S. P. Shah

Multimodal histopathologic models stratify hormone receptor-positive early breast cancer

This paper develops a multimodal transformer model using H&E images and text reports to predict recurrence scores in hormone receptor-positive breast cancer, achieving high accuracy and generalizability.

Single-cell DNA replication dynamics in genomically unstable cancers

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.

Exploiting allele-specific transcriptional effects of subclonal copy number alterations for genotype-phenotype mapping in cancer cell populations

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 Imaging and Molecular Annotation of Xenografts and Tumours (IMAXT) High Throughput Data and Analysis Infrastructure

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

Evolutionary tracking of cancer haplotypes at single-cell resolution

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

The impact of mutational processes on structural genomic plasticity in cancer cells

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

Single cell fitness landscapes induced by genetic and pharmacologic perturbations in cancer

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.

Non-coding Somatic Mutations Converge on the PAX8 Pathway in Epithelial Ovarian Cancer

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: Interactive visualization of single cell phylogenetics and spatio-temporal evolution in cancer

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