Karen Piper Hanley

This study shows that PDLIM5 regulates YAP1 localization and fibrogenic gene expression in hepatic stellate cells through mechanical cues.

DeepPathway predicts pathway expression from H&E images using contrastive learning, validated on prostate cancer and brain tumor datasets.

This study presents a transcriptomic atlas of the developing human outflow tract and its adult aortic valve derivatives, revealing persistent embryonic signatures and key regulatory factors in valve development.

PISTACHIO improves spatial cell-type deconvolution in tumours using proteomics constraints and non-negative matrix factorization.

Spartan identifies spatial domains and variable genes by integrating spatial topology and activation signals in spatial transcriptomics data.

The paper identifies novel fibrosis-associated endothelial cells in early-stage liver disease through integrated analysis of imaging, proteomic, and transcriptomic data.

This study shows that SOX9 is critical for maintaining granuloma structure and ECM barrier formation in schistosomiasis, which protects the liver from damage.

Mantpy is a framework for analyzing the extracellular matrix in spatial proteomics by representing it as spatial graphs and integrating it with cell data for joint analysis.

The paper identifies a metaplastic precursor state in Barrett's oesophagus as a reversion to a fetal epithelial cell state, revealing HNF4A's role and GWAS SNPs in regulatory regions.

The paper maps the spatial transcriptional changes in human liver cirrhosis, identifying gene signatures and cell state transitions linked to disease progression.

The paper maps histone modifications across thirteen human tissues during organogenesis to understand gene regulation and link noncoding mutations to developmental disorders.