ArticleProceedings of the National Academy of Sciences of the United States of America2022
Disentangling direct from indirect relationships in association networks.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
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- An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP).Science China. Life sciences · 2025Article
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- Multi-scale evidence for declining microbial carbon fixation along forest succession gradients.The ISME journal · 2025Article
- Climate warming enhances biodiversity and stability of grassland soil phosphorus-cycling microbial communities.The ISME journal · 2025Article
- Succession characteristics and assembly process of soil microbiome at reclaimed farmlands in coal mining area.Frontiers in microbiology · 2025Article
- Warming stimulates cellulose decomposition by recruiting phylogenetically diverse but functionally similar microorganisms.ISME communications · 2025Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Networks are vital tools for understanding and modeling interactions in complex systems in science and engineering, and direct and indirect interactions are pervasive in all types of networks. However, quantitatively disentangling direct and indirect relationships in networks remains a formidable task. Here, we present a framework, called iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity), for quantitatively inferring direct dependencies in association networks. Using copula-based transitivity, iDIRECT eliminates/ameliorates several challenging mathematical problems, including ill-conditioning, self-looping, and interaction strength overflow. With simulation data as benchmark examples, iDIRECT showed high prediction accuracies. Application of iDIRECT to reconstruct gene regulatory networks in
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