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In synthetic biology, gene regulatory circuits are often constructed by combining smaller circuit components. Connections between components are achieved by transcription factors acting on promoters. If the individual components behave as…
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.…
In many organisms the expression levels of each gene are controlled by the activation levels of known "Transcription Factors" (TF). A problem of considerable interest is that of estimating the "Transcription Regulation Networks" (TRN)…
Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
Transcription Factors (TFs) are proteins crucial for regulating gene expression. Effective regulation requires the TFs to rapidly bind to their correct target, enabling the cell to respond efficiently to stimuli such as nutrient…
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…
Cellular responses often require the fast activation or repression of specific genes, which depends on Transcription Factors (TFs) that have to quickly find the promoters of these genes within a large genome. Transcription Factors (TFs)…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
Appropriate regulation of gene expression is essential to ensure that protein synthesis occurs in a selective manner. The control of transcription is the most dominant type of regulation mediated by a complex of molecules such as…
The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…
Response time and transcription level are vital parameters of gene regulation. They depend on how fast transcription factors (TFs) find and how efficient they occupy their specific target sites. It is well known that target site search is…
We study learning of recurrent neural networks that produce temporal sequences consisting of the concatenation of re-usable "motifs". In the context of neuroscience or robotics, these motifs would be the motor primitives from which complex…
We demonstrate the effects of embedding subgraphs using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical properties of network embedded seven different…
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…
A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…
Recurrent neural networks (RNNs) are powerful dynamical models, widely used in machine learning (ML) and neuroscience. Prior theoretical work has focused on RNNs with additive interactions. However, gating - i.e. multiplicative -…
We develop a framework for self-induced phase changes in programmable matter in which a collection of agents with limited computational and communication capabilities can collectively perform appropriate global tasks in response to local…
Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction…
Dynamic network analysis has found an increasing interest in the literature because of the importance of different kinds of dynamic social networks, biological networks, and economic networks. Most available probability and statistical…