[PDF] Top 20 Mutational robustness of gene regulatory networks.
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Mutational robustness of gene regulatory networks.
... influencing robustness against mutations of network structure. The results of our analysis provide several clues towards such ...aspects of why certain types of networks are more ... See full document
Global analysis of photosynthesis transcriptional regulatory networks.
... repressor of photopigment biosynthesis operons, including bchCXYZ and bchFNBHM, with high cellular levels of this protein inhibiting photosynthetic ...much of this indirect regulation of ... See full document
Evolution of networks for body plan patterning; interplay of modularity, robustness and evolvability.
... number of domains as a side effect of producing segments, and the minimum domain network performs rather poorly at reproducing the original domain ...minimum networks, we see that only 2 genes are ... See full document
Functional alignment of regulatory networks: a study of temperate phages.
... activation of the host SOS response recombination (RecA) protein. The gene-regula- tory networks of all temperate phages have evolved to provide lysogenic and lytic states, and, moreover, to ... See full document
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) ...reconstruction of TRNs, the overwhelming combinatorics ... See full document
GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks
... The networks with colored edges (Figs. 5D–5F) display the results of a mathematical model, where the expression levels of the individual transcription factors were modeled using mass balance ordinary ... See full document
Contribution of Panton-Valentine leukocidin in community-associated methicillin-resistant Staphylococcus aureus pathogenesis.
... strains of USA300 (LAC and SF8300) and USA400 (MW2) to test whether PVL alters global gene regulatory networks and contributes to pathogenesis of bacteremia, a hallmark feature ... See full document
Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria
... construction of large protein-protein interaction networks (Wallach et ...2014). Networks generated from these studies serve to identify potential targets for future biochemical and bioinformatics ... See full document
Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation.
... region of the Cah1 gene contains at least one silencer and one enhancer region ...upstream of the translation initiation codon) and EE-2 Figure ...histogram of the approximate distances ... See full document
Phenotypic robustness and the assortativity signature of human transcription factor networks.
... expression of genes in space and time. Such spatiotemporal gene expression phenotypes arise from the binding of sequence-specific transcription factors (TFs) to DNA, and from the regulation of ... See full document
Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep.
... proof of concept validating the biological relevance of our results, we describe how genes located within in the intersecting landscape of the joint network (Figure 3) are known to be involved in ... See full document
Systematic identification of core transcription factors mediating dysregulated links bridging inflammatory bowel diseases and colorectal cancer.
... those networks were clearly grouped into three major branches (namely, cancer, inflammation and normal ...or regulatory similarity was observed among tightly clustered networks in each branch, ... See full document
RegnANN: Reverse Engineering Gene Networks using Artificial Neural Networks.
... topology of the gene regulatory network is obtained by applying a second ...each gene in the network separately, we pass a value of 1 to the input neuron of the correspondent ... See full document
Global properties and functional complexity of human gene regulatory variation.
... majority of cases, human disease and complex trait association studies do not identify plausible coding variants implicating a single ...identification of the causal gene(s) that underlie an ... See full document
Quantitative dynamic modelling of the gene regulatory network controlling adipogenesis.
... Gene regulatory networks (GRNs) coherently coordinate the expressions of genes and control the behaviors of cellular ...modeling of GRNs, we have designed a small-sample ... See full document
Modelling and Simulation of Biological Regulatory Networks by Stochastic Petri Nets
... structure of BRNs exist which are used for analysis of dynamical properties ...a gene or biological entity with a logical function having discrete ...rate of change in the levels and as a ... See full document
Robust network topologies for generating switch-like cellular responses.
... ber of networks demonstrated ultrasensitive behavior than bistable behavior ...absence of bistability [8, ...proportion of networks exhibit switch-like behavior on a large percentage ... See full document
Ground state robustness as an evolutionary design principle in signaling networks.
... the robustness principle, our approach is somewhat complementary to that of Shinar et ...set of models and highlight topological features which to our knowledge have not been considered before in the ... See full document
Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach.
... logic of the interactions (Figure ...TF–target gene logic rules from a comparison between KO and wild-type gene expression proﬁles in two growth ...target gene promoters [14–16]. In the ... See full document
Functional Trade-Offs in Promiscuous Enzymes Cannot Be Explained by Intrinsic Mutational Robustness of the Native Activity.
... characteristic of the dynamics of enzyme evolution. Various cases of laboratory evolution have unveiled a characteristic trend; a large increase in a new, promiscuous activity is often accompanied by ... See full document