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Molecular phenotyping is central in cancer precision medicine, but remains costly and standard methods only provide a tumour average profile. Microscopic morphological patterns observable in histopathology sections from tumours are…
Determining the primary site of origin for metastatic tumors is one of the open problems in cancer care because the efficacy of treatment often depends on the cancer tissue of origin. Classification methods that can leverage tumor genomic…
Mutations in proto-oncogenes (ONGO) and the loss of regulatory function of tumor suppression genes (TSG) are the common underlying mechanism for uncontrolled tumor growth. While cancer is a heterogeneous complex of distinct diseases,…
Molecular phenotyping by gene expression profiling is common in contemporary cancer research and in molecular diagnostics. However, molecular profiling remains costly and resource intense to implement, and is just starting to be introduced…
A principal component analysis of the TCGA data for 15 cancer localizations unveils the following qualitative facts about tumors: 1) The state of a tissue in gene expression space may be described by a few variables. In particular, there is…
Computer aided diagnosis (CAD) of Breast Cancer (BRCA) images has been an active area of research in recent years. The main goals of this research is to develop reliable automatic methods for detecting and diagnosing different types of BRCA…
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…
Next-generation sequencing technologies allow the measurement of somatic mutations in a large number of patients from the same cancer type. One of the main goals in analyzing these mutations is the identification of mutations associated…
Development of a tumor is known to be a result of accumulation of DNA changes in somatic cells. However, the processes of how DNA changes are produced and how they accumulate in somatic cells are not clear. DNA changes include two types:…
Sex chromosomes have evolved repeatedly across the Tree of Life, yet their evolutionary fates differ strikingly. In sharp contrast to mammals and birds with degenerated, stable Y/W chromosomes, in most amphibians, teleosts, non avian…
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than…
Double-strand breaks (DSBs) in DNA are naturally occurring destructive events in all organisms that may lead to genome instability. Cells employ various repair methods known as non-homologous end joining (NHEJ), microhomology mediated end…
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…
Gene selection plays a pivotal role in oncology research for improving outcome prediction accuracy and facilitating cost-effective genomic profiling for cancer patients. This paper introduces two gene selection strategies for deep…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
Exchange type chromosome aberrations (ETCAs) are rearrangements of the genome that occur when chromosomes break and the resulting fragments rejoin with other fragments from other chromosomes. ETCAs are commonly observed in cancer cells and…
PURPOSE: The medical literature relevant to germline genetics is growing exponentially. Clinicians need tools monitoring and prioritizing the literature to understand the clinical implications of the pathogenic genetic variants. We…
Recent studies of cancer somatic mutation profiles seek to identify mutations for targeted therapy in personalized medicine. Analysis of profiles, however, is not trivial, as each profile is heterogeneous and there are multiple confounding…
The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput…
Although cancer is known to be characterized by several unifying biological hallmarks, systems biology has had limited success in identifying molecular signatures present in in all types of cancer. The current availability of rich data sets…