ArticleProceedings of the National Academy of Sciences of the United States of America2015
Discriminating direct and indirect connectivities in biological networks.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Cellular-state control using ribozyme-scaffolded miRNA-sensing and CRISPR-mediated actuation.Cell reports methods · 2026Article
- Incorporating prior information in gene expression network-based cancer heterogeneity analysis.Biostatistics (Oxford, England) · 2025Article
- Perfluorooctanoic Acid and Its Short-Chain Substitutes Induce Cytotoxic and Prooxidative Changes in Human Peripheral Blood Mononuclear Cells: A Comparative Study.International journal of molecular sciences · 2025Article
- Gene regulatory network inference during cell fate decisions by perturbation strategies.NPJ systems biology and applications · 2025Article
- A Selective Review of Network Analysis Methods for Gene Expression Data.Methods in molecular biology (Clifton, N.J.) · 2025Review
- General relationship of local topologies, global dynamics, and bifurcation in cellular networks.NPJ systems biology and applications · 2024Article
- On network deconvolution for undirected graphs.Biometrics · 2024Article
- RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique.BMC bioinformatics · 2022Article
- Disentangling direct from indirect relationships in association networks.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Data-driven network models for genetic circuits from time-series data with incomplete measurements.Journal of the Royal Society, Interface · 2021Article
- Cell morphology-based machine learning models for human cell state classification.NPJ systems biology and applications · 2021Article
- Uncoupling gene expression noise along the central dogma using genome engineered human cell lines.Nucleic acids research · 2020Article
- Identifiability and experimental design in perturbation studies.Bioinformatics (Oxford, England) · 2020Article
- Article
- Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Reverse engineering of biological pathways involves an iterative process between experiments, data processing, and theoretical analysis. Despite concurrent advances in quality and quantity of data as well as computing resources and algorithms, difficulties in deciphering direct and indirect network connections are prevalent. Here, we adopt the notions of abstraction, emulation, benchmarking, and validation in the context of discovering features specific to this family of connectivities. After subjecting benchmark synthetic circuits to perturbations, we inferred the network connections using a combination of nonparametric single-cell data resampling and modular response analysis. Intriguingly, we discovered that recovered weights of specific network edges undergo divergent shifts under differential perturbations, and that the particular behavior is markedly different between topologies. Our results point to a conceptual advance for reverse engineering beyond weight inference. Investigating topological changes under differential perturbations may address the longstanding problem of discriminating direct and indirect connectivities in biological networks.
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