Strategic Research

Computational RNA Biology group of GRIB

Our group focuses on the development of computational methods to study and characterize DNA sequence variants that affect pre-mRNA splicing for the identification of novel risk factors and targets of therapy in cancer and other diseases. We have expertise in the development of software tools for RNA analysis (alternative splicing, regulatory motifs, RNA structure, RNA processing, RNA:RNA interactions), as well as in large-scale analysis of genomic and transcriptomic data to extract novel regulatory mechanisms linked to physiological processes and disease.

The Computational RNA Biology group of GRIB led by Eduardo Eyras is integrated in the Research Programme on Biomedical Informatics, GRIB. The GRIB is a joint research programme of the Hospital del Mar Medical Research Institute (IMIM) and the Department of Experimental and Health Sciences of the Universitat Pompeu Fabra. The GRIB mission is to develop and apply computational methods and information technologies for a better understanding and prediction of biological phenomena, giving especial emphasis to those related to the human diseases, their prevention, diagnosis and pharmacological treatment.   

Main projects

  • 1.

    SUPPA: Fast and accurate computation of differential splicing across multiple conditions

    This is a tool to study splicing across multiple conditions at high speed and accuracy. The tool has four modular operations that are run separately to generate events from an annotation, quantify event inclusion levels (PSIs) from multiple samples and calculate differential splicing across multiple conditions with replicates.

    https://bitbucket.org/regulatorygenomicsupf/suppa

  • 2.

    Characterization and detection of clinically relevant RNA-processing alterations in cancer

    Project funded by the Spanish Government (MINECO)

    http://genome.cshlp.org/content/early/2016/05/10/gr.199935.115

  • 3.

    Predictive models of RNA regulation – applications to splicing and cancer

    Project funded by the Spanish Government (MINECO)

    https://bitbucket.org/regulatorygenomicsupf/iso-ktsp

Website

Institutions

Bioinformatics expertise:

Group Leader:

Eduardo Eyras

PI

Contact:

Chus Donlo

Bioinformatics services offered

  • Biomarkers of disease

    The search of biomarkers of disease, disease subtypes, stratification, etc. based on RNA isoforms

  • pre-mRNA splicing

    Large-scale analysis of pre-mRNA splicing and regulatory mechanisms under multiple conditions

  • RNA:RNA interactions

    The detection and characterization of RNA:RNA interactions of lncRNAs on pre-mRNA/mRNA targets

  • RNA structures

    Study of RNA structures and processing of lncRNAs into small RNAs

  • More info available here:

    https://github.com/comprna/SUPPA