Publications

Computational Biomedicine Lab

2024

  1. Integrated transcriptomic landscape of the effects of anti-steatotic treatments in mouse models of fatty liver disease. I Fuster-Martínez, JF Català-Senent, MR Hidalgo, FJ Roig, JV Esplugues, N Apostolova, F García-García*, A Blas-García*. Journal of Pathology 2024 Jan. doi:  http://doi.org/10.1002/path.6242
  2. Lipid network of plasma extracellular vesicles reveals sex-based differences in the lipidomic profile from patients with alcohol use disorder. C Perpiñá-Clérigues, S Mellado, C Galiana-Roselló, M Fernández-Regueras, M Marcos, F García-García* and M Pascual*. Biology of Sex Differences 2024 Jan 25. doi: https://doi.org/10.1186/s13293-024-00584-5
  3. The role of microRNAs to understand sex-based differences in Alzheimer’s disease. J Llera-Oyola, H Carceller, Z Andreu, MR Hidalgo, I Soler-Sáez, F Gordillo, B Gómez-Cabañes, B Roson, M de la Iglesia-Vayá, R Mancuso, FR Guerini, A Mizokami, F Garcia-Garcia*. Biology of Sex Differences 2024 Jan 31. doi: https://doi.org/10.1186/s13293-024-00588-1
  4. The emerging role of mesenchymal stem cell–derived extracellular vesicles to ameliorate hippocampal NLRP3 inflammation induced by binge-like ethanol treatment in adolescence. S Mellado, MJ Morillo-Bargues, C Perpiñá-Clérigues, F García-García, V Moreno-Manzano, C Guerri, M Pascual*. Neural Regeneration Research 2024. doi: 10.4103/NRR.NRR-D-23-01397
  5. MetaFun: Unveiling sex differences in multiple omics studies through comprehensive functional meta-analysis. P Malmierca-Merlo, R Sanchez-Garcia, R Grillo-Risco, I Perez-Diez, JF Català-Senent, S Leon, H Gomez-Martinez, M de la Iglesia-Vaya, MR Hidalgo*, F Garcia-Garcia*. bioRxiv 2024 Jan 13, doi: https://doi.org/10.1101/2021.07.13.451905
  6. The impact of sex on gene expression in the brain of schizophrenic patients: a systematic review and meta-analysis of transcriptomic studies. H Carceller, MR Hidalgo, MJ Escarti, J Nacher, M Iglesia-Vaya, F Garcia-Garcia*. bioRxiv 2024, doi: https://doi.org/10.1101/2021.07.13.451905.
  7. An integrated approach to identify sex-specific genes, transcription factors, and pathways in Alzheimer’s disease. A López-Cerdán, Z Andreu, MR Hidalgo, I Soler-Saéz, A Porlan, M Pozo-Morales, S Leon, M de la Iglesia-Vayá, A Mikozami, FR Guerini, F García-García*. bioRxiv 2024 Jan 13. doi: https://doi.org/10.1101/2023.09.05.556293
  8. Unveiling common transcriptomic features between melanoma brain metastases and neurodegenerative diseases. I Soler-Sáez, A Karz, MR Hidalgo, B Gómez-Cabañes, A López-Cerdán, JF Català-Senent, M de la Iglesia-Vayá, E Hernando*, F García-García*. bioRxiv 2024 Jan 17. doi: https://doi.org/10.1101/2024.01.16.575868
  9. A spinal cord injury time and severity consensus transcriptomic reference suite in rat reveals translationally-relevant biomarker genes. R Grillo-Risco, MR Hidalgo, B Martínez Rojas, V Moreno-Manzano*, F García-García*. bioRxiv 2024 Jan 31. doi: https://doi.org/10.1101/2024.01.30.578030
  10. Single cell landscape of sex differences in the progression of multiple sclerosis. I Soler-Saez, B Gomez-Cabañes, R Grillo-Risco, C Galiana-Rosello, L Barea-Moya, H Carceller, M de la Iglesia-Vaya, S Gil-Perotin, V Tepavcevic, MR Hidalgo*, F Garcia-Garcia*. bioRxiv 2024 Jun 16. doi: https://doi.org/10.1101/2024.06.15.599139
  11. Novel diagnosis- and progression-related microRNA signatures in melanoma. H Gómez-Martínez, B Gomez-Cabañes, A Lopéz-Cerdan, E Hernando*, F Garcia-Garcia*. bioRxiv 2024 Jun 21. doi: https://doi.org/10.1101/2023.10.20.563284

