Publications

For the entire publication list, please follow the link.

See below the selected publications:


2018

  • Leif Karlsson, Michela Barbaro, Ewoud Ewing, David Gomez-Cabrero*, Svetlana Lajic*; Epigenetic Alterations Associated With Early Prenatal Dexamethasone Treatment, Journal of the Endocrine Society, 2019; 3:1 pp. 250–263, link
  • Kular et al, DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in Multiple Sclerosis. Nat. Communications, 2018; 9 article number 2397.
  • Tényi Á, Vela E, Cano I, Cleries M, Monterde D, Gomez-Cabrero D*, Roca J*, Risk and temporal order of disease diagnosis of comorbidities in patients with COPD: a population health perspective BMJ Open Respiratory Research 2018;5:e000302. doi: 10.1136/bmjresp-2018-000302
  • Schmidt, A. et al. Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg ) differentiation reveals novel regulators of FOXP3. BMC Biology. 2018; 16:47 pp.1–35.
  • James T, Linde M, Morikawa H, Fernandes SJ, Ruhrmann S, Huss M, …, Gomez-Cabrero D*, Kockum I*. Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients. Hum Mol Genet. 2018;0: 1–17. doi:10.1093/hmg/ddy001
  • Tényi Á, Cano I, Marabita F, Kiani N, Kalko SG, Barreiro E, …, Gomez-Cabrero D*, Roca J*. Network modules uncover mechanisms of skeletal muscle dysfunction in COPD patients. J Transl Med. BioMed Central; 2018;16: 34. doi:10.1186/s12967-018-1405-y
  • Pilleron, S. et al., Patterns of circulating fat-soluble vitamins and carotenoids and risk of frailty in four European cohorts of older adults. 2018. European Journal of Nutrition.

2017

  • Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, et al. Software for the Integration of Multiomics Experiments in Bioconductor. Cancer Res. 2017;77: e39–e42. doi:10.1158/0008-5472.CAN-17-0344
  • Needhamsen M, Ewing E, Lund H, Gomez-Cabrero D, Harris RARA, Kular L, et al. Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies. BMC Bioinformatics.  2017;18: 486. doi:10.1186/s12859-017-1870-y
  • Sabrina Ruhrmann, Ewoud Ewing, Eliane Piket, Lara Kular, Julio Cesar Cetrulo Lorenzi, Sunjay Jude Fernandes, et al. Hypermethylation of MIR21 in CD4+ T cells from patients with relapsing-remitting multiple sclerosis associates with lower miRNA-21 levels and concomitant up-regulation of its target genes. Mult Scler J. 2017;8: 1+13. doi:10.1177/135245
  • Gomez-Cabrero D, Tegnér J. Iterative Systems Biology for Medicine – Time for advancing from network signatures to mechanistic equations. Curr Opin Syst Biol. 2017;3: 111–118. doi:10.1016/j.coisb.2017.05.001

2016

  • Gomez-Cabrero D, Menche J, Vargas C, Cano I, Maier D, Barabási A-LA-L, et al. From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration. BMC Bioinformatics. 2016;17: 441. doi:10.1186/s12859-016-1291-3
  • Lagani V, Karozou AD, Gomez-Cabrero D, Silberberg G, Tsamardinos I. A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions. BMC Bioinformatics. 2016;17: 194. doi:10.1186/s12859-016-1038-1
  • Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, et al. Public data and open source tools for multi-assay genomic investigation of disease. Brief Bioinform. 2016;17: 603–615. doi:10.1093/bib/bbv080
  • Gomez-Cabrero D, Almgren M, Sjöholm LKLK, Hensvold AHAH, Ringh MVM V., Tryggvadottir R, et al. High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis. Genome Med. Genome Medicine; 2016;8: 124. doi:10.1186/s13073-016-0374-0
  • Kannan V, Swartz F, Kiani NANA, Silberberg G, Tsipras G, Gomez-Cabrero D, et al. Conditional Disease Development extracted from Longitudinal Health Care Cohort Data using Layered Network Construction. Scientific Reports. 2016;6: 1–14. doi:10.1038/srep26170
  • Tényi Á, de Atauri P, Gomez-Cabrero D, Cano I, Clarke K, Falciani F, et al. ChainRank, a chain prioritisation method for contextualisation of biological networks. BMC Bioinformatics. 2016;17: 17. doi:10.1186/s12859-015-0864-x

