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.

This course has been postponed from February 2022 and the selection process is finalised. Applications will not be re-opened.

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, trainers, and staff

Ricard Argelaguet

Babraham Institute


Danila Bredikhin

EMBL Heidelberg


Max Frank

EMBL Heidelberg


Ilia Kats

German Cancer Research Center


Junyan Lu

University Hospital Heidelberg


Arber Qoku

German Cancer Research Center


Oliver Stegle

EMBL Heidelberg and German Cancer Research Center


Harald Vöhringer

EMBL Heidelberg


Scientific organisers

Oliver Stegle

EMBL Heidelberg and German Cancer Research Center


Britta Velten

German Cancer Research Center


(on maternal leave)

Course organisers

Iva Gavran

Course and Conference Officer

EMBL Heidelberg



Got something to say? Tweet it with #EMBOMultiOmics

  • All times in the programme below are shown as the time in Europe/Berlin.
  • The preliminary programme below is a draft and is subject to change.

    Day 1 – Tuesday 20 September 2022
    Time SpeakersLocation
    08:50Bus shuttle to EMBLISG bus stop
    09:00–09:30RegistrationATC reception
    09:30– 09:45Welcome and safety introductions
    Wolfgang Huber – EMBL Heidelberg, Germany
    Courtyard Room
    09:45–10:00Course overview
    Oliver Stegle – EMBL Heidelberg / German Cancer Research Center, Germany
    Wolfgang Huber – EMBL Heidelberg, Germany
    Courtyard Room
    10:00–11:15Icebreaking activity: Introduction round and “Challenges and Expectations”
    EMBL Scientific Training Team
    Courtyard Room
    11:15–11:45Coffee breakFlex Lab
    11:45– 12:45Probabilistic factor models for integration of multi-omics data (MOFA)
    Oliver Stegle – EMBL Heidelberg and German Cancer Research Center, Germany
    Courtyard Room
    12:45 – 13:45Lunch breakCanteen
    13:45– 15:15Practical session: MOFA – introduction and bulk data setsComputer training lab
    15:15– 15:45Coffee breakFlex Lab
    15:45– 17:00Practical session: MOFA – introduction and bulk data sets (continued)Computer training lab
    17:00– 18:00Overview and principles of data integration strategies in different fields
    Barbara Engelhardt – Stanford University, USA (virtual)
    Courtyard Room
    18:15 – 18:30Bus shuttle to ISGEMBL bus stop
    18:30– 19:30Course dinnerISG hotel
    19:30– 21:30Participant short talks part I (their project and the challenges 7 min + Discussion)ISG hotel

    Day 2 – Wednesday 21 September 2022
    Time SpeakersLocation
    08:50Bus shuttle to EMBLISG bus stop
    09:00– 09:15Overview of the dayCourtyard Room
    09:15– 10:15Multi-omics analysis for a better understanding of complex traits and disease
    Judith Zaugg – EMBL Heidelberg, Germany
    Courtyard Room
    10:15– 10:30Coffee breakFlex Lab
    10:30– 12:30Participant short talks part II (their project and the challenges 7 min + Discussion)Courtyard Room
    12:30– 13:30Lunch breakCanteen
    13:30–13:45Group photo
    13:45– 15:15Practical session: Data handling for multi-modal single cell data using muonComputer training lab
    15:15– 16:15Computational approaches for single cell mosaic data integration
    Shila Ghazanfar – University of Sydney, Australia
    Courtyard Room
    16:15 – 16:45Coffee breakFlex Lab
    16:45– 18:45Practical session: Single-cell multi omics integration (e.g. WNN, MOFA+)Computer training lab
    18:45– 18:55Bus shuttle to ISG hotelEMBL bus stop
    19:00– 20:00Course dinnerISG hotel
    20:00– 21:00Discussion round “Problems and Challenges in Data Integration”ISG hotel

    Day 3 – Thursday 22 September 2022
    Time SpeakerLocation
    08:50Bus shuttle to EMBLISG bus stop
    09:00–09:15Overview of the dayCourtyard Room
    09:15–10:15Data preprocessing and management as a first-class citizen
    Wolfgang Huber – EMBL Heidelberg, Germany
    Courtyard Room
    10:15–11:15Practical session: Integrative analysis of own dataComputer training lab
    11:15–11:45Coffee breakFlex Lab
    11:45– 12:45Practical session: Integrative analysis of own data (continued)Computer training lab
    12:45– 13:45Lunch breakCanteen
    13:45–15:45Practical session: Integrative analysis of own data (continued)Computer training lab
    15:45–16:15Coffee breakFlex Lab
    16:15–17:15Interactive lecture on multi-table methods
    Susan Holmes – Stanford University, USA
    Courtyard Room
    17:30–20:00Bus to city centre and free afternoonEMBL bus stop
    20:00– 21:30Downtown dinner

    Day 4 – Friday 23 September 2022
    Time SpeakerLocation
    08:50Bus shuttle to EMBLISG bus stop
    09:00– 09:15Overview of the dayCourtyard Room
    09:15–10:15Encoding Domain Knowledge in Multi-view Latent Variable Models,
    Florian Buettner – Goethe-University Frankfurt, Germany
    Courtyard Room
    10:15– 11:15Practical session: Pathway informed factor models
    Florian Buettner – Goethe-University Frankfurt, Germany
    Arber Qoku – German Cancer Research Center, Germany
    Computer training lab
    11:15–11:45Coffee breakFlex Lab
    11:45– 12:45Time for participants to prepare presentationsCourtyard Room
    12:45–13:45Lunch breakCanteen
    13:45– 15:15Final discussion round and presentation of own data analysis Courtyard Room
    15:15–15:45Coffee breakFlex Lab
    15:45–16:30Final discussion round and presentation of own data analysis (continued) Courtyard Room
    16:30– 17:00Feedback and closing remarksCourtyard Room
    17:15Bus to Heidelberg train station and city centerEMBL bus stop

    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 (from 19-23 September). 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.

    COVID-19 related questions

    COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.


    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: 20 - 23 Sep 2022

    Location: EMBL Heidelberg


    Application: Closed


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

        Contact: Iva Gavran

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