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We propose an extension of a standard stochastic individual-based model in population dynamics which broadens the range of biological applications. Our primary motivation is modelling of immunotherapy of malignant tumours. In this context…

Genetic Algorithms are a popular set of optimization algorithms often used to aid software testing. However, no work has been done to apply systematic software testing techniques to genetic algorithms because of the stochasticity and the…

We built a novel Bayesian hierarchical survival model based on the somatic mutation profile of patients across 50 genes and 27 cancer types. The pan-cancer quality allows for the model to "borrow" information across cancer types, motivated…

Heterogeneity is a hallmark of all cancers. Tumor heterogeneity is found at different levels -- interpatient, intrapatient, and intratumor heterogeneity. All of them pose challenges for clinical treatments. The latter two scenarios can also…

This paper primarily addresses a dataset relating to cellular, chemical and physical conditions of patients gathered at the time they are operated upon to remove colorectal tumours. This data provides a unique insight into the biochemical…

Cluster analysis has proved to be an invaluable tool for the exploratory and unsupervised analysis of high dimensional datasets. Among methods for clustering, hierarchical approaches have enjoyed substantial popularity in genomics and other…

Melanoma is a type of skin cancer developed from melanocytes. It is one of the most lethal types of cancer, accounting for approximately 75% of skin cancer deaths. Late stage melanoma is very difficult to treat, since the cancer cells are…

In mutation testing the question whether a mutant is equivalent to its program is important in order to compute the correct mutation score. Unfortunately, answering this question is not always possible and can hardly be obtained just by…

Studies of T cells and their clonally unique receptors have shown promise in elucidating the association between immune response and human disease. Methods to identify T-cell receptor clones which expand or contract in response to certain…

Pathogenic chromosome abnormalities are very common among the general population. While numerical chromosome abnormalities can be quickly and precisely detected, structural chromosome abnormalities are far more complex and typically require…

Recent advances in types and extent of medical imaging technologies has led to proliferation of multimodal quantitative imaging data in cancer. Quantitative medical imaging data refer to numerical representations derived from medical…

Nuclear supersymmetry is reviewed and some of its applications and extensions are discussed, together with a proposal for new, more stringent and precise tests to probe the supersymmetry classification, in particular, correlations between…

In this study, we develop consistent estimators for key parameters that govern the dynamics of tumor cell populations when subjected to pharmacological treatments. While these treatments often lead to an initial reduction in the abundance…

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…

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…

Central nervous system (CNS) tumors come with the vastly heterogeneous histologic, molecular and radiographic landscape, rendering their precise characterization challenging. The rapidly growing fields of biophysical modeling and radiomics…

In cancer research, high-throughput profiling has been extensively conducted. In recent studies, the integrative analysis of data on multiple cancer patient groups/subgroups has been conducted. Such analysis has the potential to reveal the…

Cancer is a complex disease that is characterized by uncontrolled growth and division of cells. It involves a complex interplay between genetic and environmental factors that lead to the initiation and progression of tumors. Recent advances…

Identifying targets for personalized targeted therapy is the pathologist's domain and a treasure. For decades, pathologists have had to learn, understand, adopt and implement many new laboratory techniques as they arrived on the scene.…

Genetic data are frequently categorical and have complex dependence structures that are not always well understood. For this reason, clustering and classification based on genetic data, while highly relevant, are challenging statistical…