Trevor J. Pugh

The paper presents a telomere-to-telomere genome assembly of the naked mole-rat and compares it with a related species to identify gene losses and duplications associated with unique traits.

The paper analyzes spatial gene expression and tumor-microenvironment interactions in IDH-mutant gliomas across malignant transformation, finding reduced proliferation at the infiltrative margin in higher-grade tumors.

The paper uses whole-genome and transcriptome sequencing to identify two consensus cancer subtypes in biliary tract cancer, revealing divergent molecular landscapes that better explain tumor heterogeneity than anatomical classification.

The paper examines therapy-associated mutagenesis at CTCF binding sites across 4,870 tumor genomes, finding increased mutation enrichment at these sites under radiotherapy and trifluridine treatment.

The paper shows that glioblastoma stem cells form spatial patterns correlated with their transcriptional state, using image analysis to link morphology and gene expression.

The paper investigates five BRIP1/FANCJ variants for their clinical relevance in breast and ovarian cancer, finding three likely damaging variants associated with cellular sensitivity to chemotherapy drugs.

The paper assesses T-cell dynamics in pediatric cancer patients during treatment, finding that immune checkpoint proteins and T-cell subsets change with therapy, and introduces a Dynamic Immunogenomic Score to predict relapse risk.

The paper presents an updated reference genome for the naked mole-rat, identifying gene losses and gains linked to its unique physiological traits.

This paper identifies PRMT5 as a regulator of HTT mRNA splicing and alternative polyadenylation, showing that its inhibition reduces full-length HTT protein levels by promoting premature termination and cleavage.

MEDIPIPE provides an automated pipeline for cfMeDIP-seq data quality control, methylation quantification, and sample aggregation, offering ease of use and scalability for large-scale analysis.

This study identifies 13.9% of neuroblastoma patients with pathogenic germline variants in cancer predisposition genes, associated with worse survival and enriched in DNA repair genes like BARD1.

This study evaluates an integrated liquid biopsy approach for early cancer detection in Li-Fraumeni syndrome patients, showing improved detection rates compared to individual methods.

The paper identifies four immune clusters in pediatric nervous system tumors using RNA-seq data and validates them with multiple methods, highlighting the need for personalized immunogenomic profiling.

This paper identifies FANCI c.1813C>T as a candidate familial ovarian cancer risk allele in a French Canadian population with founder effects.

This study compares five data integration methods for single-cell RNA sequencing of cancer samples, finding STACAS and fastMNN most effective in correcting batch effects while preserving biological variability.

CanDIG enables secure, federated genomic and health data analysis across jurisdictions while maintaining data locality and privacy.

CReSCENT provides a web-based toolkit for analyzing scRNA-seq data in cancer research, offering preconfigured pipelines and user-editable workflows for non-experts.

This study benchmarks four methods for assigning cell type labels to cell clusters in scRNA-seq data, showing high performance but variability in precision-recall across methods and datasets.

Bamgineer simulates allele-specific copy number variants in exome and targeted sequencing data to create reference sets for benchmarking CNV calling algorithms.

The paper analyzes genomic data from pancreatic neuroendocrine tumors to identify a widespread copy neutral loss-of-heterozygosity pattern linked to tumor progression and potential therapeutic targets.