Dan J. Woodcock

3D pathology-guided microdissection

This paper introduces a 3D microdissection method combining CNC milling and light-sheet microscopy to study tumor evolution in complex 3D structures.

Assessing the effects of a 3D pathology tissue-processing workflow on downstream molecular analyses

This study evaluates the impact of a 3D pathology workflow on DNA, RNA, and protein integrity, showing minimal effect on amplifiability and transcriptomic profiles.

Redefining the topology of the human bone marrow using augmented spatial transcriptomic analysis

This study uses spatial transcriptomic analysis and machine learning to redefine the topology of human bone marrow in health and myeloproliferative neoplasms, revealing new insights into cellular heterogeneity and fibrosis.

Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of cancer

The paper evaluates the accuracy of transcript-based inferred tumor phylogenies compared to DNA-based phylogenies in prostate cancer using single-cell, spatial transcriptomic, and bulk data.

Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of heterogeneity on genomic signature scoring

The paper uses spatial transcriptomic data to show that bulk genomic signature scoring in prostate cancer biopsies is confounded by tumour heterogeneity, leading to inaccurate risk assessments.

The spatial landscape of clonal somatic mutations in benign and malignant tissue

The paper uses spatial transcriptomics to analyze copy number variations in benign and malignant tissues, revealing clonal patterns and suggesting early cancer evolution mechanisms.

Genomic copy number predicts oesophageal cancer years before transformation

This study shows genomic copy number changes can predict oesophageal cancer up to 10 years before diagnosis, enabling earlier treatment and reduced unnecessary monitoring.

Multiplexing information flow through dynamic signalling systems

This paper defines and mathematically characterizes multiplexing in signaling systems, provides experimental evidence for NF-κB's potential to multiplex information, and introduces new methods for analyzing dynamic models.

Paupar LncRNA Promotes KAP1 Dependent Chromatin Changes And Regulates Subventricular Zone Neurogenesis

The paper identifies Paupar, a lncRNA that interacts with KAP1 to regulate chromatin structure and neurogenesis in the subventricular zone.