PhD fellowship in Structural biology and Protein/Vaccine design Part-time

Research Assistant And PhD Fellowship Opportunity

We are offering a 6-month Research Assistant position and a 3-year PhD fellowship in Structural Biology and Protein/Vaccine Design commencing 15 September 2026.

The Novo Nordisk Foundation Initiative for Vaccines and Immunity (NIVI), launched in December 2023, has a unique mission to harness airway immunity through innovative vaccine research and development to prevent airborne epidemics. NIVI has two parts:

• NIVI Research Center (NIVI-R): A state-of-the-art research center anchored to the University of Copenhagen, Department of Immunology and Microbiology.
• NIVI Development (NIVI-D): A company that focuses on translational sciences and advancing vaccine development.

NIVI-R conducts scientific research, while NIVI-D works to quickly turn that research into new vaccine candidates. NIVI-D accelerates clinical trials (phases 1 and 2) and ensures a smooth transition to partners for later stages of development.

By connecting science, innovation, clinical trials, regulatory processes, and product development, NIVI aims to streamline the journey from research to real-world vaccines.

Our group and research Our group is part of the NIVI-R interdisciplinary research consortium. We develop computational and structure-guided approaches to understand immune recognition and design next-generation vaccines against respiratory pathogens. Our work integrates computational protein design, cryo-electron microscopy (cryo-EM), cryo-EM-based polyclonal serology (cryo-EMPEM), molecular dynamics simulations, machine learning, and structural biology to define epitopes and engineer improved vaccine antigens.

A central goal of the group is to understand how antibody recognition shapes protective immunity and how these insights can be translated into the rational design of broadly protective vaccine antigens and protein therapeutics.

We are a young, international, and collaborative team that values scientific curiosity, creativity, mentorship, and open exchange of ideas. The successful candidate will receive interdisciplinary training at the interface of computational biology, structural biology, immunology, and vaccinology, while working closely with collaborators across the NIVI teams and working groups.

Project description The PhD project will focus on the development and application of computational protein design approaches for vaccine and immunogen design. The successful candidate will combine state-of-the-art machine learning and protein design methods with experimental structural biology and immunological characterization.

Potential project directions include:

• Design of vaccine antigens targeting conserved B-cell and T-cell epitopes of respiratory pathogens.
• Development of de novo protein scaffolds, nanoparticles, and multivalent immunogens.
• Application of generative protein design and structure prediction tools including RFdiffusion, ProteinMPNN, AlphaFold, Chai, and related methods.
• Integration of cryo-EM, cryo-EMPEM, molecular dynamics simulations, and computational design workflows.
• Analysis of antibody-antigen interactions to guide antigen optimization and vaccine development.

The exact project will be tailored to the interests and background of the successful candidate.

Principal supervisor is Assoc. Prof. Monica Fernández-Quintero, Department of Microbiology and Immunology, monica.fernandez@sund.ku.dk.

Start: 15 September 2026

Duration: 6 months Research Assistant position and provided a positive evaluation a 3-year PhD student position

Job description Your key tasks as a Research Assistant and PhD student at NIVI Research Center are:

• Carrying through an independent research project under supervision.
• Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
• Participating in active research environments including a stay at another research team.
• Obtaining experience with teaching or other types of dissemination related to your PhD project
• Teaching and disseminating your knowledge.
• Writing a PhD thesis on the grounds of your project

Key criteria for the assessment of applicants Applicants must have qualifications corresponding to a master's degree related to the subject area of the project, e.g. Please note that your master's degree must be equivalent to a Danish master's degree (two years).

Other important criteria are:

• The grade point average achieved
• Professional qualifications relevant to the PhD project
• Previous publications
• Relevant work experience
• Other professional activities
• A curious mind-set with a strong interest in protein design and structural biology
• Language skills

Place of employment The place of employment is at NIVI-R, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen. We offer creative and stimulating working conditions in dynamic and international research environment. Our research facilities include modern laboratories and access to both computational resources as well as strong collaboration with core facilities for structural imaging.

Terms of employment The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 6 months + potentially 3 years. Within the 6-month employment as Research Assistant, it will be determined based on an individual assessment if the candidate is qualified for the PhD position. The start date is 15 September 2026 or any time soon thereafter.

The employment as PhD student is conditioned upon the applicant's successful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty's rules on achieving the degree.

Salary, pension and terms of employment are in accordance with the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.

Questions For specific information about the PhD fellowship, please contact the principal supervisor.

General information about PhD studies at the Faculty of Health and Medical Sciences is available at the Graduate School's website.

Application procedure Your application must be submitted electronically by clicking 'Apply for position' below. The application must include the following documents in PDF format:

• Motivated letter of application (max. one page)
• CV incl. education, experience, language skills and other skills relevant for the position
• Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your master's degree must be equivalent to a Danish master's degree. We encourage you to read more in the assessment database.
• Publication list (if possible)

Application deadline: 7 July 2026, 23.59pm CET We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor.

The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement.

Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You find information about the recruitment process at: https://employment.ku.dk/faculty/recruitment-process/

The applicants will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

When you will be affiliated with the University of Copenhagen or otherwise have access to their research, you may be required to undergo a background screening. The purpose is to protect the security and research integrity of the University of Copenhagen.

Interviews are expected to be held in week 32.

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.