Related papers: Chromatin Structure Changes in Human Disease: A Mi…
Across the life sciences, an ongoing effort over the last 50 years has made data and methods more reproducible and transparent. This openness has led to transformative insights and vastly accelerated scientific progress. For example,…
The GC-content is very variable in different genome regions and species but although many hypothesis we still do not know the reason why. Here we show that a relationship exists with the mutation rate, in particular we noticed a new…
Cell migration is closely linked to cell shape, yet cell size is often assumed to remain constant. This assumption is challenged by recent experiments showing that cells undergo volume loss during spreading and swelling upon activation,…
The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure.…
The implications of large-scale coherence in biological systems and possible links to quantum theory are only beginning to be explored. Whether quantum-like coherent phenomena are relevant, or even possible at all, at the high temperatures…
The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the…
Disease progression modeling provides a robust framework to identify long-term disease trajectories from short-term biomarker data. It is a valuable tool to gain a deeper understanding of diseases with a long disease trajectory, such as…
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…
With the help of a mathematical model, the metabolic process of the Krebs cycle is studied. The autocatalytic processes resulting in both the formation of the self-organization in the Krebs cycle and the appearance of a cyclicity of its…
Chromatin is repeatedly deformed in vivo during transcription, nuclear remodeling, and confined migration - yet how mechanical response varies from locus to locus, and how it relates to epigenetic state, remains unclear. We develop a theory…
A new approach to the modular, complex systems analysis of nonlinear dynamics in cell cycling network transformations involved in carcinogenesis is proposed. Carcinogenesis is a complex process that involves dynamically inter-connected…
One of the central problems in epigenetics is how epigenetic modification patterns and chromatin structure are regulated in the cell nucleus. The polymer Potts model, a recently studied model of chromatins, is introduced with an offset in…
Infectious diseases are caused by pathogenic microorganisms, such as bacteria, viruses, parasites or fungi, which can be spread, directly or indirectly, from one person to another. Infectious diseases pose a serious threat to human health,…
Atherosclerosis is one of the principle pathologies of cardiovascular disease with blood cholesterol a significant risk factor. The World Health Organisation estimates that approximately 2.5 million deaths occur annually due to the risk…
Obesity is a chronic disease that can lead to an increased risk of other serious chronic diseases and even death. We present switching and time-delayed feedback-based model free control methods for the dynamic management of body mass and…
Structured populations are ubiquitous across the biological sciences. Mathematical models of these populations allow us to understand how individual physiological traits drive the overall dynamics in aggregate. For example, linear age- or…
The aim of this paper is to study the (clinical) time-series data of three diseases with complex dynamics: Parkinson's disease, Huntington's disease and Amyotrophic Lateral Sclerosis. For this purpose, first all of the time series data are…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
Danger requires a strong rapid response. Speedy triggers are prone to false signals. False alarms can be costly, requiring strong negative regulators to oppose the initial triggers. Strongly opposed forces can easily be perturbed, leading…