Related papers: Drawing a Waddington landscape to capture dynamic …
Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of a process known as spontaneous immortalization. In this process a generic series of cell state transitions occur in…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic…
Epigenetic Tracking is a mathematical model of biological cells, originally conceived to study embryonic development. Computer simulations proved the capacity of the model to generate complex 3-dimensional cellular structures, and the…
Quantifying the adaptive landscape in a given dynamical processes has been one of most important goals in theoretical biology. It can have immediate implications for many dynamical properties, such as robustness and plasticity. Based on…
Statistical physics provides a useful perspective for the analysis of many complex systems; it allows us to relate microscopic fluctuations to macroscopic observations. Developmental biology, but also cell biology more generally, are…
DNA methylation is usually treated as an epigenetic memory mark: transcriptional history is written into regulatory DNA and later stabilizes a chosen cell identity. This picture explains persistence, but it makes memory passive. Here we…
Epigenetics has captured the attention of scientists in the past decades, yet its scope has been continuously changing. In this paper, we give an overview on how and why its definition has evolved and suggest several clarification on the…
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…
Epigenetic landscapes, represented by patterns of chemical modifications on histone tails, are essential for maintaining cell identity and tissue homeostasis. These landscapes are shaped by multiple factors, including local biochemical…
We suggest to simulate evolution of complex organisms constrained by the sole requirement of robustness in their expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence…
Genetic algorithms are a well-known example of bio-inspired heuristic methods. They mimic natural selection by modeling several operators such as mutation, crossover, and selection. Recent discoveries about Epigenetics regulation processes…
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…
In cellular reprogramming, almost all epigenetic memories of differentiated cells are erased by the overexpression of few genes, regaining pluripotency, potentiality for differentiation. Considering the interplay between oscillatory gene…
The Waddington landscape serves as a metaphor illustrating the developmental process of cells, likening it to a small ball rolling down various trajectories into valleys. Constructing an epigenetic landscape of this nature aids in…
Developmental dynamics of multicellular organism is a process that takes place in a multi-stable system in which each attractor state represents a cell type and attractor transitions correspond to cell differentiation paths. This new…
Cell fate decisions emerge as a consequence of a complex set of gene regulatory networks. Models of these networks are known to have more parameters than data can determine. Recent work, inspired by Waddington's metaphor of a landscape, has…
Epigenetic cell memory, the inheritance of gene expression patterns across subsequent cell divisions, is a critical property of multi-cellular organisms. In recent work [10], a subset of the authors observed in a simulation study how the…
Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and…
A large number of studies have shown the existence of metabolic covalent modifications in different molecular structures, able to store biochemical information that is not encoded by the DNA. Some of these covalent mark patterns can be…