Bioinformatics Unit

The Bioinformatics Unit facilitates the world-class biomedical basic and translational research by providing CRG and external researchers with services of data analyses, with a focus on NGS and HT arrays; supporting CRG data management resources; and acting as a bioinformatics knowledge hub by providing training and disseminating good practices.

In 2018, the Unit provided services to researchers from 53 labs from CRG and 18 external institutions on 96 projects and provided summer internship to two undergraduate students from Institute Provençana, Hospitalet de Llobregat.

The Unit organized and delivered to 120 attendees 52 hours of bioinformatics training, including the internal CRG courses in R and best practices in bioinformatics and external courses on NextFlow, Docker and Singularity. Three bioinformaticians from CRG groups received in-person training in the Unit.

The Unit members were active in the CRG outreach activities, including the B-Debate on Open Science, the International Day of Women and Girls in Science 2018 Wikipedia editathon, “Saca La Lengua” project and the debate with secondary school teachers on scientific and ethical challenges of biotechnologies.

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 16S and ITS amplicons, whole genome and transcriptome shotgun sequencing data.
• Support CRG Core facilities, groups and CRG-level projects with development and maintenance of data resources (databases, websites, web-tools, LIMS) and reproducible data analysis pipelines.

• “Saca La Lengua”: analysis of saliva microbiomes of Spanish school children.
• Effects of environmental enrichment on postnatal mouse cortex regulome (with Stephan Ossowski, CRG, and Roger Pique-Regi, Wayne State University, Detroit).
• Detection of sensory genes in Drosophila strains (with Matthieu Louis, CRG).
• Pergola – a web tool for interactive visualization of multi-scale genomics and behavioral data (with Cedric Notredame and Mara Dierssen, CRG).
• 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).
• 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).
• Alternative splicing and gene expression in pediatric patients with Myelodysplastic syndromes (with Lorena Zubovic, University of Trento, Italy).
• Depletion of Ring1B in Ewing sarcoma (with Sara Sanchez, Sant Joan de Deu Foundation).
• Biomarker discovery in the freely circulating exosomes implicated in colon, lung and endometrial cancers (with Eva Colas, VHIR).
• Biomarker discovery and pathway analysis of genes involved in different stages of endometriosis (with Xavier Santamaria, VHIR).

Willis JR, González-Torres P, Pittis AA, Bejarano LA, Cozzuto L, Andreu-Somavilla N, Alloza-Trabado M, Valentín A, Ksiezopolska E, Company C, Onywera H, Montfort M, Hermoso A, Iraola-Guzmán S, Saus E, Labeeuw A, Carolis C, Hecht J, Ponomarenko J, Gabaldón T.
“Citizen science charts two major “stomatotypes” in the oral microbiome of adolescents and reveals links with habits and drinking water composition.”
Microbiome, 6(1):218, 2018. doi: 10.1186/s40168-018-0592-3.

Espinosa-Carrasco J, Erb I, Hermoso Pulido T, Ponomarenko J, Dierssen M, Notredame C.
“Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools.”
iScience, 9:244-257, 2018. doi: 10.1016/j.isci.2018.10.023.