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NBS specifications

Information


Unique identifier OMICS_10483
Name NBS
Alternative name Network-Based Stratification
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB, R
Computer skills Advanced
Version 0.2
Stability Stable
Maintained Yes

Versioning


No version available

Publication for Network-Based Stratification

NBS citations

 (27)
library_books

Pan cancer analysis of somatic mutations and transcriptomes reveals common functional gene clusters shared by multiple cancer types

2018
Sci Rep
PMCID: 5902616
PMID: 29662161
DOI: 10.1038/s41598-018-24379-y

[…] mber of variants, and we only identified clustering of datasets when we investigated the number of PSGs in clusters, which were similarly sorted in order of total number of PSGs in datasets. Unlike a network-based stratification (NBS) method, high dimensional data of individual samples were lost in our procedures, which did not reflect tissue-of-origin-based classification and were not suitable to […]

library_books

Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia

2017
Malar J
PMCID: 5735551
PMID: 29258508
DOI: 10.1186/s12936-017-2140-1

[…] The population structure of 167 parasite isolates was also questioned using the method of Network Based Stratification [] which clusters the isolates together having diffusion paths associated to mutated genes in similar network regions. The list of mutated genes for each isolate was proje […]

library_books

Network dynamics based cancer panel stratification for systemic prediction of anticancer drug response

2017
Nat Commun
PMCID: 5717260
PMID: 29208897
DOI: 10.1038/s41467-017-02160-5

[…] er subtypes,. For example, method was developed to extract gene sub-networks from whole protein–protein interaction (PPI) network, based on which metastatic breast cancer was successfully classified. Network-based stratification (NBS) was also successfully employed to classify cancers based on their mutation network profiles and demonstrated improved correlation between cancer subtypes and clinica […]

library_books

Percolation transition of cooperative mutational effects in colorectal tumorigenesis

2017
Nat Commun
PMCID: 5668266
PMID: 29097710
DOI: 10.1038/s41467-017-01171-6

[…] studies showed that the topological location of somatic mutations in the protein–protein interaction (PPI) network might be closely associated with the clinical outcome. Hofree et al. proposed such a network-based stratification of cancer patients based on The Cancer Genome Atlas (TCGA), where a network propagation of somatic mutations on the PPI network was introduced by assigning high values to […]

library_books

Network propagation in the cytoscape cyberinfrastructure

2017
PLoS Comput Biol
PMCID: 5638226
PMID: 29023449
DOI: 10.1371/journal.pcbi.1005598

[…] ork propagation to discover significantly mutated subnetworks in cancer. Since then, the method has become a cornerstone of cancer genome analysis. Hofree et al. [] used a network propagation method (Network-Based Stratification, or NBS) to cluster cancer patient data, Paull et al. [] identified causal paths linking mutations to expression regulators, and Liu et al. and Zhong et al. [,] applied th […]

library_books

ndmaSNF: cancer subtype discovery based on integrative framework assisted by network diffusion model

2017
Oncotarget
PMCID: 5687665
PMID: 29179495
DOI: 10.18632/oncotarget.21643

[…] nformation about relationships between genes and biochemical pathways and comprehensive insight into tumor progress []. To deal with this problem, Hofree et al. [] brought forward a method named NBS (network-based stratification) which integrated somatic mutation data with gene networks using network diffusion model and performed clustering in a consensus clustering framework to make result robust […]

Citations

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NBS institution(s)
Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA

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