PhD Student “Integration of Multi-Omics for a Novel Therapeutic Approach to Inflammatory Bowel Disease” KU Leuven Translational Research in GastroIntestinal Disorders Belgium



The Leuven IBD research group headed by Prof. Dr. Séverine Vermeire has an extensive track record in the field of inflammatory bowel diseases. By conducting both translational and clinical research, we want to advance knowledge about the pathogenesis of these diseases, to provide better patient care and ultimately to obtain a cure. The etiology of this multifactorial disorder remains largely unknown, but complex interactions between the immune system, microbial and environmental factors, and host genotype are involved. Our research group focuses on each of these factors and combines advanced technologies (metagenomics, genomics, RNA sequencing, metabolomics, proteomics, etc.) with a deep interest in the integration of complex omics and computational modeling. Our group is now looking for a dynamic and highly motivated student to enforce our multidisciplinary research team, and to start a 4-year PhD project.

Our group is based at the Translational Research Center for Gastrointestinal Disorders (TARGID) and works closely together with gastroenterologists of the UZ Leuven, referral center for Belgian IBD patients as well as patients from neighboring countries. Moreover, our group has established a widespread network of national and international collaborations in the field of IBD.

Asavailable treatment options for inflammatory bowel disease are rapidlyincreasing, biomarkers predicting response to treatment have to be identifiedin an attempt to achieve individualized medicine. Similar to the oncologyfield, biomarker development will only move forward by applying genomics,proteomics, transcriptomics, metagenomics and/or metabolomics, and integratethese with clinical, endoscopic, histological and radiological findings.


Withthis project, we will first study if proteins (biomarkers) in the blood,measured just before start of a new therapy via mass spectrometry in 500 IBDpatients can help to predict which patients will benefit most from a particulardrug. Finding a blood-based marker would be particularly good as this is easyto study and measure. Although we discovered already several transcriptomic biomarkersat the mucosal level, patients prefer blood tests instead of mucosal biopsies.Therefore, whole blood (surrogate) transcriptomic biomarkers, reflectingformerly identified tissue or peripheral blood mononuclear cells-derivedbiomarkers, are eagerly awaited, especially as they it would be easily toimplement in daily clinical practice.


Additionally,we will study whether the combination of those transcriptomic and proteomicdata, together with the host’s genome (genomics), the microbiome (metagenomics)and the immune system will further improve the accuracy of predicting thetherapeutic response of biological agents.


Thisproject will deliver a biomarker panel, enabling a more accurate prediction of (non)responseto anti-TNF therapy, vedolizumab, ustekinumab and/or tofacitinib in patientswith Crohn’s disease and ulcerative colitis. Instead of a ‘one-size fits allprinciple’, this biomarker panel will provide a more personalised approach inindividual patients. Even if we can identify a biomarker panel which predictsnon-response to a particular drug, this is also very important as it wouldprevent un-necessary use of drugs with a very low likelihood of leading toimprovement of patients.



Develop and/or implement scripts, bioinformatics analyses pipelines, computational tools, and databases for mining and visualization of large high-throughput datasets
Generate methods for integrative analyses of multi-omics data
Provide computational guidance and supervision of masterthesis students and other members of the lab
Write peer-reviewed articles in international journals in the field of IBD and bioinformatics
Present data at national and international conferences

Master in (bio)medical sciences, bioinformatics, computer science, computational biology, (bio)statistics or equivalent
Experience in coding, machine learning, biomarker detection is a plus
Interest in analyzing and integrating complex omics- and clinical datasets
You can work independently and in a team
You can work with great precision and you are flexible
Ability to understand and translate between wet-lab scientists, clinicians and IT-professionals
Excellent English verbal and written communication skills, ideally also Dutch

A doctoral position for 4 years in a stimulating scientific environment as part of a dynamic, multidisciplinary team
Access to state-of-the-art infrastructure
Work in a leading lab with a widespread network of (inter)national collaborations.
Great expertise in the field of inflammatory bowel diseases
Competitive salary and benefits package
Starting date: 1st of October 2019


Please send a motivation letter alongwith your CV and 2 recommendation letters to Prof. Dr. Séverine Vermeire (


You can apply for this job no laterthan June 1th, 2019.


For more information please contact Prof. dr. Séverine Vermeire, tel.: +32 16 37 74 71, mail: or Mr. Bram Verstockt, tel.: +32 16 37 36 10, mail:

You can apply for this job no later than June 01, 2019 via the online application tool
KU Leuven seeks to foster an environment where all talents can flourish, regardless of gender, age, cultural background, nationality or impairments. If you have any questions relating to accessibility or support, please contact us at

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