Muchun Niu

SigFormer improves single-sample mutational signature decomposition by using a transformer framework, outperforming existing methods in high-noise and overcomplete settings.

This study benchmarks six duplex sequencing technologies to evaluate their performance in detecting somatic mutations across different genomic contexts and tissue types.

The paper introduces NanoSeq-MBN, a method improving variant detection in whole-genome sequencing, expanding the GIAB truth set with novel low-frequency variants and enabling somatic variant benchmarking.

The paper estimates the timing of homologous recombination deficiency (HRD) onset in breast cancers using HRDTimer, finding HRD occurs years before diagnosis in different subtypes.

This study develops scNanoSeq to detect somatic mutations in single tumor cells, revealing subtype-specific evolutionary patterns and a reprogramming and critical mutation co-timing model in breast cancer.

This paper introduces a new single-cell WGA method to detect DNA damage-associated variants and finds that dSNV abundance is linked to genome topological compartments.