PhD Fellowship in Molecular epidemiology/bioinformatics

This PhD project focuses on integrating genetic and epidemiological data for the purpose of understanding the molecular epidemiology and patterns of emerging infectious diseases. The project is an aspect of the PandemiX Center’s research to discover signature patterns in historical and contemporary pandemics and emerging threats.

Department of Science and Environment, Roskilde University, invites applicants for a PhD fellowship in molecular epidemiology from

January 1, 2025
, or as soon as possible thereafter. The project will be part of the PandemiX Center of Excellence, which is funded by the Danish National Research Foundation (DNRF) and led by professor of epidemiology Lone Simonsen (LS). In the interdisciplinary PandemiX Center, we use mathematical and statistical models to study the spread and impact of epidemic infectious disease, and to make predictions regarding effect of interventions such as vaccines programs. One of the four pillars of the PandemiX Center is the bioinformatics/evolutionary biology focus led by Anders Gorm Pedersen (AGP) at the Technical University of Denmark (DTU).

You will work primarily at the PandemiX Center’s offices at Statens Serum Institut (SSI), with 1-2 days weekly at DTU. working closely with AGP.

The position as PhD fellow is limited to 3 years when a full-time study.

Description of the PhD project
This PhD project focuses on the analysis of whole-genome viral genetic data, where you will use sequence data that is already in the public domain as well as data obtained via the Centers’ own sequencing efforts. You will use molecular epidemiology methods to uncover the features characterizing the emergence of a novel pathogen into the human population. An example is the current mpox situation, in which multiple clades of the virus cause different types of outbreaks in the human population in central Africa (by various modes of zoonoses, sexual transmission and skin-to-skin transmission). The work will thus straddle what can be gained from the study of genetic signatures (such as the accumulation of APOBEC3 mutations) with existing epidemiological information from surveillance efforts and special studies (such as age- and gender-patterns, disease severity and transmissibility and population-level immunity from serology studies), as well as insights into the societal context of the outbreaks. Other examples include the Nipah virus, Marburg virus, and H5N1 influenza. Depending on the problem/virus under study, you will also interact with domain experts in the fields of especially virology and immunology from our collaborators at the Statens Serum Institute and elsewhere in Danish and international academia. The research will involve both observational and theoretical research with a focus on exploring viral evolution in the pre-pandemic perspective for a pandemic threat (zoonoses), and seeking to identify the host-pathogen interactions that determine the adaptation of the virus to the human host. It may include the study of already emerged viruses in the same family, as well as the study of genetic changes in general in response to human population-level immunity from infectious and vaccination. It is expected that you briefly describe a project idea in the application; the exact PhD project will be decided later in collaboration with the supervisors LS and AGP.

Doctoral School
You will be enrolled as a PhD fellow at the Doctoral School of Science and Environment, where you will teach and conduct research in an innovative and application-oriented manner in real-world science. Basic and applied research go hand in hand here, and our research generates new knowledge and useful innovation. Read more here: https://ruc.dk/en/department-science-and-environment

Research environment at PandemiX
You will be a part of the PandemiX Center of Excellence. The overall research objective of the Center is to investigate signature features of pathogens with pandemic potential (including historical outbreaks), to better prepare for future pandemics. We strive to make breakthroughs not hitherto possible or attempted, ranging from a profound understanding of how to control transmission in the short run, to how best to secure robust population immunity in decades to come. The PandemiX Center will give rise to a new field, pandemiology, home to a growing cadre of interdisciplinary researchers ready to address the inevitable next pandemic. PandemiX is a Roskilde University (RUC) Center of Excellence, and the Center has offices at Statens Serum Institute (SSI) in Copenhagen. The PandemiX partners include the Niels Bohr Institute (NBI) at the University of Copenhagen (UCPH), the Technical University of Denmark (DTU) and North Zealand Hospital (NOH). The work environment at the PandemiX Center is highly interdisciplinary with great scientific and social interactions with many talented researchers. Read more about the PandemiX Center of Excellence here:

