Related papers: A geometrical perspective on development
Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different cell types, that elaborates this complexity, result from the activity of gene networks and…
The complexity of gene regulatory networks in multicellular organisms makes interpretable low-dimensional models highly desirable. An attractive geometric picture, attributed to Waddington, visualizes the differentiation of a cell into…
A common metaphor for describing development is a rugged "epigenetic landscape" where cell fates are represented as attracting valleys resulting from a complex regulatory network. Here, we introduce a framework for explicitly constructing…
An adult human body is made up of some 30 to 40 trillion cells, all of which stem from a single fertilized egg cell. The process by which the right cells appear to arrive in their right numbers at the right time at the right place --…
Multicellular organisms contain a wide variety of highly specialized cell types. The consistency and robustness of developmental trajectories suggest that complex gene regulatory networks effectively act as low-dimensional cell fate…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
A fundamental task in developmental biology is to identify the mechanisms which drive morphogenesis. In many cases, pattern formation is driven by the positional information determined by both the gradient of maternal factors and hard-wired…
The positioning of new cellular walls during cell division plays a key role in shaping plant tissue organization. The influence of cell geometry on the positioning of division planes has been previously captured into various geometrical…
The capacity to precisely edit genomes has outpaced our ability to predict the consequences. A cell can be genetically perfect and therapeutically useless: edited exactly as intended, yet unstable, drifting toward unintended fates, or…
There are a number of ways to procedurally generate interesting three-dimensional shapes, and a method where a cellular neural network is combined with a mesh growth algorithm is presented here. The aim is to create a shape from a genetic…
The computational modeling of genetic regulatory networks is now common place, either by fitting a system to experimental data or by exploring the behaviour of abstract systems with the aim of identifying underlying principles. This paper…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
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…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
Networks are mathematical structures that are universally used to describe a large variety of complex systems such as the brain or the Internet. Characterizing the geometrical properties of these networks has become increasingly relevant…
In this paper I present some of the most representative biological models applied to robotics. In particular, this work represents a survey of some models inspired, or making use of concepts, by gene regulatory networks (GRNs): these…
Multicellular organisms exhibit a high degree of structural organization with specific cell types always occurring in characteristic locations. The conventional framework for describing the emergence of such consistent spatial patterns is…
The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…
Genetic regulatory networks are defined by their topology and by a multitude of continuously adjustable parameters. Here we present a class of simple models within which the relative importance of topology vs. interaction strengths becomes…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…