Allele-specific expression (ASE) is a powerful signal that can be used to investigate multiple
molecular mechanisms, such as cis-regulatory effects and imprinting. Single-cell RNA …

Spatial and genomic heterogeneity of tumors are crucial factors influencing cancer
progression, treatment, and survival. However, a technology for direct mapping the clones in …

Genetic and gene expression heterogeneity is an essential hallmark of many tumors,
allowing the cancer to evolve and to develop resistance to treatment. Currently, the most …

Tumours exhibit high genotypic and transcriptional heterogeneity. Both affect cancer
progression and treatment, but have been predominantly studied separately in follicular …

Abstract Motivation Copy number variations (CNVs) are common genetic alterations in
tumour cells. The delineation of CNVs holds promise for enhancing our comprehension of …

Phenotypic plasticity, the ability of cells to adapt their behavior in response to genetic or
environmental changes, is a fundamental biological process that drives cellular diversity in …

Cell lineage tree reconstruction methods are developed for various tasks, such as
investigating the development, differentiation, and cancer progression. Single-cell …

Motivation: Reconstructing clonal lineage trees (" tumor phylogenetics") has become a core
tool of cancer genomics. Earlier approaches based on bulk DNA sequencing (DNA-seq) …

Cancer consists of genetically heterogeneous populations of cells that arise through a
process of subclonal evolution. Reconstructing the evolutionary processes that give rise to …

Tumors are comprised of subpopulations of cancer cells that harbor distinct genetic profiles
and phenotypes that evolve over time and during treatment. By reconstructing the course of …