Analysis and integration of transcriptome and proteome data – Course and Conference Office

EMBL Course

Analysis and integration of transcriptome and proteome data


Registration is not yet open for this event. If you are interested in receiving more information please register your interest.

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.


This course is targeted at 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.

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.

What past participants say about the course

“Besides of the amazing content provided by distinguished speakers, participants with diverse scientific backgrounds broadened our perspectives and created a nourishing scientific environment. We were able to learn key aspects of integrating omics data to our research and benefited from networking opportunities. Overall, it was a really nice experience.” – Damla Gunes, Koç University, Turkey

“The analysis and integration of transcriptome and proteome data course organized by EMBL allowed me to expand my horizons regarding the various bioinformatic tools and statistical analysis available that we can use for our transcriptome and proteomic. Highly Recommended!” – Diogo Estêvão, i3S – Institute for Research and Innovation in Health & CRIG – Cancer Research Institute
Ghent, Belfium


Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other events, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.


EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Date: 4 - 9 May 2025

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


  • Vladimir Benes
    EMBL Heidelberg, Germany
    • Raffaele Calogero
      University of Turin, Italy
      • Daria Fijalkowska
        University of Ghent, Belgium

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