S. P. Shah

The paper develops a method to infer DNA replication states from single-cell sequencing and analyzes replication dynamics in aneuploid cancers, finding correlations between replication timing and copy number changes.

This paper develops TreeAlign to map subclonal copy number alterations to transcriptional phenotypes in cancer cells, showing improved accuracy in clone-specific gene expression analysis.

The paper presents an infrastructure for high-throughput data and analysis of tumour and xenograft samples using multimodal imaging and molecular annotation.

The paper tracks cancer haplotypes at single-cell resolution, revealing allele-specific alterations and their role in structural variation evolution in human tumors.

The paper analyzes structural genomic variations in cancer cells to understand how mutational processes influence cell-to-cell genomic diversity and tumor evolution.

This study develops a quantitative fitness model to analyze clonal dynamics in cancer under genetic and pharmacologic perturbations, revealing how mutations and drug resistance shape tumor evolution.

The paper identifies histotype-specific regulatory elements in ovarian cancer by integrating chromatin landscapes and somatic mutations, highlighting the PAX8 pathway's role in tumor development.

E-scape provides an interactive visualization tool for analyzing cancer clonal dynamics and spatio-temporal evolution using integrated mutation, phylogenetic, and imaging data.