Related papers: A geometrical perspective on development
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
Understanding the dynamics of road networks has theoretical implications for urban science and practical applications for sustainable long-term planning. Various generative models to explain road network growth have been introduced in the…
The relationship between algebraic geometry and the inferential framework of the Bayesian Networks with hidden variables has now been fruitfully explored and exploited by a number of authors. More recently the algebraic formulation of…
Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
This paper focuses on polynomial dynamical systems over finite fields. These systems appear in a variety of contexts, in computer science, engineering, and computational biology, for instance as models of intracellular biochemical networks.…
Mathematical models of stem cell differentiation are commonly based upon the concept of subsequent cell fate decisions, each controlled by a gene regulatory network. These networks exhibit a multistable behavior and cause the system to…
In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped…
Cities are living organisms. They are out of equilibrium, open systems that never stop developing and sometimes die. The local geography can be compared to a shell constraining its development. In brief, a city's current layout is a step in…
Cell lineage decisions occur in three-dimensional spatial patterns that are difficult to identify by eye. There is an ongoing effort to replicate such patterns using mathematical modeling. One approach uses long ranging cell-cell…
Genetic regulatory networks are usually modeled by systems of coupled differential equations and by finite state models, better known as logical networks, are also used. In this paper we consider a class of models of regulatory networks…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
In densely-packed two-dimensional systems of growing cells, such as rod-shaped bacteria, a number of experimental and numerical studies report distinct patterns of nematic orientational order in the presence of confinement. So far, these…
Constructing gene regulatory networks is a fundamental task in systems biology. We introduce a Gaussian reciprocal graphical model for inference about gene regulatory relationships by integrating mRNA gene expression and DNA level…
Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns…
Biological processes underlying the basic functions of a cell involve complex interactions between genes. From a technical point of view, these interactions can be represented through a graph where genes and their connections are,…
Advances in experimental neuroscience have transformed our ability to explore the structure and function of neural circuits. At the same time, advances in machine learning have unleashed the remarkable computational power of artificial…
Turing patterns, arising from the interplay between competing species of diffusive particles, has long been an important concept for describing non-equilibrium self-organization in nature, and has been extensively investigated in many…
The remarkable range of biological forms in and around us, such as the undulating shape of a leaf or flower in the garden, the coils in our gut, or the folds in our brain, raise a number of questions at the interface of biology, physics and…
A rich class of network models associate each node with a low-dimensional latent coordinate that controls the propensity for connections to form. Models of this type are well established in the network analysis literature, where it is…