Ketan K. Badani

Organoid-T cell co-cultures functionally stratify tumor-reactive T cells and their responses to immune checkpoint inhibitors

Critical assessment of intratumor and low-biomass microbiome using long-read sequencing

The paper assesses low-biomass microbiome detection in tissues using long-read sequencing, finding that genuine microbiome signals are limited to tissues with natural microbial exposure.

Incorporating FDR into the assessment of nanopore sequencing for the reliable detection of DNA modifications in real applications

This paper introduces modFDR, a framework to assess nanopore sequencing for DNA modification detection, showing it reliably detects abundant modifications but has high false positives for rare ones.