ArticleBioinformatics (Oxford, England)2018
Classifying tumors by supervised network propagation.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- OncoBERT: Context-Aware Modeling of Somatic Mutations for Precision Oncology.bioRxiv : the preprint server for biology · 2026Article
- Deep Clustering-Based Metabolic Stratification of Non-Small Cell Lung Cancer Patients Through Integration of Somatic Mutation Profile and Network Propagation Algorithm.Interdisciplinary sciences, computational life sciences · 2025Article
- Integrating somatic mutation profiles with structural deep clustering network for metabolic stratification in pancreatic cancer: a comprehensive analysis of prognostic and genomic landscapes.Briefings in bioinformatics · 2023Article
- Article
- A network medicine approach for identifying diagnostic and prognostic biomarkers and exploring drug repurposing in human cancer.Computational and structural biotechnology journal · 2023Article
- Multi-omics peripheral and core regions of cancer.NPJ systems biology and applications · 2022Article
- A tensor-based bi-random walks model for protein function prediction.BMC bioinformatics · 2022Article
- Developing a label propagation approach for cancer subtype classification problem.Turkish journal of biology = Turk biyoloji dergisi · 2022Article
- Artificial intelligence, molecular subtyping, biomarkers, and precision oncology.Emerging topics in life sciences · 2021Review
- Evaluation and comparison of multi-omics data integration methods for cancer subtyping.PLoS computational biology · 2021Article
- A network-based deep learning methodology for stratification of tumor mutations.Bioinformatics (Oxford, England) · 2021Article
- Network-guided search for genetic heterogeneity between gene pairs.Bioinformatics (Oxford, England) · 2021Article
- Identifying modules of cooperating cancer drivers.Molecular systems biology · 2021Article
- MONTI: A Multi-Omics Non-negative Tensor Decomposition Framework for Gene-Level Integrative Analysis.Frontiers in genetics · 2021Article
- Identifying Drug Sensitivity Subnetworks with NETPHIX.iScience · 2020Article
- Constructing cancer patient-specific and group-specific gene networks with multi-omics data.BMC medical genomics · 2020Article
- NPF:network propagation for protein function prediction.BMC bioinformatics · 2020Article
- Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction.Scientific reports · 2020Article
- Classifying Breast Cancer Molecular Subtypes by Using Deep Clustering Approach.Frontiers in genetics · 2020Article
- Integrated querying and version control of context-specific biological networks.Database : the journal of biological databases and curation · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
Motivation: Network propagation has been widely used to aggregate and amplify the effects of tumor mutations using knowledge of molecular interaction networks. However, propagating mutations through interactions irrelevant to cancer leads to erosion of pathway signals and complicates the identification of cancer subtypes. Results: To address this problem we introduce a propagation algorithm, Network-Based Supervised Stratification (NBS2), which learns the mutated subnetworks underlying tumor subtypes using a supervised approach. Given an annotated molecular network and reference tumor mutation profiles for which subtypes have been predefined, NBS2 is trained by adjusting the weights on interaction features such that network propagation best recovers the provided subtypes. After training, weights are fixed such that mutation profiles of new tumors can be accurately classified. We evaluate NBS2 on breast and glioblastoma tumors, demonstrating that it outperforms the best network-based approaches in classifying tumors to known subtypes for these diseases. By interpreting the interaction weights, we highlight characteristic molecular pathways driving selected subtypes. Availability and implementation: The NBS2 package is freely available at: https://github.com/wzhang1984/NBSS. Supplementary information: Supplementary data are available at Bioinformatics online.
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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.