PhD research fellow immuno-informatics in inflammatory bowel disease

PhD research fellow immuno-informatics in inflammatory bowel disease

Published Deadline Location
15 May 1 Jun Amsterdam
We are looking for an enthusiastic PhD student who will work on personalizing the treatment of inflammatory bowel disease.

Job description

Inflammatory bowel disease (IBD) constitutes a group of incurable, chronic, relapsing diseases of the gastrointestinal tract, stemming from a dysregulated interplay between the environment and the immune system in genetically susceptible individuals. Treatment typically involves suppressing inflammation, aiming to induce or maintain a state of endoscopic remission. Currently, this is accomplished through monoclonal antibodies or small molecules targeting inflammation mediators like TNF (infliximab and adalimumab), IL12/23p40 (ustekinumab), and the JAK-STAT pathway (tofacitinib and upadacitinib), or molecules involved in immune cell recruitment to the gastrointestinal tract, such as integrin α4β7 (vedolizumab). Despite the established efficacy of these biological treatments, sustained endoscopic remission is observed in fewer than a third of patients after one year of treatment. Hence, a personalized treatment is highly warranted. Previously, we identified several epigenetic biomarkers in peripheral blood capable of prognostically predicting response, which is currently funded by the Horizon Europe consortium grant entitled METHYLOMIC.

We are looking for a highly motivated applied bioinformatician who is willing to lead the bioinformatics and data analytical side of this project in understanding response to therapy. This position is funded by the aforementioned METHYLOMIC grant in combination with a local institutional grant.

The overarching aim is to personalize treatment to ensure patients are provided the most optimal care. Your primary focus will involve the analysis of existing omics datasets from IBD patients to gather insights in driving subsequent experiments. You will be working extensively with single-cell technologies and machine learning assisted analyses of epigenetic markers to identify specific cellular subsets linked with disease progression and therapy response. Accordingly, a key aspect of your work will involve leveraging both external and internal datasets to inform subsequent experiments.


Amsterdam UMC


We are looking for a candidate with:
  • A master's degree in Biomedical Sciences, Infection & Immunity, or a related life-science field, with a strong emphasis on applied data analysis and/or machine learning;
  • Prior experience in performing (in vitro) and analyzing (in silico) omics data, such as RNA-sequencing, DNA methylation microarrays. Previous exposure to single-cell omics technologies, such as single-cell RNA-sequencing, is desired;
  • Proficiency in R, Python, and bash scripting, along with familiarity working in a Linux environment using schedulers, is expected;
  • Previous exposure to workflow management systems like Snakemake and/or Nextflow is preferred;
  • Good written and verbal communication skills in English are essential to communicate in our international team;
  • You are inherently driven, scientifically curious, and adept at collaborative teamwork.

Conditions of employment

  • A flying start to your career in scientific research.
  • Plenty of room for personal development with a wide range of training & development of academic skills
  • Working on large-scale and own research, with motivated colleagues
  • A contract for 6 months with the prospect of extension for the duration.
  • Salary scale: OIO: € 3.017 tot € 3.824 bruto (based on a fulltime workweek), depending on qualifications and experience.
  • Additional benefits including an 8.3% end-of-year bonus and 8% holiday pay. Calculate your net salary here.
  • Your pension is accrued at BeFrank. A modern, understandeble en fair pension
  • Excellent accessibility with public transportation and reimbursement of a large portion of your travel expenses. Additionally, we have plenty of parking spaces at the AMC location and a good bicycle scheme.


Amsterdam UMC

You will be collaborating with researchers at the Tytgat Institute for Liver and Intestinal Research and the Department of Gastroenterology at Amsterdam UMC. The Tytgat Institute consists of approximately 70 researchers engaged in fundamental, applied, and clinical research within the fields of gastroenterology and hepatology. While you will primarily work with colleagues at the Tytgat Institute, we actively encourage you to collaborate with peers outside the Tytgat Institute to facilitate knowledge exchange.

Additional information

During the publication period, applications will be handled continuously. If the vacancy is filled, it will be closed prematurely.

The first interviews will take place in mid-June, we ask that you take this into consideration in advance.

If you have any questions about this position, please feel free to contact Andrew Li Yim, via a.y.liyim@amsterdamumc.nlor Wouter de Jonge, via

For more information about the application procedure, please contact Chey Edwards, Recruitment Advisor, via or via +316 214 87 245.

A reference check, screening and hiring test may be part of the procedure. Read here whether that applies to you. If you join us, we ask you for a VOG (Certificate of Good Conduct).

Internal candidates will be given priority over external candidates in case of equal suitability.

Acquisition in response to this vacancy is not appreciated.


  • PhD
  • Health
  • max. 36 hours per week
  • €3017—€3824 per month
  • Doctorate
  • 11584



Meibergdreef 9, 1105AZ, Amsterdam

View on Google Maps

Interesting for you


Apply for this job

Apply for this job

This application process is managed by the employer (Amsterdam UMC). Please contact the employer for questions regarding your application.

Thank you for applying

Please contact the employer for questions regarding your application.

Tip: save this job as favorite in your AcademicTransfer account. This gives you an immediate overview and makes it easy to find the job later on. No account yet? Create it now and take advantage of other useful functionalities too!

Application procedure

Application procedure

Make sure to apply no later than 1 Jun 2024 23:59 (Europe/Amsterdam).