ArticleF1000Research2017
The PathLinker app: Connect the dots in protein interaction networks.
Article in F1000Research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Posttraumatic stress in young children at risk for maltreatment: a causal data science analysis.Frontiers in health services · 2026Article
- Integrative gene-metabolite network analysis of GLP-1 receptor agonists and related incretin pathways in cardiometabolic health.NPJ systems biology and applications · 2025Article
- Discovering anticancer drug target combinations via network-informed signaling-based approach.Communications medicine · 2025Article
- Role of Compensatory miRNA Networks in Cognitive Recovery from Heart Failure.Non-coding RNA · 2025Article
- Logic-based machine learning predicts how escitalopram attenuates cardiomyocyte hypertrophy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Anticancer Target Combinations: Network-Informed Signaling-Based Approach to Discovery.bioRxiv : the preprint server for biology · 2024Article
- Repositioning the existing drugs for neuroinflammation: a fusion of computational approach and biological validation to counter the Parkinson's disease progression.Molecular diversity · 2024Article
- Extracellular Matrix Sulfation in the Tumor Microenvironment Stimulates Cancer Stemness and Invasiveness.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- A gray box framework that optimizes a white box logical model using a black box optimizer for simulating cellular responses to perturbations.Cell reports methods · 2024Article
- Article
- Regulation of developmental gatekeeping and cell fate transition by the calpain protease DEK1 in Physcomitrium patens.Communications biology · 2024Article
- Signaling network analysis reveals fostamatinib as a potential drug to control platelet hyperactivation during SARS-CoV-2 infection.Frontiers in immunology · 2023Article
- Characterization of the SGLT2 Interaction Network and Its Regulation by SGLT2 Inhibitors: A Bioinformatic Analysis.Frontiers in pharmacology · 2022Article
- Diagnostic, Prognostic, and Immunological Roles of HELLS in Pan-Cancer: A Bioinformatics Analysis.Frontiers in immunology · 2022Article
- Integrating knowledge of protein sequence with protein function for the prediction and validation of new MALT1 substrates.Computational and structural biotechnology journal · 2022Article
- Tracing the footsteps of autophagy in computational biology.Briefings in bioinformatics · 2021Article
- Introducing the novel Cytoscape app TimeNexus to analyze time-series data using temporal MultiLayer Networks (tMLNs).Scientific reports · 2021Article
- StrongestPath: a Cytoscape application for protein-protein interaction analysis.BMC bioinformatics · 2021Article
- Computational causal discovery for post-traumatic stress in police officers.Translational psychiatry · 2020Observational
- SmartGraph: a network pharmacology investigation platform.Journal of cheminformatics · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
PathLinker is a graph-theoretic algorithm for reconstructing the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. We originally developed PathLinker to complement manual curation of signaling pathways, which is slow and painstaking. The method can be used in general to connect any set of sources to any set of targets in an interaction network. The app presented here makes the PathLinker functionality available to Cytoscape users. We present an example where we used PathLinker to compute and analyze the network of interactions connecting proteins that are perturbed by the drug lovastatin.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.