2023

  1. Lipidomic Landscape of Circulating Extracellular Vesicles Isolated from Adolescents Exposed to Ethanol Intoxication: A Sex Difference Study. C Perpiñá-Clérigues; S Mellado; JF Català-Senent; F Ibáñez; P Costa; M Marcos; C Guerri; F García-García*; M Pascual*. Biology of Sex Differences, 2023 Apr 21;14(1):22. doi: 10.1186/s13293-023-00502-1.
  2. Deciphering the Sex Bias in Housekeeping Gene Expression in Adipose Tissue: a Comprehensive Meta-analysis of Transcriptomic Studies. M Guaita-Cespedes, R Grillo-Risco, MR Hidalgo, S Fernández-Veledo, DJ Burks, M de la Iglesia-Vaya, A Galan*, F Garcia-Garcia*. Biology of Sex Differences, 2023 Apr 18;14(1):20. doi: 10.1186/s13293-023-00506-x. 
  3. A Deep Transcriptome Meta-Analysis Reveals Sex Differences in Multiple Sclerosis. JF Català-Senent, Z Andreu, MR Hidalgo, I Soler-Sáez, FJ Roig Molina, N Yanguas-Casás, A Neva-Alejo, A López-Cerdán, , M de la Iglesia-Vayá, BE Stranger, F García-García*. Neurobiology of Disease, 2023 Apr 5; 181:106113, doi: https://doi.org/10.1016/j.nbd.2023.106113.
  4. SARS-CoV-2-encoded small RNAs are able to repress the host expression of SERINC5 to facilitate viral replication. E Esplugues, S Meseguer, MP Rubio, B Lainez, B Pérez-Benavente, R Pérez-Moraga, S Romera-Giner, F García García, O Martinez-Macias, A Cremades, FJ Iborra, F Almazán. Frontiers Microbiology, 2023 Feb. doi: 10.3389/fmicb.2023.1066493.
  5. A comprehensive transcriptional signature in pancreatic ductal adenocarcinoma reveals new insights into the immune and desmoplastic microenvironment. I Perez-Diez, Z Andreu, MR Hidalgo, C Perpiñá-Clerigues, L Fantin, A Fernandez-Serra, M Iglesia-Vaya, JA Lopez-Guerrero*, F Garcia-Garcia*. Cancers 2023, 15(11), 2887; doi: https://doi.org/10.3390/cancers15112887.
  6. Vascular differences between glioblastoma IDH-wildtype and astrocytoma IDH-mutant grade 4 at imaging and transcriptomic level. MM Alvarez-Torres, A Lopez-Cerdan, M de la Iglesia-Vaya, E Fuster-Garcia, F Garcia-Garcia, JM Garcia-Gomez. NMR in Biomedicine, 2023 Jul 21; doi: https://doi.org/10.1002/nbm.5004
  7. Rapid degeneration of iPSC-derived motor neurons lacking Gdap1 engages a mitochondrial-sustained innate immune response. J Torres; M Leon; J Prieto; MM Molina Navarro; F Garcia-Garcia; M Barneo-Muñoz; X Ponsoda; R Saez; F Palau; J Dopazo; JC Izpisua Belmonte. Cell Death Discovery, 2023 Jul 1;9(1):217. doi: 10.1038/s41420-023-01531-w.
  8. Chemotherapy induces cell plasticity; controlling plasticity increases therapeutic response. F Iborra, C Marti, V Calabuig-Navarro, P Papadopoulos, S Meseguer, P Iborra, F Garcia-García, A Martínez-Lorente, F Almazan, and J Calabuig. Signal Transduction and Targeted Therapy, 2023 Jul 3;8(1):256. doi: 10.1038/s41392-023-01500-w.
  9. Acclimation and Blood Sampling: Effects on Stress Markers in C57Bl/6J Mice. N Marin, A Moragon , D Gil, F Garcia-Garcia and V Bisbal. Animals 2023, 13(18), 2816, doi:  https://doi.org/10.3390/ani13182816
  10. Exploration of SUMO2/3 Expression Levels and Autophagy Process in Fragile X-Associated Tremor/Ataxia Syndrome: Addressing Study Limitations and Insights for Future Research. MI Alvarez-Mora, G Garrabou, L Molina-Porcel, R Grillo-Risco, F Garcia-Garcia, T Barcos, J Cantó-Santos, L Rodriguez-Revenga. Cells 2023, 12(19), 2364; doi:  https://doi.org/10.3390/cells12192364
  11. SAM-UNETR: Clinically Significant Prostate Cancer Segmentation using Transfer Learning from Large Model. JA Alzate-Grisales, A Mora-Rubio, F García-García, R Tabares-Soto, M de la Iglesia-Vayá. IEEE Access 2023 Oct; doi: 10.1109/ACCESS.2023.3326882.
  12. SAMBA: Structure-Learning of Aquaculture Microbiomes Using a Bayesian Approach. Soriano B, Hafez AI, Naya-Català F, Moroni F, Moldovan RA, Toxqui-Rodríguez S, Piazzon MC, Arnau V, Llorens C, Pérez-Sánchez J. Genes 2023 Aug 19;14(8):1650 doi: 10.3390/genes14081650


