Minita J. Shah

This paper introduces MRD-EDGE, a machine learning platform for ultrasensitive ctDNA detection in plasma WGS, showing improved sensitivity and broader applicability for MRD monitoring.

This study examines how mutagenesis and extrachromosomal DNA contribute to urothelial cancer evolution, revealing clonal APOBEC3 mutations and chemotherapy-induced mutational bursts within ecDNA.

The paper introduces an updated version of the Lancet somatic variant caller that supports linked-reads sequencing data analysis by integrating barcodes and haplotype read assignments.

The paper benchmarks a new sequencing platform and develops a somatic calling pipeline using deep sequencing of cancer cell lines on two platforms.

The paper identifies three novel complex structural variation patterns in cancer genomes using genome graph analysis across 2,833 tumor WGS.

Lancet improves somatic variant calling accuracy, especially for indels, using colored DeBruijn graphs and local assembly across synthetic and real whole-genome sequencing data.