2015

  • Rodríguez-Cortez VCVC, del Pino-Molina L, Rodríguez-Ubreva J, Ciudad L, Gómez-Cabrero D, Company C, et al. Monozygotic twins discordant for common variable immunodeficiency reveal impaired DNA demethylation during naïve-to-memory B-cell transition. Nature Communications. 2015;6: 7335. doi:10.1038/ncomms8335
  • Danielsson F, James T, Gomez-Cabrero D, Huss M. Assessing the consistency of public human tissue RNA-seq data sets. Briefings in Bioinformatics. 2015;16: 941–949. doi:10.1093/bib/bbv017
  • Lippi G, Jansen-Duerr P, Viña J, Durrance-Bagale A, Abugessaisa I, Gomez-Cabrero D, et al. Laboratory biomarkers and frailty: Presentation of the FRAILOMIC initiative. Clin Chem Lab Med. 2015;53: e253–e255. doi:10.1515/cclm-2015-0147

 


2014

  • Cano-Colino M, Almeida R, Gomez-Cabrero D, Artigas F, Compte A. Serotonin regulates performance nonmonotonically in a spatial working memory network. Cereb Cortex. 2014;24: 2449–2463. doi:10.1093/cercor/bht096
  • Lindholm ME, Marabita F, Gomez-Cabrero D, Rundqvist H, Ekstrom TJ, Tegner J, et al. An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training. Epigenetics. 2014;9: 1557–1569. doi:10.4161/15592294.2014.982445
  • Miralles F, Gomez-Cabrero D, Lluch-Ariet M, Tegnér J, Cascante M, Roca J, et al. Predictive medicine: outcomes, challenges and opportunities in the Synergy-COPD project. J Transl Med. BioMed Central Ltd; 2014;12 Suppl 2: S12. doi:10.1186/1479-5876-12-S2-S12
  • Gomez-Cabrero D, Menche J, Cano I, Abugessaisa I, Huertas-Migueláñez M, Tenyi A, et al. Systems Medicine: from molecular features and models to the clinic in COPD. J Transl Med. BioMed Central Ltd; 2014;12 Suppl 2: S4. doi:10.1186/1479-5876-12-S2-S4
  • Gomez-Cabrero D, Lluch-Ariet M, Tegnér J, Cascante M, Miralles F, Roca J. Synergy-COPD: a systems approach for understanding and managing chronic diseases. J Transl Med. BioMed Central Ltd; 2014;12 Suppl 2: S2. doi:10.1186/1479-5876-12-S2-S2
  • Snir O*, Gomez-Cabrero D*, Montes A, Perez-Pampin E, Gómez-Reino JJ, Seddighzadeh M, et al. Non-HLA genes PTPN22, CDK6 and PADI4 are associated with specific autoantibodies in HLA-defined subgroups of rheumatoid arthritis. Arthritis Res Ther. 2014;16: 414. doi:10.1186/s13075-014-0414-3
  • Gomez-Cabrero D, Abugessaisa I, Maier D, Teschendorff A, Merkenschlager M, Gisel A, et al. Data integration in the era of omics: current and future challenges. BMC Syst Biol. BioMed Central Ltd; 2014;8 Suppl 2: I1. doi:10.1186/1752-0509-8-S2-I1

 


2013 and before (selected manuscripts)

  • Rodríguez-Ubreva, J. et al., 2011. Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes. Nucleic Acids Research, (10), pp.1–15.
  • Gomez-Cabrero, D., Compte, A. & Tegner, J., 2011. Workflow for generating competing hypothesis from models with parameter uncertainty. Interface Focus, 1(3), pp.438–449.
  • Taccioli, C. et al., 2011. ParkDB: a Parkinson’s disease gene expression database. Database : the journal of biological databases and curation, 2011, p.bar007.

Operations Research. Before 2010 (selected manuscripts).

  • Valls, V., Gomez-Cabrero, D., Perez, A., Quintanilla, S., 2007. Project Scheduling Optimization in Service Centre Management. Tijdschrift voor Economie en Management, LII(3), pp.341–366.
  • Gomez-Cabrero, D., Ranasinghe, D.N., , 2006, Fine-tuning the Ant Colony System algorithm through Particle Swarm Optimization. 2006 paper. Presented in conference. Technical report in “Universitat de Valencia”. Link at: https://arxiv.org/abs/1803.08353