2022

  1. Overall survival and biomarker analysis of neoadjuvant nivolumab plus chemotherapy in operable stage IIIA non-small-cell lung cancer (NADIM phase II trial). M Provencio-Pulla, R Serna-Blasco, E Nadal, A Insa, MR García-Campelo, J Casal Rubio, M Dómine, M Majem, D Rodríguez-Abreu, A Martínez-Martí, J de Castro Carpeño, M Cobo, G López Vivanco, E del Barco, R Bernabé Caro, N Viñolas, I Barneto Aranda, S Viteri, E Pereira, A Royuela, V Calvo, J Martín-López, F García-García, M Casarrubios, F Franco, E Sánchez-Herrero, B Massuti, A Cruz-Bermúdez, A Romero. Journal of Clinical Oncology, 2022 May 16. https://ascopubs.org/doi/10.1200/JCO.21.02660
  2. Beyond the Brain: MIDS Extends BIDS to Multiple Modalities and Anatomical Regions. JM Saborit-Torres, S Nadal-Almela, JA Montell-Serrano, E Oliver-Garcia, H Carceller, JA Gómez-Ádrian, M Caparrós-Redondo, F García-García, J Domenech-Fernández, M de la Iglesia-Vayá. Stud Health Technol Inform. 2022 May 25;294:413-414. doi: 10.3233/SHTI220488.
  3. Ptpn1 deletion protects oval cells against lipoapoptosis by favoring lipid droplet formation and dynamics. I Barahona Sanz, P Rada, S Calero, R Grillo-Risco, L Pereira, MC Soler-Vazquez, L María LaIglesia, MJ Moreno-Aliaga, L Herrero, D Serra, C García–Monzón, A Gonzalez-Rodriguez, J Balsinde, F García-García, MP Valdecantos, A Valverde. Cell Death and Differentiation, 2022 Jun 9. https://doi.org/10.1038/s41418-022-01023-x
  4. NPC transplantation rescues SCI-driven cAMP/EPAC2 alterations, leading to neuroprotection and microglial modulation. B Martínez-Rojas, E Giraldo, R Grillo-Risco, MR Hidalgo, E López-Mocholi, A Alastrue-Agudo, F García-García, V Moreno-Manzano. Cellular and Molecular Life Sciences 2022 Jul 29;79(8):455. doi: 10.1007/s00018-022-04494-w.
  5. Bioenergetic and autophagic characterization of skin fibroblasts from C9orf72 patients. MI Alvarez-Mora, G Garrabaou, T Barcos, F Garcia-Garcia, R Grillo-Risco, E Peruga, L Gort, S Borrego-Écija, R Sanchez-Valle, J Canto-Santos, P Navarro-Navarro, L Rodriguez-Revenga. Antioxidants. 2022 Jun 8. https://doi.org/10.3390/antiox11061129
  6. Population-based sequencing of Mycobacterium tuberculosis reveals how current population dynamics are shaped by past epidemics. I Cancino-Muñoz, MG López, M Torres-Puente, LM Villamayor, R Borrás, M Borrás-Máñez, M Bosque, JJ Camarena, C Colijn, E Colomer-Roig, J Colomina, I Escribano, O Esparcia-Rodríguez, F García-García, A Gil-Brusola, C Gimeno, A Gimeno-Gascón, B Gomila-Sard, D González-Granda, N Gonzalo-Jiménez, M Remedio Guna-Serrano, JL López-Hontangas, C Martín-González, R Moreno-Muñoz, D Navarro, M Navarro, N Orta, E Pérez, J Prat, JC Rodríguez, M Montserrat Ruiz-García, H Vanaclocha, Valencia Region Tuberculosis Working Group, Iñaki Comas. eLife 2022 Jul 26;11:e76605. doi: 10.7554/eLife.76605.
  7. Minimal hepatic encephalopathy is associated to alterations in eye movements. F Casanova-Ferrer, CE García-Cena, JJ Gallego, A Fiorillo, A Urios, A Calvo-Córdoba, MP Ballester, MP Ríos, L Durbán, MR Hidalgo, F García-García, V Felipo & C Montoliu. Sci Rep . 2022 Oct 7;12(1):16837. doi: 10.1038/s41598-022-21230-3.
  8. Unveiling sex-based differences in Parkinson Disease: a comprehensive meta-analysis of transcriptomic studies. A López-Cerdán, Z Andreu, MR Hidalgo, R Grillo-Risco, JF Català-Senent, I Soler-Sáez, A Neva-Alejo, F Gordillo, M de la Iglesia Vaya, F Garcia-Garcia*. Biology of Sex Differences 2022 Nov 22;13(1):68. doi: 10.1186/s13293-022-00477-5.


