Amy Xin Wei Zhang

Extra-lineage tissue programs define the transcription states of human pancreatic cancer

The paper identifies four epithelial transcription states in pancreatic cancer and links their origins to early developmental processes.

Transcriptomic, Genomic, and Clinical Characterization of Morphological Classes in Localized and Metastatic Pancreatic Cancer

This study characterizes morphological classes in pancreatic cancer using transcriptomic, genomic, and clinical data to identify molecular associations and prognostic implications.

scDNA: Single Cell DNA analysis software toolkit for subclonality discovery and assessment.

scDNA is a toolkit for analyzing single-cell DNA data to identify subclonal structures, mutation trajectories, and sample quality, with applications in cancer research.

The subclonal footprint of pervasive early dissemination in pancreatic cancer

This study analyzes ctDNA shedding in pancreatic cancer using paired tissue and plasma whole genomes, finding that subclones contribute significantly to early dissemination and ctDNA levels.

Integrated spatial proteomics of human PDAC uncovers an expanded tumour-immune-stroma spectrum with genomic associations

This study integrates spatial proteomics and genomics in PDAC to identify tumour-immune-stroma interactions and their genomic associations, showing multi-omics models improve patient survival prediction.

Inferring tumour microenvironment ecosystems from scRNA-seq atlases

The paper infers multicellular ecosystems from nonspatial scRNA-seq data and shows they predict therapy response and are linked to somatic mutations.

Whole Genomes Define Concordance of Matched Primary, Xenograft, and Organoid Models of Pancreas Cancer

The paper compares whole-genome data from primary pancreatic cancer, xenografts, and organoids to assess genetic concordance across different models.