David G.P. van IJzendoorn

Resolving the immune response across clonal cancer evolution in situ with Atera whole transcriptome profiling

This study evaluates Atera, a spatial transcriptomics platform, showing its ability to resolve clonal cancer evolution and immune response in situ using DCIS samples.

Machine Learning Analysis to Define Cell Lineage in Leiomyosarcoma

This paper uses machine learning to classify leiomyosarcoma based on methylation signatures, finding differences in PD-1 pathway activation and immune cell composition between tumor subtypes.

Identification and Characterization of Neoplastic Cells in Keratin-Positive Giant Cell-Rich Tumors

This paper uses single-nuclei RNA sequencing and spatial transcriptomics to characterize KPGCT, showing neoplastic cells express HMGA2::NCOR2 fusions and activate the hippo pathway, driving CSF1 production and macrophage recruitment.

TissueViewer: A Web-Based Multiplexed Image Viewer

TissueViewer is a web-based tool for viewing large multiplexed image datasets from spatial biology techniques efficiently over the internet.

The Network Zoo: a multilingual package for the inference and analysis of biological networks

The paper introduces netZoo, an open-source software suite for analyzing biological networks, demonstrating its use on cancer cell line data to identify drug resistance and cancer development factors.