Annique Claringbould
Erasmus Medical Centre Rotterdam
The Netherlands
Overview
Funded by EMBO for excellence in the life sciences
Course overview
Biological and biomedical research frequently employs multiple ‘omics methods
(“multi-omics”) to investigate biological systems comprehensively. This approach simultaneously examines various molecular layers (DNA, RNAs, proteins, metabolites) and helps to overcome limitations inherent in individual technologies. These modalities are increasingly profiled at single-cell and/or spatial resolutions. Integrating and analysing these complex datasets poses significant challenges. How can we interpret perturbation effects, establish associations between molecular profiles and study variables, or detect latent variables representing key biological elements like cell types or states? Crucially, how can we achieve these goals with statistical robustness and scientific rigor, facilitating clear and convincing reporting?
This course addresses those essential questions, providing participants with foundational mathematical and conceptual understanding of integrative multi-modal data analysis methods. Through hands-on sessions using state-of-the-art datasets, attendees will explore different software tools, assess data quality and results, identify potential pitfalls, evaluate performance, optimize model parameters, interpret outcomes effectively, and embrace open-science practices. Methods covered include factor analysis, multi-table ordination and dimensionality reduction techniques, notably the widely utilised Multi-Omics Factor Analysis (MOFA) and more recent approaches, developed by the course faculty.
Audience
This course is aimed at bioinformatics scientists, PhD students and post-docs aiming to improve their skills in multi-omics data integration methodologies. Scientists who themselves have a training role are particularly encouraged to apply. Experience with R and/or Python and willingness to work with both is a prerequisite for this course.
Modules
- Multi-table integration: motivation, concepts and theory
- Multi-omics case studies, single cell multi-omics, spatial omics
- Data management and open science related topics in multi-modal data integration
- Visualisation and interactive data analysis
Learning outcomes
The course will provide researchers with an overview and the theoretical foundations of state-of-the-art methods for multi-modal integration, with a focus on omics data. In practical sessions on relevant real-world examples from single-cell and bulk multi-omics studies, participants will gain familiarity with software implementations and learn about practical aspects, including quality assessment of inputs and outputs, method performance assessment, choice of tuning parameters, interpretation of the model fit and potential pitfalls.
What past participants say about the course
“The course was a fantastic overview of the state-of-the-art in multi-omics integration with exposure to the top methods and researchers in the field. Getting to discuss open problems with the speakers and other participants was invaluable and I’ve made some great connections with other attendees which I hope to continue to develop.” – Eleanor Williams, Wellcome-MRC Cambridge Stem Cell Institute, UK
“The course provides a comprehensive overview of different multiomics data integration techniques with real-life applications and an excellent opportunity to network with fellow participants, speakers, and method developers.” – Adhideb Ghosh, ETH Zurich, Switzerland
Speakers, trainers, and staff
Helena Crowell
Centro Nacional de Análisis Genómico
Spain
Sascha Dietrich
Universitätsklinikum Düsseldorf
Germany
Wolfgang Huber
EMBL Heidelberg
Germany
Junyan Lu
Heidelberg University
Germany
Mor Nitzan
The Hebrew University of Jerusalem
Israel
Denis Schapiro
Heidelberg University
Germany
Oliver Stegle
EMBL Heidelberg/ DKFZ
Germany
Jonan Tanevski
Heidelberg University
Germany
Scientific organisers
Wolfgang Huber
EMBL Heidelberg
Germany
Junyan Lu
Heidelberg University
Germany
Oliver Stegle
EMBL Heidelberg/ DKFZ
Germany
Britta Velten
Heidelberg University
Germany
Programme
Day 0: Date tbc
| Time (Europe/Berlin) | Session |
|---|---|
| Introduction to EMBLeCampus – pre-course briefing, software package installations |
Day 1: Tuesday, 28 July 2026
| Time (Europe/Berlin) | Session | Location |
|---|---|---|
| 08:40 | Bus to EMBL ATC | ISG Hotel |
| 08:50 – 09:00 | Registration | Courtyard Room A & B |
| 09:00 – 09:15 | Welcome and safety instructions | Courtyard Room A & B |
| 09:15 – 09:30 | Course Overview | Courtyard Room A & B |
| 09:30 – 10:15 | Networking: Ice breaking activity | Courtyard Room A & B |
| 10:15 – 11:15 | Lecture 1: Probabilistic factor models for integration of multi-omic data (MOFA) | Courtyard Room A & B |
| 11:15 – 11:45 | Coffee break and meet the speaker | Courtyard Room A & B |
| 11:45 – 12:45 | Lunch | EMBL Canteen |
| 12:45 – 14:15 | Practical 1: First steps with Multi-Omics Factor Analysis (MOFA): data setup, method calling, troubleshooting, and results interpretation | Courtyard Room A & B |
