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Collecting genomics data across multiple heterogeneous populations (e.g., across different cancer types) has the potential to improve our understanding of disease. Despite sequencing advances, though, resources often remain a constraint…
While we once thought of cancer as single monolithic diseases affecting a specific organ site, we now understand that there are many subtypes of cancer defined by unique patterns of gene mutations. These gene mutational data, which can be…
In recent years, cancer genome sequencing and other high-throughput studies of cancer genomes have generated many notable discoveries. In this review, Novel genomic alteration mechanisms, such as chromothripsis (chromosomal crisis) and…
Cancer is known as a disease mainly caused by gene alterations. Discovery of mutated driver pathways or gene sets is becoming an important step to understand molecular mechanisms of carcinogenesis. However, systematically investigating…
In order to analyze data from cancer genome sequencing projects, we need to be able to distinguish causative, or "driver," mutations from "passenger" mutations that have no selective effect. Toward this end, we prove results concerning the…
Lung cancer is one of the death threatening diseases among human beings. Early and accurate detection of lung cancer can increase the survival rate from lung cancer. Computed Tomography (CT) images are commonly used for detecting the lung…
Cancer is a disease that takes millions of lives every year. Then, to propose treatments, avoid recurrence, and improve the patient's life quality, we need to analyze this disease from a biophysical perspective with a solid mathematical…
Motivation: Driver (epi)genomic alterations underlie the positive selection of cancer subpopulations, which promotes drug resistance and relapse. Even though substantial heterogeneity is witnessed in most cancer types, mutation accumulation…
Statistical inference on the cancer-site specificities of collective ultra-rare whole genome somatic mutations is an open problem. Traditional statistical methods cannot handle whole-genome mutation data due to their…
Theoretical reasoning suggests that human cancer may result from knocking down the genetic constraints evolved for maintenance of the metazoan multicellularity, which, however, requires a critical test. Using xenograft-based experimental…
Cancer cell lines have frequently been used to link drug sensitivity and resistance with genomic profiles. To capture genomic complexity in cancer, the Cancer Genome Project (CGP) (Garnett et al., 2012) screened 639 human tumor cell lines…
Mutations can arise from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell…
Cancer is a complex genetic disease involving uncontrolled cell growth and proliferation, and necessitates effective targeting of dysregulated cellular pathways underlying cancer progression. Multiple genetic and epigenetic alterations…
In The Cancer Genome Atlas (TCGA) data set, there are many interesting nonlinear dependencies between pairs of genes that reveal important relationships and subtypes of cancer. Such genomic data analysis requires a rapid, powerful and…
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…
Motivation: Gene selection has become a common task in most gene expression studies. The objective of such research is often to identify the smallest possible set of genes that can still achieve good predictive performance. The problem of…
Quantum theory is a tremendously successful physical theory, but nevertheless suffers from two serious problems: the measurement problem and the problem of interpretational underdetermination. The latter, however, is largely overlooked as a…
Cancer cells are widely known to be protected from apoptosis, which is a major hurdle to successful anti-cancer therapy. Over-expression of several anti-apoptotic proteins, or mutations in pro-apoptotic factors, has been recognized to…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
Tumor synthesis enables the creation of artificial tumors in medical images, facilitating the training of AI models for tumor detection and segmentation. However, success in tumor synthesis hinges on creating visually realistic tumors that…