Jeff A. Wintersinger

This paper introduces REPRESS, a deep learning model that predicts cell-type-specific microRNA binding and mRNA degradation from RNA sequences, outperforming existing methods in multiple tasks.

The paper benchmarks 31 subclonal reconstruction algorithms on simulated tumours, finding that algorithm choice significantly impacts performance and no single algorithm excels across all tasks.

Pairtree reconstructs clone trees from multiple bulk DNA samples to infer cancer evolutionary histories with higher accuracy and scalability.

This paper introduces SubMARine, a polynomial-time algorithm for reconstructing tumor clone trees that efficiently captures uncertainty and scales to large datasets.

This study develops quantitative metrics and simulated datasets to evaluate subclonal reconstruction methods in tumours.

This study compares two genomes of Haemonchus contortus to identify technical errors and biological differences, finding significant assembly and annotation discrepancies.