| 14:15 – 15:15 | Lecture 2 Oliver Stegle – EMBL Heidelberg/ German Cancer Research Center (DKFZ), Germany | Courtyard Room A & B |
| 15:15 – 15:45 | Coffee break and meet the speaker – Oliver Stegle | Courtyard Room A & B |
| 15:45 – 17:15 | Pratical 1: First steps with Multi-Omics Factor Analysis (MOFA): data setup, method calling, troubleshooting, and results interpretation | Courtyard Room A & B |
| 17:15 – 19:15 | Participant flash talks | Courtyard Room A & B |
| 19:15 – 20:15 | Dinner | EMBL Canteen |
| 20:15 | Bus to ISG Hotel | ATC Entrance |
Day 2: Wednesday, 29 July 2026
| Time (Europe/Berlin) | Session | Location |
|---|---|---|
| 08:40 | Bus to EMBL ATC | ISG Hotel |
| 08:50 – 09:00 | Overview of the day | Courtyard Room A & B |
| 09:00 – 10:00 | Lecture 3: Integrating single-cell transcriptomics and large-scale genetics to understand complex diseases Annique Claringbould – Erasmus Medical Centre Rotterdam, The Netherlands | Courtyard Room A & B |
| 10:00 – 10:15 | Coffee break and meet the speaker – Annique Claringbould | Courtyard Room A & B |
| 10:15 – 12:15 | Participants Presentations | Networking | Courtyard Room A & B |
| 12:15 – 12:30 | Group Photo | Courtyard Room A & B |
| 12:30 – 13:15 | Lunch Break | |
| 13:15 – 14:45 | Practical 2: MOFA for single-cell multi-omics data | Courtyard Room A & B |
| 14:45 – 15:45 | Lecture 4 Wolfgang Huber – EMBL Heidelberg, Germany | Courtyard Room A & B |
| 15:45 – 16:15 | Coffee break and meet the speaker – Wolfgang Huber | Courtyard Room A & B |
| 16:15 – 18:15 | Pratical 2: Mosaic integration of multi-omics single-cell data | Courtyard Room A & B |
| 18:15 – 18:30 | Bus to ISG Hotel | ATC Entrance |
| 18:30 – 19:30 | Dinner | ISG Hotel |
| 19:30 – 20:30 | Round table discussion: Problems and challenges in data integration (including RCR principles) | ISG Hotel |
Day 3: Thursday, 30 July 2026
| Time (Europe/Berlin) | Session | Location |
|---|---|---|
| 08:40 | Bus to EMBL ATC | ISG Hotel |
| 08:50 – 09:00 | Overview of the day | Courtyard Room A & B |
| 09:00 – 10:00 | Lecture 5: Integrative Spatial-omic data analysis Denis Schapiro – Heidelberg University, Germany | Courtyard Room A & B |
| 10:00 – 11:00 | Practical 3: Integrative analysis of spatial omics data | Courtyard Room A & B |
| 11:00 – 11:15 | Coffee break and meet the speaker – Denis Schapiro | Courtyard Room A & B |
| 11:15 – 12:15 | Practical 3 (cont.): Integrative analysis of spatial omics data | Courtyard Room A & B |
| 12:15 – 13:15 | Lunch | EMBL Canteen |
| 13:15 – 14:15 | Lecture 6: Spatial-Resolved Transcriptomic Analysis Helena L. Crowell – Centro Nacional de Análisis Genómico, Spain | Courtyard Room A & B |
| 14:15 – 14:45 | Coffee break and meet the speaker – Helena L. Crowell | Courtyard Room A & B |
| 14:45 – 16:15 | Practical 3 (cont.): Integrative analysis of spatial omics data | Courtyard Room A & B |
| 16:15 – 17:15 | Lecture 7: Multi-Omics for Precision Medicine Junyan Lu – Heidelberg University, Germany | Courtyard Room A & B |
| 17:15 – 18:00 | Bus transfer downtown | ATC Entrance |
| 18:00 – 19:30 | Guided city tour | |
| 19:30 – 21:30 | Course dinner |
Day 4: Friday, 31 July 2026
| Time (Europe/Berlin) | Session | Location |
|---|---|---|
| 08:40 – 08:50 | Bus to EMBL ATC | ISG Hotel |
| 08:50 – 09:00 | Overview of the day | Courtyard Room A & B |
| 09:00 – 09:30 | Discussion: Open science and responsible conduct of research in data sciences Wolfgang Huber – EMBL Heidelberg, Germany Oliver Stegle – EMBL Heidelberg/ German Cancer Research Center (DKFZ), Germany | Courtyard Room A & B |
| 09:30 – 10:30 | Lecture 8: AI and Multi-Modal Data Integration in Clinical Studies Sascha Dietrich – University Clinic Düsseldorf, Germany | Courtyard Room A & B |
| 10:30 – 10:45 | Coffee break and meet the speaker – Sascha Dietrich | |
| 10:45 – 11:45 | Lecture 9: Understanding complex and dynamic biological systems with single-cell omic data Mor Nitzan – The Hebrew University of Jerusalem, Germany | Courtyard Room A & B |
| 11:45 – 12:30 | Discussion in small groups + time for participants to prepare presentations | Courtyard Room A & B |
| 12:30 – 13:15 | Lunch Break | Courtyard Room A & B |
| 13:15 – 14:00 | Discussion in small groups + time for participants to prepare presentations | Courtyard Room A & B |
| 14:00 – 14:30 | Coffee break and meet the speaker – Mor Nitzan | |
| 14:30 – 16:00 | Presentations/ Discussion | Courtyard Room A & B |
| 16:00 – 16:15 | Coffee Break / | Courtyard Room A & B |
| 16:15 – 17:30 | Presentations/ Discussion | Courtyard Room A & B |
| 17:30 – 17:45 | Feedback and closing remarks | Courtyard Room A & B |
| 17:45 – 00:00 | Bus to Heidelberg train station and city center |
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Media kit
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Date: 28 - 31 Jul 2026
Location: EMBL Heidelberg
Venue: EMBL Advanced Training Centre
Deadline(s):
Application: 21 Apr 2026
Organisers:
-
Wolfgang Huber
EMBL Heidelberg, Germany -
Junyan Lu
University Hospital Heidelberg, Germany -
Oliver Stegle
EMBL Heidelberg, Germany -
Britta Velten
Heidelberg University, Germany
Contact: Aline Schnieder
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