NBS statistics

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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

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Publication for Network-Based Stratification

NBS in publications

 (8)
PMCID: 5902616
PMID: 29662161
DOI: 10.1038/s41598-018-24379-y

[…] 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 […]

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

[…] was used as the statistical test and the benjamini–hochberg method was used to correct p values., 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 […]

PMCID: 5638226
PMID: 29023449
DOI: 10.1371/journal.pcbi.1005598

[…] 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 […]

PMCID: 5430742
PMID: 28432308
DOI: 10.1038/s41598-017-01064-0

[…] into bi-clustering to improve the performance of discovering cancer subtypes–. knowing the subtype of a cancer patient can provide directional clues for precise treatment. hofree et al. proposed a network-based stratification method to integrate somatic cancer with gene interaction networks. this approach initially groups cancer patients with mutations in similar network regions […]

PMCID: 4902951
PMID: 27287041
DOI: 10.1186/s13073-016-0319-7

[…] low-dimensional representation; loocv, leave-one-out cross-validation; map, maximum a posteriori; mgl, module graphical lasso; msc, mesenchymal stem cell; msigdb, molecular signatures database; nbs, network-based stratification; ov, ovarian cancer; pc, principal component; pca, principal component analysis; ppi, protein-protein interaction; roc, receiver operator characteristic; sam, […]


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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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