Modeling cellular machinery through biological network comparison

By Roded Sharan, Trey Ideker. Nature Biotechnology, 2006

569 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/610019414e6179f8db0a7948625677efe68cd043

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Citations in the corpus

Associating Genes and Protein Complexes with Disease via Network Propagation (2010, methodology): “This score was further enhanced, as in [28] to accommodate for information on the reliability of interactions.”
Complex network measures of brain connectivity: Uses and interpretations (2010, unknown): “The increased emphasis on structure – function and between-subject comparisons in studies of brain networks will require the development of accurate statistical comparison tools, similar to those in cellular and molecular biology (Sharan and Ideker, 2006).”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, methodology): “All these greatly help drug design (Yu et al., 2004b; Sharan et al., 2005; Leicht et al., 2006; Sharan & Ideker, 2006; Zhang et al., 2008; McGary et al., 2010; Korcsmáros et al., 2011).”
Graph Kernels (2008, unknown): “Machine learning in domains such as bioinformatics (Sharan and Ideker, 2006), chemoinformatics (Bonchev and Rouvray, 1991), drug discovery (Kubinyi, 2003), web data mining (Washio and Motoda, 2003), and social networks (Kumar et al., 2006) involves the study of relationships between structured…”
Protein networks in disease. (2008, background): “In yeast, there is now a sizable literature reporting methods to align, contrast, and compare protein networks across species spanning a wide range of evolutionary distances (see above and Sharan and Ideker 2006 ).”
Integrative approaches for finding modular structure in biological networks (2013, background): “Additionally, comparative analyses of conserved modules can supplement sequence-matching techniques for the prediction of function 113,126–129 , on the basis of the premise that interaction partners of orthologous genes or proteins are also likely to be functionally conserved.”
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins (2009, background): “routinely performed to reveal new functional relationships in model eukaryotes such as yeast, worm, and fly [14–19], few analogous studies of the global functional architecture of E.”
Network-based prediction of protein function (2007, background): “…set of works attempted to identify evolutionarily conserved functional modules via the integration of networks from multiple organisms (Kelley et al , 2003; Sharan et al , 2005; Campillos et al , 2006; Flannick et al , 2006; Gandhi et al , 2006; see also the review in Sharan and Ideker, 2006).”
The skew spectrum of graphs (2008, background): “…Kondor risi@gatsby.ucl.ac.uk Gatsby Computational Neuroscience Unit, UCL, 17 Queen Square, London, WC1N 3AR, U.K. Karsten M. Borgwardt kmb51@cam.ac.uk Department of Engineering, University of Cambridge, Trumpington Street, Cambridge, CB2 1PZ, U.K. Abstract The central issue in representing…”
Systematic Functional Annotation and Visualization of Biological Networks (2016, background): “Quantitative comparison of biological networks is indeed a major goal of systems biology (Sharan and Ideker, 2006).”
Disease candidate gene identification and prioritization using protein interaction networks (2009, background): “Net-work-based analyses have been developed with a number of goals [9], including protein function prediction [10], identification of functional modules [11], interaction prediction [12,13], identification of disease candidate genes [14,15] and drug targets [16,17], and the study of network…”
Gromov-Wasserstein Learning for Graph Matching and Node Embedding (2019, background): “This task is important for many applications, e.g., matching the protein networks from different species (Sharan & Ideker, 2006; Singh et al., 2008), linking accounts in different social networks (Zhang & Philip, 2015), and feature matching in computer vision (Cordella et al., 2004; Zanfir &…”