Masahiro Ono @ Tocky Lab

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...

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...

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

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.

TockyPrep: data preprocessing methods for flow cytometric fluorescent timer analysis - BMC Bioinformatics Background: Fluorescent Timer proteins, which display time-dependent changes in their emission spectra, are invaluable for analyzing the temporal dynamics of cellular events at the single-cell level. ...

🌟 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🐭

TockyPrep: data preprocessing methods for flow cytometric fluorescent timer analysis - BMC Bioinformatics Background: Fluorescent Timer proteins, which display time-dependent changes in their emission spectra, are invaluable for analyzing the temporal dynamics of cellular events at the single-cell level. ...

🌟 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...

Figure 1 E) A flowchart of the new package ‘TockyDevelopment’

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