相关论文: Serially-regulated biological networks fully reali…

Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…

Two different types of directed networks are investigated, transcriptional regulation networks and neural networks. The directed network structure are studied and also shown to reflect the different processes taking place on the networks.…

The control of complex networks is of paramount importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that perturbations to one node can affect other nodes,…

We develop a general method to explore how the function performed by a biological network can constrain both its structural and dynamical network properties. This approach is orthogonal to prior studies which examine the functional…

Nature is rife with networks that are functionally optimized to propagate inputs in order to perform specific tasks. Whether via genetic evolution or dynamic adaptation, many networks create functionality by locally tuning interactions…

The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…

Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…

Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…

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 networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…

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…

Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…

Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…

Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…

Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous…

Many biological, technological, and social systems can be effectively described as networks of interacting subsystems. Typically, these networks are not isolated objects, but interact with their environment through both signals and…

The identification of the limiting factors in the dynamical behavior of complex systems is an important interdisciplinary problem which often can be traced to the spectral properties of an underlying network. By deriving a general relation…

Genetic regulatory networks (GRNs) have been widely studied, yet there is a lack of understanding with regards to the final size and properties of these networks, mainly due to no network currently being complete. In this study, we analyzed…

We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…

Cells are regulated by networks of controllers having many targets, and targets affected by many controllers, but these "many-to-many" combinatorial control systems are poorly understood. Here we analyze distinct cellular networks…