Related papers: Metabolic network modularity arising from simple g…
A biologically motivated individual-based framework for evolution in network-structured populations is developed that can accommodate eco-evolutionary dynamics. This framework is used to construct a network birth and death model. The…
"Evolution behaves like a tinkerer" (Francois Jacob, Science, 1977). Software systems provide a unique opportunity to understand biological processes using concepts from network theory. The Debian GNU/Linux operating system allows us to…
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…
From biosystem to complex system,the study of life is always an important area. Inspired by hyper-cycle theory about the evolution of non-life system, we study the metabolism, self-replication and mutation behavior in the Internet based on…
We propose a discrete model to determine the metabolic scaling exponent based on Fibonacci growth patterns and discrete biological development phases. In contrast to continuous fractal models such as the West-Brown-Enquist (WBE) theory, the…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
We propose a natural model of evolving weighted networks in which new links are not necessarily connected to new nodes. The model allows a newly added link to connect directly two nodes already present in the network. This is plausible in…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
Many researchers have hypothesised models which explain the evolution of the topology of a target network. The framework described in this paper gives the likelihood that the target network arose from the hypothesised model. This allows…
Behavioral changes in animals and humans, as a consequence of an error or a verbal instruction, can be extremely rapid. Improvement in behavioral performances are usually associated in machine learning and reinforcement learning to synaptic…
Biomolecular networks have already found great utility in characterizing complex biological systems arising from pair-wise interactions amongst biomolecules. Here, we review how graph theoretical approaches can be applied not only for a…
Genome-scale metabolic models have become a fundamental tool for examining metabolic principles. However, metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes, but also affected by regulatory…
Wagner's modularity inducing problem domain is a key contribution to the study of the evolution of modularity, including both evolutionary theory and evolutionary computation. We study its behavior under classical genetic algorithms. Unlike…
We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of…
Cooperation is observed widely in nature and is thought an essential component of many evolutionary processes, yet the mechanisms by which it arises and persists are still unclear. Among several theories, network reciprocity -- a model of…
Mechanistic models can provide an intuitive and interpretable explanation of network growth by specifying a set of generative rules. These rules can be defined by domain knowledge about real-world mechanisms governing network growth or may…
Cells adapt their metabolic fluxes in response to changes in the environment. We present a framework for the systematic construction of flux-based graphs derived from organism-wide metabolic networks. Our graphs encode the directionality of…
The metabolic wiring of patient cells is altered drastically in many diseases, including cancer. Understanding the nature of such changes may pave the way for new therapeutic opportunities, as well as the development of personalized…
The modular structure of brain networks supports specialized information processing, complex dynamics, and cost-efficient spatial embedding. Inter-individual variation in modular structure has been linked to differences in performance,…
We present a simple physical model that recapitulates several features of biological evolution, while being based only on thermally-driven attachment and detachment of elementary building blocks. Through its dynamics, this model samples a…