PhD position in Data-driven epidemiology and biology of infection

The Department of Medical Biochemistry and Microbiology (IMBIM) at Uppsala University provides a broad international environment for research and teaching. Research at IMBIM) broadly spans the areas of biochemistry, cell and molecular biology, tumour biology, comparative genetics, functional genomics, immunology, bacteriology, and virology. The research is essentially of fundamental nature, but with relevance and application in health and disease in both animals and humans. More info: Research - Uppsala University

Data-driven life science (DDLS) uses data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) aims to recruit and train the next generation of data-driven life scientists and to create globally leading computational and data science capabilities in Sweden. The program is funded with a total of 3.3 billion SEK (about 290 MUSD) over 12 years from the Knut and Alice Wallenberg (KAW) Foundation.

In 2025 the DDLS Research School will be expanded with the recruitment of 19 academic and 7 industrial PhD students. During the course of the DDLS program more than 260 PhD students and 200 postdocs will be part of the Research School. The DDLS program has four strategic research areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and biology of infection. For more information, please see DDLS Research school - SciLifeLab

The future of life science is data-driven. Will you be part of that change? Then join us in this unique program!

At Uppsala University, we are announcing the position as DDLS PhD student in Data driven epidemiology and biology of infection.

Data driven epidemiology and biology of infection covers research that will transform our understanding of pathogens, their interactions with hosts and the environment, and how they are transmitted through populations. Research will have a strong focus on computational analysis or predictive modelling of pathogen biology or host-microbe systems for which multidimensional, genome-scale experimental data are now available or it may use population-scale genetic, clinical, or public health data from pathogen surveillance efforts and biobanks.

We seek a highly motivated individual, with an ability to work independently and a strong interest in pursuing a PhD degree in Data driven epidemiology and biology of infection. The expected starting date is September 2025, or as otherwise agreed.

Project description: This PhD project is part of the Data-Driven Life Science (DDLS) research school supported by the SciLifeLab and Wallenberg National Program. The research group at the Department of Medical Biochemistry and Microbiology where the candidate will be joining is focusing on mechanisms and dynamics of plasmid copy number in pathogenic bacteria, with a strong focus on infection biology and evolution of antibiotic resistance. The goals for this project are i) to better understand the role of small cryptic plasmids in the development and spread of antibiotic resistance, and ii) Use machine learning tools to examine the complex interplay between bacterial hosts, various plasmids and resistance. To reach these goals, the successful candidate will have access to a large collection of genetically well-characterized microorganisms, infection models, and an interactive and stimulating working environment.

Duties: The successful candidate will primarily engage in research work and doctoral studies. Other duties at the institution are administration and teaching that may be included in the employment at a maximum level of 20 %.

Requirements
To meet the entry requirements for doctoral studies, you must

• hold a Master’s (second-cycle) degree in Machine learning, Computer science, Bioinformatics, Infection Biology or a related field, or
• have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
• have acquired substantially equivalent knowledge in some other way.

We are looking for a candidate who has a strong interest in data-driven research in infection biology. Previous practical experience in machine learning, deep learning and relevant software framework (R and Python) is highly desired. Very good oral and written communication skills in English are required. Emphasis will also be given on personal qualities such as collaboration and communication skills as well as analytical capacity. Ability to take own initiatives as well as to work well independently and in interaction with other research groups is an asset.

Additional qualifications
Working knowledge in statistics and infection biology is highly appreciated.

Part of the DDLS program, to be employed as a PhD student, the applicant must be accepted in a doctoral programme at Uppsala University. Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date September 2025 or as agreed. Placement: Uppsala

For further information about the position, please contact: Asso. Prof. Helen Wang, helen.wang@imbim.uu.se.

Please submit your application by May 28 2025, UFV-PA 2025/1038.

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