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Signal processing in biological systems is delicately executed by specialised networks, which are modular assemblies of network motifs. The motifs are independently functional circuits found in enormous numbers in any living cell. A very…
We investigate bifurcations in feedforward coupled cell networks. Feedforward structure (the absence of feedback) can be defined by a partial order on the cells. We use this property to study generic one-parameter steady state bifurcations…
Directed cycles form the fundamental motifs in natural, social and artificial networks, yet their distinct computational roles remain under-explored, particularly in the context of higher-order structure and function. In this work, we…
The global dynamics of gene regulatory networks are known to show robustness to perturbations in the form of intrinsic and extrinsic noise, as well as mutations of individual genes. One molecular mechanism underlying this robustness has…
The formalism of partial information decomposition provides independent or non-overlapping components constituting total information content provided by a set of source variables about the target variable. These components are recognised as…
We demonstrate the advantages of feedforward loops using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical behaviors of network embedded feedback and…
We consider possible designs and experimental realiza-tions in synthesized rather than naturally occurring bio-chemical systems of a selection of basic bio-inspired information processing steps. These include feed-forward loops, which have…
We analyze a class of network motifs in which a short, two-node positive feed- back motif is inserted in a three-node negative feedback loop. We demonstrate that such networks can undergo a bifurcation to a state where a stable fixed point…
Recurrent neural network architectures can have useful computational properties, with complex temporal dynamics and input-sensitive attractor states. However, evaluation of recurrent dynamic architectures requires solution of systems of…
Using the formalism of information theory, we analyze the mechanism of information transduction in a simple one-step signaling cascade S$\rightarrow$X representing the gene regulatory network. Approximating the signaling channel to be…
Representation of intracellular signaling networks as directed graphs allows for the identification of regulatory motifs. Regulatory motifs are groups of nodes with the same connectivity structure, capable of processing information. The…
Intracellular biochemical networks fluctuate dynamically due to various internal and external sources of fluctuation. Dissecting the fluctuation into biologically relevant components is important for understanding how a cell controls and…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
Studies on the role of fluctuations in signal propagation and on gene regulation in monoclonal bacterial population have been extensively pursued based on the machinery of two-component system. The bacterial two-component system shows noise…
In a previous paper, the authors developed a method for computing normal forms of dynamical systems with a coupled cell network structure. We now apply this theory to one-parameter families of homogeneous feed-forward chains with…
Network motifs are patterns of over-represented node interactions in a network which have been previously used as building blocks to understand various aspects of the social networks. In this paper, we use motif patterns to characterize the…
In contrast to engineering applications, in which the structure of control laws are designed to satisfy prescribed function requirements, in biology it is often necessary to infer gene-circuit function from incomplete data on gene-circuit…
The design of biologically-inspired wireless communication systems using bacteria as the basic element of the system is initially motivated by a phenomenon called \emph{Quorum Sensing}. Due to high randomness in the individual behavior of a…
MicroRNAs are endogenous non-coding RNAs which negatively regulate the expression of protein-coding genes in plants and animals. They are known to play an important role in several biological processes and, together with transcription…
Biological and technological networks contain patterns, termed network motifs, which occur far more often than in randomized networks. Network motifs were suggested to be elementary building blocks that carry out key functions in the…