Inherent size constraints on prokaryote gene networks due to "accelerating" growth
, 2004 Networks exhibiting "accelerating" growth have total link numbers growing faster than linearly with network size and can exhibit transitions from stationary to nonstationary statistics and from random to scale-free to regular statistics at particular ...
Gagen, M. J., Mattick, J. S.
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Weighted-Lasso for Structured Network Inference from Time Course Data [PDF]
, 2009 We present a weighted-Lasso method to infer the parameters of a first-order vector auto-regressive model that describes time course expression data generated by directed gene-to-gene regulation networks. These networks are assumed to own a prior internal
Ambroise, Christophe +2 more
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Existence of Oscillations in Cyclic Gene Regulatory Networks with Time Delay [PDF]
, 2012 This paper is concerned with conditions for the existence of oscillations in gene regulatory networks with negative cyclic feedback, where time delays in transcription, translation and translocation process are explicitly considered.
Hara, Shinji +2 more
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Optimal first-passage time in gene regulatory networks
, 2014 The inherent probabilistic nature of the biochemical reactions, and low copy number of species can lead to stochasticity in gene expression across identical cells.
Ghusinga, Khem Raj, Singh, Abhyudai
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Evolving Gene Regulatory Networks with Mobile DNA Mechanisms
, 2013 This paper uses a recently presented abstract, tuneable Boolean regulatory network model extended to consider aspects of mobile DNA, such as transposons.
Adamatzky, Andrew, Bull, Larry
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Noise control in gene regulatory networks with negative feedback
, 2016 Genes and proteins regulate cellular functions through complex circuits of biochemical reactions. Fluctuations in the components of these regulatory networks result in noise that invariably corrupts the signal, possibly compromising function.
Hinczewski, Michael, Thirumalai, D.
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Inference of Sparse Networks with Unobserved Variables. Application to Gene Regulatory Networks
, 2014 Networks are a unifying framework for modeling complex systems and network inference problems are frequently encountered in many fields. Here, I develop and apply a generative approach to network inference (RCweb) for the case when the network is sparse ...
Slavov, Nikolai
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A Posterior Probability Approach for Gene Regulatory Network Inference in Genetic Perturbation Data
, 2016 Inferring gene regulatory networks is an important problem in systems biology. However, these networks can be hard to infer from experimental data because of the inherent variability in biological data as well as the large number of genes involved.
Raftery, Adrian E. +2 more
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Failed "nonaccelerating" models of prokaryote gene regulatory networks
, 2004 Much current network analysis is predicated on the assumption that important biological networks will either possess scale free or exponential statistics which are independent of network size allowing unconstrained network growth over time. In this paper,
Gagen, M. J., Mattick, J. S.
core
On the basic computational structure of gene regulatory networks
, 2009 Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and their target genes.
Albert +65 more
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