Related papers: On dynamic network entropy in cancer
Cancers remain the lead cause of disease-related, pediatric death in North America. The emerging field of complex systems has redefined cancer networks as a computational system with intractable algorithmic complexity. Herein, a tumor and…
In cancer research, the comparison of gene expression or DNA methylation networks inferred from healthy controls and patients can lead to the discovery of biological pathways associated to the disease. As a cancer progresses, its signalling…
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…
The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable…
The use of networks to integrate different genetic, proteomic, and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases. Here we introduce a new phenotypic database summarizing…
Genetic regulatory networks control ontogeny. For fifty years Boolean networks have served as models of such systems, ranging from ensembles of random Boolean networks as models for generic properties of gene regulation to working dynamical…
Phenotypic heterogeneity in cancer cells is widely observed and is often linked to drug resistance. In several cases, such heterogeneity in drug sensitivity of tumors is driven by stochastic and reversible acquisition of a drug tolerant…
Cancer progresses with a change in the structure of the gene network in normal cells. We define a measure of organizational hierarchy in gene networks of affected cells in adult acute myeloid leukemia (AML) patients. With a retrospective…
Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of…
New entropy measures have been recently introduced for the quantification of the complexity of networks. Most of these entropy measures apply to static networks or to dynamical processes defined on static complex networks. In this paper we…
Cancer complexome comprises a heterogeneous and multifactorial milieu that varies in cytology, physiology, signaling mechanisms and response to therapy. The combined framework of network theory and spectral graph theory along with the…
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…
Random boolean networks are a model of genetic regulatory networks that has proven able to describe experimental data in biology. They not only reproduce important phenomena in cell dynamics, but they are also extremely interesting from a…
In this study, we provide a dynamical systems perspective to the modelling of pathological states induced by tumors or infection. A unified disease model is established using the innate immune system as the reference point. We propose a…
Background: Differential expression analysis of (individual) genes is often used to study their roles in diseases. However, diseases such as cancer are a result of the combined effect of multiple genes. Gene products such as proteins seldom…
The field of complex networks studies a wide variety of interacting systems by representing them as networks. To understand their properties and mutual relations, the randomisation of network connections is a commonly used tool. However,…
From the perfect radial symmetries of radiolarian mineral skeletons to the broken symmetry of homochirality, the logic of Nature's regularities has fascinated scientists for centuries. Some of Nature's symmetries are clearly visible in…
Cancer invasion and metastasis depend on angiogenesis. The cellular processes (growth, migration, and apoptosis) that occur during angiogenesis are tightly regulated by signaling molecules. Thus, understanding how cells synthesize multiple…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
The aim of this paper is to discuss the role of robustness and diversity in population dynamics in particular to some properties of the multi-step from healthy tissue to fully malignant tumours. Recent evidence shows that diversity within…