Research groups

Translational Bioinformatics group (TransBio)

Our research activities comprise two main blocks: (i) own methodological research, and (ii) collaborative projects. Our methodological work revolves around the identification and prediction of pathological sequence variants from NGS or directed sequencing projects, in the clinical setting. We develop our own bioinformatics tools and test them in collaboration with biomedical research teams at the Vall d'Hebron Institute (VHIR). Regarding our collaborative projects, they involve the processing of large amounts of heterogeneous information (NGS, epigenomic, structural, etc) to answer biomedical problems, whether in the discovery or in the clinical applications fields.

The expertise of our group comprises a broad series of bioinformatics, covering from sequence (multiple sequence alignments, conservation patterns) and structure analyses (characterization of functional sites, interaction sites, etc) to NGS-related techniques (gene panel and exome processing, including quality control, variant annotation, etc). Technically, we are fluid in scripting (Perl, Python, R) and in machine learning usage.

Main projects

  • 1.

    Development of computational tools for the prediction of pathological mutations in proteins

    Since a few years ago, we have been working in the development of computational tools for the prediction of pathological mutations in proteins (PMID: 11812146, 15390262, 15879453, 16208716, 17059831). In this work we have followed a two-step approach. First, we have characterized pathological mutations in terms of sequence, structure and evolutionary properties (PMID: 11812146). Second, we have used the results of this descriptive work to identify those parameters with the best predictive power. Also we have used these results to train a neural network and obtain an empirical model that allows the identification of disease-causing mutations with moderately high accuracies (around 70%; PMID: 15390262, 15879453, 16208716).

    http://www.vhir.org/portal1/grup-lines.asp?s=recerca&contentid=9196&idrefer=9067

Website

Institutions

Bioinformatics expertise:

Group Leader:

Xavier de la Cruz

Bioinformatics services offered

  • Analysis and interpretation of gene panel and exome experiments using both standard protocols and novel, in-house, tools for variant scoring