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Directed information transmission is paramount for many social, physical, and biological systems. For neural systems, scientists have studied this problem under the paradigm of feedforward networks for decades. In most models of feedforward…
Transcriptional regulation by transcription factors and post-transcriptional regulation by microRNAs constitute two major modes of regulation of gene expression. While gene expression motifs incorporating solely transcriptional regulation…
One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an…
Regulation of gene expression is the consequence of interactions between the promoter of the gene and the transcription factors (TFs). In this paper, we explore the features of a genetic network where the TFs (activators and repressors)…
We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. The gene sets…
To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the…
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
Transcription is regulated through interplay between transcription factors, an RNA polymerase(RNAP), and a promoter. Even for a simple repressive transcription factor that disturbs promoter activity at the initial binding of RNAP, its…
We model the transcription factor based regulation network of yeast using a content-based network model that mimicks the recognition of binding motifs on the regulatory regions of the genes. We are thereby able to faithfully reproduce many…
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…
Developing and maintaining life requires a lot of computation. This is done by gene regulatory networks. But we have little understanding of how this computation is organized. I show that there is a direct correspondence between the…
Motifs, which have been established as building blocks for network structure, move beyond pair-wise connections to capture longer-range correlations in connections and activity. In spite of this, there are few generative graph models that…
We characterize the connectivity structure of feed-forward, deep neural networks (DNNs) using network motif theory. To address whether a particular motif distribution is characteristic of the training task, or function of the DNN, we…
Understanding how transcription factors (TFs) regulate mammalian gene expression in space and time is a central topic in biology. To activate a gene, a TF has first to diffuse in the available space of the nucleus until it reaches a target…
It is well known that, under suitable conditions, microRNAs are able to fine tune the relative concentration of their targets to any desired value. We show that this function is particularly effective when one of the targets is a…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
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.…
Gene regulatory networks present a wide variety of dynamical responses to intrinsic and extrinsic perturbations. Arguably, one of the most important of such coordinated responses is the one of amplification cascades, in which activation of…
Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diffusion (a combination of 3D diffusion around and 1D random…