J. William Harbour

BAP1 loss and PRAME expression converge to remodel the tumor-immune ecosystem during uveal melanoma progression

The paper profiles single-cell data from uveal melanoma to show BAP1 loss and PRAME expression drive convergent immunoregulatory changes and immune resistance.

Surface Complex V couples proton gradient across the plasma membrane to ATP production in cancer

The paper shows cancer cells use a proton gradient from lactate export to drive ATP production via plasma membrane-localized ATP synthases, resolving the Warburg effect's energetic inefficiency.

Identification of targetable epigenetic vulnerabilities for uveal melanoma

This study identifies BET inhibition as a promising therapeutic strategy for uveal melanoma by demonstrating its efficacy in reducing metastasis and improving survival in a mouse model.

A multi-step immune-competent genetic mouse model reveals phenotypic plasticity in uveal melanoma

This paper develops a genetically engineered mouse model of uveal melanoma that recapitulates human disease progression and immune microenvironment features, revealing phenotypic plasticity and cooperative genetic drivers.

GDF15 reprograms the microenvironment to drive the development of uveal melanoma liver metastases

This study identifies GDF15 as a driver of uveal melanoma liver metastasis by reprogramming hepatic stellate cells to promote angiogenesis and matrix deposition.

UPhyloplot2: Visualizing Phylogenetic Trees from Single-Cell RNA-seq Data

UPHyloplot2 generates phylogenetic plots from inferCNV output files to visualize tumor clonality inferred from single-cell RNA-seq data.

PieParty: Visualizing cells from scRNA-seq data as pie charts

PieParty visualizes scRNA-seq data as pie charts where each cell's slices represent gene expression, enabling intuitive and dense visualization of multiple genes and networks.

Fate of developmental mechanisms of myocardial plasticity in the postnatal heart

The paper investigates the postnatal fate of developmental gene regulatory networks in the heart, identifying persistent contributions from neural crest-derived cardiomyocytes.

SparK: A Publication-quality NGS Visualization Tool

Command-line Python tool that turns sequencing tracks into editable vector figures, averaging replicates, drawing standard-deviation tracks and marking significantly changed regions.