ELIXIR Omics Integration and Systems Biology



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6 - 10 September 2021



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The aim of this workshop is to provide an integrated view of data-driven hypothesis generation through biological network analysis, constraint-based modelling, and supervised and unsupervised integration methods. 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 and pitfalls in their integration. The techniques will be discussed in terms of their rationale and applicability.



Covered topics

  • Data pre-processing and cleaning prior to integration;
  • Application of key machine learning methods for multi-omics analysis including deep learning;
  • Multi-omics integration, clustering and dimensionality reduction;
  • Biological network inference, community and topology analysis and visualization;
  • Condition-specific and personalized modeling through Genome-scale Metabolic models for integration of transcriptomic, proteomic, metabolomic and fluxomic data;
  • Identification of key biological functions and pathways;
  • Identification of potential biomarkers and targetable genes through modeling and biological network analysis;
  • Application of network approaches in meta-analyses;
  • Similarity network fusion and matrix factorization techniques;
  • Integrated data visualization techniques


Learning objectives

At the end of the course, students should:

  • Identify key methods for analysis and integration of omics data based on a given dataset;
  • Perform standard feature selection techniques;
  • Understand the differences and apply dimensionality reduction techniques;
  • Understand strengths and pitfalls of key machine learning techniques in multi-omic analysis;
  • Apply unsupervised and supervised data integration techniques;
  • Build biological networks based on different omics data including integrated multi-omics networks;
  • Perform centrality and community analyses in graphs;
  • Apply network approaches in meta-analyses;
  • Apply similarity network fusion of patient data;
  • Compare different cell-types or conditions through the application of different biological network analysis techniques;
  • Simulate biological functions using constraint-based models and flux balance analysis;
  • Identify potential confounding factors and sources of bias.



Course open for PhD students, postdocs, group leaders and core facility staff from European institutions looking for an introduction to multi-omics integration and systems biology approaches. This course can accommodate a maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria including entry requirements, motivation to attend the course as well as gender and geographical balance.  Please note that NBIS training events do not provide any formal university credits. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

Applications are closed. Click here if you would like to be notified of the next course instance.

Fee This online training event has no fee. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK. Please note that NBIS cannot invoice individuals.


Entry requirements

Practical exercises can be performed using R or Python, so we only accept students with previous experience in one of those programming languages. We will not discuss how to process specific omics, and the students are referred to other NBIS courses for this matter.


  • Basic knowledge in R or Python;
  • Basic understanding of frequentist statistics;
  • A computer with web camera and Zoom.


  • Experience with analysis of NGS and other omic data;
  • Completing NBIS courses “Introduction to Bioinformatics using NGS data” and “Introduction to biostatistics and machine learning”
  • Basic docker knowledge




Course staff

Rui Benfeitas (Stockholm University, course leader)
Nikolay Oskolkov (Lund University, course leader)
Ashfaq Ali (Lund University, course leader)
Sergiu Netotea (Chalmers University of Technology)
Ricard Argelaguet (Babraham Institute, United Kingdom)
Kim-Anh Lê Cao (Melbourne University, Australia)
Pedro Beltrao (EMBL-EBI, United Kingdom)
Nikolaus Sonnenschein (DTU Technical University of Denmark, Denmark)




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