Integrative Analysis of Multi-Omics Data – Course and Conference Office

EMBO Practical Course

Integrative Analysis of Multi-Omics Data


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

Course Overview

Experimental designs in basic biology research and biomedicine increasingly involve the use of multiple omics technologies to characterise a set of samples e.g. genomic variants, epigenetic marks, transcriptome, proteome, metabolome, functional assays, imaging. This is true for both bulk and single cell analyses. Therefore, data analysis techniques are required that are able to cope with such data in an efficient and generalisable manner. Thus, the proposed advanced course addresses one of the major data challenges scientists face today. Its core objective is to convey the conceptual and mathematical foundations that underpin integrative multimodal data analysis strategies and the practical trade-offs of different methods.


Course is aimed at PhD students and post-docs working in computational biology aiming to improve their skills in multi-omics data integration methodologies. Solid experience with R and/or Python 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 give students and postdocs and overview of the state-of-the-art methods, with a focus on omics data. In practical sessions using relevant real-world examples from single-cell and bulk multi-omics studies, participants will gain familiarity with software implementations, practical aspects and quality assessment of inputs and outputs and pitfalls, method performance assessment and tuning, and model fit interpretation.

Speakers and Trainers

Simon Anders

Center for Molecular Biology of Heidelberg University


Ricard Argelaguet

Babraham Institute


Barbara Engelhardt

Princeton University


Oliver Stegle

EMBL Heidelberg and German Cancer Research Center


Scientific Organisers

Oliver Stegle

EMBL Heidelberg and German Cancer Research Center


Course Organisers

Iva Gavran

Course and Conference Officer

EMBL Heidelberg


Irena Provaznikova

Training Lab Technician

EMBL Heidelberg


Preliminary programme

Got something to say? Tweet it with #EMBOMultiOmics

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

Day 1 – Tuesday, 22 February 2022
Time (Europe/Berlin)Session
09:00-09:30Introduction and housenote slides
EMBL Course and Conference Office
09:30-09:45Course overview
Oliver Stegle, EMBL Heidelberg and German Cancer Research Center, Germany,
Wolfgang Huber, EMBL Heidelberg, Germany,
Britta Velten, German Cancer Research Center, Germany
09:45-11:00Icebreaking activity: Introduction round and “Challenges and Expectations”
EMBL Scientific Training Team
11:00-11:30Coffee break
11:30-12:30Overview and principles of data integration strategies in different fields
Barbara Engelhardt, Princeton University, USA
12:30-13:30Lunch break
13:30-14:30Probabilistic factor models for integration of multi-omics data (MOFA)
Britta Velten, German Cancer Research Center, Germany
14:30-16:00Practical session: MOFA – introduction and bulk data sets
16:00-16:30Coffee break
16:30-18:00Practical session: MOFA – introduction and bulk data sets (continued)
18:00-20:00Participant short talks part I (their project and the challenges 7 min + Discussion)
with concurrent Pizza Dinner
20:00Return to hotel
Day 2 – Wednesday, 23 February 2022
Time (Europe/Berlin)
09:00-09:15Overview of the day
09:15-10:15Multi-omics analysis for a better understanding of complex traits and disease
Judith Zaugg, EMBL Heidelberg, Germany
10:15-10:30Coffee break
10:30-12:30Participant short talks part II (their project and the challenges 7 min + Discussion)
12:30-13:30Lunch break
Practical session: Single-cell multi omics integration
13:30-15:00Practical session: Data handling for multi-modal single cell data using muon
15:00-16:00Pitfalls and challenges for single cell data integration
Rahul Satija, New York Genome Center, USA (remotely)
16:00-16:30Coffee break
16:30-18:30Practical session: Single-cell multi omics integration (e.g. WNN, MOFA+)
18:30-20:30Dinner in ATC rooftop lounge and discussion round “Problems and Challenges in Data Integration”
20:30 Return to hotel

Day 3 – Thursday, 24 February 2022
Time (Europe/Berlin)
09:00-09:15Overview of the day
09:15-10:15Data preprocessing and management as a first-class citizen
Wolfgang Huber, EMBL Heidelberg, Germany
10:15-11:15Practical session: Integrative analysis of own data
11:15-11:30Coffee break
11:30-12:30Practical session: Integrative analysis of own data (continued)
12:30-13:30Lunch break
13:30-15:30Practical session: Integrative analysis of own data (continued)
15:30-16:00Coffee break
16:00-17:00Interactive lecture on multi-table methods
Susan Holmes, Stanford University, USA (remotely)
17:00-19:30Bus down town and guided tour of Heidelberg
19:30Dinner at local restaurant
Day 4 – Friday, 25 February 2022
Time (Europe/Berlin)
09:00-09:15Overview of the day
09:15-10:15Visualization and interactive data exploration
Simon Anders, Center for Molecular Biology of Heidelberg University, Germany
10:15-11:15Theory and principles for differentiating biological signal from confounding
Oliver Stegle, EMBL Heidelberg and German Cancer Research Center, Germany
11:15-11:30Coffee break
11:30-12:30Time for participants to prepare presentation 1
12:30-13:30Lunch break
13:30-15:00Final discussion round and presentation of own data analysis
15:00-15:30Coffee break
15:30-16:15Final discussion round and presentation of own data analysis (continued)
16:15-16:45Feedback and closing remarks
17:00Bus 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.


Registration Fees (include admission, course materials, meals and coffee breaks):
This EMBO course includes accommodation and transportation to and from the hotel to the venue.

PhD Studenttba

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:

Motivation letter length: 
The maximum limit of 2000 characters (ca. 200 words) refers to manually typed text (spaces included).

Free field text length: The maximum characters for your answers in the free field text boxes is 255 (spaces included).Text only: If you copy-paste the text, hidden formatting might still be included and you will be informed that your text exceeds the character limit. We recommend either:

  1. saving your text as text only in your editor or Email programme, OR
  2. copy-pasting it into Notepad and then onto the website.

Symbols: If you have special symbols in your text make sure you are using Unicode characters, otherwise these will not be recognised by the tool.

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 the EMBL Advanced Training Centre Corporate Partnership Programme and 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.

Boehringer Ingelheim Fonds Travel Grant

Applies to selected courses only. Availability will be indicated during the abstract or motivation letter submission process.

This grant covers costs related to your attendance to the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.
Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course
– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course


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


EMBO Courses: The registration fee includes accommodation for 5 nights in a shared twin room with another course participant. 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.

Participants staying at a different hotel are welcome to use the complimentary course shuttle bus – please check the timetable for departure location and times. Alternatively, you can use public transportation.


Further course information will be shared with accepted course participants via Slack (a digital workspace and messaging app).

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.


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


  • Wolfgang Huber
    EMBL Heidelberg

EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

Corporate partners

Associate partners

Stay in touch

What's new on our blog