Responsibilities and tasks
The PhD position is an educational position and the main tasks are in accordance with chapter 3, Ministerial Order on the PhD Programme at the Universities and Certain Higher Artistic Educational Institutions (https://ufm.dk/en/legislation/prevailing-laws-and-regulations/education/files/engelsk-ph-d-bekendtgorelse.pdf)

Qualifications
We are looking for a talented, highly motivated and creative applicant with a Master's degree in Bioinformatics/Molecular epidemiology, and with documented skills in methods for analysing viral genomic data. Special emphasis is put on having experience with methods for phylogenetic and evolutionary analysis. We are looking for someone who is interested in pursuing quantitative studies of epidemic infectious diseases in human populations. We are looking for someone who is equally interested in the analytical aspects of the question (what one can find out from viral genetic patterns), to basic research type of questions in the exciting field of molecular epidemiology. The successful candidate must be imaginative, enjoy an interdisciplinary workplace, and above all have strong skills in bioinformatics and be interested in embracing through course work and collaborations also other methods and applications that we use to study emerging pathogens in the Center. The candidate must have excellent English skills, both written and orally. Finally, we value initiative and good collaboration and communication skills. We expect you to participate in the daily activities of the Center and engage in interdisciplinary exchange of ideas and collaborations.

Assessment process
In the assessment regarding employment, the following will be considered:

• Relevant Master's degree or the equivalent according to the Danish Qualifications Framework for Higher Education in molecular epidemiology or bioinformatics
• Other academic qualifications as described in this job posting.

The assessment will further include:

• Educational competencies and further relevant qualifications
• Grades from Master’s degree or the equivalent
• Quality and relevance of your project idea
  • Your project description may not exceed 3 pages (of each 2.400 incl. spaces)
• Quality and relevance of the methodological and theoretical choices
• Consistency and coherence between the project and the choice of method and theory
• Whether the project appears realistic and feasible
• Whether the candidate has adequate qualifications and experiences to carry out the PhD project
• Relevance of the project for the Doctoral School of Science and Environment

More information
For further information about the position please contact Professor Lone Simonsen Tel. +45 23 42 95 03 E-mail: [email protected].

Terms of employment
The employment is full-time, 37 hours/week. The principal supervisor will be Lone Simonsen, Department of Science and Environment, Roskilde University, Denmark. E-mail: Professor Anders Gorm Petersen at DTU and a co-investigator at PandemiX will be co-supervising the student

The position will be filled according to the Agreement between the Danish Ministry of Finance and the Danish Confederation of Professional Associations (AC) and Job Structure for Academic Staff at Universities.

Application procedure
After the deadline for applications the Dean will shortlist applicants for assessment with assistance from the recruitment committee including the chairperson of the assessment committee.

Shortly after the application deadline all applicants will be notified whether or not their application has been selected for assessment.

The shortlisted applicants will be informed about the composition of the assessment committee, and each applicant will be given the opportunity to comment on the composition of the committee and - later on - their assessment.

Once the recruitment process is completed, all applicants will be informed of the outcome of their application.

Application
To apply for the position go to www.ruc.dk/en/job/

Only applications in English are accepted.

Applications must include:

1. Cover Letter detailing motivation and background for applying for the specific PhD project.

2. PhD project idea with original research idea (max 3 pages, of each 2.400 incl. spaces).

3. Curriculum vitae (CV) including information about education, research experience, language skills, and other relevant qualifications.

4. Original diplomas for a Master’s degree, and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish.

5. Publication list (if applicable).

6 . Reference letters (if available).

Please submit your application no later than November 1, 2024.

Material received after this date will not be taken into consideration.

Roskilde University wishes to reflect the diversity of society and welcomes applications from all qualified candidates regardless of personal background.

Department: Universitetsvej 1, Roskilde

Location: Roskilde Universitet