Related papers: A geometrical perspective on development

Gene regulatory networks arise in all living cells, allowing the control of gene expression patterns. The study of their topology has revealed that certain subgraphs of interactions or "motifs" appear at anomalously high frequencies. We ask…

Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and…

A cellular model introduced for the evolution of the fluvial landscape is revisited using extensive numerical and scaling analyses. The basic network shapes and their recurrence especially in the aggregation structure are then addressed.…

Transport in crowded, complex environments occurs across many spatial scales. Geometric restrictions can hinder the motion of individuals and, combined with crowding between individuals, can have drastic effects on global transport…

Adaptation mechanism of cells on the basis of stochastic gene expression and epigenetic modification is proposed. From marginally stable states generated by epigenetic modification, a gene expression pattern that achieves greater cell…

The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives…

Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…

Networks have been used to model many real-world phenomena to better understand the phenomena and to guide experiments in order to predict their behavior. Since incorrect models lead to incorrect predictions, it is vital to have a correct…

We present a general computational theory of stem cell networks and their developmental dynamics. Stem cell networks are special cases of developmental control networks. Our theory generates a natural classification of all possible stem…

The use of artificial neural networks as models of chaotic dynamics has been rapidly expanding. Still, a theoretical understanding of how neural networks learn chaos is lacking. Here, we employ a geometric perspective to show that neural…

A continuously evolving geography requires a good understanding in networks. As such, this paper accounts for theories and applications of complex networks and their role both in geography in general, as well as in determining various…

Cell type-specific gene expression patterns are represented as memory states of a Hopfield neural network model. It is shown that order parameters of this model can be interpreted as concentrations of master transcription regulators that…

The space of possible behaviors complex biological systems may exhibit is unimaginably vast, and these systems often appear to be stochastic, whether due to variable noisy environmental inputs or intrinsically generated chaos. The brain is…

Landscapes are meaningful ecological units that strongly depend on the environmental conditions. Such dependencies between landscapes and the environment have been noted since the beginning of Earth sciences and cast into conceptual models…

Geometry can be used to explain many properties commonly observed in real networks. It is therefore often assumed that real networks, especially those with high average local clustering, live in an underlying hidden geometric space.…

In a highly simplified view, a disease can be seen as the phenotype emerging from the interplay of genetic predisposition and fluctuating environmental stimuli. We formalize this situation in a minimal model, where a network (representing…

Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…

Graphical modelling has a long history in statistics as a tool for the analysis of multivariate data, starting from Wright's path analysis and Gibbs' applications to statistical physics at the beginning of the last century. In its modern…

The movement changes the underlying spatial representation of the participated mobile objects or nodes. In real world scenario, such mobile nodes can be part of any biological network, transportation network, social network, human…

High-throughput experiments are shedding light on the topology of large regulatory networks and at the same time their functional states, namely the states of activation of the nodes (for example transcript or protein levels) in different…