Paul Christopher Boutros

This study examines how sex and ancestry influence the genomic heterogeneity of pancreatic adenocarcinoma across multiple datasets.

The paper quantifies urinary proteome differences between Black and White prostate cancer patients, finding immune pathway dysregulation and aggressive cancer features in Black patients after controlling for age, PSA, and cISUP.

The paper quantifies sex differences in the cancer proteome across eight cancer types, identifying sex-differential protein abundance and linking some differences to copy number aberrations.

This study maps epigenomic heterogeneity in prostate cancer by analyzing 3,001 methylomes and identifies four subtypes with distinct clinical and molecular features.

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

The paper analyzes genetic and health record data from a diverse population to uncover gene-phenotype associations and assess polygenic score performance across ancestries.

Metapipeline-DNA automates comprehensive analysis of DNA sequencing data from raw reads to visualization, supporting germline and somatic genomic features.

The paper identifies genomic deletions as the rate-limiting mutational processes in breast and ovarian cancer initiation, requiring 1-3 deletions for tumor development.

This study quantifies mutation rates, selection coefficients, and epistatic interactions across prostate cancer stages, revealing dynamic selective pressures and therapeutic implications.

moPepGen identifies non-canonical peptides from genetic and transcriptomic data across species and technologies by generating them in linear time.

This study provides a multiomics resource of cancer extracellular vesicles, showing correlations between LO proteins and prostate cancer progression, and demonstrating the feasibility of single-cell RNA-Seq on EVs.

This study identifies OGDHL as a regulator of tumor growth, neuroendocrine marker expression, and nucleotide abundance in prostate cancer, with implications for treatment resistance.

This study demonstrates that RNA transcripts can serve as templates for double-strand break repair in human cells, identifying DNA polymerase-zeta as a key enzyme and revealing genomic scars associated with this process.

The paper introduces a method to assign single-cell RNA-seq data to donor-of-origin without prior genetic information, achieving high concordance in tumor-derived data.

The paper investigates how patient sex affects cancer cell function by analyzing gene essentiality and drug sensitivity across 1,209 cell lines.

The paper creates a variant benchmark for X and Y chromosomes using a complete assembly of HG002, highlighting challenges in variant detection in complex regions.

The paper develops a benchmark for detecting low-frequency mosaic variants in the HG002 reference material using high-coverage sequencing data and validates its utility across multiple technologies.

The paper quantifies the impact of genome build differences on variant calling and introduces StableLift, an algorithm to predict cross-build variant stability.

The paper quantifies secreted and extracellular vesicle (EV) urinary proteomes in men with and without prostate cancer, showing their stability and utility in distinguishing malignant from benign lesions.

This paper introduces a platform for establishing and screening patient-derived cutaneous neurofibroma organoids to support drug discovery for NF1-associated tumors.

This study evaluates how different random seeds affect subclonal reconstruction algorithms in cancer genomics, finding significant variability in subclone estimates across seeds.

The paper benchmarks 31 subclonal reconstruction algorithms on simulated tumours, finding that algorithm choice significantly impacts performance and no single algorithm excels across all tasks.

This study examines telomere length in prostate cancer, finding associations with genomic instability and clinical outcomes.

iSubGen generates disease subtypes by integrating multiple data types, handling missing data and identifying clinically distinct patient groups.

The paper quantifies tumor-specific total mRNA expression from bulk data and shows its association with clinical outcomes across 15 cancer types.

An ensemble of six imputation methods, built through the NCI-CPTAC Proteogenomics DREAM Challenge, fills missing values in labeled LC-MS/MS proteomics data, helping most for low-abundance proteins.

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