Margaret Gibson

A comprehensive bulk and single-cell transcriptional atlas of pediatric leukemias

This study presents a comprehensive bulk and single-cell transcriptional dataset of 69 pediatric leukemia patients, demonstrating its utility in improving leukemia characterization and clinical testing.

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies

DeepSomatic is a deep learning method for detecting somatic variants from short-read and long-read sequencing data, outperforming existing callers, especially for indels.

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

Severus detects and characterizes somatic structural variations in tumor genomes using long reads, outperforming existing methods in accuracy and revealing clinically relevant rearrangements.

Successful classification of clinical pediatric leukemia genetic subtypes via structural variant detection using HiFi long-read sequencing

This study shows that HiFi long-read sequencing can detect clinically relevant structural variants in pediatric leukemia, improving subtype classification.

Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort

The paper uses HiFi sequencing to identify hypermethylation outliers in a rare disease cohort, finding allele-specific loss of regulatory elements linked to disease.

Neonatal hyperoxia induces sex-dependent pulmonary cellular and transcriptomic changes in an experimental mouse model of bronchopulmonary dysplasia

This study investigates sex-dependent molecular and cellular changes in mouse lungs exposed to hyperoxia, identifying distinct progenitor and reparative responses in males and females.

Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes

The paper presents diagnostic analyses of 960 pediatric rare disease families using genomic sequencing and machine learning, finding higher diagnostic rates with long-read sequencing and highlighting challenges in variant interpretation.