ArticlePloS one2012
AlignNemo: a local network alignment method to integrate homology and topology.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- 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
- Pairwise Biological Network Alignment Based on Discrete Bat Algorithm.Computational and mathematical methods in medicine · 2021Article
- A novel algorithm for finding top-k weighted overlapping densest connected subgraphs in dual networks.Applied network science · 2021Article
- ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks.BMC genomics · 2020Article
- L-HetNetAligner: A novel algorithm for Local Alignment of Heterogeneous Biological Networks.Scientific reports · 2020Article
- NAIGO: An Improved Method to Align PPI Networks Based on Gene Ontology and Graphlets.Frontiers in bioengineering and biotechnology · 2020Article
- Data-driven network alignment.PloS one · 2020Article
- From homogeneous to heterogeneous network alignment via colored graphlets.Scientific reports · 2018Article
- PrimAlign: PageRank-inspired Markovian alignment for large biological networks.Bioinformatics (Oxford, England) · 2018Article
- An extensive assessment of network alignment algorithms for comparison of brain connectomes.BMC bioinformatics · 2017Article
- Unified Alignment of Protein-Protein Interaction Networks.Scientific reports · 2017Article
- Robust cell tracking in epithelial tissues through identification of maximum common subgraphs.Journal of the Royal Society, Interface · 2016Article
- Local versus global biological network alignment.Bioinformatics (Oxford, England) · 2016Article
- The post-genomic era of biological network alignment.EURASIP journal on bioinformatics & systems biology · 2015Article
- Time dynamics of protein complexes in the AD11 transgenic mouse model for Alzheimer's disease like pathology.BMC neuroscience · 2015Article
- Global multiple protein-protein interaction network alignment by combining pairwise network alignments.BMC bioinformatics · 2015Article
- Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison.Algorithms for molecular biology : AMB · 2015Article
- Fair evaluation of global network aligners.Algorithms for molecular biology : AMB · 2015Article
- HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks.Bioinformatics (Oxford, England) · 2014Article
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Authors and funding
5 authors.
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Abstract
Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.
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