Gene networks
How to Knock Out Feedback Circuits in Gene Networks?
... It would be interesting to apply this algorithm to actual gene networks. When edges in G are endowed with a sign, one would also like to have an efficient algorithm for depriving G of its positive (resp. ...
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Time course study of the response to LPS targeting the pig immune gene networks
... JUNB gene (a member of Jun family) also participates in the immune response; it is activated by the TLR signalling path- way [39] and can induce expression of interleukins [40– ...inflammatory gene ...
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Some considerations for analyzing biodiversity using integrative metagenomics and gene networks
... simple gene networks (Figure 3A and ...specific gene families, abundant families, rare families, transferred families and what parts of the graph singled out markers that are amenable to popula- tion ...
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Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks
... In the convergent orientation, once TetR-GFP is expressed in the high state, it continuously dominates by propagating supercoils into the LacI-RFP transcript region. These supercoils may impose a higher activation ...
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Spectral analysis of gene expression profiles using gene networks
... the gene expression analysis process, and several attempts have been carried out in that direction so ...for gene expression from an a priori model of gene networks; for example, by deriving ...
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Foxp2 regulates gene networks implicated in neurite outgrowth in the developing brain.
... Abstract Forkhead-box protein P2 is a transcription factor that has been associated with intriguing aspects of cognitive function in humans, non-human mammals, and song-learning birds. Heterozygous mutations of the human ...
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Weighted gene co-expression network analysis unveils gene networks associated with the Fusarium head blight resistance in tetraploid wheat
... decoy/guard gene-for-gene interaction model [126], leading likely to ...for gene co- expression analysis based on the expression of the whole transcriptome suggested that BB differed from other ...
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dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data
... of the putative edges. This probability is estimated from 100,000 random edge rankings. A higher AUPR score thus indicates a better overall performance over the n networks. Results We first evaluated the ...
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Reconstruction and clustering with graph optimization and priors on gene networks and images
... the gene to be ...the gene promoters — is statistically compared to those obtained at the module ...of gene promoters, randomly chosen among all the gene promoters, instead of using all ...
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Constraint Identification Using Modified Hoare Logic on Hybrid Models of Gene Networks
... and give precise trajectories in terms of concentrations; qualitative models [16, 15] focus on the major features that explain the observations (only main causalities are taken into account); and hybrid models link ...
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Contribution of gene duplications to the evolution of genetic networks
... genetic networks in a controlled ...genetic networks but also of behavior in analogous systems in which features of networks of interacting agents get selectively enhanced over ...
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Refining Dynamics of Gene Regulatory Networks in a Stochastic π-Calculus Framework
... 5. Blossey, R., Cardelli, L., Phillips, A.: A compositional approach to the stochastic dynamics of gene networks. Transactions in Computational Systems Biology 3939 (Jan 2006) 99–122 6. Popova-Zeugmann, ...
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A semiquantitative framework for gene regulatory networks: increasing the time and quantitative resolution of Boolean networks
... biological networks is impeded by a scarcity in ki- netic information on the biochemical reactions that form them, a focus in systems biology, pio- neered by the work of Kauffman [ 2 ] and Thomas [ 3 ], lies on ...
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Reduction of the chemical master equation for gene regulatory networks using proper generalized decompositions
... But noteworthy, the ease of the approximation allows for an easy treatment of unknown parameters (as is frequently the case when modeling gene regulatory networks, for instance). These unknown parameters ...
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Efficient algorithms for reconciling gene trees and species networks via duplication and loss events
... a gene tree and a network, which was solved in [4] for a more general model but with a very high complexity, was re-studied here for a simpler model, which is more pertinent for same parts of the Tree of Life, and ...
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A Cloud-aware autonomous workflow engine and its application to Gene Regulatory Networks inference
... cell gene expression data from chicken erythrocyte progenitors acquired during their differentiation process (Richard et ...of gene expression, the Ran- dom Telegraph model (Peccoud and Ycart, ...new ...
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Kinetic Theory Modeling and Efficient Numerical Simulation of Gene Regulatory Networks Based on Qualitative Descriptions
... Appendix A. Qualitative Modeling: Process Hitting Process hitting is a powerful simple tool for the analysis of large regulatory networks. Historically related to the discrete models of Stuart Kauffman [11] and ...
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Kinetic Theory Modeling and Efficient Numerical Simulation of Gene Regulatory Networks Based on Qualitative Descriptions
... j=1 a j (z − v j , t)Ψ(z − v j , t) − a j (z, t)Ψ(z, t) (2) with the propensity a j depending on the system state and time. The result is a system of linear, time-dependent, differential equations, defined given an ...
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Reduction of the chemical master equation for gene regulatory networks using proper generalized decompositions
... governing gene regulatory networks and cell signaling processes remains a challenging task owing to its complexity, exponentially growing with the number of species ...
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Predicting interactome networks perturbations in human cancer: application to gene fusions in acute lymphoblastic leukemia.
... B-cell gene expression profiles representing 24 distinct phe- notypes of normal and diseased B cells (Lefebvre et ...of gene expression levels and increase the accuracy of our predictions (Wang et ...
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