Integrative analysis of multi-omics data – Course and Conference Office

EMBO Practical Course

Integrative analysis of multi-omics data


Proof of COVID-19 vaccination or recovery is required to attend this on-site course. Please see EMBL’s COVID-19 safety policy for on-site events.

Course Overview

Multi-omics studies that combine genomics, transcriptome, proteome and other modalities are increasingly common in fundamental biology research and biomedicine. Using multi-omics experimental designs at bulk or single-cell resolution can help identifying novel biomarkers or reveal insights into biological mechanisms. This course addresses the conceptual and mathematical foundations of state-of-the-art methods for analyzing the data that results from multi-omics studies. The course will provide an overview of advanced applications of multi-omics methods, provide insights into how to select the most appropriate methods and convey practical experiences by providing participants with hands-on training. Finally, we will provide opportunities for participants to apply the taught principles to their own problems and data.


This course is aimed at PhD students and post-docs in computational biology aiming to improve their skills in multi-omics data integration methodologies. Solid experience with R and/or Python and willingness to work with both is a prerequisite for this course.


  • Probabilitic factor models for multi-omics integration (MOFA)
  • Multi-table methods for multi-omics integration
  • Data visualization and interactive exploration
  • Pre-processing and data management
  • Detection of hidden confounders and technical effects
  • Hands-on exercises with bulk and single cell multi-omics data sets

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.

Speakers and Trainers

Constantin Ahlmann-Eltze

EMBL Heidelberg


Simon Anders

Center for Molecular Biology of Heidelberg University


Ricard Argelaguet

Babraham Institute


Danila Bredikhin

EMBL Heidelberg


Barbara Engelhardt

Princeton University


Max Frank

EMBL Heidelberg


Ilia Kats

German Cancer Research Center


Junyan Lu

EMBL Heidelberg


Oliver Stegle

EMBL Heidelberg and German Cancer Research Center


Harald Vöhringer

EMBL Heidelberg


Scientific Organisers

Oliver Stegle

EMBL Heidelberg and German Cancer Research Center


Course Organisers

Iva Gavran

Course and Conference Officer

EMBL Heidelberg



Got something to say? Tweet it with #EMBOMultiOmics

The preliminary programme below is a draft and is subject to change.

Day 1 – Tuesday, 22 February 2022
Time (Europe/Berlin)SessionLocation
09:15-09:45Introduction and housenote slides
EMBL Course and Conference Office
Courtyard Room A & B
09:45-10:00Course overview
Oliver Stegle, EMBL Heidelberg and German Cancer Research Center, Germany,
Wolfgang Huber, EMBL Heidelberg, Germany,
Britta Velten, German Cancer Research Center, Germany
Courtyard Room A & B
10:00-11:15Icebreaking activity: Introduction round and “Challenges and Expectations”
EMBL Scientific Training Team
Courtyard Room A & B
11:15-11:45Coffee breakFoyer
11:45-12:45Overview and principles of data integration strategies in different fields
Barbara Engelhardt, Princeton University, USA
Courtyard Room A & B
12:45-14:15Lunch breakFoyer
14:15-15:15Probabilistic factor models for integration of multi-omics data (MOFA)
Britta Velten, German Cancer Research Center, Germany
Courtyard Room A & B
15:15-16:45Practical session: MOFA – introduction and bulk data setsCourtyard Room A & B
16:45-17:15Coffee breakFoyer
17:15-18:45Practical session: MOFA – introduction and bulk data sets (continued)Courtyard Room A & B
18:45-19:45Course dinnertbd
19:45-21:45Participant short talks part I (their project and the challenges 7 min + Discussion)tbd
21:45Return to hotel
Day 2 – Wednesday, 23 February 2022
Time (Europe/Berlin)Location
09:00-09:15Overview of the dayCourtyard Room A & B
09:15-10:15Multi-omics analysis for a better understanding of complex traits and disease
Judith Zaugg, EMBL Heidelberg, Germany
Courtyard Room A & B
10:15-10:30Coffee breakFoyer
10:30-12:30Participant short talks part II (their project and the challenges 7 min + Discussion)tbd
12:30-14:00Lunch breakFoyer
14:00-15:30Practical session: Data handling for multi-modal single cell data using muonCourtyard Room A & B
15:30-16:30Pitfalls and challenges for single cell data integration
Rahul Satija, New York Genome Center, USA (remotely)
Courtyard Room A & B
16:30-17:00Coffee breakFoyer
17:00-19:00Practical session: Single-cell multi omics integration (e.g. WNN, MOFA+)Courtyard Room A & B
19:00-20:00Dinner tbd
20:00-21:00Discussion round “Problems and Challenges in Data Integration”tbd
21:00 Return to hotel

Day 3 – Thursday, 24 February 2022
Time (Europe/Berlin)SpeakerLocation
09:00-09:15Overview of the dayCourtyard Room A & B
09:15-10:15Data preprocessing and management as a first-class citizen
Wolfgang Huber, EMBL Heidelberg, Germany
Courtyard Room A & B
10:15-11:15Practical session: Integrative analysis of own dataCourtyard Room A & B
11:15-11:30Coffee breakFoyer
11:30-12:30Practical session: Integrative analysis of own data (continued)Courtyard Room A & B
12:30-14:00Lunch breakFoyer
14:00-16:00Practical session: Integrative analysis of own data (continued)Courtyard Room A & B
16:00-16:30Coffee breakFoyer
16:30-17:30Interactive lecture on multi-table methods
Susan Holmes, Stanford University, USA (remotely)
Courtyard Room A & B
17:30-19:30Social programmetbd
19:30-21:00Course dinnertbd

