Research

TransBio is involved in several research lines including single-cell analysis, patient stratification, Translational Applications of Whole Genome Sequencing or Oral Microbiome characterization among others. Some highlights are:

STATegRa: a Data Integration Framework.

 STATegRa is a Bioconductor package with classes and tools for multi-omics data integration. The new biomedical research environment, where many data types (multi-omics) are being generated in a daily basis, opens a new world around data integration. If we are able to combine different data or regulatory layers, we’ll gain information and move to a holistic world view. However, new tools to deal with these large and heterogeneous data sets in an integrative manner are needed. STATegRa package wants to provide not only the tools but a consolidated framework for data integration.

 

NAGEN 1000: Whole Genome Sequencing for Rare Diseases in Navarra.

The Navarre 1000 Genomes Project (NaGen1000) was launched in 2016 as an initiative promoted by the biomedical research center Navarrabiomed to set the stage for future implementation of sequencing as a routine resource for the development of genomic medicine in SNS-Osasunbidea.

This project, pioneering in the scope of the Spanish National Health System, is based on whole genome sequencing and focused on personalized medicine. It aims to sequence the whole genomes of over a thousand patients with rare diseases or certain types of cancer, and their families, to understand the genetic components of the disease in order to provide better diagnosis and, ultimately, better treatments.

At the Translational Bioinformatics Unit, we provide bioinformatics and computational support to the NAGEN project. We are developing and implementing bioinformatics analysis pipelines (from sequence to annotated variants), data analysis and visualization tools, and clinical data management databases for storing all the information related to the participants, their samples and results obtained.

In addition, we keep constant communication and learning from experiences from other genome analysis centers in Spain such as FPS (Sevilla, Joaquin Dopazo) and CNAG (Barcelona, Sergi Beltran). During 2018 PharmaNAGEN, a project extending the genomic applications to pharmacogenetics started and we are involved in the bioinformatics pipeline and software deployment.

Characterizing Oral Microbiome

In TransBio we are collaborating with the Center for Host Microbiome Interaction to identify and characterize the human Oral Microbiome. We are working in the generation and characterization of the oral microbiome gene catalog and its applications in health and disease. We are part of a collaobration including King´s College London and MetaGenoPolis.

Systems Biology

The rise and growth of Systems Biology following the sequencing of the human genome has been astounding. Early on, an iterative wet-dry methodology was formulated which turned out to be a successful approach in deciphering biological Complexity. Such type of analysis effectively iden- tified and associated molecular network signatures operative in biological processes across different systems. Yet, it has proven difficult to distinguish between causes and conse- quences, thus making it challenging to attack medical questions where we require precise causative drug targets and disease mechanisms beyond a web of associated markers.

While we find that the underlying challenge of finding the governing mechanistic system equations enabling precision medicine remains open thus rendering clinical translation of Systems Biology arduous, stunning advances in raw computational power, generation of high-precision multi-faceted biological data, combined with powerful algorithms hold promise to set the stage for data-driven identification of equations implicating a fundamental understanding of living systems during health and disease.

Text adapted from Gomez-Cabrero, Tegner, 2017, Current Opinion in Systems Biology.

Single-cell analysis