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2021
Carbonell-Caballero J, López-Quílez A, Conesa D, Dopazo J. Deciphering Genomic Heterogeneity and the Internal Composition of Tumour Activities through a Hierarchical Factorisation Model. Mathematics. 2021;9(21):2833. doi:10.3390/math9212833.
2019
Amadoz A, Hidalgo MR, Cubuk C, Carbonell-Caballero J, Dopazo J. A comparison of mechanistic signaling pathway activity analysis methods. Brief Bioinform. 2019;20(5):1655-1668. doi:10.1093/bib/bby040.
Cubuk C, Hidalgo MR, Amadoz A, et al. Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models. NPJ Syst Biol Appl. 2019;5:7. doi:10.1038/s41540-019-0087-2.
2018
Ferreira PG, Muñoz-Aguirre M, Reverter F, et al. The effects of death and post-mortem cold ischemia on human tissue transcriptomes. Nat Commun. 2018;9(1):490. doi:10.1038/s41467-017-02772-x.
Cubuk C, Hidalgo MR, Amadoz A, et al. Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape. Cancer Res. 2018;78(21):6059-6072. doi:10.1158/0008-5472.CAN-17-2705.
Wu GAlbert, Terol J, Ibañez V, et al. Genomics of the origin and evolution of Citrus. Nature. 2018;554(7692):311-316. doi:10.1038/nature25447.
Hidalgo MR, Amadoz A, Cubuk C, Carbonell-Caballero J, Dopazo J. Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome. Biol Direct. 2018;13(1):16. doi:10.1186/s13062-018-0219-4.
Ibáñez M, Carbonell-Caballero J, Such E, et al. The modular network structure of the mutational landscape of Acute Myeloid Leukemia. PLoS One. 2018;13(10):e0202926. doi:10.1371/journal.pone.0202926.
2017
Hidalgo MR, Cubuk C, Amadoz A, Salavert F, Carbonell-Caballero J, Dopazo J. High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes. Oncotarget. 2017;8(3):5160-5178. doi:10.18632/oncotarget.14107.
Carbonell-Caballero J, Amadoz A, Alonso R, et al. Reference genome assessment from a population scale perspective: an accurate profile of variability and noise. Bioinformatics. 2017;33(22):3511-3517. doi:10.1093/bioinformatics/btx482.
2016
Salavert F, Hidago MR, Amadoz A, et al. Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models. Nucleic acids research. 2016. doi:10.1093/nar/gkw369.
Ibáñez M, Carbonell-Caballero J, García-Alonso L, et al. The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations. PLoS One. 2016;11(2):e0148346. doi:10.1371/journal.pone.0148346.
Falco MM, Bleda M, Carbonell-Caballero J, Dopazo J. The pan-cancer pathological regulatory landscape. Scientific Reports. 2016;6(1). doi:10.1038/srep39709.
Falco MM, Bleda M, Carbonell-Caballero J, Dopazo J. The pan-cancer pathological regulatory landscape. Scientific reports. 2016;6:39709. doi:10.1038/srep39709.
2015
Alonso R, Salavert F, Garcia-Garcia F, et al. Babelomics 5.0: functional interpretation for new generations of genomic data. Nucleic acids research. 2015;43:W117-W121. doi:10.1093/nar/gkv384.
Ewing AD, Houlahan KE, Hu Y, et al. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. participants ICGC-TCGADREAMSoma, Xi L, Dewal N, et al., eds. Nature methods. 2015. doi:10.1038/nmeth.3407.
Carbonell-Caballero J, Alonso R, Ibañez V, Terol J, Talon M, Dopazo J. A phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the genus Citrus. Molecular biology and evolution. 2015;32:2015-2035. doi:10.1093/molbev/msv082.
2014
García-Alonso L, Jiménez-Almazán J, Carbonell-Caballero J, et al. The role of the interactome in the maintenance of deleterious variability in human populations. Mol Syst Biol. 2014;10:752. doi:10.15252/msb.20145222.
Larriba E, Jaime MDLA, Carbonell-Caballero J, et al. Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia. Fungal Genet Biol. 2014;65:69-80. doi:10.1016/j.fgb.2014.02.002.