Timothy R. Chu

Wavelet Based Whole Genome Doubling Aware Single Cell Copy Number Calling

Songbird is a single cell whole genome sequencing copy number caller that detects whole genome duplication and outperforms existing tools in breakpoints identification and true copy number detection.

Comprehensive Molecular Characterization of High-Grade Endometrial Cancer in an Ancestrally-Diverse Cohort

This study characterizes the molecular differences in high-grade endometrial cancer across an ancestrally diverse cohort, identifying ancestry-associated mutations and immune microenvironment differences.

Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graph

Lancet2 improves somatic variant calling with faster runtime and better performance, especially for InDels, using enhanced methods and machine learning.

An explainable boosting machine model for identifying artifacts caused by formalin-fixed paraffin embedding

This paper introduces an explainable boosting machine model to identify and filter variant artifacts caused by formalin-fixed paraffin embedding in cancer genomics.

The Interplay between Mutagenesis and Extrachromosomal DNA Shapes Urothelial Cancer Evolution

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