ArticleScientific reports2016
Network diffusion-based analysis of high-throughput data for the detection of differentially enriched modules.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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Who cites it
26 citing papers in PubMed, 43 citations in OpenAlex.
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- Identification of antimicrobial resistance genes in Escherichia coli through network diffusion.The Journal of antimicrobial chemotherapy · 2026Article
- Proteome analysis refines molecular processes underlying metamorphosis in the ascidian Ciona intestinalis.PloS one · 2026Article
- The mutational landscape and its longitudinal dynamics in relapsed and refractory classic Hodgkin lymphoma.Annals of hematology · 2025Article
- Genetic Contribution to Medium-Term Disease Activity in Multiple Sclerosis.Molecular neurobiology · 2025Article
- Article
- Identification of Tumor Budding-Associated Genes in Breast Cancer through Transcriptomic Profiling and Network Diffusion Analysis.Biomolecules · 2024Article
- CausNet: generational orderings based search for optimal Bayesian networks via dynamic programming with parent set constraints.BMC bioinformatics · 2023Article
- A statistical physics approach for disease module detection.Genome research · 2022Article
- Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease.Respiratory research · 2022Article
- Identification of recurrent genetic patterns from targeted sequencing panels with advanced data science: a case-study on sporadic and genetic neurodegenerative diseases.BMC medical genomics · 2022Article
- Characterization and comparison of gene-centered human interactomes.Briefings in bioinformatics · 2021Article
- The effect of statistical normalization on network propagation scores.Bioinformatics (Oxford, England) · 2021Article
- Differential Network Analysis Reveals Regulatory Patterns in Neural Stem Cell Fate Decision.Interdisciplinary sciences, computational life sciences · 2021Article
- Ranking cancer drivers via betweenness-based outlier detection and random walks.BMC bioinformatics · 2021Article
- Systems biology analysis identifiesComputational and structural biotechnology journal · 2021Article
- NetCore: a network propagation approach using node coreness.Nucleic acids research · 2020Article
- Frailness and resilience of gene networks predicted by detection of co-occurring mutations via a stochastic perturbative approach.Scientific reports · 2020Article
- Gene relevance based on multiple evidences in complex networks.Bioinformatics (Oxford, England) · 2020Article
- Molecular targets and system biology approaches for drug repurposing against SARS-CoV-2.Bulletin of the National Research Centre · 2020Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A relation exists between network proximity of molecular entities in interaction networks, functional similarity and association with diseases. The identification of network regions associated with biological functions and pathologies is a major goal in systems biology. We describe a network diffusion-based pipeline for the interpretation of different types of omics in the context of molecular interaction networks. We introduce the network smoothing index, a network-based quantity that allows to jointly quantify the amount of omics information in genes and in their network neighbourhood, using network diffusion to define network proximity. The approach is applicable to both descriptive and inferential statistics calculated on omics data. We also show that network resampling, applied to gene lists ranked by quantities derived from the network smoothing index, indicates the presence of significantly connected genes. As a proof of principle, we identified gene modules enriched in somatic mutations and transcriptional variations observed in samples of prostate adenocarcinoma (PRAD). In line with the local hypothesis, network smoothing index and network resampling underlined the existence of a connected component of genes harbouring molecular alterations in PRAD.
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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.