2021

  1. Hepatic Steatosis and Steatohepatitis: A Functional Meta-analysis of Sex-based Differences in Transcriptomic Studies. José F. Català-Senent; Marta R. Hidalgo; Marina Berenguer; Gopanandan Parthasarathy; Harmeet Malhi; Pablo Malmierca-Merlo; María de la Iglesia-Vayá; Francisco Garcia-Garcia*. Biology of Sex Differences 2021, 12:29; https://doi.org/10.1186/s13293-021-00368-1.
  2. Functional Signatures in Non-Small-Cell Lung Cancer: A Systematic Review and Meta-Analysis of Sex-Based Differences in Transcriptomic Studies. I Pérez-Díez, MR Hidalgo, P Malmierca-Merlo, Z Andreu, S Romera-Giner, R Farràs, M de la Iglesia-Vayá, M Provencio, A Romero and F García-García*. Cancers 2021, 13(1), 143; https://doi.org/10.3390/cancers13010143.
  3. Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers. Sergio Romera-Giner, Zoraida Andreu Martínez, Francisco García-García, Marta R Hidalgo*. Biol Direct 2021 May 26; 16(1):9, doi: 10.1186/s13062-021-00293-8.
  4. CSVS, a crowdsourcing database of the Spanish population genetic variability. Peña-Chilet M, Roldán G, Perez-Florido J, Ortuño FM, Carmona R, Aquino V, Lopez-Lopez D, Loucera C, Fernandez-Rueda JL, Gallego A, García-Garcia F, González-Neira A, Pita G, Núñez-Torres R, Santoyo-López J, Ayuso C, Minguez P, Avila-Fernandez A, Corton M, Moreno-Pelayo MÁ, Morin M, Gallego-Martinez A, Lopez-Escamez JA, Borrego S, Antiñolo G, Amigo J, Salgado-Garrido J, Pasalodos-Sanchez S, Morte B, Carracedo Á, Alonso Á, Dopazo J. Nucleic Acids Res. 2020 Sep 29;. doi: 10.1093/nar/gkaa794. PubMed PMID: 32990755.
  5. Genomic Analysis of the First European Bacteriophages with Depolymerase Activity and Biocontrol Efficacy Against the Phytopathogen Ralstonia solanacearum. EG Biosca, JF Català-Senent, A Figàs-Segura, E Bertolini, MM López, B Álvarez. Viruses 2021 Dec 17;13(12):2539. doi: 10.3390/v13122539.
  6. De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (Solanum betaceum Cav.) with Different Fruit Color. Juan Pacheco, Santiago Vilanova, Rubén Grillo-Risco, Francisco García-García, Jaime Prohens, Pietro Gramazio. Horticulturae 2021, 7(11), 31.
  7. TLR4 deficiency affects the microbiome and reduces intestinal dysfunctions and inflammation in chronic alcohol- fed mice. Carlos M. Cuesta, María Pascual, Raúl Pérez-Moraga, Irene Rodríguez-Navarro, Francisco García-García, Juan R. Ureña-Peralta, Consuelo Guerri. Int J Mol Sci. 2021 Nov 27;22(23). doi: 10.3390/ijms222312830. PMID: 34884634.
  8. Developmental disruption of Erbb4 in Pet1+ neurons impairs serotonergic sub-system connectivity and memory formation. Candela Barettino, Alvaro Ballesteros-González, Andrés Aylón, Xavier Soler, Leticia Ortí, Selene Díaz, Isabel Reillo, Francisco García García, Francisco José Iborra, Cary Lai, Nathalie Dehorter, Xavier Leinekugel, Nuria Flames, Isabel Del Pino. Front. Cell Dev. Biol. 10 December 2021 | https://doi.org/10.3389/fcell.2021.770458.
  9. Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. Kinza Rian, Marta R. Hidalgo, Cankut Çubuk, Matias M. Falco, Carlos Loucera, Marina Esteban-Medina, Inmaculada Alamo-Alvarez, María Peña-Chilet, Joaquín Dopazo. Computational and Structural Biotechnology Journal 2021, 19: 2968-2978.
  10. Mechanistic modeling of the SARS-CoV-2 disease map. Rian K, Esteban-Medina M, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Gunyel D, Ostaszewski M, Peña-Chilet M, Dopazo J. BioData Min. 2021 Jan 21;14(1):5. doi: 10.1186/s13040-021-00234-1. PMID: 33478554; PMCID: PMC7817765.
  11. De-identifying Spanish medical texts – named entity recognition applied to radiology reports. I Pérez-Díez, R Pérez-Moraga, A López-Cerdán, JM Salinas-Serrano & M de la Iglesia-Vayá. Journal of Biomedical Semantics, volume 12, Article number: 6 (2021).
  12. Transcriptomic Analysis of a Diabetic Skin-Humanized Mouse Model Dissects Molecular Pathways Underlying the Delayed Wound Healing Response. C León, F García-García, S Llames, E García-Pérez, M Carretero, MC Arriba, J Dopazo, M del Río, MJ Escámez and L Martínez-Santamaría. Genes 2021, 12(1), 47; https://doi.org/10.3390/genes12010047.

