The DOI matches its Crossref record; 69 of the 69 references it cites were found in a registry or an index.
Græmlin: General and robust alignment of multiple large interaction networks
Open accessAbstract
The recent proliferation of protein interaction networks has motivated research into network alignment: the cross-species comparison of conserved functional modules. Previous studies have laid the foundations for such comparisons and demonstrated their power on a select set of sparse interaction networks. Recently, however, new computational techniques have produced hundreds of predicted interaction networks with interconnection densities that push existing alignment algorithms to their limits. To find conserved functional modules in these new networks, we have developed Græmlin, the first algorithm capable of scalable multiple network alignment. Græmlin's explicit model of functional evolution allows both the generalization of existing alignment scoring schemes and the location of conserved network topologies other than protein complexes and metabolic pathways. To assess Græmlin's performance, we have developed the first quantitative benchmarks for network alignment, which allow comparisons of algorithms in terms of their ability to recapitulate the KEGG database of conserved functional modules. We find that Græmlin achieves substantial scalability gains over previous methods while improving sensitivity.
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Cited by
Network‐based prediction of protein function
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A Survey of Statistical Network Models
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Integrative approaches for finding modular structure in biological networks
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Topological network alignment uncovers biological function and phylogeny
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Metadata
- Authors
- Flannick, J., Novak, A., Srinivasan, B. S., McAdams, H. H., & Batzoglou, S.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2006-08-09
- Volume
- 16
- Issue
- 9
- Pages
- 1169-1181
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2171081680
- Cited by
- 320
- References
- 69
- Type
- posted content
- Language
- en
- Open access
- hybrid
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- Flannick, J., Novak, A., Srinivasan, B. S., McAdams, H. H., & Batzoglou, S. (2006). Græmlin: General and robust alignment of multiple large interaction networks. Genome Research. https://doi.org/10.1101/gr.5235706
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