Challenges within and between omics data integration

General context

In the era of Big Data, the tsunami of massive ‘omics’ data production is shifting the way we do science. Life science researchers are no longer obliged to utilize one data set at a time, and are moving towards multi-disciplinary integrative biology. It has been demonstrated that integration of different ‘omics’ data platforms (including genome, transcriptome, proteome, and epigenome, etc..), boost biological discoveries and improve functional predictions of the underlying interactions and regulation among molecular entities, such as genes. Integrating different ‘omics’ profiles is a challenging task, reminiscent of pattern mining in large datasets or clustering problems in multiple dimensions. One must account for the effects of each data type, thereby alleviating the problems associated with processing data across different platforms, and variable reliability levels of heterogeneous data.

In this first 2-day training of a series of three, we will introduce computational approaches that are at hand to analyze, integrate and interpret omics data. We target scientists with no or limited knowledge on omics data integration, more advanced levels will be addressed in following sessions in 2019. During a first day of lectures (Monday 19 November), experts in the field will illustrate their know-how, discuss applications and stir new ideas to integrate and interpret data from different omics technologies. The first session of the day will deal with different sources of data, data management, data standardization, etc. Next, field experts will showcase algorithms and tools they developed and/or use for different types of omics data integration (both supervised and unsupervised methods) and explain opportunities and challenges of the specific algorithms. A third session will be dedicated to interpretation and validation of results. During a round table discussion, the trainers will address questions/issues that were raised by the participants, to stimulate the interaction and to make the training as relevant as possible for your own research. We will end the day with a keynote talk that will integrate several of the methodologies that were discussed during the day into a biological story.      

On Tuesday 20 November, there is the opportunity to follow a hands-on training in Bio-Accelerator Ghent. During this training, we will showcase VIB’s efforts to make integrative biology accessible to the wider research community of VIB through its activities across the Centers and Core Facilities. First, we will cover the main aspects of experimental design, data acquisition and file formatting, data normalization and filtration. Then we will move on to describe our arsenal for selecting our ‘weapon of choice’ (Bayesian networks, PCA, Feature selection, Machine learning, SVM, Random Forest, Deep Learning, etc.). Finally, we will provide a clear biological interpretation to the results.

Focus for the hands-on training will be on transcriptomics, metabolomics and proteomics data. During the morning session we will illustrate a variety of computational approaches using predefined datasets. In the afternoon, you can start exploring your own datasets. We prefer that you bring your own laptop, we will let you know upfront what you need to install. A basic knowledge of R is essential to follow this hands-on part. 

Note that you need to indicate upon registration that you would like to follow the hands-on session and that places are limited!


Target audience

This first training in a series of three targets scientists interested in learning on omics data processing and integration with no or limited experience. It is aimed at PhD students, postdoctoral fellows, technicians or other scientists with a molecular biology background.


Scientific Committee

Yvan Saeys (VIB-UGent Center for Inflammation Research)
Frederik Coppens (VIB-UGent Center for Plant Systems Biology)
Shoshana Wodak (VIB-VUB Center for Structural Biology)
Steven Maere (VIB-UGent Center for Plant Systems Biology)
Oren Tzfadia (VIB Bioinformatics Core)


Confirmed speakers

Shoshana Wodak, VIB-VUB Center for Structural Biology
Lana Garmire, University of Hawai Cancer Center, Honolulu, US
Roded Sharan, School of Computer Science, Tel Aviv University, IL
Tom Michoel, Computational Biology Unit, Dept. of Informatics, University of Bergen, NO
Patrick Aloy, Structural Biofinformatics lab, Institute for Research in Biomedicine, Barcelona, ES
Zeynep Kalender Atak, VIB-KU Leuven Center for Brain & Disease Research, Leuven, BE
Gary Bader, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, CA





Registration info
  • Participation is free for VIB participants.
  • Registration fee for Academics from Universities and Centers of Excellence is € 50 (21% VAT incl.) to attend the lectures session on 19 November. If you are selected for the hands-on session, we will contact you to pay an additional € 50 (21% VAT incl.).
  • Registration fee for participants of EU-LIFE partner institutes is € 50 (21% VAT incl.) to attend the lectures session on 19 November. If you are selected for the hands-on session, we will contact you to pay an additional € 50 (21% VAT incl.).
  • Registration fee for industry is € 300 (21% VAT incl.). The hands-on session is not open for participants from industry.
  • Note that upon no-show without valid justification you will be blacklisted for the VIB training program for 1 year and for VIB participants the reimbursement of the catering costs (€ 50) will be charged to the research group. Click here for more information.




19 & 20 November 2018


FSVM Research Building - Shell auditorium
Technologiepark 927
9052 Ghent


Internal and external field experts
Registration is closed.

Registration start date:

30 August 2018

Registration end date:

5 November 2018