ArticleBMC bioinformatics2013
Steiner tree methods for optimal sub-network identification: an empirical study.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- KGBN: Augmenting and optimizing logical gene regulatory networks using knowledge graphs.bioRxiv : the preprint server for biology · 2026Article
- Assessing individual head and neck squamous cell carcinoma patient response to therapy through integration of functional and genomic data.Scientific reports · 2025Article
- A framework towards digital twins for type 2 diabetes.Frontiers in digital health · 2024Article
- Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study.Frontiers in gastroenterology (Lausanne, Switzerland) · 2023Article
- C3: connect separate connected components to form a succinct disease module.BMC bioinformatics · 2020Article
- Analyzing the genes and pathways related to major depressive disorder via a systems biology approach.Brain and behavior · 2020Article
- Large scale study of anti-sense regulation by differential network analysis.BMC systems biology · 2018Article
- The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways.BMC bioinformatics · 2017Article
- Article
- Ror2 Signaling and Its Relevance in Breast Cancer Progression.Frontiers in oncology · 2017Article
- A physarum-inspired prize-collecting steiner tree approach to identify subnetworks for drug repositioning.BMC systems biology · 2016Article
- PheNetic: network-based interpretation of molecular profiling data.Nucleic acids research · 2015Article
- Decoding Cellular Dynamics in Epidermal Growth Factor Signaling Using a New Pathway-Based Integration Approach for Proteomics and Transcriptomics Data.Frontiers in genetics · 2015Article
- Newly Constructed Network Models of Different WNT Signaling Cascades Applied to Breast Cancer Expression Data.PloS one · 2015Article
- NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases.BMC genomics · 2015Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundAnalysis and interpretation of biological networks is one of the primary goals of systems biology. In this context identification of sub-networks connecting sets of seed proteins or seed genes plays a crucial role. Given that no natural node and edge weighting scheme is available retrieval of a minimum size sub-graph leads to the classical Steiner tree problem, which is known to be NP-complete. Many approximate solutions have been published and theoretically analyzed in the computer science literature, but far less is known about their practical performance in the bioinformatics field.
resultsHere we conducted a systematic simulation study of four different approximate and one exact algorithms on a large human protein-protein interaction network with ~14,000 nodes and ~400,000 edges. Moreover, we devised an own algorithm to retrieve a sub-graph of merged Steiner trees. The application of our algorithms was demonstrated for two breast cancer signatures and a sub-network playing a role in male pattern baldness.
conclusionWe found a modified version of the shortest paths based approximation algorithm by Takahashi and Matsuyama to lead to accurate solutions, while at the same time being several orders of magnitude faster than the exact approach. Our devised algorithm for merged Steiner trees, which is a further development of the Takahashi and Matsuyama algorithm, proved to be useful for small seed lists. All our implemented methods are available in the R-package SteinerNet on CRAN (http://www.r-project.org) and as a supplement to this paper.
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