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bioNMF: a versatile tool for non-negative matrix factorization in biology

Alberto Pascual-Montano1*, Pedro Carmona-Saez2, Monica Chagoyen12, Francisco Tirado1, Jose M Carazo2 and Roberto D Pascual-Marqui3

Author Affiliations

1 Computer Architecture Department, Facultad de Ciencias Físicas, Universidad Complutense de Madrid, 28040, Spain

2 BioComputing Unit, National Center of Biotechnology, Campus Universidad Autónoma de Madrid, 28049, Spain

3 The KEY Institute for Brain-Mind Research, University Hospital of Psychiatry. Lenggstr. 31, CH-8029 Zurich, Switzerland

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BMC Bioinformatics 2006, 7:366  doi:10.1186/1471-2105-7-366

Published: 28 July 2006



In the Bioinformatics field, a great deal of interest has been given to Non-negative matrix factorization technique (NMF), due to its capability of providing new insights and relevant information about the complex latent relationships in experimental data sets. This method, and some of its variants, has been successfully applied to gene expression, sequence analysis, functional characterization of genes and text mining. Even if the interest on this technique by the bioinformatics community has been increased during the last few years, there are not many available simple standalone tools to specifically perform these types of data analysis in an integrated environment.


In this work we propose a versatile and user-friendly tool that implements the NMF methodology in different analysis contexts to support some of the most important reported applications of this new methodology. This includes clustering and biclustering gene expression data, protein sequence analysis, text mining of biomedical literature and sample classification using gene expression. The tool, which is named bioNMF, also contains a user-friendly graphical interface to explore results in an interactive manner and facilitate in this way the exploratory data analysis process.


bioNMF is a standalone versatile application which does not require any special installation or libraries. It can be used for most of the multiple applications proposed in the bioinformatics field or to support new research using this method. This tool is publicly available at webcite.