monotockylab.bsky.social
Masahiro Ono @ Tocky Lab
@monotockylab.bsky.social
700 followers 470 following 61 posts
Immunologist | Creator and Developer of Tocky | Integrative Experimental and Computational Immunology | T cells | Cancer Immunology | Immunotherapy Imperial College London, Reader Website: monotockylab.github.io GitHub: github.com/MonoTockyLab
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monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Jul 5
🚀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!
2 4
Reposted by Masahiro Ono @ Tocky Lab
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Jul 27
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
www.telegraph.co.uk
1 1
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Jul 27
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
www.telegraph.co.uk
1 1
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Jul 20
🚀 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!
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...
www.nature.com
4
Reposted by Masahiro Ono @ Tocky Lab
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Jul 13
🚀 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. 💻
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 ....
onlinelibrary.wiley.com
1 3 4
Reposted by Masahiro Ono @ Tocky Lab
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Jul 2
🚀 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...
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...
www.nature.com
1 3
Reposted by Masahiro Ono @ Tocky Lab
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Jul 13
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. 🌳
1 2
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Jul 13
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. 🌳
1 2
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Jul 13
🚀 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. 💻
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 ....
onlinelibrary.wiley.com
1 3 4
Reposted by Masahiro Ono @ Tocky Lab
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Jul 5
🚀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!
2 4
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Jul 5
🚀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!
2 4
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Jul 2
🚀 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...
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...
www.nature.com
1 3
Reposted by Masahiro Ono @ Tocky Lab
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · May 17
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 📄✨
natmicrobiol.nature.com
Nature Microbiology @natmicrobiol.nature.com · May 13
🚨Out now!

An intragenic open chromatin region in human T cell leukemia virus type 1 functions as a transcriptional silencer and regulates transcriptional burst by recruiting the host transcription factor RUNX.

#MicroSky 🧬🦠

www.nature.com/articles/s41...
Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment - Nature Microbiology
An intragenic open chromatin region in human T cell leukaemia virus type 1 functions as a transcriptional silencer and regulates transcriptional burst by recruiting the host transcription factor RUNX.
www.nature.com
1 4
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · May 17
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 📄✨
natmicrobiol.nature.com
Nature Microbiology @natmicrobiol.nature.com · May 13
🚨Out now!

An intragenic open chromatin region in human T cell leukemia virus type 1 functions as a transcriptional silencer and regulates transcriptional burst by recruiting the host transcription factor RUNX.

#MicroSky 🧬🦠

www.nature.com/articles/s41...
Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment - Nature Microbiology
An intragenic open chromatin region in human T cell leukaemia virus type 1 functions as a transcriptional silencer and regulates transcriptional burst by recruiting the host transcription factor RUNX.
www.nature.com
1 4
Reposted by Masahiro Ono @ Tocky Lab
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Apr 26
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
academic.oup.com
1 5 12
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Apr 26
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...?
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
academic.oup.com
1
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Apr 26
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/...
1
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Apr 26
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)
1
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Apr 26
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
academic.oup.com
1 5 12
Reposted by Masahiro Ono @ Tocky Lab
discovimmunol.bsky.social
Discovery Immunology @discovimmunol.bsky.social · Apr 25
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
2 3
Reposted by Masahiro Ono @ Tocky Lab
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Mar 24
🔍 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.
Masahiro Ono | The Dogma of Treg and The True Origins of Tocky
What is Preventing Advancements and Whats is Required for the Future?
monotockylab.github.io
1 6
Reposted by Masahiro Ono @ Tocky Lab
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Apr 12
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
1 1
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Apr 12
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
1 1
Reposted by Masahiro Ono @ Tocky Lab
discovimmunol.bsky.social
Discovery Immunology @discovimmunol.bsky.social · Apr 4
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
1 4
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Mar 24
🔍 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.
Masahiro Ono | The Dogma of Treg and The True Origins of Tocky
What is Preventing Advancements and Whats is Required for the Future?
monotockylab.github.io
1 6
Reposted by Masahiro Ono @ Tocky Lab
monotockylab.bsky.social
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · Feb 8
🌟 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. ...
link.springer.com
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