Jiazhen Rong

This study creates a longitudinal multiomic atlas of pediatric high-grade glioma, revealing distinct tumor cell states and therapeutic targets not seen in adult glioblastoma.

Clonalscope detects cancer subclones using DNA copy number data from single-cell and spatial omic sequencing, identifying spatially segregated subclones and validating them with matched scDNA-seq data.

SUMMIT traces mitochondrial mutations in human tissues to identify spatially localized clones and their transcriptomic profiles.

ntsm detects sample swaps in heterogeneous sequencing data without alignment, using k-mer variants and coverage information to improve QC efficiency.

The paper identifies clonal cell states in Barrett's esophagus and links them to esophageal adenocarcinoma progression through single-cell lineage tracing and transcriptional profiling.

The paper introduces niche-differential expression analysis to identify context-dependent cell-cell interactions in spatial transcriptomics data and applies it to colorectal cancer metastases.

CytoCommunity identifies tissue cellular neighborhoods from spatial data using graph neural networks, revealing condition-specific patterns in cancer tissues.

bedtk is a toolkit for genomic interval manipulation that uses an implicit interval tree to enable fast overlap queries, outperforming existing tools in speed and memory usage.