Herein we provide a detailed molecular analysis of the spatial heterogeneity of clinically
localized, multifocal prostate cancer to delineate new oncogenes or tumor suppressors. We …

To the Editor: In addition to single-nucleotide variations and small insertions-deletions (indels),
larger-sized structural variations (for example, insertions, deletions, inversions, …

Recent years have witnessed an increase in research activity for the detection of structural
variants (SVs) and their association to human disease. The advent of next-generation …

The current paradigm of cancer care relies on predictive nomograms which integrate detailed
histopathology with clinical data. However, when predictions fail, the consequences for …

Cancers adapt to increasingly potent targeted therapies by reprogramming their phenotype.
Here we investigated such a phenomenon in prostate cancer, in which tumours can escape …

Motivation: The high throughput sequencing (HTS) platforms generate unprecedented amounts
of data that introduce challenges for the computational infrastructure. Data management, …

High-throughput sequencing (HTS) data are commonly stored as raw sequencing reads in
FASTQ format or as reads mapped to a reference, in SAM format, both with large memory …

Background Malignant peritoneal mesothelioma (PeM) is a rare and fatal cancer that
originates from the peritoneal lining of the abdomen. Standard treatment of PeM is limited to …

Available computational methods for tumor phylogeny inference via single-cell sequencing (SCS)
data typically aim to identify the most likely perfect phylogeny tree satisfying the infinite …

Human genomes are now being rapidly sequenced, but not all forms of genetic variation are
routinely characterized. In this study, we focus on Alu retrotransposition events and seek to …