Related papers: Dynamics of cell-type transition mediated by epige…
This paper deals with a model of cellular growth called "Epigenetic Tracking", whose key features are: i) distinction bewteen "normal" and "driver" cells; ii) presence in driver cells of an epigenetic memory, that holds the position of the…
The mechanism through which cells determine their fate is intimately related to the spreading of certain biochemical (so-called epigenetic) marks along their genome. The mechanisms behind mark spreading and maintenance are not yet fully…
Extrachromosomal DNA (ecDNA) can drive oncogene amplification, gene expression and intratumor heterogeneity, representing a major force in cancer initiation and progression. The phenomenon becomes even more intricate as distinct types of…
Cell size is a fundamental determinant of cellular physiology, influencing processes such as growth, division, and function. In this study, we develop a segmented mathematical framework to investigate how different control mechanisms…
Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underly many morphogenetic events and involve spatial gradients in active cellular forces…
To maintain renewing epithelial tissues in a healthy, homeostatic state, (stem) cell divisions and differentiation need to be tightly regulated. Mechanisms of homeostatic control often rely on crowding control: cells are able to sense the…
In epidemiological modelling, dynamics on networks, and in particular adaptive and heterogeneous networks have recently received much interest. Here we present a detailed analysis of a previously proposed model that combines heterogeneity…
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including…
Phenotype transition takes place in many biological processes such as differentiation, and understanding how a cell reprograms its global gene expression profile is a problem of rate theories. A cell phenotype transition accompanies with…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
The process controlling the diferentiation of stem, or progenitor, cells into one specific functional direction is called lineage specification. An important characteristic of this process is the multi-lineage priming, which requires the…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a…
Understanding to what extent stem cell potential is a cell-intrinsic property, or an emergent behavior coming from global tissue dynamics and geometry, is a key outstanding question of systems and stem cell biology. Here, we propose a…
The emergence of acquired drug resistance in cancer represents a major barrier to treatment success. While research has traditionally focused on genetic sources of resistance, recent findings suggest that cancer cells can acquire transient…
Human embryonic stem cells (ESC) are undifferentiated and are endowed with the capacities of self renewal and pluripotential differentiation. Adult stem cells renew their own tissue, but whether they can trans-differentiate to other tissues…
The compartmentalization of distinct templates in protocells and the exchange of templates between them (migration) are key elements of a modern scenario for prebiotic evolution. Here we use the diffusion approximation of population…
Identifying control strategies for biological networks is paramount for practical applications that involve reprogramming a cell's fate, such as disease therapeutics and stem cell reprogramming. Here we develop a novel network control…
We present the epithelial-to-mesenchymal transition (EMT) from two perspectives: experimental/technological and theoretical. We review the state of the current understanding of the regulatory networks that underlie EMT in three…