Focus on the group's mission

The Vital-IT team provides bioinformatics collaborative support to life science projects in Switzerland and abroad through collaborations with academic and industry partners. Thanks to its diverse expertise in computational biology, data management and software engineering, the team is able to find custom-made solutions to answer complex biological questions including biomedical & omics data. The value it delivers to its partners is a deep commitment to advancing science effectively and independently.

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Data stewardship and management

We organize, clean & control the quality of your datasets for subsequent analysis. In addition, we can process, transform and align your datasets to existing standards and make them available as a database. We can propose different data storage solutions depending on project needs (e.g. federated versus integrated). We are specialized in handling different types of omics data (RNA-Seq, metabolomics, lipidomics, gene expression, proteomics, transcriptomics, microbiomics) as well as sensitive clinical data, for which we provide solutions through latest-generation encrypted systems (e.g. setting up federated database solutions for remote analysis).

In practice:

  • Set up of a federated database for biomarker discovery in type 2 diabetes (T2D) as part of the IMI RHAPSODY consortium. In this database, 10 observational clinical cohorts with a combined total of 50K patients were standardized, harmonized and made available for statistical analysis. We developed data mining and statistical tools in an analysis package for researchers to use within the consortium. Read more and watch the video
  • Set up of a database composed of ~100 clinical trials as part of the IMI Hypo-RESOLVE consortium. The work has involved setting up ETL (extract, transform, load) pipeline for feeding trial data into a secure Oracle database and the creation of a virtual analysis environment accessible via remote desktop and secured by 2 factor authentication.
  • Read more about SIB's role as Data Coordination Centre in pan-European projects

Biostatistics and bioinformatics analysis

We propose analysis pipelines adapted to each research context, including multi-omics models and results interpretation.

In practice:

  • Development of a method for interpreting gene expression data with metabolic models which has helped to identify key genes in obesity-related inflammation in adipose tissue (read the paper)
  • Integrative analysis of mouse and human lipidomics data which led to the discovery of novel lipid biomarker candidates for T2D (read the paper)
  • Transcript assembly and functional characterization of heart-specific lncRNAs in collaboration with the University of Lausanne Medical School (read the paper)
  • Transcriptomics data analysis from muscle biopsies in a human clinical trial investigating the effect of Urolithin A on muscle function (read the paper)

Software engineering & tailoring

We develop tailored web applications and software tools to present, analyze, visualize and interpret data and results. We use various standards as appropriate to ensure interoperability and reusability (e.g. W3C standards such as RDF).

In practice:

  • Development, in collaboration with EMBO, of SourceData - a web-based platform for curating and annotating figures in scientific publications (read the paper).
  • Development, in collaboration with the SIB Clinical Bioinformatics Group and the Geneva University Hospitals (HUG), of Oncobench ® - a software platform to help cancer diagnosis (read the news)

Our approach

We strive to establish partnerships: even for one-off collaborations, we seek to deeply understand the data and the objectives of the project we work on. Our partners appreciate our reliability, commitment and team spirit.

Our track record spans biomedical research projects of different sizes - from punctual help to long-term European projects.

We are recognized for our flexibility and independence, allowing us to tailor efficient solutions and propose advisory services to each situation. For example, the collaboration can be customized to include our partner's own ontologies, provide support to validate internal approaches or integrate large and complex amounts of data of various types and origins.

We train both beginners and experts in bioinformatics methods, languages and best practices.

Our highly qualified team of 30 people has an average seniority of 9 years at SIB.

Publications

 

Members

View our group members here

Domain(s) of activity:

  • Core facility and competence centre
  • Structural biology
  • Systems biology
  • Data management
  • Data mining
  • Genome reconstruction
  • Machine learning
  • Mass spectrometry
  • Next generation sequencing
  • Personalised medicine
  • Software engineering

Domain(s) of application:

  • Basic research
  • Medicine and health

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