ArticleJournal of the Royal Society, Interface2010
Topological network alignment uncovers biological function and phylogeny.
Article in Journal of the Royal Society, Interface, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
- Network rewiring conserves the topology of drought-impaired food webs.Communications biology · 2025Article
- Ten practical tips and tricks to improve the effectiveness of biological network alignment.PLoS computational biology · 2025Article
- Changes in species composition and community structure during plant-pollinator community assembly.Ecology · 2025Article
- Exact p-values for global network alignments via combinatorial analysis of shared GO terms : REFANGO: Rigorous Evaluation of Functional Alignments of Networks using Gene Ontology.Journal of mathematical biology · 2024Article
- Current and future directions in network biology.Bioinformatics advances · 2024Article
- Network-Based Structural Alignment of RNA Sequences Using TOPAS.Methods in molecular biology (Clifton, N.J.) · 2023Article
- SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment.NPJ systems biology and applications · 2022Article
- Challenges and Limitations of Biological Network Analysis.Biotech (Basel (Switzerland)) · 2022Article
- An Extensive Assessment of Network Embedding in PPI Network Alignment.Entropy (Basel, Switzerland) · 2022Article
- The protein-protein interaction network alignment using recurrent neural network.Medical & biological engineering & computing · 2021Article
- Alignments of biomolecular contact maps.Interface focus · 2021Article
- Juxtapose: a gene-embedding approach for comparing co-expression networks.BMC bioinformatics · 2021Article
- Data-driven biological network alignment that uses topological, sequence, and functional information.BMC bioinformatics · 2021Article
- A network-based framework for shape analysis enables accurate characterization of leaf epidermal cells.Nature communications · 2021Article
- Protein Function Prediction Based on PPI Networks: Network Reconstruction vs Edge Enrichment.Frontiers in genetics · 2021Article
- Pairwise Biological Network Alignment Based on Discrete Bat Algorithm.Computational and mathematical methods in medicine · 2021Article
- Comparative Analyses of Gene Co-expression Networks: Implementations and Applications in the Study of Evolution.Frontiers in genetics · 2021Review
- L-HetNetAligner: A novel algorithm for Local Alignment of Heterogeneous Biological Networks.Scientific reports · 2020Article
- A review of protein-protein interaction network alignment: From pathway comparison to global alignment.Computational and structural biotechnology journal · 2020Review
- NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families.PloS one · 2020Article
27 more citing papers are in PubMed but not listed here.
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology and disease. Comparison and alignment of biological networks will probably have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for purely topological alignment has yet been devised. In this paper, we present a novel algorithm based solely on network topology, that can be used to align any two networks. We apply it to biological networks to produce by far the most complete topological alignments of biological networks to date. We demonstrate that both species phylogeny and detailed biological function of individual proteins can be extracted from our alignments. Topology-based alignments have the potential to provide a completely new, independent source of phylogenetic information. Our alignment of the protein-protein interaction networks of two very different species-yeast and human-indicate that even distant species share a surprising amount of network topology, suggesting broad similarities in internal cellular wiring across all life on Earth.
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