Joshua A. Bull

MuSpAn: a toolbox for multiscale spatial analysis

Joshua A. Bull, Joshua W. Moore

Advances in multiplex imaging and spatial omics have revolutionised spatial data generation in biology, revealing complex tissue organisation across multiple scales. However, methods for analysing these data have lagged behind, with fragmented, study-specific pipelines and limited guidance for tool selection. To address …

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netPCF: Geometry-aware pair correlation functions for spatial biology

Joshua W. Moore, Joshua A. Bull, Helen M. Byrne

Abstract Spatial organisation is a defining feature of biological systems, underpinning cellular interactions, tissue function, disease progression and therapeutic response. Identifying and quantifying spatial organisation may require methods that resolve relationships across spatial scales. The pair correlation function (PCF) quantifies spatial dependence …

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Exploring the relationship between vascular remodelling and tumour growth using agent-based modelling

Nicholas Fan, Joshua A. Bull, Helen M. Byrne

Abstract We develop a multiscale agent-based model (ABM) to investigate the effect that mechanical interactions between proliferating tumour cells and the surrounding vasculature have on the oxygen supply to the tumour microenvironment (TME), the tumour’s growth dynamics, and its response to radiotherapy. …

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Topology of Multi-species Localization

Abhinav Natarajan, Thomas Chaplin, Joshua A. Bull, Eoghan J. Mulholland-Illingworth et autres

Spatial relationships in multi-species data can indicate and affect system outcomes and behaviors, ranging from disease progression in cancer to coral reef resilience in ecology; therefore, quantifying these relationships is an important problem across scientific disciplines. Persistent homology (PH), a key mathematical …

Topology of Multi-species Localization

Abhinav Natarajan, Thomas Chaplin, Joshua A. Bull, Eoghan J. Mulholland-Illingworth et autres

Spatial relationships in multi-species data can indicate and affect system outcomes and behaviors, ranging from disease progression in cancer to coral reef resilience in ecology; therefore, quantifying these relationships is an important problem across scientific disciplines. Persistent homology (PH), a key mathematical …

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Therapeutic manipulation and spatial quantification of the tumor microenvironment in colorectal cancer

Eoghan J. Mulholland-Illingworth, Joshua W. Moore, Muyang Lin, Raheleh Amirkhah et autres

, reconfiguring local immune neighborhoods and indirectly altering epithelial stem cell states. Finally, we demonstrate that multiscale spatial analysis provides a quantitative readout of stromal-immune-epithelial remodeling following therapy. These findings establish a simplified, translationally relevant CAF framework and highlight spatially resolved stromal …

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Topological classification of tumour-immune interactions and dynamics

Jingjie Yang, Heidi Fang, Jagdeep Dhesi, Iris H. R. Yoon et autres

The complex and dynamic crosstalk between tumour and immune cells results in tumours that can exhibit distinct qualitative behaviours-elimination, equilibrium, and escape-and intricate spatial patterns, yet share similar cell configurations in the early stages. We offer a topological approach to analyse time …

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Temporo-spatial cellular atlas of the regenerating alveolar niche in idiopathic pulmonary fibrosis

Praveen Weeratunga, Bethany Hunter, Martin J. Sergeant, Joshua A. Bull et autres

Abstract Healthy alveolar repair relies on the ability of alveolar stem cells to differentiate into specialized epithelial cells for gas exchange. In chronic fibrotic lung diseases such as idiopathic pulmonary fibrosis (IPF), this regenerative process is abnormal but the underlying mechanisms remain …

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Spatial Transcriptomics Identifies Aberrant Communication between Dendritic Cells and Leukemia Stem Cells As a Therapeutically Targetable Axis in Juvenile Myelomonocytic Leukemia

Eleni Louka, Kristian Gurashi, Sean Wen, Mariolina Salio et autres

Juvenile Myelomonocytic Leukemia (JMML) is a RAS-driven aggressive childhood leukemia characterised by aberrant proliferation of myelomonocytic cells and very poor prognosis. Unlike other leukemias, children with JMML have no disease modifying treatments and notably Bone Marrow (BM) transplantation, the only curative treatment, …

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Relational Persistent Homology for Multispecies Data with Application to the Tumor Microenvironment

Bernadette J. Stolz, Jagdeep Dhesi, Joshua A. Bull, Heather A. Harrington et autres

Topological data analysis (TDA) is an active field of mathematics for quantifying shape in complex data. Standard methods in TDA such as persistent homology (PH) are typically focused on the analysis of data consisting of a single entity (e.g., cells or molecular …

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Integrating diverse statistical methods to analyse stage-discriminatory cell interactions in colorectal neoplasia

Joshua A. Bull, Eoghan J. Mulholland, Joshua W. Moore, Jesús J. Bosque et autres

Summary Spatial biology has the potential to unlock information about the disrupted cellular ecosystems that define human disease. Quantitative analysis of spatially-resolved cell interactions allows mapping of tissue self-organisation and assessment of why cells interact differently in physiological and pathological contexts. However, …

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Publisher Correction: Semaphorin 3A causes immune suppression by inducing cytoskeletal paralysis in tumour-specific CD8+ T cells

Mike Bogetofte Barnkob, Yale S. Michaels, Violaine André, Philip S. Macklin et autres

In this article the title was incorrectly written as ‘Semmaphorin 3A causes immune suppression by inducing cytoskeletal paralysis in tumour-specific CD8+ T cells’ but should have been ‘Semaphorin 3A causes immune suppression by inducing cytoskeletal paralysis in tumour-specific CD8+ T cells’. The …

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