PhD in Medical Science

PhD in the subject Medical Science and the research area Microbiology in the Medical Area

Description of research environment
The Systems Virology Group is located at the Department of Translational Medicine and is led by Associate Professor Joakim Esbjörnsson. The group uses various bioinformatics and phylogenetics methods to combine genetic, clinical, and epidemiological data to explain how viruses evolve and adapt to new environments—both at the population level and within individual hosts. In addition, various experimental model systems are used to study in detail how virus-host interactions regulate disease progression. The research is therefore often based on complex and multifaceted (often longitudinally collected) data that require advanced biostatistics and modelling. Furthermore, identified key markers and regulators of disease progression are evaluated functionally in various human cell and tissue model systems to assess their potential as treatment or vaccine targets. Here you can read more about our exciting research.

Within the research group, we value a good working environment with respect and care in our relationships with one another. We strive for a workplace that is perceived as both rewarding and stimulating for all employees, and we continuously work to create conditions for job satisfaction, development, and participation for everyone. We care for both physical safety and the psychosocial work environment.

The Department of Translational Medicine is now announcing a doctoral position and employment as a PhD student in the Systems Virology group at the department.

Subject
Medical Science

Project description
Curbing the human immunodeficiency virus (HIV) epidemic represents one of the major challenges of our time with approximately 40.8 (37.0-45.6) million people infected globally. Acute HIV-1 infection is characterized by high levels of virus replication; that is manifested as a peak rise in plasma HIV-1 RNA levels up to 6-8 log/ml, a decline in CD4+ T cells approximately two weeks after infection and sometimes accompanied by non-specific flu-like symptoms. The viral replication comes under control when the host defenses are mobilized against the virus, leading to a slow decline to a steady-state viral load, or set point, of between 3-5 log/ml at approximately four months post-infection. Peak viral load levels in adults are not predictive of the rate of disease progression. However, the viral set point (the level at which viral load is maintained during this early, asymptomatic period) is predictive of the length of the asymptomatic period and AIDS-free survival. This is most likely a measure of the dynamics between the virulence of the infecting virus strain, and the ability of the host immune system to contain the virus. The rate of progression of HIV-1 infection to AIDS is highly variable among individuals, developing an average of 9-10 years after infection in most adults in the absence of antiretroviral therapy. 

The overall objective of the PhD project is to study HIV-1 evolution and human immune responses in acute HIV-1 infection, and ultimately how the interplay between virus and host dictates HIV-1 pathogenesis.

Tasks
The PhD student’s main tasks will be to conduct one's own postgraduate education. This includes, in addition to completing mandatory doctoral courses, using sequence analysis (including phylogenetics [both maximum-likelihood and Bayesian analysis], molecular properties analysis, analysis of adaptation and selection), proteomics analysis (including differential expression analysis, enrichment analysis, structural equation modelling, and supervised dimensionality reduction methods), systems biology analysis (including machine learning and other AI techniques), statistical tools focusing on analysis of complex longitudinal data, and how different types of data are interconnected (including mixed effects modelling). In addition, hands-on experience will be gained from applying all the experimental methods that were used to generate the existing data in the laboratory. An important part of doctoral education is to analyse generated results and present them in the form of scientific manuscripts and articles.

Eligibility
Students with basic eligibility for third-cycle studies are those who have:

• completed a second-cycle degree.
• have completed courses of at least 240 credits, of which at least 60 credits are from second-cycle courses, or
• have acquired largely equivalent knowledge in some other way, in Sweden or abroad.

The requirement for special qualifications are met by those who have:

• at least 60 credits in the field of medical science
• applicants must have knowledge equivalent to at least 3 years of upper secondary school proficiency in English

Specific requirements for the position:

• degree of master in bioinformatics
• knowledge of virus-host interactions, immunology and how this relates to disease development
• experience in biostatistical analysis and programming in R

Merits for the position:

• knowledge of virus-host interactions, immunology and how this relates to disease development
• experience in relevant evolutionary biology and phylogenetic sequence analysis
• publications in peer-reviewed scientific journals
• great importance will be placed on personal qualities. The tasks require that you are independent, driven, and cooperative

Basis of assessment and selection
In accordance with the provisions of the Higher Education Ordinance, the selection shall primarily be based on an assessment of the applicants' ability to benefit from the education. When making admissions, it is primarily the applicant's qualifications from the basic education that can normally be assessed. In this regard, breadth, depth and relevance, as well as elements of independent work, shall be considered.

Terms
As a doctoral student at Lund University, you are both admitted as a student and an employee.

The employment is a fixed-term employment for a total of four years, 100% with a start date 2026-02-01, or according to agreement. The main rule is that employment at Lund University is conducted in Sweden, you are therefore expected to be able to perform your work on site in Malmö. Further information regarding regulations regarding admission and employment as a doctoral student can be found on the faculty's website.

We offer
Lund University is a government agency, which means you get special benefits, generous vacation time and a favorable occupational pension. Read more about being employed with us on the university's website. 

How to apply
The position is applied for via the university's recruitment system. The application should include a personal letter explaining why you are interested in the position and how the position matches your qualifications. The application should also include a CV, degree certificate or equivalent and any other information you wish to refer to (copies of grades, information for references, letters of recommendation, etc.).