Protein complexes and functional modules in molecular networks

By V. Spirin, Leonid A. Mirny. Proceedings of the National Academy of Sciences of the United States of America, 2003

1,495 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7cc43461c033fa027a853cb20cbca373e3ed6ad0

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Citations in the corpus

Protein interaction networks from yeast to human. (2004, background): “Modules are being sought for a variety of networks: metabolic networks [55], high-throughput experimental interaction data [56–60] and in silico predicted networks [37 ,61].”
Evaluation of clustering algorithms for protein-protein interaction networks (2006, background): “Developper King AD Van Dongen S Bader GD and Hogue CWV Blatt M, Wiseman S, Domany E References [21] [35] [19] [18]”
Computational approaches for detecting protein complexes from protein interaction networks: a survey (2010, methodology): “Spirin and Mirny [17] proposed three methods for protein complex prediction from PPI network.”
Automated Network Analysis Identifies Core Pathways in Glioblastoma (2010, background): “This community structure or network modularity has been identified in diverse network systems, including social [18,19], scientific collaboration [20], metabolic [21], and molecular interaction networks [22–24].”
Reconstruction of cellular signalling networks and analysis of their properties (2005, background): “A reconstruction of associations involves a description of simple connectivity (for example, NF-κB is functionally connected to IκB kinase (IKK)) or a more involved set of relationships that shows more intermediates between a signalling input and a signalling output (for example, NF-κB is functional”
Network-based prediction of protein function (2007, background): “The functions enriched within the module (i.e. obtaining P-value below some threshold) are then predicted for all the genes in the module.”
Comparative Genomics in Eukaryotes (2005, background): “Locally densely connected networks reflect stable physical complexes, whereas less connected networks correlate with signaling pathways and transient interactions (Pereira-Leal et al., 2004; Spirin and Mirny, 2003).”
Interactome: gateway into systems biology. (2005, background): “A common theme pervading biological investigation is that most proteins generally function as components of complexes that contain other macromolecules to carry out speciﬁc biological processes, and networks of interactions connect multiple, different cellular processes (43–46).”
Analysis of Biological Networks (2008, background): “Though there is increasing interest in the analysis of dynamic aspects of complex networks, the precise relationship between structure and function of complex networks is still largely unclear [30,37,55,63,68].”
Identifying gene-disease associations using centrality on a literature mined gene-interaction network (2008, background): “, 2003), for identifying functional modules and network motifs (Spirin and Mirny, 2003) and for predicting functional annotations based on network connectivity (Schwikowski et al.”
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps (2005, background): “It is well known that the reliability of different data sources vary, even if they are based on the same underlying technology (von Mering et al., 2002; Deng et al., 2003; Sprinzak et al., 2003).”
Integrative approaches for finding modular structure in biological networks (2013, methodology): “At the molecular level, modules have been variously described as groups of genes, gene products or metabolites that are functionally coordinated, physically interacting and/or co-regulated 1–7 .”
Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. (2008, background): “The study of interaction networks has proven fruitful in many areas of biological research, highlighting distinct modularity in metabolic networks,(54) cellular networks,(55) and protein-interaction networks.(56) Although such an approach has not been previously applied to the epigenome, recent evid”
A core-attachment based method to detect protein complexes in PPI networks (2009, background): “Since proteins in the same complex are highly interactive with each other, protein complexes generally correspond to dense subgraphs in the PPI network [6,7] and many previous studies have been proposed based on this observation.”