Bioinformatics Unit

The Bioinformatics Unit provided researchers at CRG/PRBB and external organizations with services of consultation, planning and budgeting NGS experiments, data analysis and management, software and database development, and training. The Unit works in close synergy with the other CRG core facilities, with the focus on delivering reproducible results using the state-of-the-art bioinformatics software.

In 2017, the Unit provided services to researchers from 52 labs from CRG, 17 other public institutions and a European start-up company, thus being well recognizable outside the CRG. The Unit hosted the Spanish Women in Africa Foundation awardee Dr. Elizabeth Kizito from Uganda Christian University.

The Unit organized and delivered to more than 100 attendees 66 hours of bioinformatics training, including the internal CRG courses, CRG NextFlow course and Bioinformatics Bootcamp by the Bioinformatics Barcelona (BIB). Two PhD students from the University Cape Town, South Africa, awardees of the Novartis-Africa-CRG program, obtained training in the Unit for 6 months each.

The Unit members were active in the CRG outreach activities, including the Barcelona Science Fair, International Day of Women and Girls in Science, Core Facilities Management Workshop, Open Science Week, and Wikipedia editathon by the Catalan Society of Biology.

The Unit offers the following services:

• Genomics: Genome assembly, functional annotation and comparative analysis; variant calling from WGS and WES data; analysis of ChIP-seq and ATAC-seq.
• Transcriptomics: Analysis of data from RNA-seq, RIP-seq, HT-qPCR, and other high-throughput experiments, including commercial and custom microarrays; analysis of B- and T-cell repertoires sequencing.
• Metagenomics: Analysis of amplicon, whole genome and transcriptome shotgun sequencing data.
• Proteomics and Structural bioinformatics: Protein functional annotation and prediction; analysis of SNPs’ effects on protein structure and function; protein structure comparison and 3D homology modelling; immune epitope prediction.
• Development of databases, websites, web tools, LIMS, custom pipelines, including containerization of the NextFlow pipelines.
• Submission data to public repositories, mining public databases, and statistical analysis.
• Manuscript preparation and support of grant submissions.

• “Saca La Lengua”: analysis of saliva microbiomes of Spanish school children.
• VastDB – a database of alternative splicing (with Manuel Irimia, CRG).
• CRISPETa – a web tool for designing paired sgRNA (with Roderic Guigo and Rory Johnson, CRG).
• Wnt/β-catenin signalling pathway safeguards epigenetic stability and homeostasis of mouse embryonic stem cells (with Pia Cosma, CRG).
• Detection of sensory genes in Drosophila strains (with Matthieu Louis, CRG).
• Pergola – a web tool for interactive visualization of multi-scale genomics and behavioural data (with Cedric Notredame & Mara Dierssen, CRG).
• Analysis of structural variants from WGS data of a family trio affected with a rare disease (with Susana Balcells and Daniel Grinberg, University of Barcelona).
• Assembly and annotation of three fly species Clogmia albipunctata, Megaselia abdita, and Episyrphus balteatus (with Karl Wotton, Exeter University, UK).
• Development of a robust set of genomic tools for more efficient breeding in Solanum aethiopicum (with Elizabeth Kizito, Uganda Christian University).
• Microbiome profiles of HIV/HPV infected couples (with Harris Onywera and Tracy Meiring, University of Cape Town, South Africa).
• Intron retaining in pombe (with Jose Ayete, UPF).
• ATAC-seq profiling of NFAT5 ko and wild type macrophages derived from bone marrow (with Christina Lopez-Rodriguez, UPF).
• Parp2 ko expression profiling in β-cells over-expressing cMyc (with Jose Yelamos, IMIM).
• Differentiation of human cardiomyocytes (with Nuria Montserrat, IBEC).
• Genetic analysis of replicating pancreatic β-cells in old islets (with Noelia Tellez, University of Barcelona).
• WES and variant identification in treatment-resistant juvenile-onset ophthalmoplegic complicated Myasthenia Gravis patients (with Melissa Nel and Jeanine Heckmann, U. Cape Town, South Africa).
• In vivo transcriptional profiling of Mycobacterium tuberculosis from highly infectious TB patients (with Jason Limberes, U. Cape Town, South Africa).