Nikhil Wagle

SlideCNA detects spatial copy number alterations from Slide-seq data to identify sub-clones in metastatic breast cancer.

SCHAF generates spatially resolved single-cell transcriptomes from H&E histology images using vision transformers and adversarial learning, showing good agreement with ground-truth data.

cDNA-detector identifies and removes exogenous cDNA contamination in DNA sequencing data, improving accuracy in downstream analysis.

ExSeq enables multiplexed RNA mapping at nanoscale resolution by expanding biological specimens for in situ sequencing.

The paper develops a toolbox for scRNA-Seq and snRNA-Seq of fresh and frozen human tumors, testing it across eight tumor types and optimizing protocols for different tissue characteristics.

This study finds that 5% of breast cancers have high tumor mutation burden, more common in metastatic tumors, with APOBEC activity as the most common mutational process and potential benefit from PD-1 inhibitors.