ArticleNucleic acids research2016
NetDecoder: a network biology platform that decodes context-specific biological networks and gene activities.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
23 citing papers in PubMed.
- Mini-Galaxy: Rethinking Complex Human Diseases Through the Lens of Systems Biology and Multilayered AI Network Perspectives.International journal of molecular sciences · 2026Review
- Glucagon-like Peptide-1 Receptor Agonists: A New Frontier in Treating Alcohol Use Disorder.Brain sciences · 2025Review
- GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data.PLoS computational biology · 2025Article
- Unique transcriptional signatures correlate with behavioral and psychological symptom domains in Alzheimer's disease.Translational psychiatry · 2024Article
- Review
- Mapping cellular senescence networks in human diabetic foot ulcers.GeroScience · 2024Article
- Multiorgan locked-state model of chronic diseases and systems pharmacology opportunities.Drug discovery today · 2024Review
- Network-based approaches for modeling disease regulation and progression.Computational and structural biotechnology journal · 2023Review
- Article
- De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens.Genome research · 2022Article
- Uncovering Pharmacological Opportunities for Cancer Stem Cells-A Systems Biology View.Frontiers in cell and developmental biology · 2022Review
- Gene utility recapitulates chromosomal aberrancies in advanced stage neuroblastoma.Computational and structural biotechnology journal · 2022Article
- Genome-wide discovery of hidden genes mediating known drug-disease association using KDDANet.NPJ genomic medicine · 2021Article
- Modular network mechanism of CCN1-associated resistance to HSV-1-derived oncolytic immunovirotherapies for glioblastomas.Scientific reports · 2021Article
- Synthetic and systems biology principles in the design of programmable oncolytic virus immunotherapies for glioblastoma.Neurosurgical focus · 2021Review
- Machine Learning and Systems Biology Approaches to Characterize Dosage-Based Gene Dependencies in Cancer Cells.Journal of bioinformatics and systems biology : Open access · 2021Article
- Dysregulation of RNA Splicing in Tauopathies.Cell reports · 2019Article
- Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches.Briefings in bioinformatics · 2019Review
- Article
- Reconstruction of complex single-cell trajectories using CellRouter.Nature communications · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The sequential chain of interactions altering the binary state of a biomolecule represents the 'information flow' within a cellular network that determines phenotypic properties. Given the lack of computational tools to dissect context-dependent networks and gene activities, we developed NetDecoder, a network biology platform that models context-dependent information flows using pairwise phenotypic comparative analyses of protein-protein interactions. Using breast cancer, dyslipidemia and Alzheimer's disease as case studies, we demonstrate NetDecoder dissects subnetworks to identify key players significantly impacting cell behaviour specific to a given disease context. We further show genes residing in disease-specific subnetworks are enriched in disease-related signalling pathways and information flow profiles, which drive the resulting disease phenotypes. We also devise a novel scoring scheme to quantify key genes-network routers, which influence many genes, key targets, which are influenced by many genes, and high impact genes, which experience a significant change in regulation. We show the robustness of our results against parameter changes. Our network biology platform includes freely available source code (http://www.NetDecoder.org) for researchers to explore genome-wide context-dependent information flow profiles and key genes, given a set of genes of particular interest and transcriptome data. More importantly, NetDecoder will enable researchers to uncover context-dependent drug targets.
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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.