Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as
biological signals representing no or low gene expression, while others regard zeros as …

Simple Summary Most malignant tumours are highly heterogeneous at molecular and
phenotypic levels. Tumour variability poses challenges for the management of patients, as it …

Background Heterogeneity in single-cell RNA-seq (scRNA-seq) data is driven by multiple
sources, including biological variation in cellular state as well as technical variation …

Chemotherapy resistance is a critical contributor to cancer mortality and thus an urgent
unmet challenge in oncology. To characterize chemotherapy resistance processes in high …

We perform a thorough analysis of RNA velocity methods, with a view towards
understanding the suitability of the various assumptions underlying popular …

Spatial transcriptomics are a collection of genomic technologies that have enabled
transcriptomic profiling on tissues with spatial localization information. Analyzing spatial …

Cancer cells within a tumour have heterogeneous phenotypes and exhibit dynamic
plasticity. How to evaluate such heterogeneity and its impact on outcome and drug response …

Spatially resolved transcriptomics (SRT)-specific computational methods are often
developed, tested, validated, and evaluated in silico using simulated data. Unfortunately …

Dimension reduction and (spatial) clustering is usually performed sequentially; however, the
low-dimensional embeddings estimated in the dimension-reduction step may not be …

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating
cellular biology at an unprecedented resolution, enabling the characterization of cellular …