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2007
Hernández P, Huerta-Cepas J, Montaner D, et al. Evidence for systems-level molecular mechanisms of tumorigenesis. BMC Genomics. 2007;8:185. doi:10.1186/1471-2164-8-185.
Al-Shahrour F, Minguez P, Tárraga J, et al. FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res. 2007;35(Web Server issue):W91-6. doi:10.1093/nar/gkm260.
Al-Shahrour F, Arbiza L, Dopazo H, et al. From genes to functional classes in the study of biological systems. BMC Bioinformatics. 2007;8:114. doi:10.1186/1471-2105-8-114.
Conde L, Montaner D, Burguet-Castell J, Tárraga J, Al-Shahrour F, Dopazo J. Functional profiling and gene expression analysis of chromosomal copy number alterations. Bioinformation. 2007;1(10):432-5. doi:10.6026/97320630001432.
Minguez P, Al-Shahrour F, Montaner D, Dopazo J. Functional profiling of microarray experiments using text-mining derived bioentities. Bioinformatics. 2007;23(22):3098-9. doi:10.1093/bioinformatics/btm445.
Conde L, Montaner D, Burguet-Castell J, et al. ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. Nucleic Acids Res. 2007;35(Web Server issue):W81-5. doi:10.1093/nar/gkm257.
2008
Conesa A, Bro R, Garcia-Garcia F, et al. Direct functional assessment of the composite phenotype through multivariate projection strategies. Genomics. 2008;92(6):373-83. doi:10.1016/j.ygeno.2008.05.015.
Tárraga J, Medina I, Carbonell J, et al. GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Res. 2008;36(Web Server issue):W308-14. doi:10.1093/nar/gkn303.
2009
Montaner D, Minguez P, Al-Shahrour F, Dopazo J. Gene set internal coherence in the context of functional profiling. BMC Genomics. 2009;10:197. doi:10.1186/1471-2164-10-197.
Medina I, Montaner D, Bonifaci N, et al. Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. Nucl. Acids Res. 2009;37:W340-344. doi:10.1093/nar/gkp481.
Medina I, Montaner D, Bonifaci N, et al. Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. Nucleic Acids Res. 2009;37(Web Server issue):W340-4. doi:10.1093/nar/gkp481.
van Heerden JH, Conesa A, Stein DJ, Montaner D, Russell V, Illing N. Parallel changes in gene expression in peripheral blood mononuclear cells and the brain after maternal separation in the mouse. BMC Res Notes. 2009;2:195.
Silbiger V, Luchessi A, Hirata R, et al. Peripheral blood cells transcriptome to study new biomarkers for myocardial infarction follow up. In: ; 2009.
Minguez P, Götz S, Montaner D, Al-Shahrour F, Dopazo J. SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucleic Acids Res. 2009;37(Web Server issue):W109-14. doi:10.1093/nar/gkp402.
Minguez P, Gotz S, Montaner D, Al-Shahrour F, Dopazo J. SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucl. Acids Res. 2009;37:W109-114. doi:10.1093/nar/gkp402.
2010
Medina I, Carbonell J, Pulido L, et al. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Research. 2010;38:W210-W213. Featured in NAR. Available at: http://nar.oxfordjournals.org/content/38/suppl_2/W210.full.
Bediaga NG, Acha-Sagredo A, Guerra I, et al. DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Res. 2010;12(5):R77. doi:10.1186/bcr2721.
Moreno-Manzano V, Rodríguez-Jiménez FJ, Aceña-Bonilla JL, et al. FM19G11, a new hypoxia-inducible factor (HIF) modulator, affects stem cell differentiation status. The Journal of biological chemistry. 2010;285:1333-42.
Galan A, Montaner D, M Póo E, et al. Functional genomics of 5- to 8-cell stage human embryos by blastomere single-cell cDNA analysis. PLoS One. 2010;5(10):e13615. doi:10.1371/journal.pone.0013615.
Prado-Lopez S, Conesa A, Armiñán A, et al. Hypoxia promotes efficient differentiation of human embryonic stem cells to functional endothelium. Stem Cells. 2010;28(3):407-18. doi:10.1002/stem.295.
Németh A, Conesa A, Santoyo-López J, et al. Initial genomics of the human nucleolus. PLoS genetics. 2010;6:e1000889. doi:10.1371/journal.pgen.1000889.
Shi L, Campbell G, Jones WD, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature biotechnology. 2010;28:827-38. Available at: http://www.nature.com/nbt/journal/v28/n8/full/nbt.1665.html.
Montaner D, Dopazo J. Multidimensional gene set analysis of genomic data. PLoS One. 2010;5(4):e10348. doi:10.1371/journal.pone.0010348.
2011
Prieur X, Mok CYL, Velagapudi VR, et al. Differential Lipid Partitioning Between Adipocytes and Tissue Macrophages Modulates Macrophage Lipotoxicity and M2/M1 Polarization in Obese Mice. Diabetes. 2011;60:797-809.
Yung S, Ledran M, Moreno-Gimeno I, et al. Large-scale transcriptional profiling and functional assays reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human embryonic stem cells. Hum Mol Genet. 2011;20(24):4932-46. doi:10.1093/hmg/ddr431.