Several miRNA-mRNA relationship databases have been reported, most of them based on sequence complementarities. However, the number of false positives in these databases is large and they do not overlap completely. Talasso application uses Lasso regression with non-negative constraints to integrate both sources of information. Lasso enforces the sparseness of the solution and non negative constraints restrict the search to down-regulation of the mRNA by the miRNAs making this approach very convenient to solve the miRNA-mRNA relationship.

Quantification of miRNA-mRNA interactions. Ander Muniategui; Rubén Nogales-Cadenas; Miguél Vázquez; Xabier L. Aranguren; Xabier Agirre; Aernout Luttun; Felipe Prosper; Alberto Pascual-Montano; Angel Rubio (Submitted)

Functional analysis of large sets of genes and proteins is becoming more and more necessary with the increase of experimental biomolecular data at omic scale. Enrichment analysis is by far the most popular available methodology to derive functional implications of sets of cooperating genes. The problem with these techniques relies in the redundancy of resulting information, that in most of the cases generate lots of trivial results with high risk to mask the reality of key biological events. Gtlinker filters and links enriched output data identifying sets of genes and terms to produce metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations.

Functional Analysis beyond Enrichment: Non-Redundant Reciprocal Linkage of Genes and Biological Terms. Celia Fontanillo, Ruben Nogales-Cadenas, Alberto Pascual-Montano and Javier De Las Rivas. 2011. PLoS ONE 6 (9) p. e24289
[Medline] [Online version]

GeneCodis is a web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list

Ruben Nogales-Cadenas, Pedro Carmona-Saez, Miguel Vazquez, Cesar Vicente, Xiaoyuan Yang, Francisco Tirado, Jose M. Carazo and Alberto Pascual-Montano. GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. Nucleic Acids Research 2009; doi: 10.1093/nar/gkp416
[Medline] [On-line version] 

MARq is an online tool to mine GEO for experiments with similar or opposite gene expression signatures. It allows searching experiments by content, comparing the query gene expression signatures with those found in GEO database

MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. Miguel Vazquez,  Ruben Nogales-Cadenas, Javier Arroyo, Pedro Botías, Raul García, Jose M. Carazo,  Francisco Tirado, Alberto Pascual-Montano and Pedro Carmona-Saez. Nucleic Acids Research 2010. Jul 1;38 Suppl:W228-32. Epub 2010 May 31
[Medline] [Online version]

bioNMF is a web-based tool for performing non-negative matrix factorization of biological data. This application is a useful tool for bioinformatics researchers that need to use the NMF algorithm in an easy and efficient way.

Mejía-Roa, E., Carmona-Saez, P., Nogales, R., Vicente, C., Vázquez, M., Yang, XY., García, C., Tirado, F., Pascual-Montano, A.. bioNMF: A web-based tool for Non-negative Matrix Factorization in biology. Nucleic Acid Research. 2008.  Nucleic Acids Research 2008; doi: 10.1093/nar/gkn335
[Medline] [On-line version] 

Sent is a web-based tool to brings structure and semantics to a list of genes by means of literature analysis. It takes a list of genes given as input and returns a collection of functionally related groups along with a list of words that provide them with a functional description.

Miguel Vazquez, Ruben Nogales-Cadenas, Monica Chagoyen, Pedro Carmona-Saez and Alberto Pascual-Montano. SENT: Semantic Features in Text. Nucleic Acids Research 2009; doi: 10.1093/nar/gkp392
[Medline] [On-line version] 

Moara is a project developed by BioComputing unit at Centro Nacional de Biotecnologia (CNB) for the development of biological text mining tools

Mariana Lara Neves, Jose Maria Carazo and Alberto Pascual-Montano. Moara: a Java library for extracting and normalizing gene and protein mentions. BMC Bioinformatics. 2010 Mar 26;11:157.
[Medline] [Online version]

Centrosome:db contains a set of human genes encoding proteins that are localized in the centrosome, either as centrosome constituents or as centrosome visitors. Genes have been considered as centrosomal on the basis of different kinds of evidences including high-throughput proteomics assays, annotations in public databases and orthology relationships to centrosomal genes in closely related species (e.g. mouse)