Omics Integration and Systems Biology

Course open for PhD students, postdocs, and researchers looking for an introduction to multi-omics integration and systems biology.

Important dates

Application closed

Application closes: 28 June

Confirmation to accepted students: 5 July

Responsible teachers: Rui Benfeitas, Nikolay Oskolkov, Ashfaq Ali

If you do not receive information according to the above dates please contact: Rui Benfeitas, Nikolay Oskolkov
or Ashfaq Ali

Course fee

A course fee of 2000 SEK will be invoiced to accepted participants. This includes lunches, coffee, snacks and course dinner. Please note that NBIS cannot invoice individuals

Course content

The aim of this workshop is to provide an integrated view of biological network construction and integration, constraint-based modelling, multi-omics integration and hypothesis generation.

A general description of different methods for analysing different omics data (e.g. transcriptomics and genomics) will be presented with some of the lectures discussing key methods in omics integration. The various techniques are discussed in terms of their rationale and applicability, with a particular focus on possible confounding factors. Attendants will further get hands-on experience in their application. Some of the covered topics include:

  • Condition-specific and personalized metabolic modeling based on integration of transcriptomic and proteomic data;
  • Identification of potential biomarkers and targetable genes;
  • Identification of key biological functions and pathways;
  • Co-expression and association networks, gene modules, and network topology analysis;
  • Multi-omics integration, clustering and dimensionality reduction;
  • Application of key machine learning methods for multi-omics analysis.

While basic understanding of NGS techniques is desirable it is not essential to fully follow the course. Further details about the course content may be found on the course homepage at .

Entry requirements

The course is aimed at M.Sc., PhD- or postdoc-level researchers with basic programming experience (e.g. R, Python). We will not discuss how to process the raw omics data and the students are referred to other NBIS courses for this matter:


  • Basic programming/scripting experience in R, Python or Linux programming
  • Ability to bring your own laptop with R/Python installed for the practical exercises


  • Experience with omics and NGS analysis
  • Basic statistics understanding
  • Differential expression/abundance analysis
  • Completing NBIS courses “Introduction to Bioinformatics using NGS data”

Link to application