2020

  1. Plasmatic Membrane Expression of Adhesion Molecules in Human Cardiac Progenitor/Stem Cells Might Explain Their Superior Cell Engraftment after Cell Transplantation. I Ontoria-Oviedo , I Palacios, J Panadero, B Sánchez, F García-García, A López-Cerdán, A Dorronsoro, D Castellano, L Rodríguez-Borlado, A Bernad, and P Sepúlveda. Stem Cells International. 2020 Oct 10, https://doi.org/10.1155/2020/8872009.
  2. Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies. Casanova Ferrer F, Pascual M, Hidalgo MR, Malmierca-Merlo P, Guerri C, García-García F*. Genes (Basel). 2020 Sep 21;11(9). doi: 10.3390/genes11091106. PubMed PMID: 32967293.
  3. Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.  Yang M, Petralia F, Li Z, Li H, Ma W, Song X, Kim S, Lee H, Yu H, Lee B, Bae S, Heo E, Kaczmarczyk J, Stępniak P, Warchoł M, Yu T, Calinawan AP, Boutros PC, Payne SH, Reva B, Boja E, Rodriguez H, Stolovitzky G, Guan Y, Kang J, Wang P, Fenyö D, Saez-Rodriguez J. Cell Syst. 2020 Aug 26;11(2):186-195.e9. doi: 10.1016/j.cels.2020.06.013. PubMed PMID: 32710834.
  4.  Lack of TLR4 modifies the miRNAs profile and attenuates inflammatory signaling pathways. Ureña-Peralta JR, Pérez-Moraga R, García-García F, Guerri C. PLoS One. 2020;15(8):e0237066. doi: 10.1371/journal.pone.0237066. PubMed PMID: 32780740; PubMed Central PMCID: PMC7418977.
  5. Exploring sunflower responses to Sclerotinia head rot at early stages of infection using RNA-seq analysis. Fass MI, Rivarola M, Ehrenbolger GF, Maringolo CA, Montecchia JF, Quiroz F, García-García F, Blázquez JD, Hopp HE, Heinz RA, Paniego NB, Lia VV. Sci Rep. 2020 Aug 7;10(1):13347. doi: 10.1038/s41598-020-70315-4. PubMed PMID: 32770047; PubMed Central PMCID: PMC7414910.
  6.  Sex is a strong prognostic factor in stage IV non-small-cell lung cancer patients and should be considered in survival rate estimation. Barquín M, Calvo V, García-García F, Nuñez B, Sánchez-Herrero E, Serna-Blasco R, Auglytė M, Carcereny E, Rodriguez-Abreu D, López Castro R, Guirado M, Camps C, Bosch-Barrera J, Massuti B, Ortega AL, Del Barco E, Gonzalez-Larriba JL, Aguiar D, García-Campelo R, Dómine M, Agraso S, Sala MA, Oramas J, Bernabé R, Blanco R, Parejo C, Cruz A, Menasalvas E, Royuela A, Romero A, Provencio M. Cancer Epidemiol. 2020 Aug;67:101737. doi: 10.1016/j.canep.2020.101737.  PubMed PMID: 32450544.
  7.  Uterine disorders affecting female fertility: what are the molecular functions altered in endometrium?. Devesa-Peiro A, Sebastian-Leon P, Garcia-Garcia F, Arnau V, Aleman A, Pellicer A, Diaz-Gimeno P. Fertil Steril. 2020 Jun;113(6):1261-1274. doi: 10.1016/j.fertnstert.2020.01.025. PubMed PMID: 32482256.
