Matthew M. Meyerson

HipHap improves haplotype assignment and confidence scoring for diploid genomes by aligning reads to each haplotype separately and introducing a quality score.

This study presents complete subtelomeric sequences from diverse populations, revealing extensive haplotype diversity and gene copy-number variation associated with chromosome arms.

This study shows that U2AF1 mutations can rescue exon skipping caused by KRAS mutations in lung adenocarcinoma, revealing a dynamic interplay between splicing factor and oncogenic mutations.

This study identifies that 3q-gain aneuploidy in squamous cell carcinomas creates a vulnerability to SREBP-pathway inhibition, offering a target for lipid-targeted therapies.

The paper identifies foldback artifacts in long-read sequencing data and introduces Breakinator, a tool to detect these artifacts and chimeric reads across different sequencing platforms.

The paper shows that p53 protein abundance in TP53 mutant cancers can be exploited to selectively kill these cells using proximity-inducing small molecules.

This study shows PACT inhibits PKR activation by endogenous dsRNA through restricting PKR movement on dsRNA, without sequestering dsRNA, thereby adjusting the activation threshold for long dsRNA.

This paper resolves ring chromosomes, Robertsonian translocations, and complex structural variants using long-read sequencing and telomere-to-telomere assembly, revealing breakpoint structures and methylation changes.

The paper uses long-read sequencing to identify four types of telomere repeat variations in cancer genomes, including neotelomeres and telomere-spanning fusions.

The paper identifies repeat-calling errors in nanopore sequencing of telomeres and shows that tuning basecalling models improves telomere analysis.

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

The paper develops DNA- and RNA-based models combining immune and tumor features to predict outcomes of checkpoint inhibition in melanoma.

The paper introduces a method to screen large variant libraries with mutations across wide regions using improved mutant detection software, enabling accurate variant calling and counting from sequencing data.

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.

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

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.

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.

The paper analyzes RNA alterations across 27 cancer types using whole-genome sequencing data, identifying gene expression associations with DNA variants and structural fusions.