Yvan Saeys Lab

Research focus

​Our group studies the design and application of novel data mining and machine learning techniques, motivated by specific questions in biology and medicine.  To this end, our group combines the expertise of both strong analytical skills, exemplified by solid backgrounds in applied mathematics, computer science and engineering, with expertise in applied bioinformatics.

In the field of systems immunology, our group develops new computational approaches to unravel the regulatory landscape of immune cell differentiation and functioning.  High-throughput methods such as microarrays, next-generation-sequencing (NGS), multiplexed flow cytometry and imaging are currently revolutionizing the field of immunology, allowing us to study cells and their interactions into unprecedented depth.  While these technologies are able to generate massive amounts of data on cell behavior and functioning, interpreting these data and making sense out of it is currently the next challenge.  Our group develops novel systems biology approaches to model the regulatory landscape of immune cells using module networks and computational flow cytometry.

On the more algorithmic side, our research group develops new machine learning approaches to deal with challenging extensions of the classical learning paradigms, including high-dimensional, small sample settings, semi-supervised learning, imbalanced data, and structured input and output representations.  Our group has a solid expertise in the development of feature selection (biomarker selection) algorithms, and is currently exploring the potential of these techniques for new data types, such as flow cytometry and imaging.  A great part of our research effort also goes to the analysis of integrated “omics” approaches, where we take a network approach to integrate various data sources, and make use of novel graph mining approaches to formulate biological questions as machine learning questions on graphs.

In addition to our methodological research, we also aim to provide the scientific community with freely available, easy-to-use webtools, databases and other publicly available resources that result from our newly developed algorithms.  An overview of our tools can be found here.


NicheNet: modeling intercellular communication by linking ligands to target genes.Browaeys Robin Saelens Wouter° Saeys Yvan@NATURE METHODS, 17, 159-162, 2020* or °: authors contributed equally@: corresponding authors
A comparison of single-cell trajectory inference methodsSaelens W* Cannoodt R* Todorov H Saeys YNATURE BIOTECHNOLOGY, 37, 547-554, 2019* or °: authors contributed equally
A Computational Pipeline for the Diagnosis of CVID Patients.Emmaneel Annelies Bogaert Delfien Van Gassen Sofie Tavernier Simon Dullaers Melissa Haerynck Filomeen Saeys Yvan@Frontiers in Immunology, 10, 2009, 2019@: corresponding authors
Network Inference from Single-Cell Transcriptomic DataTodorov Helena Cannoodt Robrecht Saelens Wouter Saeys YvanMethods in Molecular Biology, 1883, 235-249, 2019
Computational flow cytometry: helping to make sense of high-dimensional immunology dataSaeys Yvan Van Gassen Sofie Lambrecht BartNATURE REVIEWS IMMUNOLOGY, 16, 449-62, 2016

Job openings


The first Cell Atlas for the human Thymus

28/02/2020 - Scientists from the VIB Center for Inflammation Research, Ghent University, The Wellcome Sanger Institute (UK), and Newcastle University (UK) have composed a complete map of the cells in the developing human thymus.

Scientists develop ‘Twitter’ for cells

10/01/2020 - Computational biologists led by Yvan Saeys (VIB-UGent) developed new bioinformatics method to better study communication between cells. This helps researchers to gain insight into how the gene expression of cells is regulated by interacting cells.

Detailed brain map uncovers hidden immune cells that may be involved in neurodegenerative disorders

06/05/2019 - A team led by Kiavash Movahedi (VIB-VUB) has developed a comprehensive cell atlas of the brain's immune compartment. This revealed not only the striking diversity of brain macrophages, but also found microglia where they were not expected

Artificial intelligence sheds new light on cell developmental dynamics

01/04/2019 - ​What happens inside a cell when it is activated, changing, or responding to variations in its environment? Researchers from the VIB-UGent Center for Inflammation Research have developed a map of how to best model these cellular dynamics.

Artificial intelligence empowers core facilities to stay ahead

20/03/2019 - A common theme across all VIB core facilities is the generation of potentially huge datasets that require powerful analysis tools to make sense of the data being generated.

VIB research hits bioRxiv’s most downloaded top 10

31/01/2019 - Every year, Rxivist compiles a list of the most downloaded bioRxiv preprints. The organization has recently put together the list for 2018​. At number 10, we find a paper from the Yvan Saeys group at the VIB-UGent Center for Inflammation Research.

VIB scientists develop best methods for automated flow cytometry analysis

16/07/2016 - Flow cytometry has been widely used by immunologists and cancer biologists for more than 30 years as a biomedical research tool to distinguish different cell types in mixed populations based on the expression of cellular markers.

GenomeView wins 'Most Creative Visualization' Award

15/09/2011 - Thomas Abeel, VIB Department of Plant Systems Biology, UGent, is one of the winners in the first iDEA (Illumina’s Data Excellence Award) Challenge

VIB scientists win DREAM-5 for systems biology

18/03/2011 - The DREAM is the most important benchmark for the comparison of computational models used in systems biology. Among all the top labs, their test was unanimously rated the overall best performer based on a number of gold standard data sets.

Yvan Saeys

Yvan Saeys

Research area(s)


PhD: Ghent Univ., Ghent, Belgium, 2004
Postdoc: Univ. Claude Bernard, Lyon, France, 2009
Postdoc: Ghent Univ., Ghent, Belgium, 2009-2013
Professor: Ghent Univ., Ghent, Belgium, since 2015
VIB Group leader since 2015

Contact Info

VIB-UGent Center for Inflammation ResearchUGent-VIB Research Building FSVMTechnologiepark 71 9052 GENTRoute description