomic manifolds within the Tocky framework. monotockylab.github.io/CanonicalToc...

Delighted to share our new bioRxiv preprint: www.biorxiv.org/content/10.6... We present a new approach to resolve T cell temporal states at single-cell resolution in cancer immunotherapy. My thanks to all co-authors and collaborators. #Immunology #CancerResearch

Honoured that our T-cell immunotherapy research at Imperial is featured in The Telegraph via Cancer Research UK. Using Tocky, we reveal the behaviour of therapy-responsive and anti-cancer T cells, aiming to further improve immunotherapy approaches to melanoma. www.telegraph.co.uk/science/canc...

Honoured that our T-cell immunotherapy research at Imperial is featured in The Telegraph via Cancer Research UK. Using Tocky, we reveal the behaviour of therapy-responsive and anti-cancer T cells, aiming to further improve immunotherapy approaches to melanoma. www.telegraph.co.uk/science/canc...

🚀 Thrilled to share our new paper using Deep Learning and Tocky! www.nature.com/articles/s41... 👉 We build on our original Tocky method by integrating CRISPR & deep learning to decode transcriptional dynamics. 🔥 7 years of work - toward data-driven immunology!

🚀 Our next-generation cytometry tool GatingTree now published in #CytometryPartA! 🔗 onlinelibrary.wiley.com/doi/10.1002/... GatingTree enables systematic analysis of high-dimensional flow cytometry data, without relying on dimensionality reduction. 💻

🚀 New paper out! Our ConvNet + Grad-CAM approach decodes Fluorescent Timer (Tocky) data at single-cell resolution. Using Foxp3 Tocky, we reveal CNS2-controlled and developmental transcriptional dynamics. Built on 7 years of work with AI and CRISPR! www.nature.com/articles/s41...

Bored of black-box UMAP and clustering in #Cytometry? GatingTree skips such methods, directly analyses high-dimensional data, builds reproducible tree paths across markers, and reveals group-specific effects. No dimensionality reduction, just interpretable gates. 🌳

🚀 Our next-generation cytometry tool GatingTree now published in #CytometryPartA! 🔗 onlinelibrary.wiley.com/doi/10.1002/... GatingTree enables systematic analysis of high-dimensional flow cytometry data, without relying on dimensionality reduction. 💻

🚀Thrilled to announce our new Tocky-CRISPR-Deep Learning paper! ✅ConvNet + Grad-CAM decodes fluorescent timer (Tocky) data ✅Enables single-cell identification of enhancer-dependent Foxp3 transcription dynamics www.nature.com/articles/s41... 🔥A step toward data-driven immunology!

🚀Thrilled to announce our new Tocky-CRISPR-Deep Learning paper! ✅ConvNet + Grad-CAM decodes fluorescent timer (Tocky) data ✅Enables single-cell identification of enhancer-dependent Foxp3 transcription dynamics www.nature.com/articles/s41... 🔥A step toward data-driven immunology!

🚀 New paper out! Our ConvNet + Grad-CAM approach decodes Fluorescent Timer (Tocky) data at single-cell resolution. Using Foxp3 Tocky, we reveal CNS2-controlled and developmental transcriptional dynamics. Built on 7 years of work with AI and CRISPR! www.nature.com/articles/s41...

Excellent work from my long-term collaborator of over 17 years, @Sato_Y_Lab (on X) 🔬 on Runx/HTLV-1! The start of our collaboration goes back to my own Runx paper in 2007: www.nature.com/articles/nat... This Runx/HTLV-1 study is the latest milestone 🔬. Honoured to be a co-author 📄✨

Excellent work from my long-term collaborator of over 17 years, @Sato_Y_Lab (on X) 🔬 on Runx/HTLV-1! The start of our collaboration goes back to my own Runx paper in 2007: www.nature.com/articles/nat... This Runx/HTLV-1 study is the latest milestone 🔬. Honoured to be a co-author 📄✨

What if Tregs are not a separate lineage, but part of spontaneously activated T cells? In this work, we integrate this idea with our recent findings: Adult T cell leukemia (ATL) is not 'Treg cancer', challenging the current concept of Treg as a distinct entity.🧵(1/4) academic.oup.com/discovimmuno...

What if Tregs are not a separate lineage, but part of spontaneously activated T cells? In this work, we integrate this idea with our recent findings: Adult T cell leukemia (ATL) is not 'Treg cancer', challenging the current concept of Treg as a distinct entity.🧵(1/4) academic.oup.com/discovimmuno...

Explore how HTLV-1 hijacks self-reactive T cells via Periodic TCR signalling - a fresh lens on Treg biology and immune regulation. Game-changing insights from single-cell analysis. 👇 📄 Ono & Satou (2024) 🧬 bit.ly/42gRcuR

🔍 New Blog Post: The Dogma of Treg and The True Origins of Tocky monotockylab.github.io/blog/2025/As... The blog explores what is certain in Treg immunology and what is not, unraveling the past two decades of my research life that have been triggered by the non-reproducible evidence in Treg biology.

Single-cell analysis reveals how periodic TCR signalling defines the spectrum of Treg and self-reactive T cells—and how HTLV-1 may hijack this for immune evasion and transformation. The study fills key gaps in Treg biology and viral #immunology. 🔗 bit.ly/42gRcuR

🔍 New Blog Post: The Dogma of Treg and The True Origins of Tocky monotockylab.github.io/blog/2025/As... The blog explores what is certain in Treg immunology and what is not, unraveling the past two decades of my research life that have been triggered by the non-reproducible evidence in Treg biology.

🌟 Excited to share my new publication on TockyPrep, now published in BMC Bioinformatics🚀 link.springer.com/article/10.1... The TockyPrep R package automates and standardizes flow cytometric analysis of Fluorescent Timer reporters, unlocking the analysis of Nr4a3 Tocky mice and other Timer reporters🐭

🌟 Excited to share my new publication on TockyPrep, now published in BMC Bioinformatics🚀 link.springer.com/article/10.1... The TockyPrep R package automates and standardizes flow cytometric analysis of Fluorescent Timer reporters, unlocking the analysis of Nr4a3 Tocky mice and other Timer reporters🐭

Pleased to announce TockyPrep update - the R package for preprocessing flow cytometric Fluorescent Timer data 🚀 monotockylab.github.io/TockyPrep/in... Now featuring an Interactive application to fine-tune your analysis! 🛠️ monotockylab.github.io/TockyPrep/ar...

A multidimensional toolkit for elucidating temporal trajectories in cell development in vivo Read this Techniques and Resources Article by Masahiro Ono @monotockylab.bsky.social and Tessa Crompton: https://doi.org/10.1242/dev.204255

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 20

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 19

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 18

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 17

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 16

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 15

🚀 A new paper has been published: a novel computational toolkit to fully harness the power of Fluorescent Timer reporters through multidimensional analysis! 🕒🧪💻 journals.biologists.com/dev/article/...

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 14

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 13

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 12

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 11

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 10

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 9

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 8

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 7

Choose 20 books that have stayed with you or influenced you. One book per day for 20 days, in no particular order. No explanations, no reviews, just covers. #Books #BookSky💙📚 #BookChallenge Day 6