PhD scholarship in Bioinformatics/Mucosal Immunology

Wednesday 19 May 21

Apply for this job

Apply no later than 30 June 2021
Apply for the job at DTU Health Tech by completing the following form.

Apply online

We are looking for a bright and motivated PhD student in bioinformatics/mucosal immunology with documented experience in the analysis of single cell-RNA sequencing (scRNA-seq) data sets to join our team within the Mucosal Immunology group at the Section of Experimental and Translational Immunology, DTU HealthTech.

You will join an exceptional team of mucosal immunologists, bioinformaticians and imaging specialists at DTU and Stanford University focused on generating a single cell Atlas of human intestinal immune compartments in health and in Inflammatory Bowel Disease. The team was established as a result of one of several consortium  grants awarded by the Helmsley Trust, USA dedicated to establishing an atlas of the human intestine in health and in Crohn’s disease at single cell resolution and is part of the broader International ‘Gut Cell Atlas’ consortium. As such this position offers a unique opportunity to join a team of scientists working at the very forefront of the field of human gut immunology in health and disease and to work together with international experts in the field of bioinformatics, immunology, gastroenterology and spacial trancriptomics.

Responsibilities and qualifications
You will contribute to driving the analysis of scRNA-seq data sets of human intestinal immune (T cells, antigen presenting cells, B cells) and stromal (endothelial and mesenchymal stromal cells) isolated from the human healthy and Crohn’s disease intestine and associated lymphoid tissues. In doing this you will work closely with wet lab and bioinformatic colleagues at DTU HealthTech, clinical collaborators at nearby Hvidovre, Herlev Hospitals as well as expert bioinformatics and immunologists at Stanford University.

Types of analysis will include processing of single cell RNA, CITE-seq and TCR/BCR data from raw sequencing data to publication ready plots including:

  • Establishment of pipelines integrating current and novel bioinformatic tools and algorithms
  • Identification of cellular subsets and cellular states, cellular trajectories, intra- and inter-cellular signaling and communication modules,
  • Tracing of T (TCR) and B cell (BCR) clonality and transcriptional states during activation in intestinal lymphoid tissues
  • Assessment of tissue and disease specific alterations cellular composition and states

You must have prior experience/expertise in the analysis of scRNA-seq data. Experience in in R and unix based systems is necessary as our main pipelines are based on these. Prior documented experience and/or courses in the field of Immunology will be seen as a considerable strength in the final judgement of applicants for this position.

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

Approval and Enrolment
The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see the DTU PhD Guide

The assessment of the applicants will be made by the Laboratory head Professor William Agace. 

We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

Salary and appointment terms
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. The period of employment is 3 years. Starting date is 1st October 2021 (or according to mutual agreement). 

You can read more about career paths at DTU here

Further information
Further information about the group can be obtained by visiting our website: Mucosal Immunology group and about the project by contacting Professor William Agace at

You can read more about DTU Health Tech at

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark

Application procedure
Your complete online application must be submitted no later than 30 June 2021 (Danish time)Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

  • A letter motivating the application (cover letter)
  • Curriculum vitae
  • Grade transcripts and BSc/MSc diploma
  • Excel sheet with translation of grades to the Danish grading system (see guidelines and Excel spreadsheet here)
  • A one page summary documenting experiences/training with single-cell RNA-seq analysis and, where applicable, the field of Immunology.

You may apply prior to ob­tai­ning your master's degree but cannot begin before having received it.

All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.

DTU Health Tech
DTU Health Tech engages in research, education, and innovation base on technical and natural science for the healthcare sector. The Healthcare sector is a globally expanding market with demands for the most advanced technological solutions. DTU Health Tech creates the foundation for companies to develop new and innovative services and products which benefit people and create value for society. DTU Health Techs expertise spans from imaging and biosensor techniques, across digital health and biological modelling, to biopharma technologies. The department has a scientific staff of about 175 persons, 130 PhD students and a technical/administrative support staff of about 80 persons.

Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear vision to develop and create value using science and engineering to benefit society. That vision lives on today. DTU has 12,900 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. Our main campus is in Kgs. Lyngby north of Copenhagen and we have campuses in Roskilde and Ballerup and in Sisimiut in Greenland.