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Understanding how microenvironmental heterogeneity influences tumor progression is essential for advancing both cancer biology and therapeutic strategies. In this study, we develop a cellular automata (CA) model to simulate tumor growth…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
As immunotherapies become standard cancer treatments, it is increasingly important to identify a patient's immune profile, which encompasses the activity of immune cells within the tumor microenvironment and the presence of specific…
Tumor recurrence, driven by the evolution of drug resistance is a major barrier to therapeutic success in cancer. Resistance is often caused by genetic alterations such as point mutation, which refers to the modification of a single genomic…
In the genomic era, the identification of gene signatures associated with disease is of significant interest. Such signatures are often used to predict clinical outcomes in new patients and aid clinical decision-making. However, recent…
Recent technological advancements have enabled detailed investigation of associations between the molecular architecture and tumor heterogeneity, through multi-source integration of radiological imaging and genomic (radiogenomic) data. In…
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…
Breast cancer is a health problem that affects mainly the female population. An early detection increases the chances of effective treatment, improving the prognosis of the disease. In this regard, computational tools have been proposed to…
The unwelcome evolution of malignancy during cancer progression emerges through a selection process in a complex heterogeneous population structure. In the present work, we investigate evolutionary dynamics in a phenotypically heterogeneous…
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…
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…
The availability of cancer measurements over time enables the personalised assessment of tumour growth and therapeutic response dynamics. However, many tumours are treated after diagnosis without collecting longitudinal data, and cancer…
The popular use of histopathology images, such as hematoxylin and eosin (H&E), has proven to be useful in detecting tumors. However, moving such cancer cases forward for treatment requires accurate on the amount of the human epidermal…
One of the mechanisms that ensure cancer robustness is tumor heterogeneity, and its effects on tumor cells dynamics have to be taken into account when studying cancer progression. There is no unifying theoretical framework in mathematical…
Thyroid cancer is currently the fifth most common malignancy diagnosed in women. Since differentiation of cancer sub-types is important for treatment and current, manual methods are time consuming and subjective, automatic computer-aided…
Cancer development is a multistep process often starting with a single cell in which a number of epigenetic and genetic alterations have accumulated thus transforming it into a tumor cell. The progeny of such a single benign tumor cell…
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…
The ability to locally degrade the extracellular matrix (ECM) and interact with the tumour microenvironment is a key process distinguishing cancer from normal cells, and is a critical step in the metastatic spread of the tumour. The…
Cancer typically arises not from a single genetic mutation (i.e., hit) but from multi-hit combinations that accumulate within cells. However, enumerating multi-hit combinations becomes exponentially more expensive computationally as the…
The mutational heterogeneity of tumours can be described with a tree representing the evolutionary history of the tumour. With noisy sequencing data there may be uncertainty in the inferred tree structure, while we may also wish to study…