Midhat S. Farooqi

Owl quantifies microsatellite instability from long-read data, identifying MSI-high genomes and motif-specific patterns in cancer samples.

This study integrates transcriptomic, proteomic, and phosphoproteomic data from two pediatric B-ALL subtypes to identify subtype-specific regulatory interactions and potential therapeutic targets.

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.

Wakhan reconstructs chromosome-scale copy number profiles of tumor genomes using long-read sequencing, showing better consistency with data than existing methods.

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

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