Job Description

Course overview

Systems biology is a still expanding field of research aiming to understand at the molecular level how cells, tissues, and organisms operate in their biological context. Among the key technologies driving this forward, are next-generation sequencing and proteomics as they provide powerful means to determine global expression levels of genes and proteins. Both fields have matured to a degree that they have now become accessible to researchers in many areas of biology.

During this course, participants will gain theoretical insight in the structure of sequencing and proteomic data, and they will receive training in data analysis for the annotation, quantification, and statistical analysis of gene and protein expression using various computational tools. In addition, training will be provided in the use of Cytoscape to derive biological insights from the integration of both data types.

Audience

This course is for biologists and biochemists who are (starting to be) involved in both next-generation sequencing and mass spectrometry-based proteomics, but who are not experts in these fields.

Modules/resources

• Principles of mRNA quantification
• Principles of protein identification and quantification
• Principles and application of bioinformatic tools for mining of transcriptome and proteome data
• Data integration by Cytoscape

Learning outcomes

The aim of this practical course is to provide insight in techniques that are frequently used for transcriptome and proteome analysis and to provide hands-on experience turning primary data into information that can be used for further biological interpretation. To achieve these goals, participants will gain insight in the basic principles of gene expression analysis (RNAseq data quantification and differential expression analysis), protein identification and quantification, and they will be trained in the use of software tools to analyse sequencing and proteomic data (SearchGUI, PeptideShaker, MaxQuant). In addition, the course will provide insight in the complementarity of transcriptome and proteome data by their integrative analysis via Cytoscape.

Date: 3 – 8 May 2026

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre

Deadline(s):

Application: 25 Jan 2026