  8.  Rilpivirine attenuates liver fibrosis through selective STAT1-mediated apoptosis in hepatic stellate cells. Martí-Rodrigo A, Alegre F, Moragrega ÁB, García-García F, Martí-Rodrigo P, Fernández-Iglesias A, Gracia-Sancho J, Apostolova N, Esplugues JV, Blas-García A. Gut. 2020 May;69(5):920-932. doi: 10.1136/gutjnl-2019-318372. PubMed PMID: 31530714.
  9.  Optimised molecular genetic diagnostics of Fanconi anaemia by whole exome sequencing and functional studies. Bogliolo M, Pujol R, Aza-Carmona M, Muñoz-Subirana N, Rodriguez-Santiago B, Casado JA, Rio P, Bauser C, Reina-Castillón J, Lopez-Sanchez M, Gonzalez-Quereda L, Gallano P, Catalá A, Ruiz-Llobet A, Badell I, Diaz-Heredia C, Hladun R, Senent L, Argiles B, Bergua Burgues JM, Bañez F, Arrizabalaga B, López Almaraz R, Lopez M, Figuera Á, Molinés A, Pérez de Soto I, Hernando I, Muñoz JA, Del Rosario Marin M, Balmaña J, Stjepanovic N, Carrasco E, Cuesta I, Cosuelo JM, Regueiro A, Moraleda Jimenez J, Galera-Miñarro AM, Rosiñol L, Carrió A, Beléndez-Bieler C, Escudero Soto A, Cela E, de la Mata G, Fernández-Delgado R, Garcia-Pardos MC, Sáez-Villaverde R, Barragaño M, Portugal R, Lendinez F, Hernadez I, Vagace JM, Tapia M, Nieto J, Garcia M, Gonzalez M, Vicho C, Galvez E, Valiente A, Antelo ML, Ancliff P, Garcia F, Dopazo J, Sevilla J, Paprotka T, Pérez-Jurado LA, Bueren J, Surralles J. J Med Genet. 2020 Apr;57(4):258-268. doi: 10.1136/jmedgenet-2019-106249. PubMed PMID: 31586946.
  10.  Association of a single nucleotide polymorphism in the ubxn6 gene with long-term non-progression phenotype in HIV-positive individuals. Díez-Fuertes F, De La Torre-Tarazona HE, Calonge E, Pernas M, Bermejo M, García-Pérez J, Álvarez A, Capa L, García-García F, Saumoy M, Riera M, Boland-Auge A, López-Galíndez C, Lathrop M, Dopazo J, Sakuntabhai A, Alcamí J. Clin Microbiol Infect. 2020 Jan;26(1):107-114. doi: 10.1016/j.cmi.2019.05.015. PubMed PMID: 31158522.
  11. Transcriptomic Analysis Reveals a Differential Gene Expression Profile Between Two Sunflower Inbred Lines with Different Ability to Tolerate Water Stress. M Escalante, A Vigliocco, Sebastián Moschen, P Fernández, R Heinz, F Garcia-Garcia, J A Di Rienzo, A Andrade, S Alemano. Plant Mol Biol Rep 38, 222–237 (2020). https://doi.org/10.1007/s11105-020-01192-4.
  12. Mechanistic models of signaling pathways deconvolute the glioblastoma single-cell functional landscape. MM Falco, M Peña-Chilet, C Loucera, MR Hidalgo, J Dopazo. NAR Cancer, Volume 2, Issue 2, June 2020, zcaa011, https://doi.org/10.1093/narcan/zcaa011.

