Related papers: Epigenetic Dynamics of Cell Reprogramming
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
We investigate the mechanisms of histone sliding and detachment with a stochastic model that couples thermally-induced, passive histone sliding with active motor-driven histone unwrapping. Analysis of a passive loop or twist defect-mediated…
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…
Heterogeneity is ubiquitous in stem cells (SC), cancer cells (CS), and cancer stem cells (CSC). SC and CSC heterogeneity is manifested as diverse sub-populations with self-renewing and unique regeneration capacity. Moreover, the CSC progeny…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that…
We present a hybrid vertex/cell-centred model for mechanically simulating planar cellular monolayers undergoing cell reorganisation. Cell centres are represented by a triangular nodal network, while the cell boundaries are formed by an…
Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…
Program synthesis aims to automatically construct human-readable programs that satisfy given task specifications, such as input/output pairs or demonstrations. Recent works have demonstrated encouraging results in a variety of domains, such…
The homeostasis of epithelial tissue relies on a balance between the self-renewal of stem cell populations, cellular differentiation, and loss. Although this balance needs to be tightly regulated to avoid pathologies, such as tumor growth,…
A shortcut to adiabaticity (STA) is concerned with the fast and robust manipulation of the dynamics of a quantum system that reproduces the effect of an adiabatic process. A recently proposed method enables the generation of shortcuts from…
We propose and analyze a stochastic model to investigate epigenetic mutations, i.e., modifications of the genetic information that control gene expression patterns in a cell but do not alter the DNA sequence. Epigenetic mutations are…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
The mechanical environment of a substrate plays a key role in influencing the behavior of adherent biological cells. Traditional tunable substrates have limitations as their mechanical properties cannot be dynamically altered in-situ during…
Cell fate determination, the process through which cells commit to differentiated states is commonly mediated by gene regulatory motifs with mutually exclusive expression states. The classical deterministic picture for cell fate…
We study a stochastic model proposed recently in the genetic literature to explain the heterogeneity of cell populations or of gene products. Cells are located in two colonies, whose sizes fluctuate as birth and migration processes in…
Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. MtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The…
We introduce a machine learning approach for extracting fine-grained representations of protein evolution from molecular dynamics datasets. Metastable switching linear dynamical systems extend standard switching models with a…
Hematopoiesis is a complex biological process that leads to the production and regulation of blood cells. It is based upon differentiation of stem cells under the action of growth factors. A mathematical approach of this process is proposed…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…