Genomics of Gene Expression

Current research projects

  • LongTREC (Horizon Europe, MSCA-DN-2021-101072892): The Long Reads European Transcriptomics Consortium. The next generation transcriptome biology revealed by single molecule sequencing technologies.
  • NSF. Identifying the determinants of high protein content in seeds of Phaseolus
  • MO4D. (MICIN, PID2020-119537RB-100).  Integration of multi-omics data to infer multi-layered disease models.
  • SQANTI4. (NIH, 1R21HG011280-01). Development of methods for transcript quantification and differential expression analysis using long-read sequencing technologies
  • Cell2Spine. (PROMETEO-CIPROM/2022/25). Spatial transcriptomics and cell communication models applied to tissue regeneration and treatment in spinal cord injury with precision nanomedicine.

Past research projects

  • Microbial Dark Matter. (NASA, 19-EXO19-0029, 2020-2022). Network modelling of stromatolite microbial communities to identify unknown species of successful adaptation.
  • Functional analysis at the isoform resolution (University of Florida Start-up package, 2014): Development of a computational methodology to investigate the functional impact of alternative splicing, using long-read technologies.
  • RFA-RM-17-001 (NIH-R03, 2017-2018): Galaxy platform for integrative metabolomics and transcriptomics analysis.
  • A Novel Antimicrobial Approach To Combat Huanglongbing D. (USDA-SCRI, USA, 2015-2018): Computational modelling of detoxification pathways in citrus using RNA-seq data to investigate the response to greening disease treatment.
  • Proyecto Intergrupo 2017 (Centro de Investigación Príncipe Felipe, 2017-2019): Identification and modelling of molecular and cellular events of the immune response associated to the appearance of Minimal Hepatic Encephalopathy in cirrhotic patients.
  • UFII Seed Funds 2017 (University of Florida Informatics Institute, 2017-2018):  Understanding the functional role of alternative splicing in crop traits.
  • ChroMe (H2020, European Comision, 2016-2019):  Training network to study the nexus between chromatin and metabolism for understanding the epigenetic adaptation in metabolic health and disease.
  • PROMETEO 2016 (Conselleria d’Educació, Investigació, Cultura i Esport, Generalitat Valenciana, 2016-2019): The Next Systems Biology: desarrollo de métodos estadísticos para la biología de sistemas multiómica.
  • NOVELSEQ (Spanish Ministry MINECO, 2016-2018): Novel methods for new challenges in the analysis of high-throughput sequencing data such as the application of long reads to the transcriptome study, the transcriptome assays of single cells and the integration of multi-omic data.
  • DEANN (Marie Curie IRSES, European Comision, 2014-2017): Developing a European American NGS analysis Network
  • Integrative Analysis of TEDDY data to improve T1D diagnosis (Helmsley Charitable Trust, USA, 2015-2017): Integrative analysis of  multiomics, nutritional, demographic and clinical data from a cohort of 1.000 T1D patients to find Type 1 Diabetes triggers.
  • STATegra (FP7 Health, European Comision, 2012-2015): User-driven development of statistical methods for experimental planning, data gathering, and integrative analysis of Next Generation Sequencing, proteomics and metabolomics data.
  • AYUDA COMPLEMENTARIA para proyecto STATegra (Conselleria d’Educació de la Generalitat Valenciana, 2015).
  • Annot-lincRNA (Spanish Ministry MINECO, 2013-2015): Development of Computational Approaches for the characterization and functional annotation of long-non-coding RNA.
  • GentxGent 2012-2013: Analysis of Discordant twins to study the relationship of gene expression and methylation associated to Systemic lupus erythematosus.
  • Ayuda Complementaria para PATHOGENOMICS – Metabolomics and Interactiomics of the relationship host-pathogen (Conselleria d’Educació, Cultura i Esport, Generalitat Valenciana, 2012).
  • Técnico de Apoyo para Redes Transcripcionales Controladoras de Virulencia en Hongos Filamentosos Patógenos (Conselleria d’Educació, Cultura i Esport, Generalitat Valenciana, 2012-2013).
  • PIB2010AR (Spanish MICINN, 2010): Genomics and transcriptomics of dexotification pathways in Drosophila.
  • Exploring novel genome-transcriptome relationships by Next Generation Sequencing approaches (Spanish MICINN, 2010): Development of computer platforms for  the study of genomic regulation with deep sequencing techniques.
  • TRANSPAT (ERA-NET, Spanish MICINN, 2009-2011): Development of transcriptional networks regulating virulence in filamentous fungi from RNA-seq data.
  • Pathomics (ERA-NET, Spanish MICINN, 2009-2011): Metabolomics and Interactiomics of the relationship host-pathogen.