2019

  1.  Using mechanistic models for the clinical interpretation of complex genomic variation. Peña-Chilet M, Esteban-Medina M, Falco MM, Rian K, Hidalgo MR, Loucera C, Dopazo J. Sci Rep. 2019 Dec 12;9(1):18937. doi: 10.1038/s41598-019-55454-7. PubMed PMID: 31831811; PubMed Central PMCID: PMC6908734.
  2. Differences in gene expression profiling and biomarkers between histological colorectal carcinoma subsets from the serrated pathway. García-Solano J, Turpin-Sevilla MDC, García-García F, Carbonell-Muñoz R, Torres-Moreno D, Conesa A, Conesa-Zamora P. Histopathology. 2019 Oct;75(4):496-507. doi: 10.1111/his.13889. PubMed PMID: 31025430.
  3.  A comparison of mechanistic signaling pathway activity analysis methods. Amadoz A, Hidalgo MR, Çubuk C, Carbonell-Caballero J, Dopazo J. Brief Bioinform. 2019 Sep 27;20(5):1655-1668. doi: 10.1093/bib/bby040. Review. PubMed PMID: 29868818; PubMed Central PMCID: PMC6917216.
  4.  Fibroblast activation and abnormal extracellular matrix remodelling as common hallmarks in three cancer-prone genodermatoses. Chacón-Solano E, León C, Díaz F, García-García F, García M, Escámez MJ, Guerrero-Aspizua S, Conti CJ, Mencía Á, Martínez-Santamaría L, Llames S, Pévida M, Carbonell-Caballero J, Puig-Butillé JA, Maseda R, Puig S, de Lucas R, Baselga E, Larcher F, Dopazo J, Del Río M. Br J Dermatol. 2019 Sep;181(3):512-522. doi: 10.1111/bjd.17698. PubMed PMID: 30693469; PubMed Central PMCID: PMC6850467.
  5. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J. Nat Commun. 2019 Jun 17;10(1):2674. doi: 10.1038/s41467-019-09799-2. PubMed PMID: 31209238; PubMed Central PMCID: PMC6572829.
  6. Characterization of molecular mechanisms underlying the axonal Charcot-Marie-Tooth neuropathy caused by MORC2 mutations.  Sancho P, Bartesaghi L, Miossec O, García-García F, Ramírez-Jiménez L, Siddell A, Åkesson E, Hedlund E, Laššuthová P, Pascual-Pascual SI, Sevilla T, Kennerson M, Lupo V, Chrast R, Espinós C. Hum Mol Genet. 2019 May 15;28(10):1629-1644. doi: 10.1093/hmg/ddz006. PubMed PMID: 30624633.
  7.  Differential expression of circulating miRNAs as a novel tool to assess BAG3-associated familial dilated cardiomyopathy. Zaragoza C, Saura M, Hernández I, Ramirez-Carracedo R, García-García F, Zamorano JL, Mangas A, Toro R. Biosci Rep. 2019 Mar 29;39(3). doi: 10.1042/BSR20180934. Print 2019 Mar 29. PubMed PMID: 30792263; PubMed Central PMCID: PMC6418398.
  8. Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models. Çubuk C, Hidalgo MR, Amadoz A, Rian K, Salavert F, Pujana MA, Mateo F, Herranz C, Carbonell-Caballero J, Dopazo J. NPJ Syst Biol Appl. 2019;5:7. doi: 10.1038/s41540-019-0087-2. PubMed PMID: 30854222; PubMed Central PMCID: PMC6397295.

