Related papers: A theoretical basis for cell deaths
Telomeres are repetitive sequences of nucleotides at the end of chromosomes, whose evolution over time is intrinsically related to biological ageing. In most cells, with each cell division, telomeres shorten due to the so-called end…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation, signaling, or metabolic mechanisms, and computational…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
The intratumor heterogeneity has been recognized to characterize cancer cells impairing the efficacy of cancer treatments. We here propose an extension of constraint-based modeling approach in order to simulate metabolism of cell…
Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…
Interactions between crawling cells, which are essential for many biological processes, can be quantified by measuring cell-cell collisions. Conventionally, experiments of cell-cell collisions are conducted on two-dimensional flat…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
Cell tracking algorithms which automate and systematise the analysis of time lapse image data sets of cells are an indispensable tool in the modelling and understanding of cellular phenomena. In this study we present a theoretical framework…
Recent evidence suggests that nongenetic (epigenetic) mechanisms play an important role at all stages of cancer evolution. In many cancers, these mechanisms have been observed to induce dynamic switching between two or more cell states,…
While it is commonly observed that the shape dynamics of mammalian cells can undergo large random fluctuations, theoretical models aiming at capturing cell mechanics often focus on the deterministic part of the motion. In this paper, we…
Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
The organization of live cells into tissues and their subsequent biological function involves inter-cell mechanical interactions, which are mediated by their elastic environment. To model this interaction, we consider cells as spherical…
Aging research has produced powerful explanatory frameworks -- evolutionary theories, the Hallmarks of Aging, SENS, geroscience, hyperfunction, and information-loss models -- yet none provides quantitative rules for determining which…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…
This work introduces a generic quantitative framework for studying dynamical processes that involve interactions of polymer sequences. Possible applications range from quantitative studies of the reaction kinetics of polymerization…
A key challenge in systems biology is the elucidation of the underlying principles, or fundamental laws, which determine the cellular phenotype. Understanding how these fundamental principles are altered in diseases like cancer is important…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology. Constraint-based models in particular play a key role in the attempt to…