Regulatory networks
Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors
... gene regulatory networks from expression data is very challenging and depends on (A) the time point when data are measured, (B) the kind of the external stimulation and (C) the interconnectedness of the ...
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Inference of gene regulatory networks with sparse structural equation models exploiting genetic perturbations.
... of regulatory network topology inference, but also enables learning of causal regulatory relations between ...gene regulatory networks in accordance with biological evidence about genes ...
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GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks
... gene regulatory networks (GRNs). A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of ...
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Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation.
... Lcr2, the promoter of which contains sequence motifs similar to those found in the Lcr1 promoter, suggesting that both genes may be regulated by the same or similar upstream DNA- binding protein(s) domains ensuring ...
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A relative variation-based method to unraveling gene regulatory networks.
... gene regulatory networks (GRN) from experimental data and other a priori ...Boolean networks [3,4], Bayesian networks [5,6], information theory based algorithms [7–10], ordinary differential ...
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Functional alignment of regulatory networks: a study of temperate phages.
... As a case study, we considered the regulatory networks of two well-characterized temperate bacteriophages of E. coli, k and 186 (Figure 1). These two phages represent two distinct classes of temperate ...
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Harnessing diversity towards the reconstructing of large scale gene regulatory networks.
... transcriptional regulatory networks and their corresponding expression data from large-scale microarray experiments, together with synthetic network and corresponding expression datasets ...
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Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.
... on regulatory networks comprising genes, proteins, and small ...tory networks are often very complicated, such that for even the simplest functions many components are involved and entangled with ...
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Regulatory networks controlling nitrogen sensing and uptake in Candida albicans.
... Nitrogen is one of the key nutrients for microbial growth. During infection, pathogenic fungi like C. albicans need to acquire nitrogen from a broad range of different and changing sources inside the host. Detecting the ...
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Studying Dynamic Features in Myocardial Infarction Progression by Integrating miRNA-Transcription Factor Co-Regulatory Networks and Time-Series RNA Expression Data from Peripheral Blood Mononuclear Cells.
... complex regulatory interactions underlying diseases [12, 13]. Gene regulatory networks control gene expression and protein formation, and therefore influence the cell ...gene regulatory ...
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ZNF675 evolutionary history and its novel role in neuronal regulatory networks
... in regulatory regions, they can change their expression levels, thus altering the network on which that gene acts on (Ayarpadikannan & Kim, ...gene regulatory networks over mammalian evolution ...
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A parallel attractor-finding algorithm based on Boolean satisfiability for genetic regulatory networks.
... genetic regulatory network are modeled as a set of functions of the Boolean network, while the state transitions in the Boolean network reflect the dynamic property of a genetic regulatory ...genetic ...
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Modelling and Simulation of Biological Regulatory Networks by Stochastic Petri Nets
... Abstract – Biological Regulatory Networks (BRNs) depicts the basic interactions in between various nodes in all biological systems. Inherently, all chemical and biological actions are governed by continuous ...
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Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach.
... regulatory networks. Given the physical and logical complexity of these networks, the various sources of (often noisy) data that can be utilized for their elucidation, the monetary costs involved, ...
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Metabolic constraint-based refinement of transcriptional regulatory networks.
... transcriptional regulatory networks (TRNs) focus primarily on proximal data such as gene co-expression and transcription factor (TF) ...possible networks limits identification of mechanistic ...
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Mutational robustness of gene regulatory networks.
... gene regulatory networks, systems of ordinary differential equations (ODEs) were used, which describe TF-TF dimerization and TF-target gene regulation (via Hill ...the regulatory interactions of the ...
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Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks.
... gene regulatory networks (GRN) can be difficult to interpret due to a tangle of edges interconnecting thousands of ...core regulatory genes (transcription factors and ...core regulatory genes ...
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High-precision, in vitro validation of the sequestration mechanism for generating ultrasensitive dose-response curves in regulatory networks.
... genetic networks in which genetic elements are ‘‘mixed and matched’’ in order to create artificial bistable ‘‘toggle switches,’’ genetic oscillators and other complex, non-linear input/output behaviors ...genetic ...
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Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks.
... Collier, the single Drosophila COE (Collier/EBF/Olf-1) transcription factor, is required in sev- eral developmental processes, including head patterning and specification of muscle and neuron identity during ...
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Evolution of gene regulatory networks by fluctuating selection and intrinsic constraints.
... (iii) Mutational bias. We next examined the influence of mutational bias on GRN evolution. In other words, we wanted to determine the properties of GRNs that are more sensitive to mutational bias. Lynch (2007) proposed ...
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