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CentrosomeDB: a new generation of the centrosomal proteins database for Human and Drosophila melanogaster.
Alves-Cruzeiro JM, Nogales-Cadenas R, Pascual-Montano AD. Alves-Cruzeiro JM, et al. Among authors: pascual montano ad. Nucleic Acids Res. 2014 Jan;42(Database issue):D430-6. doi: 10.1093/nar/gkt1126. Epub 2013 Nov 21. Nucleic Acids Res. 2014. PMID: 24270791 Free PMC article.
bioNMF: a web-based tool for nonnegative matrix factorization in biology.
Mejía-Roa E, Carmona-Saez P, Nogales R, Vicente C, Vázquez M, Yang XY, García C, Tirado F, Pascual-Montano A. Mejía-Roa E, et al. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W523-8. doi: 10.1093/nar/gkn335. Epub 2008 May 30. Nucleic Acids Res. 2008. PMID: 18515346 Free PMC article.
3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.
Nogales-Cadenas R, Jonic S, Tama F, Arteni AA, Tabas-Madrid D, Vázquez M, Pascual-Montano A, Sorzano CO. Nogales-Cadenas R, et al. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W363-7. doi: 10.1093/nar/gkt385. Epub 2013 May 13. Nucleic Acids Res. 2013. PMID: 23671335 Free PMC article.
Moara: a Java library for extracting and normalizing gene and protein mentions.
Neves ML, Carazo JM, Pascual-Montano A. Neves ML, et al. BMC Bioinformatics. 2010 Mar 26;11:157. doi: 10.1186/1471-2105-11-157. BMC Bioinformatics. 2010. PMID: 20346105 Free PMC article.
Assessment of protein set coherence using functional annotations.
Chagoyen M, Carazo JM, Pascual-Montano A. Chagoyen M, et al. BMC Bioinformatics. 2008 Oct 20;9:444. doi: 10.1186/1471-2105-9-444. BMC Bioinformatics. 2008. PMID: 18937846 Free PMC article.
Quantification of miRNA-mRNA interactions.
Muniategui A, Nogales-Cadenas R, Vázquez M, Aranguren XL, Agirre X, Luttun A, Prosper F, Pascual-Montano A, Rubio A. Muniategui A, et al. PLoS One. 2012;7(2):e30766. doi: 10.1371/journal.pone.0030766. Epub 2012 Feb 14. PLoS One. 2012. PMID: 22348024 Free PMC article.
NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning.
Setoain J, Franch M, Martínez M, Tabas-Madrid D, Sorzano CO, Bakker A, Gonzalez-Couto E, Elvira J, Pascual-Montano A. Setoain J, et al. Nucleic Acids Res. 2015 Jul 1;43(W1):W193-9. doi: 10.1093/nar/gkv445. Epub 2015 May 4. Nucleic Acids Res. 2015. PMID: 25940629 Free PMC article.
Proteogenomics Dashboard for the Human Proteome Project.
Tabas-Madrid D, Alves-Cruzeiro J, Segura V, Guruceaga E, Vialas V, Prieto G, García C, Corrales FJ, Albar JP, Pascual-Montano A. Tabas-Madrid D, et al. J Proteome Res. 2015 Sep 4;14(9):3738-49. doi: 10.1021/acs.jproteome.5b00466. Epub 2015 Jul 16. J Proteome Res. 2015. PMID: 26144527
MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures.
Vazquez M, Nogales-Cadenas R, Arroyo J, Botías P, García R, Carazo JM, Tirado F, Pascual-Montano A, Carmona-Saez P. Vazquez M, et al. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W228-32. doi: 10.1093/nar/gkq476. Epub 2010 May 31. Nucleic Acids Res. 2010. PMID: 20513648 Free PMC article.