Publications

For the entire publication list, please follow the link.

See publications in review or to be submitted (bioRxiv):

  • Carr VR, Witherden E, Lee S, Shoaie S, Mullany P, Proctor GB, et al. Abundance and diversity of resistomes differ between healthy human oral cavities and gut. bioRxiv. Cold Spring Harbor Laboratory; 2019; 644922. doi:10.1101/644922
  • Magnusson R, Rundquist O, Kim MJ, Hellberg S, Na CH, Benson M, et al. On the prediction of protein abundance from RNA. bioRxiv. Cold Spring Harbor Laboratory; 2019; 599373. doi:10.1101/599373
  • Gomez-Cabrero D, Tarazona S, Ferreirós-Vidal I, Ramirez RN, Company C, Schmidt A, et al. STATegra: a comprehensive multi-omics dataset of B-cell differentiation in mouse. bioRxiv. Cold Spring Harbor Laboratory; 2019; 587477. doi:10.1101/587477
  • Ruiz-Villalba A, Romero JP, Hernandez SC, Vilas-Zornoza A, Fortelny N, Castro L, et al. Single-cell RNA-seq analysis reveals the crucial role of Collagen Triplex Helix Repeat Containing 1 (CTHRC1) cardiac fibroblasts for ventricular remodeling after myocardial infarction. bioRxiv. Cold Spring Harbor Laboratory; 2019; 643130. doi:10.1101/643130
  • Sumida N, Sifakis E, Scholz BA, Woodbridge AF, Kiani N, Gomez-Cabrero D, et al. The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulating MYC in 3D: Implications for the fitness of cancer cells. bioRxiv. Cold Spring Harbor Laboratory; 2018; 286583. doi:10.1101/286583
  • Elias S, Schmidt A, Gomez-Cabrero D, Tegner J. Gene regulatory network of human GM-CSF secreting T helper cells. bioRxiv. Cold Spring Harbor Laboratory; 2019; 555433. doi:10.1101/555433

See below the selected publications:


2019

  • Kular L, Needhamsen M, Adzemovic MZ, Kramarova T, Gomez-Cabrero D, Ewing E, et al. Neuronal methylome reveals CREB-associated neuro-axonal impairment in multiple sclerosis. Clin Epigenetics. 2019;11: 86. doi:10.1186/s13148-019-0678-1
  • Gossec L, Kedra J, Servy H, Pandit A, Stones S, Berenbaum F, et al. EULAR points to consider for the use of big data in rheumatic and musculoskeletal diseases. Ann Rheum Dis. 2019;  doi:10.1136/annrheumdis-2019-215694
  • Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, et al. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nat Commun. 2019;10: 2674. doi:10.1038/s41467-019-09799-2
  • Butcher L, Carnicero JA, Gomez Cabrero D, Dartigues J-F, Pérès K, Garcia-Garcia FJ, et al. Increased levels of soluble Receptor for Advanced Glycation End-products (RAGE) are associated with a higher risk of mortality in frail older adults. Age Ageing. 2019; 1–7. doi:10.1093/ageing/afz073
  • Carlström KE, Ewing E, Granqvist M, Gyllenberg A, Aeinehband S, Enoksson SL, et al. Therapeutic efficacy of dimethyl fumarate in relapsing-remitting multiple sclerosis associates with ROS pathway in monocytes. Nat Commun. Springer US; 2019;10: 3081. doi:10.1038/s41467-019-11139-3
  • Ferreirós-Vidal I, Carroll T, Zhang T, Lagani V, Ramirez RN, Ing-Simmons E,… , Gomez-Cabrero D. Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation. PLOS Biol. 2019;17.
  • Ewing E, Kular L, Fernandes SJ, Karathanasis N, Lagani V, Ruhrmann S, …, Gomez-Cabrero D*, Jagodic M*. Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression. EBioMedicine. 2019.
  • Pilleron S, Weber D, Pérès K, Colpo M, Gomez-Cabrero D, Stuetz W, et al. Patterns of circulating fat-soluble vitamins and carotenoids and risk of frailty in four European cohorts of older adults. Eur J Nutr. Springer Berlin Heidelberg; 2019;58: 379–389.
  • Joshi et al. Phosphatase inhibitor PPP1R11 modulates resistance of human T cells toward Treg‐mediated suppression of cytokine expression. J Leukoc Biol. 2019.
  • Karlsson L, Barbaro M, Ewing E, Gomez-Cabrero D*, Lajic S*; Epigenetic Alterations Associated With Early Prenatal Dexamethasone Treatment, Journal of the Endocrine Society, 2019; 3:1 pp. 250–263, link

2018

  • 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

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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