Related papers: The coherent feed-forward loop acts as an efficien…
Construction of a scaffold structure that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes. But a general solution to this motif-scaffolding problem remains open. Current…
Biochemical signalling cascades transduce extracellular stimuli into cellular responses through sequences of discrete, node-to-node activations. While signal fidelity depends critically on local interaction kinetics, the mechanisms…
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that…
A prominent feature of gene transcription regulatory networks is the presence in large numbers of motifs, i.e, patterns of interconnection, in the networks. One such motif is the feed forward loop (FFL) consisting of three genes X, Y and Z.…
Feed-forward loops (FFLs) are among the most ubiquitously found motifs of reaction networks in nature. However, little is known about their stochastic behavior and the variety of network phenotypes they can exhibit. In this study, we…
Motivation: Recent studies of genomic-scale regulatory networks suggested that a feed-forward loop (FFL) circuitry is a key component of many such networks. This led to a study of the functional properties of different FFL types, where the…
We investigate the structural and dynamical properties of the transcriptional regulatory network of the yeast {\it Saccharomyces cerevisiae} and compare it with two unbiased ensembles: one obtained by reshuffling the edges and the other…
This note studies feedforward circuits as models for perfect adaptation to step signals in biological systems. A global convergence theorem is proved in a general framework, which includes examples from the literature as particular cases. A…
We study reliable communication in uncoordinated vehicular communication from the perspective of Shannon theory. Our system model for the information transmission is that of an Arbitrarily Varying Channel (AVC): One sender-receiver pair…
In this paper, we consider a bidirectional relay network with half-duplex nodes and block fading where the nodes transmit with a fixed transmission rate. Thereby, user 1 and user 2 exchange information only via a relay node, i.e., a direct…
Many biological regulatory systems process signals out of steady state and respond with a physiological delay. A simple model of regulation which respects these features shows how the ability of a delayed output to transmit information is…
Networks are abundant in biological systems. Small sized over-represented network motifs have been discovered, and it has been suggested that these constitute functional building blocks. We ask whether larger dynamical network motifs exist…
The mining of graphs in terms of their local substructure is a well-established methodology to analyze networks. It was hypothesized that motifs - subgraph patterns which appear significantly more often than expected at random - play a key…
The back-propagation (BP) algorithm has been considered the de-facto method for training deep neural networks. It back-propagates errors from the output layer to the hidden layers in an exact manner using the transpose of the feedforward…
In this paper, we study the bidirectional/two-way relaying of molecular communication and propose a relaying scheme with two time slots. Compared to the four-time-slot and three-time-slot schemes, the proposed two-time-slot scheme improves…
The mating pathway in \emph{Saccharomyces cerevisiae} is one of the best understood signal transduction pathways in eukaryotes. It transmits the mating signal from plasma membrane into the nucleus through the G-protein coupled receptor and…
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…
Associative memory has been a prominent candidate for the computation performed by the massively recurrent neocortical networks. Attractor networks implementing associative memory have offered mechanistic explanation for many cognitive…
During batch growth on mixtures of two growth-limiting substrates, microbes consume the substrates either sequentially or simultaneously. These growth patterns are manifested in all types of bacteria and yeasts. The ubiquity of these growth…
In this paper, we consider a network communications problem in which multiple correlated sources must be delivered to a single data collector node, over a network of noisy independent point-to-point channels. We prove that perfect…