Total: 24 publication(s)


Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P. (2014)

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.

Nucleic Acids Res. doi:10.1093/nar/gku1081
Europe PMC | doi

Sebastian-Leon P, Vidal E, Minguez P, Conesa A, Tarazona S, Amadoz A, Armero C, Salavert F, Vidal-Puig A, Montaner D, Dopazo J. (2014)

Understanding disease mechanisms with models of signaling pathway activities.

BMC Syst Biol 8 doi:10.1186/s12918-014-0121-3


Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. (2013)

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

Nucleic Acids Res. 41(Database issue):D808-15. doi:10.1093/nar/gks1094
Europe PMC | doi

Minguez P, Letunic I, Parca L, Bork P. (2013)

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins

Nucleic Acids Res. 41(Database issue):D306-11. doi:10.1093/nar/gks1230
Europe PMC | doi


García-Alonso L, Alonso R, Vidal E, Amadoz A, de María A, Minguez P, Medina I, Dopazo J. (2012)

Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments

Nucleic Acids Res. 40(20):e158. doi:10.1093/nar/gks699
Europe PMC | doi

Chen WH, Minguez P, Lercher MJ, Bork P. (2012)

OGEE: an online gene essentiality database

Nucleic Acids Res. 40(Database issue):D901-6. doi:10.1093/nar/gkr986
Europe PMC | doi

Doerks T, van Noort V, Minguez P, Bork P. (2012)

Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins

PLoS ONE 7(4):e34302. doi:10.1371/journal.pone.0034302
Europe PMC | doi

Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P. (2012)

Deciphering a global network of functionally associated post-translational modifications

Mol. Syst. Biol. 8:599. doi:10.1038/msb.2012.31
Europe PMC | doi


Minguez P, Dopazo J. (2011)

Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties

PLoS ONE 6(3):e17474. doi:10.1371/journal.pone.0017474
Europe PMC | doi

Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C. (2011)

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

Nucleic Acids Res. 39(Database issue):D561-8. doi:10.1093/nar/gkq973
Europe PMC | doi


Minguez P, Dopazo J. (2010)

Functional genomics and networks: new approaches in the extraction of complex gene modules

Expert Rev Proteomics 7(1):55-63. doi:10.1586/epr.09.103
Europe PMC | doi

Al-Shahrour F, Minguez P, Marqués-Bonet T, Gazave E, Navarro A, Dopazo J. (2010)

Selection upon genome architecture: conservation of functional neighborhoods with changing genes

PLoS Comput. Biol. 6(10):e1000953. doi:10.1371/journal.pcbi.1000953
Europe PMC | doi


Minguez P, Götz S, Montaner D, Al-Shahrour F, Dopazo J. (2009)

SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks

Nucleic Acids Res. 37(Web Server issue):W109-14. doi:10.1093/nar/gkp402
Europe PMC | doi

Montaner D, Minguez P, Al-Shahrour F, Dopazo J. (2009)

Gene set internal coherence in the context of functional profiling

BMC Genomics 10:197. doi:10.1186/1471-2164-10-197
Europe PMC | doi


Horcajadas JA, Mínguez P, Dopazo J, Esteban FJ, Domínguez F, Giudice LC, Pellicer A, Simón C. (2008)

Controlled ovarian stimulation induces a functional genomic delay of the endometrium with potential clinical implications

J. Clin. Endocrinol. Metab. 93(11):4500-4510. doi:10.1210/jc.2008-0588
Europe PMC | doi

Al-Shahrour F, Carbonell J, Minguez P, Goetz S, Conesa A, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J. (2008)

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments

Nucleic Acids Res. 36(Web Server issue):W341-6. doi:10.1093/nar/gkn318
Europe PMC | doi

Tárraga J, Medina I, Carbonell J, Huerta-Cepas J, Minguez P, Alloza E, Al-Shahrour F, Vegas-Azcárate S, Goetz S, Escobar P, Garcia-Garcia F, Conesa A, Montaner D, Dopazo J. (2008)

GEPAS, a web-based tool for microarray data analysis and interpretation

Nucleic Acids Res. 36(Web Server issue):W308-14. doi:10.1093/nar/gkn303
Europe PMC | doi


Minguez P, Al-Shahrour F, Montaner D, Dopazo J. (2007)

Functional profiling of microarray experiments using text-mining derived bioentities

Bioinformatics 23(22):3098-3099. doi:10.1093/bioinformatics/btm445
Europe PMC | doi

Al-Shahrour F, Minguez P, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J. (2007)

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments

Nucleic Acids Res. 35(Web Server issue):W91-6. doi:10.1093/nar/gkm260
Europe PMC | doi

Al-Shahrour F, Arbiza L, Dopazo H, Huerta-Cepas J, Mínguez P, Montaner D, Dopazo J. (2007)

From genes to functional classes in the study of biological systems

BMC Bioinformatics 8:114. doi:10.1186/1471-2105-8-114
Europe PMC | doi


Al-Shahrour F, Minguez P, Tárraga J, Montaner D, Alloza E, Vaquerizas JM, Conde L, Blaschke C, Vera J, Dopazo J. (2006)

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments

Nucleic Acids Res. 34(Web Server issue):W472-6. doi:10.1093/nar/gkl172
Europe PMC | doi

Montaner D, Tárraga J, Huerta-Cepas J, Burguet J, Vaquerizas JM, Conde L, Minguez P, Vera J, Mukherjee S, Valls J, Pujana MA, Alloza E, Herrero J, Al-Shahrour F, Dopazo J. (2006)

Next station in microarray data analysis: GEPAS

Nucleic Acids Res. 34(Web Server issue):W486-91. doi:10.1093/nar/gkl197
Europe PMC | doi

Minguez P, Al-Shahrour F, Dopazo J. (2006)

A function-centric approach to the biological interpretation of microarray time-series

Genome Inform 17(2):57-66.
Europe PMC


Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J. (2005)

BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments

Nucleic Acids Res. 33(Web Server issue):W460-4. doi:10.1093/nar/gki456
Europe PMC | doi