相关论文: A phylogenetic latent feature model for clonal dec…
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…
The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…
The ability of tumors to evolve and adapt by developing subclones in different genetic and epigenetic states is a major challenge in oncology. Traditional tools like multi-regional sequencing used to study tumor evolution and the resultant…
Recent experimental evidence suggests that acute myeloid leukemias may originate from multiple clones of malignant cells. Nevertheless it is not known how the observed clones may differ with respect to cell properties such as proliferation…
Tumor cell populations can be thought of as being composed of homogeneous cell subpopulations, with each subpopulation being characterized by overlapping sets of single nucleotide variants (SNVs). Such subpopulations are known as subclones…
In this dissertation, we develop nonparametric Bayesian models for biomedical data analysis. In particular, we focus on inference for tumor heterogeneity and inference for missing data. First, we present a Bayesian feature allocation model…
An unsolved fundamental problem in biology and ecology is to predict observable traits (phenotypes) from a new genetic constitution (genotype) of an organism under environmental perturbations (e.g., drug treatment). The emergence of…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
Medical imaging is a critical initial tool used by clinicians to determine a patient's cancer diagnosis, allowing for faster intervention and more reliable patient prognosis. At subsequent stages of patient diagnosis, genetic information is…
Determination of functions for poorly characterized genes is crucial for understanding biological processes and studying human diseases. Functionally associated genes are often gained and lost together through evolution. Therefore…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
We present a mathematical model that describes how tumour heterogeneity evolves in a tissue slice that is oxygenated by a single blood vessel. Phenotype is identified with the stemness level of a cell, $s$, that determines its proliferative…
Explicit accounting for copy number alterations can dramatically improve mutation frequency estimates, leading to more accurate phylogeny reconstructions and subclone characterizations.
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…
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…
Phase-field models of tumour growth have proved useful as theoretical tools to investigate cancer invasion. A key implicit assumption underlying mathematical models of this type which have so far been proposed, though, is that cells in the…
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…
In order to identify clusters of objects with features transformed by unknown affine transformations, we develop a Bayesian cluster process which is invariant with respect to certain linear transformations of the feature space and able to…
Biological tools such as genetic lineage tracing, three dimensional confocal microscopy and next generation DNA sequencing are providing new ways to quantify the distribution of clones of normal and mutated cells. Population-wide clone size…
It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…