Core Facilities

jean-francois-taly
Bioinformatics Unit

Unit Structure

ACTING HEAD OF THE UNIT:
Jean-François Taly
DATA ANALYST:
Luca Cozzuto
SCIENTIFIC PROGRAMMER:
Antonio Hermoso

Summary

The Bioinformatics core facility aims to provide expertise and infrastructure on different aspects of the Bioinformatics field to all researchers at the Centre for Genomic Regulation (CRG), PRBB, and other external entities. More specifically, the unit is operated as a full service facility focused on providing services of consultation, data analysis and management, software development, and access to computing resources. Furthermore, the unit is involved in different dissemination activities such as courses, workshops and symposiums designed to train researchers on the use of the different bioinformatics tools available for conducting their research projects. More information in our wiki: http://biocore.crg.cat.


Services

Basic services:

  • Consultation on bioinformatics methods and resources
  • Assistance with the computational aspects of research by providing support and consultation in relation to data management, statistical data analysis, and interpretation of experimental data, focusing primarily on high-throughput genomics technologies.
  • Software evaluation, implementation, and training
  • Support on the evaluation and implementation of new bioinformatics software (gathering of users requirements, scheduling, implementation, validation, documentation, training, and end-users support).
  • Customization of bioinformatics resources
  • Local implementation of genome-related software (e.g. genomics browsers like Ensembl, UCSC, and GBrowse) and most common bioinformatics tools (Galaxy, EMBOSS, among others).
  • High-throughput data analysis of genomics, transcriptomics, and proteomics datasets; the unit is specialized in genome resequencing, ChIP-Seq transcription factor analysis, RNA-Seq differential expression analysis and de novo assembly.
  • Downstream analysis for the interpretation of gene lists, including gene set enrichment and over-representation of biological functions using Gene Ontology terms;
  • Identification of functional genomics elements, such as genes and regulatory sequences, through comparative genomics approaches;
  • Construction of ad-hoc databases and web interfaces to allow systematically storage, management, analysis, and search of biologically relevant information;
  • Development of bioinformatics scripts and more advanced pipelines to automate sequence analyses and genome annotation tasks

Advanced services:

  • High-throughput data analysis of genomics, transcriptomics, and proteomics datasets; the unit is specialized in genome resequencing, ChIP-Seq transcription factor analysis, RNA-Seq differential expression analysis and de novo assembly.
  • Downstream analysis for the interpretation of gene lists, including gene set enrichment and over-representation of biological functions using Gene Ontology terms;
  • Identification of functional genomics elements, such as genes and regulatory sequences, through comparative genomics approaches;
  • Construction of ad-hoc databases and web interfaces to allow systematically storage, management, analysis, and search of biologically relevant information;
  • Development of bioinformatics scripts and more advanced pipelines to automate sequence analyses and genome annotation tasks
  • The unit will be also focused on the education of biologists in the analysis and interpretation of their experimental data through the provision of custom advice and training in bioinformatics as well as in the acquisition of basic programming skills.

Selected Publications

  1. Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J.
    “Comparative transcriptomics of early dipteran development.”
    BMC Genomics, 14:123 (2013).
  2. Simboeck E, Gutierrez A, Cozzuto L, Beringer M, Caizzi L, Keyes WM, Di Croce L.
    “DPY30 regulates pathways in cellular senescence through ID protein expression.”
    EMBO J, 32(16):2217-30 (2013).
  3. Chang JM, Taly JF, Erb I, Sung TY, Hsu WL, Tang CY, Notredame C, Su EC.
    “Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations.”
    PLoS One, 8(10):e75542 (2013).
  4. Sanseverino W, Hermoso A, D’Alessandro R, Vlasova A, Andolfo G, Frusciante L, Lowy E, Roma G, Ercolano MR.
    “RGdb 2.0: Towards a community-based database model for the analysis of R-genes in plants.”
    Nucleic Acids Res, 41(Database issue):D1167-71 (2013).
  5. Morey L, Aloia L, Cozzuto L, Benitah SA, Di Croce L.
    “RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells.”
    Cell Rep, 3(1):60-9 (2013).