Jose Espejo Valle-Inclán

This study shows that a single chromosome 3p break initiates ccRCC evolution by creating a fitness bottleneck that selects for recurrent aneuploidies.

SAVANA improves detection of somatic structural variants and copy number aberrations in cancer using long-read sequencing with higher sensitivity and specificity than existing tools.

ReConPlot is an R package for visualizing and interpreting complex genome rearrangements by integrating somatic copy number aberrations and structural variants.

The paper compiles a comprehensive reference dataset of true somatic structural variations by analyzing melanoma and normal cell lines with multiple sequencing technologies and experimental validation.

SHARC rapidly identifies somatic genomic structural variations from nanopore sequencing for blood-based cancer monitoring, detecting ten SVs per sample and enabling treatment response tracking in metastatic prostate cancer.

GRIDSS2 identifies somatic structural variants by analyzing single breakends and phasing, achieving a 3.1% false negative rate in metastatic cancers and uncovering a novel duplication signature.

This paper introduces FUDGE, a method for detecting fusion genes using CRISPR/Cas9 enrichment and long-read sequencing, achieving high sensitivity and specificity across various cancer types.

A three-tool chain calls somatic structural variants, purity, ploidy and copy number from paired tumour/normal whole genomes, then clusters breakpoints into derivative chromosome structures and gene fusions.

LoReAn improves genome annotation by integrating long-read cDNA sequencing with other data types, outperforming existing pipelines in gene structure prediction and discovery.

This study uses nanopore sequencing to detect and phase structural variants in patient genomes, identifying novel variants missed by short-read sequencing.

This paper presents the first nanopore-only assembly of the ~54 MB genome of Rhizoctonia solani, demonstrating improved contiguity through optimized DNA isolation and sequencing.