news
| Mar 18, 2026 | π New Preprint Published π§ Our new bioRxiv preprint introduces mCanonicalTockySeq, a framework that brings an experimental time anchor into single-cell transcriptomics to analyse temporal and developmental progression together. Using the Nr4a3-Tocky Fluorescent Timer system, this study resolves signalling-linked temporal progression alongside thymocyte differentiation and shows that the learned reference structure can be transferred across species to organise human thymic single-cell data.
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| Mar 13, 2026 | π New Preprint Published π Our new bioRxiv preprint introduces CanonicalTockySeq, a framework that integrates Nr4a3-Tocky Fluorescent Timer signalling history with single-cell RNA-seq to resolve dynamic T-cell states in cancer immunotherapy. Using an experimentally anchored canonical manifold, this study separates temporal progression from signalling strength at single-cell resolution and shows that effective checkpoint blockade is associated with reduced persistence of antigen engagement, suppression of exhaustion-associated TCR signalling programmes, and maintenance of progenitor-like features linked to durable antitumour responses.
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| Jul 02, 2025 | π New Paper Published π Our paper in Biology Methods and Protocols introduces TockyLocus, an open-source framework for the quantitative and standardised analysis of Fluorescent Timer flow cytometry data in Nr4a3-Tocky and Foxp3-Tocky mice. By optimising analysis of Timer Angle and establishing a biologically grounded five-locus categorisation scheme, this study provides a robust and interpretable method for analysing transcriptional dynamics, enabling reproducible statistical testing and visualisation without reliance on arbitrary gating.
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| Jul 01, 2025 | π New Paper Published π Our paper in Nature Communications presents a new framework for decoding temporal transcriptional dynamics from Fluorescent Timer data using an integrative combination of molecular genetics, flow cytometry, and machine learning. Using a convolutional neural network (ConvNet)-based approach together with Foxp3-Tocky Fluorescent Timer reporter mice and CRISPR gene editing, this study reveals previously unrecognised features of Foxp3 transcriptional dynamics, including roles of CNS2 in regulating transcription frequency and age-dependent differences from neonatal to aged mice.
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| Feb 09, 2025 | π New Paper Published π Excited to share my new publication on TockyPrep, now published in BMC Bioinformaticsπ The TockyPrep R package automates and standardizes flow cytometric analysis of Fluorescent Timer reporters, unlocking the analysis of Nr4a3 Tocky mice and other Timer reportersπ |
| Dec 01, 2024 | π New Paper Published: π Thrilled to share our latest research! Our study, βA multidimensional toolkit for elucidating temporal trajectories in cell development in vivo,β is now available in Development.
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| Nov 15, 2024 | π» New R Package Released β TockyLocus: Our second Tocky package has been released at our GitHube site! TockyLocus is essential for quantitative analysis of Fluorescent Timer data π
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| Nov 06, 2024 | π» New R Package Released β TockyPrep: We have released the TockyPrep package, which offers data preprocessing methods for Tocky data (and any Fluorescent Timer data). Such data would not be fully useful without these proper analytic methods.
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| Nov 05, 2024 | π» New R Package Released β GatingTree: A ground-breaking R package for analysing high-dimensional cytometry data without the use of dimensional reduction. π This innovative approach allows for more precise and detailed data analysis, revolutionizing how we understand complex biological datasets.
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| Jun 13, 2024 | π New Paper Published: Our review article on the relationship between Foxp3+ regulatory T cells and the human retrovirus infection. We show that T cells constitute a spectrum of self-reactivity and the activation mechanisms within self-reactive T cells are exploited by HTLV-1 infection.
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| Mar 25, 2024 | π A new website has launched! πβ¨ |