Using the Grid to Analyze the Pharmacokinetic Modelling after Contrast Administration in Dynamic MRI. - Ignacio Blanquer; Vicente Hernández; Daniel Monleón; José Carbonell; David Moratal; Bernardo Celda; Montserrat Robles; Luis Martí-Bonmatí (HealthGrid, 2006)

A nonparametric MRI inhomogeneity correction method. - José V. Manjón; Juan José Lull; José Carbonell-Caballero; Gracián García-Martí; Luis Martí-Bonmatí; Montserrat Robles (Medical Image Anal., 2007)

MRI denoising using Non-Local Means. - José V. Manjón; José Carbonell-Caballero; Juan José Lull; Gracián García-Martí; Luis Martí-Bonmatí; Montserrat Robles (Medical Image Anal., 2008)

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. - Fátima Al-Shahrour; José Carbonell; Pablo Minguez; Stefan Götz 003; Ana Conesa; Joaquín Tárraga; Ignacio Medina; Eva Alloza; David Montaner; Joaquín Dopazo (Nucleic Acids Res., 2008)

GEPAS, a web-based tool for microarray data analysis and interpretation. - Joaquín Tárraga; Ignacio Medina; José Carbonell; Jaime Huerta-Cepas; Pablo Minguez; Eva Alloza; Fátima Al-Shahrour; Susana Vegas-Azcárate; Stefan Götz 003; Pablo Escobar; Francisco García-García 002; Ana Conesa; et al. (Nucleic Acids Res., 2008)

Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. - Ignacio Medina; David Montaner; Nuria Bonifaci; Miguel Angel Pujana; José Carbonell; Joaquín Tárraga; Fátima Al-Shahrour; Joaquín Dopazo (Nucleic Acids Res., 2009)

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. - Ignacio Medina; José Carbonell; Luis Pulido; Sara C. Madeira; Stefan Götz 003; Ana Conesa; Joaquín Tárraga; Alberto D. Pascual-Montano; Rubén Nogales-Cadenas; Javier Santoyo; Francisco García-García 002; Martina Marbà; et al. (Nucleic Acids Res., 2010)

Serial Expression Analysis: a web tool for the analysis of serial gene expression data. - María José Nueda; José Carbonell; Ignacio Medina; Joaquín Dopazo; Ana Conesa (Nucleic Acids Res., 2010)

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. - Rubén Sánchez 002; François Serra; Joaquín Tárraga; Ignacio Medina; José Carbonell; Luis Pulido; Alejandro de María; Salvador Capella-Gutiérrez; Jaime Huerta-Cepas; Toni Gabaldón; Joaquín Dopazo; Hernán Dopazo (Nucleic Acids Res., 2011)

Qualimap: evaluating next-generation sequencing alignment data. - Fernando García-Alcalde; Konstantin Okonechnikov; José Carbonell; Luis M. Cruz; Stefan Götz 003; Sonia Tarazona; Joaquín Dopazo; Thomas F. Meyer; Ana Conesa (Bioinform., 2012)

Inferring the functional effect of gene expression changes in signaling pathways. - Patricia Sebastián-León; José Carbonell; Francisco Salavert; Rubén Sánchez 002; Ignacio Medina; Joaquín Dopazo (Nucleic Acids Res., 2013)

Babelomics 5.0: functional interpretation for new generations of genomic data. - Roberto Alonso; Francisco Salavert; Francisco García-García 002; José Carbonell-Caballero; Marta Bleda; Luz Garcia-Alonso; Alba Sanchis-Juan; Daniel Perez-Gil; Pablo Marín-García; Rubén Sánchez 002; Cankut Çubuk; Marta R. Hidalgo; et al. (Nucleic Acids Res., 2015)

Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models. - Francisco Salavert; Marta R. Hidalgo; Alicia Amadoz; Cankut Çubuk; Ignacio Medina; Daniel Crespo; José Carbonell-Caballero; Joaquín Dopazo (Nucleic Acids Res., 2016)

Reference genome assessment from a population scale perspective: an accurate profile of variability and noise. - José Carbonell-Caballero; Alicia Amadoz; Roberto Alonso; Marta R. Hidalgo; Cankut Çubuk; David V. Conesa; Antonio López-Quílez; Joaquín Dopazo (Bioinform., 2017)

A comparison of mechanistic signaling pathway activity analysis methods. - Alicia Amadoz; Marta R. Hidalgo; Cankut Çubuk; José Carbonell-Caballero; Joaquín Dopazo (Briefings Bioinform., 2019)

Lessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation. - Marc Clascà; Marta Garcia-Gasulla; Arnau Montagud; José Carbonell-Caballero; Alfonso Valencia (PASC, 2023)