ArticleNature biotechnology2013
Network link prediction by global silencing of indirect correlations.
Article in Nature biotechnology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed.
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- Inferring networks of chemical reactions by curvature analysis of kinetic trajectories.Physical chemistry chemical physics : PCCP · 2025Article
- Determining interaction directionality in complex biochemical networks from stationary measurements.Scientific reports · 2025Article
- Link prediction of heterogeneous complex networks based on an improved embedding learning algorithm.PloS one · 2025Article
- Higher order interaction analysis quantifies coordination in the epigenome revealing novel biological relationships in Kabuki syndrome.Briefings in bioinformatics · 2024Article
- Networked dynamic systems with higher-order interactions: stability versus complexity.National science review · 2024Article
- Reverse network diffusion to remove indirect noise for better inference of gene regulatory networks.Bioinformatics (Oxford, England) · 2024Article
- Reconstructing the evolution history of networked complex systems.Nature communications · 2024Article
- The maximum capability of a topological feature in link prediction.PNAS nexus · 2024Article
- MICA: a multi-omics method to predict gene regulatory networks in early human embryos.Life science alliance · 2024Article
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- Gene communities in co-expression networks across different tissues.PLoS computational biology · 2023Article
- Widening the landscape of transcriptional regulation of green algal photoprotection.Nature communications · 2023Article
- Network regression analysis in transcriptome-wide association studies.BMC genomics · 2022Article
- Distribution equality as an optimal epidemic mitigation strategy.Scientific reports · 2022Article
- RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique.BMC bioinformatics · 2022Article
- Monocarboxylate Transporters Are Involved in Extracellular Matrix Remodelling in Pancreatic Ductal Adenocarcinoma.Cancers · 2022Article
- Disentangling direct from indirect relationships in association networks.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
29 more citing papers are in PubMed but not listed here.
Corrections and comments
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2 authors.
Funding
Abstract
Predictions of physical and functional links between cellular components are often based on correlations between experimental measurements, such as gene expression. However, correlations are affected by both direct and indirect paths, confounding our ability to identify true pairwise interactions. Here we exploit the fundamental properties of dynamical correlations in networks to develop a method to silence indirect effects. The method receives as input the observed correlations between node pairs and uses a matrix transformation to turn the correlation matrix into a highly discriminative silenced matrix, which enhances only the terms associated with direct causal links. Against empirical data for Escherichia coli regulatory interactions, the method enhanced the discriminative power of the correlations by twofold, yielding >50% predictive improvement over traditional correlation measures and 6% over mutual information. Overall this silencing method will help translate the abundant correlation data into insights about a system's interactions, with applications ranging from link prediction to inferring the dynamical mechanisms governing biological networks.
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Registered trials
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