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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 the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
High-throughput experiments are shedding light on the topology of large regulatory networks and at the same time their functional states, namely the states of activation of the nodes (for example transcript or protein levels) in different…
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…
Recurrent neural networks are frequently studied in terms of their information-processing capabilities. The structural properties of these networks are seldom considered, beyond those emerging from the connectivity tuning necessary for…
Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions -- lists of the most important players and the pairwise interactions between them.…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
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…
Networked systems display complex patterns of interactions between a large number of components. In physical networks, these interactions often occur along structural connections that link components in a hard-wired connection topology,…
The rapidly developing theory of complex networks indicates that real networks are not random, but have a highly robust large-scale architecture, governed by strict organizational principles. Here, we focus on the properties of biological…
The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation, signaling, or metabolic mechanisms, and computational…
Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
We examine the modular structure of the metabolic network when combined with the regulatory network representing direct regulation of enzymes by small metabolites in E.coli. In order to identify the modular structure we introduce clustering…
Neural systems show a modular and typically also a hierarchical organisation across different levels and across different species. Topology relates to function, but it is also influences dynamics as earlier studies showed its effect on…
In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model was recently proposed to explain this scaling for metabolic enzymes and their…
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…
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…
We propose a general method to predict functions of vertices where: 1. The wiring of the network is somehow related to the vertex functionality. 2. A fraction of the vertices are functionally classified. The method is influenced by…