Rameen Beroukhim

This study identifies genomic subtypes and immune features of mucosal melanoma, linking CD163+ macrophages to immune resistance and suggesting TIM-3 blockade as a therapeutic target.

TangentXY improves copy-number estimation for sex chromosomes, revealing associations between chrX and chrY copy-number alterations and cancer features.

TRACER improves cellular profile coherence in spatial transcriptomics by resolving mixed profiles and reconstructing undetected cells, enhancing downstream analyses.

The paper studies mutations and structural variants during double-strand break repair in budding yeast, finding that repair-associated deletions and template switches depend on microhomology and homeology.

The paper identifies O-mannosylation and protein maturation as therapeutic targets in BRAF fusion oncogenesis by showing their necessity for fusion-induced transformation.

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.

This paper identifies how PVT1 rearrangements in MYC+ cancers generate oncogenic peptides that synergistically activate MYC, AKT, and RAS-MAPK pathways, enhancing tumor aggressiveness.

The paper identifies ARGOS genes, which are amplified in cancer, have low expression relative to copy number, and are toxic when overexpressed, and validates several as pan-cancer targets.

The paper tests how N-terminal epitope tags affect H3K27M-mediated loss of H3K27 trimethylation and finds that they abrogate this effect.

This study uses deep mutational scanning to analyze KRAS variants, identifying gain- and loss-of-function mechanisms and their impact on oncogenic activity.

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 investigates mutation patterns during double-strand break repair in yeast, finding that deletions and tandem duplications occur with specific microhomology preferences and structural constraints.

The paper compares germline and somatic structural variants in cancer, identifying differences in their generating processes and selection, and develops a classifier to distinguish them in tumor samples without matched normals.

This study identifies distinct structural variation patterns in prostate cancer across disease states, defining clinically actionable subgroups based on whole genome profiling.

The paper identifies ancestry-specific germline variants in cancer predisposition genes and their somatic effects across diverse populations.

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 introduces the Cancer LncRNA Census (CLC), a curated resource of lncRNAs with causative roles in cancer, and shows their genomic and evolutionary features.

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

This study identifies germline genetic variants influencing somatic mutation patterns in 2,642 cancer genomes across 39 cancer types.

This study characterizes mitochondrial genomes in 2,700 cancer patients across 37 types using whole-genome sequencing and RNA-seq, revealing mutational patterns, truncating mutations, and nuclear transfer of mitochondrial DNA.

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 hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

ActivePathways integrates multivariate omics data to identify enriched pathways, revealing cancer driver genes and prognostic pathways in breast cancer.

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

CloneRetriever identifies and retrieves rare clones from heterogeneous populations to study clonal fitness and selection mechanisms.

The paper introduces Tangent and Pseudo-Tangent pipelines for copy-number inference from cancer genome data, improving noise reduction and accuracy in SNP array and WES analyses.

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.