ArticleBioinformatics (Oxford, England)2008
Ensemble non-negative matrix factorization methods for clustering protein-protein interactions.
Article in Bioinformatics (Oxford, England), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Incorporating Machine Learning into Established Bioinformatics Frameworks.International journal of molecular sciences · 2021Review
- Transcranial direct current stimulation modulates brain functional connectivity in autism.NeuroImage. Clinical · 2020Article
- Large-Scale Validation of Hypothesis Generation Systems via Candidate Ranking.Proceedings : ... IEEE International Conference on Big Data. IEEE International Conference on Big Data · 2018Article
- A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks.BMC bioinformatics · 2017Article
- Protein complex detection based on partially shared multi-view clustering.BMC bioinformatics · 2016Article
- A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps.Bioinformatics (Oxford, England) · 2016Article
- A two-layer integration framework for protein complex detection.BMC bioinformatics · 2016Article
- A novel one-class SVM based negative data sampling method for reconstructing proteome-wide HTLV-human protein interaction networks.Scientific reports · 2015Article
- Microbial community pattern detection in human body habitats via ensemble clustering framework.BMC systems biology · 2014Article
- Paradigm of tunable clustering using Binarization of Consensus Partition Matrices (Bi-CoPaM) for gene discovery.PloS one · 2013Article
- Protein complex detection via weighted ensemble clustering based on Bayesian nonnegative matrix factorization.PloS one · 2013Article
- An overview of the statistical methods used for inferring gene regulatory networks and protein-protein interaction networks.Advances in bioinformatics · 2013Article
- Co-clustering phenome-genome for phenotype classification and disease gene discovery.Nucleic acids research · 2012Article
- Recent advances in clustering methods for protein interaction networks.BMC genomics · 2010Article
- Defining the plasticity of transcription factor binding sites by Deconstructing DNA consensus sequences: the PhoP-binding sites among gamma/enterobacteria.PLoS computational biology · 2010Article
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4 authors.
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Abstract
motivationWhen working with large-scale protein interaction data, an important analysis task is the assignment of pairs of proteins to groups that correspond to higher order assemblies. Previously a common approach to this problem has been to apply standard hierarchical clustering methods to identify such a groups. Here we propose a new algorithm for aggregating a diverse collection of matrix factorizations to produce a more informative clustering, which takes the form of a 'soft' hierarchy of clusters.
resultsWe apply the proposed Ensemble non-negative matrix factorization (NMF) algorithm to a high-quality assembly of binary protein interactions derived from two proteome-wide studies in yeast. Our experimental evaluation demonstrates that the algorithm lends itself to discovering small localized structures in this data, which correspond to known functional groupings of complexes. In addition, we show that the algorithm also supports the assignment of putative functions for previously uncharacterized proteins, for instance the protein YNR024W, which may be an uncharacterized component of the exosome.
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