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Masahiro Ono @ Tocky Lab

@monotockylab.bsky.social
722 followers 498 following 66 posts

Immunologist | Creator and Developer of Tocky & GatingTree | Integrative Experimental and Computational Immunology | T cells | Cancer Immunology | Immunotherapy Website: monotockylab.github.io GitHub: github.com/MonoTockyLab

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Reposted by Masahiro Ono @ Tocky Lab
Medicine at Cambridge @medcambridge.bsky.social · 26/06/2026
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 04/06/2026
Thank you for highlighting our work. It has been a pleasure to develop this research through the Centre’s support for Imperial–ICR collaboration.
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 25/03/2026
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.
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 25/03/2026
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.
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 25/03/2026
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.
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 13/03/2026
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...
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 13/03/2026
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
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Reposted by Masahiro Ono @ Tocky Lab
Waggoner Lab @labwaggoner.bsky.social · 14/03/2026
@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...
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 13/03/2026
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...
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 13/03/2026
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
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 27/07/2025
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...
telegraph.co.uk
How good bugs are fighting back against skin cancer
The answer lies in the microbiome. Read about the breakthrough research offering new hope
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 27/07/2025
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...
telegraph.co.uk
How good bugs are fighting back against skin cancer
The answer lies in the microbiome. Read about the breakthrough research offering new hope
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 20/07/2025
🚀 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!
nature.com
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...
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 13/07/2025
🚀 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. 💻
onlinelibrary.wiley.com
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 ....
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 02/07/2025
🚀 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...
nature.com
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...
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 13/07/2025
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. 🌳
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 13/07/2025
🚀 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. 💻
onlinelibrary.wiley.com
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 ....
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 05/07/2025
🚀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!
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 05/07/2025
🚀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!
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 02/07/2025
🚀 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...
nature.com
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...
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 17/05/2025
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 📄✨
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 17/05/2025
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 📄✨
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 26/04/2025
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...
academic.oup.com
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 26/04/2025
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...
academic.oup.com
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
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Reposted by Masahiro Ono @ Tocky Lab
Discovery Immunology @discovimmunol.bsky.social · 25/04/2025
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
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 24/03/2025
🔍 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.
monotockylab.github.io
Masahiro Ono | The Dogma of Treg and The True Origins of Tocky
What is Preventing Advancements and Whats is Required for the Future?
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 12/04/2025
www.linkedin.com/posts/cancer...
linkedin.com
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...
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 12/04/2025
www.linkedin.com/posts/cancer...
linkedin.com
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...
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Reposted by Masahiro Ono @ Tocky Lab
Discovery Immunology @discovimmunol.bsky.social · 04/04/2025
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 24/03/2025
🔍 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.
monotockylab.github.io
Masahiro Ono | The Dogma of Treg and The True Origins of Tocky
What is Preventing Advancements and Whats is Required for the Future?
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Reposted by Masahiro Ono @ Tocky Lab
Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 08/02/2025
🌟 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🐭
link.springer.com
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. ...
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 08/02/2025
🌟 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🐭
link.springer.com
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. ...
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 18/01/2025
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...
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Reposted by Masahiro Ono @ Tocky Lab
Development @dev-journal.bsky.social · 29/12/2024
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: doi.org/10.1242/dev.204255
Figure 1 E) A flowchart of the new package ‘TockyDevelopment’
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 25/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 24/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 23/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 22/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 21/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 20/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 19/12/2024
🚀 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/...
journals.biologists.com
A multidimensional toolkit for elucidating temporal trajectories in cell development in vivo
Summary: A novel toolkit, utilising Tocky-canonical correspondence analysis, enables the identification of developmental trajectories in vivo through flow cytometric analysis using Fluorescent Timer p...
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 19/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 18/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 17/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 16/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 15/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 14/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 13/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 12/12/2024
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
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Masahiro Ono @ Tocky Lab @monotockylab.bsky.social · 10/12/2024
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
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