Integrative approaches for finding modular structure in biological networks

By Koyel Mitra, Anne-Ruxandra Carvunis, S. Ramesh, Trey Ideker. Nature reviews genetics, 2013

548 citations recorded by the source corpus.

A central goal of systems biology is to elucidate the structural and functional architecture of the cell. To this end, large and complex networks of molecular interactions are being rapidly generated for humans and model organisms. A recent focus of bioinformatics research has been to integrate these networks with each other and with diverse molecular profiles to identify sets of molecules and interactions that participate in a common biological function — that is, 'modules'. Here, we classify such integrative approaches into four broad categories, describe their bioinformatic principles and review their applications.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/06482e7f6fbead4d7ca3f526a99e83daca9c0097

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Citations in the corpus

Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015, background): “Alternative depictions of the network analysis process are also available elsewhere 28,41,169 .”
Systematic Functional Annotation and Visualization of Biological Networks (2016, methodology): “For example, several network algorithms have been developed to search for sets of interconnected nodes that share a common phenotype or a consistent response across experimental conditions (Ideker et al., 2002; Mitra et al., 2013).”
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data (2015, unknown): “They include obvious aspects such as control versus treatment used in challenge studies, but when applied to a complex data set (e.g., humans with a specific disease) they can include demographic information about sex, weight,”
Network propagation: a universal amplifier of genetic associations (2017, background): “Although most studies have so far focused on a single network, the integration of multiple networks has been repeatedly shown to improve the predictive power of different methods 22 .”
The BioGRID interaction database: 2019 update (2018, background): “To this end, the accurate annotation of protein, genetic and other forms of interaction data from the literature by a host of databases and metadatabases has expedited the formulation of both intuitive and more formal models of cellular functions (16), as well as the interpretation of complex genome”
Disentangling Interactions in the Microbiome: A Network Perspective (2016, unknown): “We refer the reader to a recent review of integrative approaches for finding modules in biological networks through merging topological data with ‘omics data [27].”