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Assessing regulatory information in developmental gene regulatory networks [PDF]
Proceedings of the National Academy of Sciences, 2017 Gene regulatory networks (GRNs) provide a transformation function between the static genomic sequence and the primary spatial specification processes operating development. The regulatory information encompassed in developmental GRNs thus goes far beyond the control of individual genes.
Peter, Isabelle S., Davidson, Eric H.
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Exact reconstruction of gene regulatory networks using compressive sensing. [PDF]
, 2014 BackgroundWe consider the problem of reconstructing a gene regulatory network structure from limited time series gene expression data, without any a priori knowledge of connectivity.
Chang, Young Hwan +2 more
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The hardwiring of development: Organization and function of genomic regulatory systems [PDF]
, 1997 The gene regulatory apparatus that directs development is encoded in the DNA, in the form of organized arrays of transcription factor target sites. Genes are regulated by interactions with multiple transcription factors and the target sites for the ...
Arnone, Maria I., Davidson, Eric H.
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Adaptive gene regulatory networks [PDF]
EPL (Europhysics Letters), 2009 5 pages ...
Stauffer, Franck, Berg, Johannes
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Quantum gene regulatory networks
npj Quantum Information, 2022 AbstractIn this work, we present a quantum circuit model for inferring gene regulatory networks (GRNs) from single-cell transcriptomic data. The model employs qubit entanglement to simulate interactions between genes, resulting in competitive performance and promising potential for further exploration.
Cristhian Roman-Vicharra, James J. Cai
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SynTReN : a generator of synthetic gene expression data for design and analysis of structure learning algorithms [PDF]
, 2006 Background: The development of algorithms to infer the structure of gene regulatory networks based on expression data is an important subject in bioinformatics research. Validation of these algorithms requires benchmark data sets for which the underlying
Van den Bulcke, Tim +7 more
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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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Gene Regulatory Network v1 [PDF]
, 2020 Gene regulatory networks (GRNs) provide a platform for integrating multiomic data and can be used to characterize the dynamics of perturbations during biological transitions such as puberty and other complex traits. We used a multiomics approach, which has the power to identify the control mechanisms underpinning complex traits (Argelaguet et al 2019 ...
Amin R Mohamed +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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