Journal ArticleDOI
Network motifs: theory and experimental approaches
TLDR
Network motifs are reviewed, suggesting that they serve as basic building blocks of transcription networks, including signalling and neuronal networks, in diverse organisms from bacteria to humans.Abstract:
Transcription regulation networks control the expression of genes. The transcription networks of well-studied microorganisms appear to be made up of a small set of recurring regulation patterns, called network motifs. The same network motifs have recently been found in diverse organisms from bacteria to humans, suggesting that they serve as basic building blocks of transcription networks. Here I review network motifs and their functions, with an emphasis on experimental studies. Network motifs in other biological networks are also mentioned, including signalling and neuronal networks.read more
Citations
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Journal ArticleDOI
Link prediction in complex networks: A survey
TL;DR: Recent progress about link prediction algorithms is summarized, emphasizing on the contributions from physical perspectives and approaches, such as the random-walk-based methods and the maximum likelihood methods.
Journal ArticleDOI
Temporal Networks
Petter Holme,Jari Saramäki +1 more
TL;DR: This review presents the emergent field of temporal networks, and discusses methods for analyzing topological and temporal structure and models for elucidating their relation to the behavior of dynamical systems.
Posted Content
Learning Convolutional Neural Networks for Graphs
TL;DR: This work proposes a framework for learning convolutional neural networks for arbitrary graphs that operate on locally connected regions of the input and demonstrates that the learned feature representations are competitive with state of the art graph kernels and that their computation is highly efficient.
Journal ArticleDOI
Transcriptional architecture of the mammalian circadian clock
TL;DR: Genome-wide analyses of the clock transcriptional feedback loop have revealed a global circadian regulation of processes such as transcription factor occupancy, RNA polymerase II recruitment and initiation, nascent transcription, and chromatin remodelling.
PatentDOI
Connecting microrna genes to the core transcriptional regulatory circuitry of embryonic stem cells
TL;DR: The transcriptional regulatory circuitry of ES cells that incorporates protein-coding and miRNA genes based on high-resolution ChIP-seq data, systematic identification of miRNA promoters, and quantitative sequencing of short transcripts in multiple cell types reveals how key ES cell transcription factors promote the ES cell miRNA expression program and integrate miRNAs into the regulatory circuitry controlling ES cell identity.
References
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Book
Introduction To The Theory Of Neural Computation
TL;DR: This book is a detailed, logically-developed treatment that covers the theory and uses of collective computational networks, including associative memory, feed forward networks, and unsupervised learning.
Journal ArticleDOI
Network Motifs: Simple Building Blocks of Complex Networks
TL;DR: Network motifs, patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks, are defined and may define universal classes of networks.
Journal ArticleDOI
The structure of the nervous system of the nematode Caenorhabditis elegans
TL;DR: The structure and connectivity of the nervous system of the nematode Caenorhabditis elegans has been deduced from reconstructions of electron micrographs of serial sections as discussed by the authors.
Journal ArticleDOI
Comprehensive Identification of Cell Cycle–regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization
Paul T. Spellman,Gavin Sherlock,Gavin Sherlock,Michael Q. Zhang,Vishwanath R. Iyer,Kirk R. Anders,Michael B. Eisen,Patrick O. Brown,Patrick O. Brown,David Botstein,Bruce Futcher +10 more
TL;DR: A comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle is created, and it is found that the mRNA levels of more than half of these 800 genes respond to one or both of these cyclins.
Journal ArticleDOI
A synthetic oscillatory network of transcriptional regulators
TL;DR: This work used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli, which periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells.