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.

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.

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

How good bugs are fighting back against skin cancer The answer lies in the microbiome. Read about the breakthrough research offering new hope

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...

How good bugs are fighting back against skin cancer The answer lies in the microbiome. Read about the breakthrough research offering new hope

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...

Machine learning-assisted decoding of temporal transcriptional dynamics via fluorescent timer - Nature Communications Transcriptional dynamics govern gene regulation across development and immunity. Here, the authors combine CRISPR-engineered Timer reporter mice with machine learning to reveal age- and enhancer-depen...

🚀 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!

GatingTree: Pathfinding Analysis of Group‐Specific Effects in Cytometry Data Advancements in cytometry technologies have led to a remarkable increase in the number of markers that can be analyzed simultaneously, presenting significant challenges in data analysis. Traditional ....

🚀 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. 💻

Machine learning-assisted decoding of temporal transcriptional dynamics via fluorescent timer - Nature Communications Transcriptional dynamics govern gene regulation across development and immunity. Here, the authors combine CRISPR-engineered Timer reporter mice with machine learning to reveal age- and enhancer-depen...

🚀 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. 🌳

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. 🌳

GatingTree: Pathfinding Analysis of Group‐Specific Effects in Cytometry Data Advancements in cytometry technologies have led to a remarkable increase in the number of markers that can be analyzed simultaneously, presenting significant challenges in data analysis. Traditional ....

🚀 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!

Machine learning-assisted decoding of temporal transcriptional dynamics via fluorescent timer - Nature Communications Transcriptional dynamics govern gene regulation across development and immunity. Here, the authors combine CRISPR-engineered Timer reporter mice with machine learning to reveal age- and enhancer-depen...

🚀 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 📄✨

Spectrum of Treg and self-reactive T cells: single cell perspectives from old friend HTLV-1 Summary. Despite extensive regulatory T cell (Treg) research, fundamental questions on in vivo dynamics remain to be answered. The current study aims to di

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...

Spectrum of Treg and self-reactive T cells: single cell perspectives from old friend HTLV-1 Summary. Despite extensive regulatory T cell (Treg) research, fundamental questions on in vivo dynamics remain to be answered. The current study aims to di

Message:
- Foxp3⁺ T cells are part of a broader spectrum of self-reactive T cells.
- HTLV-1 can transform this broader pool into leukemic cells.
- Analysis of the dynamics of Foxp3 and TCR signalling is key, instead of relying on 'Treg', an inflexible concept.(4/4)
academic.oup.com/discovimmuno...?

What are self-reactive T cells? Self-reactivity is a vaguely defined concept.
To be quantitative, here is our working model: Self-reactive T cells receive cognate antigen signals in the absence of inflammation or infection, and become Timer⁺ in the Nr4a3-Tocky system(3/4)
rupress.org/jcb/article/...

Recent single-cell data support that HTLV-1 transforms activated T cells into leukemia cells by accelerating the activation of spontaneously activated T cells, irrespective of Foxp3.
Thus, ATL is better modelled as a cancer of self-reactive T cells, rather than 'Treg cancer' — but why? (2/4)

Spectrum of Treg and self-reactive T cells: single cell perspectives from old friend HTLV-1 Summary. Despite extensive regulatory T cell (Treg) research, fundamental questions on in vivo dynamics remain to be answered. The current study aims to di

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

Masahiro Ono | The Dogma of Treg and The True Origins of Tocky What is Preventing Advancements and Whats is Required for the Future?

🔍 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.

Dr Masahiro Ono at Imperial College London is working to develop ways to… | Cancer Research UK (CRUK) Dr Masahiro Ono at Imperial College London is working to develop ways to activate immune cells more effectively in the lab, so that we can make immunotherapy treatments more successful for people with...

www.linkedin.com/posts/cancer...