PhD scholarship in T cell immunoinformatics

DTU Bioinformatics
Tuesday 28 Nov 17

Apply for this job

Apply no later than 22 December 2017
Apply for the job at DTU Bioinformatics by completing the following form.

Apply online

A PhD scholarship is available in the Immunoinformatics and Machine-Learning group headed by Professor Morten Nielsen, at the Department of Bio and Health Informatics, DTU Lyngby.

T cells scrutinize the surface of cells for foreign peptides presented in complex with MHC (Major histocompatibility complex) molecules to check if the cell has been infected. Only a minor proportion of possible peptide produced within a cell are presented by MHC on the cell surface, and only a minor proportion of these are recognized by T cells. The PhD project will be focused on further advancing our understanding of the rules associated with this process of antigen presentation and T cell recognition, in particular in context of MHC class II and post-translational modifications.

Responsibilities and tasks
Over the last decade, our understanding and ability to predict the MHC class I pathway antigen presentation has improved substantially. This however does not hold for post-transnationally modified (PTM) antigens, where our understanding on how PTM’s impact the potential for antigen presentation remains limited. Likewise, is our ability to predict MHC class II antigen presentation limited, and data suggest that properties other that MHC binding plays a critical role for the prediction of CD4 epitopes. Finally, is our understanding of the role of the T cell and the similarity of the presented peptide to the self proteome in the context of peptide immunogenicity very limited.

Driven by data obtained from Mass-spectroscopy and in-vitro binding assays, the PhD will seek to

  • Learn the rules of antigen presentation of PTM modified peptides
  • Investigate the role of properties other than MHC binding for MHC class II antigen presentation
  • Investigate the role of self-similarity in the context of peptide immunogenicity (in particular for MHC class II)

The tools used in the project will by focused around conventional and deep neural networks.

Candidates should have a master degree or equivalent.

The successful candidate will have a bioinformatics, biology, or computer science background and must have strong computational skills and prior experience with Unix/Linux command line environments, as well as either C, Perl, Python or a comparable scripting language. The applicant must have a strong background within machine learning, bioinformatics and structural biology.

Approval and Enrolment
The scholarships for the PhD degree are subject to academic approval, and the candidates will be enrolled in one of the general degree programmes of DTU. For information about the general requirements for enrolment and the general planning of the scholarship studies, please see the DTU PhD Guide.

We offer
We offer an interesting and challenging job in an international environment focusing on education, research, scientific advice and innovation, which contribute to enhancing the economy and improving social welfare. We strive for academic excellence, collegial respect and freedom tempered by responsibility. The Technical University of Denmark (DTU) is a leading technical university in northern Europe and benchmarks with the best universities in the world.

Salary and appointment terms
The appointment will be based on the collective agreement with the Confederation of Professional Associations. The allowance will be agreed with the relevant union.

The period of employment is 3 years starting from 1 February 2018 or ASAP hereafter.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from Morten Nielsen;, tel.: +45 4525 2480.

You can read more about the Department of Bio and Health Informatics on

Please submit your online application no later than 22 December 2017 (Local time). Apply online at

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill in 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)

Applications and enclosures received after the deadline will not be considered.

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

DTU Bioinformatics has its main research and teaching activities in bio-medical and bio-technological informatics, metagenomics, epidemiology, quantitative genomics, integrative systems biology, artificial intelligence and machine learning. Research involves the use of vast amounts of phenotypic, clinical, environmental, biological and multi-omic information in humans, animals, plants and microbes. We run projects combining big data and laboratory research via the national supercomputing center or Computerome and the molecular genomics laboratories.

DTU is a technical university providing internationally leading research, education, innovation and scientific advice. Our staff of 5,800 advance science and technology to create innovative solutions that meet the demands of society; and our 11,000 students are being educated to address the technological challenges of the future. DTU is an independent academic university collaborating globally with business, industry, government, and public agencies.
16 DECEMBER 2017