Day 4 – Friday, 25 February 2022
Time (Europe/Berlin)SpeakerLocation
09:00-09:15Overview of the dayCourtyard Room A & B
09:15-10:15Visualization and interactive data exploration
Simon Anders, Center for Molecular Biology of Heidelberg University, Germany
Courtyard Room A & B
10:15-11:15Theory and principles for differentiating biological signal from confounding
Oliver Stegle, EMBL Heidelberg and German Cancer Research Center, Germany
Courtyard Room A & B
11:15-11:30Coffee breakFoyer
11:30-12:30Time for participants to prepare presentation 1Courtyard Room A & B
12:30-14:00Lunch break Foyer
14:00-15:30Final discussion round and presentation of own data analysis Courtyard Room A & B
15:30-16:00Coffee breakFoyer
16:00-16:45Final discussion round and presentation of own data analysis (continued) Courtyard Room A & B
16:45-17:15Feedback and closing remarksCourtyard Room A & B
17:30Bus to Heidelberg train station and city center

Practical Information

Registration Fees and Motivation Letter

For selection purposes, please note that your application will not be considered without a letter of motivation.

Important: We strongly encourage participants to run this R self-assessment prior to application in order to better asses their knowledge necessary to follow the course: https://forms.gle/JZJnbWpLiN6gBUKh6.


Registration Fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks. This EMBO course includes accommodation and transportation to and from the hotel to the venue.

PhD Student€250

NO visa support letters will be issued until payment of the registration fee is confirmed.

Confirmation and Payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation Letter Submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.


  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For more detailed information, follow the instructions provided in our video on how to submit a course motivation letter.

Further Details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial Assistance

Financial Assistance

Registration Fee Waivers

All academic and student registrants are invited to apply for a registration fee waiver, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO. The registration fee waiver covers the registration sum that you have paid to attend the meeting. Conference participants are not required to pre-pay the registration fee to be selected for a fee waiver for a virtual meeting. If you have already paid the registration fee and are awarded a fee waiver, it will be reimbursed after the meeting. Course participants are required to pay the course fee in advance, which will then be reimbursed after the recipient has attended the course.

Childcare Grants

For participants and speakers with childcare responsibilities there is the possibility to apply for a grant, provided by EMBO, to offset childcare costs incurred when participating at a virtual event. Eligible costs include fees for a babysitter or childcare facility or travel costs for a care giver. Please note that priority will be given to early stage researchers. Costs will be reimbursed after the meeting only once a reimbursement form and original receipts have been received. Attendance at the event is required in order to be eligible to receive the reimbursement. In order to apply for this grant, you must be registered by the abstract submission deadline.


Applications for financial assistance can be submitted via the submission portal* (for the submission of abstracts for conferences or the submission of motivation letters for courses) by completing the Financial Assistance Application Section (underneath the section for entering abstract/motivation letter information). The link to the portal can be found in the registration confirmation email that you will receive after registering for the conference or course.

For conferences, if you are not submitting an abstract, you can still apply for financial assistance in the submission portal. Read the instructions on how to apply for financial assistance.

Note that priority will be given to those submitting an abstract to present at the conference. In your application you will be asked to answer questions regarding your motivation for applying, and, for registration fee waivers, the reasons why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

*For some events, applications for Childcare Grants will still be done by email. Information about the grant will be sent out shortly after the abstract/motivation letter deadline. Please contact the event Conference Officer if you have any questions.


The scientific organisers will select the recipients of registration fee waivers during the abstract selection process for conferences and the participant selection process for courses. Results will be announced approximately 3 – 4 weeks before the event start date. Selection results do not impact your admission to the meeting. Registration fee waiver selection is based on your current work or study location, your motivation for applying, the reasons for needing financial support and the impact this event will have on your career. Childcare grants are allocated based on career stage, with priority given to early stage researchers.

Further details

Check out this list of external funding opportunities or get more information on attending the conference as an event reporter.

For further information about financial assistance please refer to the FAQ page.

Accommodation and Shuttles


The registration fee includes accommodation for 4 nights in a single room. Any additional nights need to be booked and paid personally at the hotel.

Local Transport

Participants staying at the ISG Hotel (near EMBL): Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further Details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For further information on getting to EMBL Heidelberg visit our Travel Information page.

For enquiries about accommodation and local transportation please refer to the FAQ page.

Technical Requirements and Event Software

Technical Requirements

Below you will find the software and technical requirements for this course.

  • Participants need to bring their own laptops, which will be used to remotely access EMBL virtual machines with pre-installed software.
  • You will need admin rights to install the software required to access the virtual machines. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.
  • If you have a non-standard HDMI port (other than type A), you need to bring an adaptor.
  • Keyboard and PC mouse are available for use with a standard USB port. If you have a different port type, such as USB-C, you will need to bring your own.

Event Software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Additional Information

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.


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 conferences, 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.

Date: 22 - 25 Feb 2022

Location: EMBL Heidelberg


Application: 30 Nov 2021


  • Wolfgang Huber
    EMBL Heidelberg
    • Oliver Stegle
      EMBL Heidelberg and German Cancer Research Center
      • Britta Velten
        German Cancer Research Center

      Contact: Iva Gavran

      Download event poster

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