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We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…
In cancer research, the term epigenetics was used in the 1970s in its modern sense encompassing non-genetic events modifying the chromatin state, mainly to oppose the emerging oncogene paradigm. However, starting from the establishment of…
Breast cancer ranks as the most prevalent form of cancer diagnosed in women, and diagnosis faces several challenges, a change in the size, shape and appearance of breasts, dense breast tissue, lumps or thickening in the breast especially if…
The Galleri (R) (GRAIL) multi-cancer early detection test measures circulating tumour DNA (ctDNA) to predict the presence of more than 50 different cancers, from a blood test. If sensitivity of the test to detect early-stage cancers is…
Lung cancer is a condition where there is abnormal growth of malignant cells that spread in an uncontrollable fashion in the lungs. Some common treatment strategies are surgery, chemotherapy, and radiation which aren't the best options due…
Many machine learning models have been proposed to classify phenotypes from gene expression data. In addition to their good performance, these models can potentially provide some understanding of phenotypes by extracting explanations for…
Comparative studies of cancer-related genes allow us to gain novel information about the evolution and function of these genes, but also to understand cancer as a driving force in biological systems and species life histories. So far,…
Transcriptional profiling on microarrays to obtain gene expressions has been used to facilitate cancer diagnosis. We propose a deep generative machine learning architecture (called DeepCancer) that learn features from unlabeled microarray…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Multi-cancer early detection (MCED) tests offer to screen for multiple types of cancer with a single blood sample. Despite their promising diagnostic performance, evidence regarding their population benefit is not yet available. Expecting…
The prediction plays the important role in detecting efficient protection and therapy of cancer. The prediction of mutations in gene needs a diagnostic and classification, which is based on the whole database (big dataset), to reach…
Tomasetti and Vogelstein (2015a) find that the incidence of a set of cancer types is correlated with the total number of normal stem cell divisions. Here, we separate the effects of standing stem cell number (i.e., organ or tissue size) and…
Deciphering cell type heterogeneity is crucial for systematically understanding tissue homeostasis and its dysregulation in diseases. Computational deconvolution is an efficient approach estimating cell type abundances from a variety of…
Although somatic mutations are the main contributor to cancer, underlying germline alterations may increase the risk of cancer, mold the somatic alteration landscape and cooperate with acquired mutations to promote the tumor onset and/or…
The discovery of important biomarkers is a significant step towards understanding the molecular mechanisms of carcinogenesis; enabling accurate diagnosis for, and prognosis of, a certain cancer type. Before recommending any diagnosis,…
Lung cancer has been one of the most prevalent disease in recent years. According to the research of this field, more than 200,000 cases are identified each year in the US. Uncontrolled multiplication and growth of the lung cells result in…
Machine learning promises to revolutionize clinical decision making and diagnosis. In medical diagnosis a doctor aims to explain a patient's symptoms by determining the diseases \emph{causing} them. However, existing diagnostic algorithms…
A variety of genome-wide profiling techniques are available to probe complementary aspects of genome structure and function. Integrative analysis of heterogeneous data sources can reveal higher-level interactions that cannot be detected…
It is proposed that cancer results from the breakdown of universal control mechanisms which developed in mutual association as part of the historical process that brought individual cells together into multi-cellular communities. By…
Metastatic prostate cancer is one of the most common cancers in men. In the advanced stages of prostate cancer, tumours can metastasise to other tissues in the body, which is fatal. In this thesis, we performed a genetic analysis of…