Related papers: Metabolic network modularity arising from simple g…
Networks effectively capture interactions among components of complex systems, and have thus become a mainstay in many scientific disciplines. Growing evidence, especially from biology, suggest that networks undergo changes over time, and…
The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used…
The study of network structural controllability focuses on the minimum number of driver nodes needed to control a whole network. Despite intensive studies on this topic, most of them consider static networks only. It is well-known, however,…
Developing reliable mechanisms for continuous local learning is a central challenge faced by biological and artificial systems. Yet, how the environmental factors and structural constraints on the learning network influence the optimal…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed…
We present a general computational theory of cancer and its developmental dynamics. The theory is based on a theory of the architecture and function of developmental control networks which guide the formation of multicellular organisms.…
Biological phenomena differ significantly from physical phenomena. At the heart of this distinction is the fact that biological entities have computational abilities and thus they are inherently difficult to predict. This is the reason why…
In several applications, including in synthetic biology, one often has input/output data on a system composed of many modules, and although the modules' input/output functions and signals may be unknown, knowledge of the composition…
We study the effect of extrinsic noise in metabolic networks. We introduce external random fluctuations at the kinetic level, and show how these lead to a stochastic generalization of standard Metabolic Control Analysis. While Summation and…
Molecular signaling networks are believed to determine cancer robustness. Although cancer patient survivability was reported to correlate with the heterogeneous connectivity of the signaling networks inspired by theoretical studies on the…
In this work we study the problem of network morphism, an effective learning scheme to morph a well-trained neural network to a new one with the network function completely preserved. Different from existing work where basic morphing types…
The response of complex networks to perturbations is of utmost importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that the perturbation of one node can…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
To understand the structure of a large-scale biological, social, or technological network, it can be helpful to decompose the network into smaller subunits or modules. In this article, we develop an information-theoretic foundation for the…
We describe the dynamics of a simple adaptive network. The network architecture evolves to a number of disconnected components on which the dynamics is characterized by the possibility of differently synchronized nodes within the same…
We propose a model for the growth of weighted networks that couples the establishment of new edges and vertices and the weights' dynamical evolution. The model is based on a simple weight-driven dynamics and generates networks exhibiting…
A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this…
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 central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…