Jeremiah A. Wala

The paper introduces statistical tools to analyze immune cluster patterns in prostate cancer and finds high-grade tumors show more immune infiltration and active immune features.

The paper identifies immune spatial organization as a biomarker predicting metastasis risk in high-grade prostate cancer using computational pathology and H&E slides.

This study shows that BRD4 gene deletions reduce toxicity from overexpression in ovarian and breast cancers, providing evidence for a novel mechanism in cancer progression.

The paper identifies a subset of mismatch repair proficient colorectal cancers with high immune infiltration that may benefit from immune checkpoint inhibitors, using spatial profiling and genomics.

This paper introduces two methods to detect recurrent genomic rearrangements in cancer genomes and identifies 80 simple and 29 complex rearrangements across 2,500 cancers.

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

The paper identifies three novel complex structural variation patterns in cancer genomes using genome graph analysis across 2,833 tumor WGS.

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

The paper analyzes somatic retrotransposition events in 2,954 cancer genomes, identifying L1 insertions as significant contributors to structural variations and oncogenesis.

SvABA detects structural variants and indels using genome-wide local assembly, showing improved sensitivity and specificity, especially for small variants and complex rearrangements in cancer genomes.

This paper identifies driver mutations across 2,500 tumors from 37 cancer types, revealing a whole-genome panorama of genomic events that underlie tumor development.

The paper analyzes somatic rearrangements in cancer genomes using whole-genome sequencing data, identifying recurrent breakpoints and their genomic features.

The paper identifies nine structural variation signatures in cancer genomes, revealing patterns of deletions, tandem duplications, and translocations linked to replication mechanisms and oncogenic activation.