SNMNMF specifications


Unique identifier OMICS_12515
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Source code URL
Maintained Yes


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  • person_outline Shihua Zhang <>
  • person_outline Xianghong Jasmine Zhou <>

Publication for SNMNMF

SNMNMF in publications

PMCID: 5259869
PMID: 28155675
DOI: 10.1186/s12918-016-0357-1

[…] the networks composed of both genes and mirnas, a good module should include both genes and mirnas with connections. to better identify the gene-mirna modules, zhang et al. developed a framework of snmnmf, which is based on non-negative matrix factorization and utilized a variety of data, including gene-gene interaction (ggi) and transcription factor binding sites (tfbs) []. however, snmnmf […]

PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] of more than two genomic data types is still at its infancy and not yet extensively applied to functional sequencing techniques, but there are already some tools that combine several data types. snmnmf [] and pimim [] combine mrna and mirna expression data with protein–protein, dna–protein, and mirna–mrna interaction networks to identify mirna–gene regulatory modules. mona [] combines […]

PMCID: 4331711
PMID: 25707620
DOI: 10.1186/1471-2164-16-S2-S11

[…] only an incomplete part of the modules in a certain biological context., recently, zhang et al. (2011) developed a framework of sparse network-regularized multiple non-negative matrix factorization (snmnmf) to discover mirna-gene comodules based on factorized coefficient matrices by integrating diverse data sources []. le et al. (2013) designed a iterative learning framework of protein […]

PMCID: 3866260
PMID: 24564886
DOI: 10.1186/1752-0509-7-S2-S11

[…] the mirna regulatory network [-] or tfs and target genes regulatory networks []. as a result, many computational tools have been proposed to predict the mirna-mrna regulations (embl [], miranda [], snmnmf[,], pictar [], mirconnx [], and targetscan []), or the tf-mrna regulations (trrd[], jaspar[], and transfac [,]). recently there are several attempts to discover the combinational links […]

PMCID: 3896928
PMID: 23175680
DOI: 10.1093/bib/bbs075

[…] to find the co-expressed mirnas and mrnas, then ppis are further used to refine the structures. a novel machine learning method sparse network regularized multiple non-negative matrix factorization (snmnmf) was developed in this work to integrate three heterogeneous data sources. they tested this method on a data set of ovarian cancer samples, and 49 significant mrms were identified, […]

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SNMNMF institution(s)
Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA; Academy of Mathematics and Systems Science, CAS, Beijing, China; School of Computer Science, Wuhan University, Wuhan, China
SNMNMF funding source(s)
Supported by the National Institutes of Health (Grants R01GM074163); National Science Foundation (Grants 0515936; and 0747475); National Natural Science Foundation of China (No. 11001256); Innovation Project of Chinese Academy of Sciences (CAS) (kjcx-yw-s7); the Special Presidential Prize - Scientific Research Foundation of the CAS, and the Special Foundation of President of AMSS at CAS for ‘Chen Jing-Run’ Future Star Program.

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