相关论文: Inferring clonal evolution of tumors from single n…
According to the National Cancer Institute, there were 9.5 million cancer-related deaths in 2018. A challenge in improving treatment is resistance in genetically unstable cells. The purpose of this study is to evaluate unsupervised machine…
Analysis of somatic mutation profiles from cancer patients is essential in the development of cancer research. However, the low frequency of most mutations and the varying rates of mutations across patients makes the data extremely…
The purpose of cancer genome sequencing studies is to determine the nature and types of alterations present in a typical cancer and to discover genes mutated at high frequencies. In this article we discuss statistical methods for the…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
Cancer is responsible for millions of deaths worldwide every year. Although significant progress has been achieved in cancer medicine, many issues remain to be addressed for improving cancer therapy. Appropriate cancer patient…
Recent studies at individual cell resolution have revealed phenotypic heterogeneity in nominally clonal tumor cell populations. The heterogeneity affects cell growth behaviors, which can result in departure from the idealized uniform…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
Changes in the number of copies of certain parts of the genome, known as copy number alterations (CNAs), due to somatic mutation processes are a hallmark of many cancers. This genomic complexity is known to be associated with poorer…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
We investigate a partial differential equation model of a cancer cell population, which is structured with respect to age and telomere length of cells. We assume a continuous telomere length structure, which is applicable to the clonal…
In this work, we investigate the population dynamics of tumor cells under therapeutic pressure. Although drug treatment initially induces a reduction in tumor burden, treatment failure frequently occurs over time due to the emergence of…
In this paper we study a class of stochastic individual-based models that describe the evolution of haploid populations where each individual is characterised by a phenotype and a genotype. The phenotype of an individual determines its…
Recent progress in genetic techniques has shed light on the complex co-evolution of malignant cell clones in leukemias. However, several aspects of clonal selection still remain unclear. In this paper, we present a multi-compartmental…
Motivation: Epigenetic heterogeneity within a tumour can play an important role in tumour evolution and the emergence of resistance to treatment. It is increasingly recognised that the study of DNA methylation (DNAm) patterns along the…
Cancer results from a sequence of genetic and epigenetic changes which lead to a variety of abnormal phenotypes including increased proliferation and survival of somatic cells, and thus, to a selective advantage of pre-cancerous cells. The…
Liver cancer is a leading cause of cancer-related mortality worldwide, with its high genetic heterogeneity complicating diagnosis and treatment. This study introduces DLSOM, a deep learning framework utilizing stacked autoencoders to…
The cellular composition of the tumor microenvironment can directly impact cancer progression and the efficacy of therapeutics. Understanding immune cell activity, the body's natural defense mechanism, in the vicinity of cancerous cells is…
In cancer, treatment failure and disease recurrence have been associated with small subpopulations of cancer cells with a stem-like phenotype. In this paper, we develop and investigate a phenotype-structured model of solid tumour growth in…
The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich…