Related papers: On Gene Duplication Models for Evolving Regulatory…
Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed…
Genes communicate with each other through different regulatory effects, which lead to the emergence of complex structures in cells, and such structures are expected to be different for normal and cancerous cells. To study breast cancer…
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…
We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
From the proliferative mechanisms generating neurons from progenitor cells to neuron migration and synaptic connection formation, several vicissitudes culminate in the mature brain. Both component loss and gain remain ubiquitous during…
Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…
We introduce a network growth model based on complete redirection: a new node randomly selects an existing target node, but attaches to a random neighbor of this target. For undirected networks, this simple growth rule generates unusual,…
Dynamic gene-regulatory networks are complex since the number of potential components involved in the system is very large. Estimating dynamic networks is an important task because they compromise valuable information about interactions…
We consider an evolving network of a fixed number of nodes. The allocation of edges is a dynamical stochastic process inspired by biological reproduction dynamics, namely by deleting and duplicating existing nodes and their edges. The…
The yeast galactose network has provided many insights into how eukaryotic gene circuits regulate metabolic function. However, there is currently no consensus model of the network that incorporates protein dilution due to cellular growth.…
Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node…
Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here, we show that a large fraction of…
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…
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…
In this paper we present a generalized model for network growth that links the microscopical agent strategies with the large scale behavior. This model is intended to reproduce the largest number of features of the Internet network at the…
The evolution of species habitat range is an important topic over a wide range of research fields. In higher organisms, habitat range evolution is generally associated with genetic events such as gene duplication. However, the specific…
Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the…
Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…
We study the spreading dynamics on graphs with a power law degree distribution p_k ~ k^-gamma with 2<gamma<3, as an example of a branching process with diverging reproductive number. We provide evidence that the divergence of the second…