ReviewFrontiers in genetics2019
A Comprehensive Survey of Tools and Software for Active Subnetwork Identification.
Review in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
27 citing papers in PubMed.
- MAAMOUL: metabolic network-based discovery of microbiome-metabolome shifts in disease.Bioinformatics (Oxford, England) · 2026Article
- MAAMOUL: Metabolic network-based discovery of microbiome-metabolome shifts in disease.bioRxiv : the preprint server for biology · 2026Article
- A new Similarity Based Adapted Louvain Algorithm (SIMBA) for active module identification in p-value attributed biological networks.Scientific reports · 2025Article
- Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review.Briefings in bioinformatics · 2024Review
- Selective loss of Y chromosomes in lung adenocarcinoma modulates the tumor immune environment through cancer/testis antigens.bioRxiv : the preprint server for biology · 2024Article
- A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data.Briefings in bioinformatics · 2024Review
- A network embedding approach to identify active modules in biological interaction networks.Life science alliance · 2023Article
- SEMtree: tree-based structure learning methods with structural equation models.Bioinformatics (Oxford, England) · 2023Article
- A comprehensive survey of the approaches for pathway analysis using multi-omics data integration.Briefings in bioinformatics · 2022Review
- A new machine learning method for cancer mutation analysis.PLoS computational biology · 2022Article
- SUBATOMIC: a SUbgraph BAsed mulTi-OMIcs clustering framework to analyze integrated multi-edge networks.BMC bioinformatics · 2022Article
- Temporal and sequential order of nonoverlapping gene networks unraveled in mated female Drosophila.Life science alliance · 2022Article
- Prospects and challenges of cancer systems medicine: from genes to disease networks.Briefings in bioinformatics · 2022Review
- Improving Analysis and Annotation of Microarray Data with Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Connections for Matters of the Heart: Network Medicine in Cardiovascular Diseases.Frontiers in cardiovascular medicine · 2022Review
- Construction and contextualization approaches for protein-protein interaction networks.Computational and structural biotechnology journal · 2022Review
- gcMECM: graph clustering of mutual exclusivity of cancer mutations.BMC bioinformatics · 2021Article
- TopoFun: a machine learning method to improve the functional similarity of gene co-expression modules.NAR genomics and bioinformatics · 2021Article
- A Graph Feature Auto-Encoder for the prediction of unobserved node features on biological networks.BMC bioinformatics · 2021Article
- A multi-objective genetic algorithm to find active modules in multiplex biological networks.PLoS computational biology · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A recent focus of computational biology has been to integrate the complementary information available in molecular profiles as well as in multiple network databases in order to identify connected regions that show significant changes under different conditions. This allows for capturing dynamic and condition-specific mechanisms of the underlying phenomena and disease stages. Here we review 22 such integrative approaches for active module identification published over the last decade. This article only focuses on tools that are currently available for use and are well-maintained. We compare these methods focusing on their primary features, integrative abilities, network structures, mathematical models, and implementations. We also provide real-world scenarios in which these methods have been successfully applied, as well as highlight outstanding challenges in the field that remain to be addressed. The main objective of this review is to help potential users and researchers to choose the best method that is suitable for their data and analysis purpose.
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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.