2018

  1.  Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape. Cubuk C, Hidalgo MR, Amadoz A, Pujana MA, Mateo F, Herranz C, Carbonell-Caballero J, Dopazo J. Cancer Res. 2018 Nov 1;78(21):6059-6072. doi: 10.1158/0008-5472.CAN-17-2705. PubMed PMID: 30135189.
  2. Deep sequencing and miRNA profiles in alcohol-induced neuroinflammation and the TLR4 response in mice cerebral cortex. Ureña-Peralta JR, Alfonso-Loeches S, Cuesta-Diaz CM, García-García F, Guerri C. Sci Rep. 2018 Oct 29;8(1):15913. doi: 10.1038/s41598-018-34277-y. PubMed PMID: 30374194; PubMed Central PMCID: PMC6206094.
  3.  Extracellular Vesicles Secreted by Hypoxic AC10 Cardiomyocytes Modulate Fibroblast Cell Motility. Ontoria-Oviedo I, Dorronsoro A, Sánchez R, Ciria M, Gómez-Ferrer M, Buigues M, Grueso E, Tejedor S, García-García F, González-King H, Garcia NA, Peiró-Molina E, Sepúlveda P. Front Cardiovasc Med. 2018;5:152. doi: 10.3389/fcvm.2018.00152. PubMed PMID: 30410918; PubMed Central PMCID: PMC6209632.
  4. A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection.  Fourati S, Talla A, Mahmoudian M, Burkhart JG, Klén R, Henao R, Yu T, Aydın Z, Yeung KY, Ahsen ME, Almugbel R, Jahandideh S, Liang X, Nordling TEM, Shiga M, Stanescu A, Vogel R, Pandey G, Chiu C, McClain MT, Woods CW, Ginsburg GS, Elo LL, Tsalik EL, Mangravite LM, Sieberts SK. Nat Commun. 2018 Oct 24;9(1):4418. doi: 10.1038/s41467-018-06735-8. PubMed PMID: 30356117; PubMed Central PMCID: PMC6200745.
  5.  Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome. Hidalgo MR, Amadoz A, Çubuk C, Carbonell-Caballero J, Dopazo J. Biol Direct. 2018 Aug 22;13(1):16. doi: 10.1186/s13062-018-0219-4. PubMed PMID: 30134948; PubMed Central PMCID: PMC6106876.
  6.  The effects of death and post-mortem cold ischemia on human tissue transcriptomes. Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR, Pervouchine D, Carbonell-Caballero J, Nurtdinov R, Breschi A, Amador R, Oliveira P, Çubuk C, Curado J, Aguet F, Oliveira C, Dopazo J, Sammeth M, Ardlie KG, Guigó R. Nat Commun. 2018 Feb 13;9(1):490. doi: 10.1038/s41467-017-02772-x. PubMed PMID: 29440659; PubMed Central PMCID: PMC5811508.
  7.  Prognostic value of quantitative ctDNA levels in non small cell lung cancer patients. Provencio M, Torrente M, Calvo V, Pérez-Callejo D, Gutiérrez L, Franco F, Pérez-Barrios C, Barquín M, Royuela A, García-García F, Bueno C, Garcia-Grande A, Camps C, Massuti B, Sotomayor E, Romero A. Oncotarget. 2018 Jan 2;9(1):488-494. doi: 10.18632/oncotarget.22470. PubMed PMID: 29416630; PubMed Central PMCID: PMC5787483.

 All contributions in PubMed