Related papers: Geometrical constraints in a gene network model an…
Embryonic development involves pattern formation characterized by the emergence of spatially localized domains characterized by distinct cell fates resulting from differential gene expression. The boundaries demarcating these domains are…
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…
Developing and maintaining life requires a lot of computation. This is done by gene regulatory networks. But we have little understanding of how this computation is organized. I show that there is a direct correspondence between the…
We present a model for mechanically-induced pattern formation in growing biological tissues and discuss its application to the development of leaf venation networks. Drawing an analogy with phase transitions in solids, we use a phase field…
Neural computation in biological and artificial networks relies on the nonlinear summation of many inputs. The structural connectivity matrix of synaptic weights between neurons is a critical determinant of overall network function, but…
Graph Neural Networks (GNN) can capture the geometric properties of neural representations in EEG data. Here we utilise those to study how reinforcement-based motor learning affects neural activity patterns during motor planning, leveraging…
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…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Gene expression represents a fundamental interface between genes and environment in the development and ongoing plasticity of the human organism. Individual differences in gene expression are likely to underpin much of human diversity,…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
This work targets the influence of disorder on the relaxed structure and macroscopic mechanical properties of elastic networks. We construct network classes of different types of disorder (length, topology and stiffness), which are…
Network science provides an indispensable theoretical framework for studying the structure and function of real complex systems. Different network models are often used for finding the rules that govern their evolution, whereby the correct…
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…
Spatial organisation is a hallmark of all living cells, and recreating it in model systems is a necessary step in the creation of synthetic cells. It is therefore of both fundamental and practical interest to better understand the basic…
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
Cellular structures must organize themselves within strict physical constraints, operating with finite resources and well-defined boundaries. Classical systems demonstrate only passive responses to boundaries, from surface energy…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss…