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Social science studies dealing with control in networks typically resort to heuristics or describing the static control distribution. Optimal policies, however, require interventions that optimize control over a socioeconomic network…
A theory for qualitative models of gene regulatory networks has been developed over several decades, generally considering transcription factors to regulate directly the expression of other transcription factors, without any intermediate…
In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies…
We introduce the concept of control centrality to quantify the ability of a single node to control a directed weighted network. We calculate the distribution of control centrality for several real networks and find that it is mainly…
A reflection of our ultimate understanding of a complex system is our ability to control its behavior. Typically, control has multiple prerequisites: It requires an accurate map of the network that governs the interactions between the…
In this paper we study an important global regulation mechanism of transcription of biological cells using specific macro-molecules, 6S RNAs. The functional property of 6S RNAs is of blocking the transcription of RNAs when the environment…
Recent experimental studies of living neural networks reveal that their global activation induced by electrical stimulation can be explained using the concept of bootstrap percolation on a directed random network. The experiment consists in…
The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks…
The well-known issue of reconstructing regulatory networks from gene expression measurements has been somewhat disrupted by the emergence and rapid development of single-cell data. Indeed, the traditional way of seeing a gene regulatory…
We consider a general class of translation-invariant systems with a specific category of output nonlinearities motivated by biological sensing. We show that no dynamic output feedback can stabilize this class of systems to an isolated…
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…
In many real, directed networks, the strongly connected component of nodes which are mutually reachable is very small. This does not fit with current theory, based on random graphs, according to which strong connectivity depends on mean…
Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context specific and dynamic in…
Random boolean networks are a model of genetic regulatory networks that has proven able to describe experimental data in biology. They not only reproduce important phenomena in cell dynamics, but they are also extremely interesting from a…
A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…
Our understanding of neural computation is founded on the assumption that neurons fire in response to a linear summation of inputs. Yet experiments demonstrate that some neurons are capable of complex functions that require interactions…
This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…
We study the problem of controlling a general complex network towards an assigned synchronous evolution, by means of a pinning control strategy. We define the pinning-controllability of the network in terms of the spectral properties of an…
A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed to use statistical correlations in…
This paper highlights several properties of large urban networks that can have an impact on machine learning methods applied to traffic signal control. In particular, we show that the average network flow tends to be independent of the…