PhD position in Data driven epidemiology and biology of infection

jobs
Published

July 5, 2026

Umeå University campus buildings by the pond in summer

Before you read the ad

  • We don’t expect you to fit “a box”. Many of us don’t as we work interdisciplinary. We are looking for a computer scientist but if you think you got a similar skill set, by all means, do not self-select out!
  • Our lab is very collaborative. Few big challenges are solved by an individual in isolation
  • We value independent thinking. At the end of this PhD you should ideally be one of the best people in the world at the topic you choose; we can only guide you but the path is yet to be figured out. We are counting on you to figure out the route
  • We are not an “AI-lab”. We treat AI as a tool among any other, but nobody joining our lab will be forced to use AI. A PhD is a time to learn and we think AI poses a real danger of robbing you of this opportunity. You will however be allowed to use AI if you show that you can use it appropriately and understand the risks.
  • Our lab is rather technology-oriented; a detail-oriented mindset is probably ideal, because getting technology to work is all about the details!
  • We value honesty. Nobody wins from overselling themselves, and nobody wins from hiding failure. The license to independent thinking includes the license to fail!

This ad is a preview. A formal ad will be posted toward August. Those interested can contact us directly already.

PhD position in Data driven epidemiology and biology of infection

Background

The Department of Molecular Biology at Umeå University is searching for a DDLS PhD student in Data driven epidemiology and biology of infection with start date 1 September 2026, or as agreed. The future of life science is data-driven. Will you be part of that change? Then join us in this unique program!

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 are looking for a PhD student with an interest in algorithms, data structures, high-performance computing, but also with aspects of machine learning and microbiology. A PhD will be awarded in the topic of Molecular Biology, but the PhD will primarily focus on developing new algorithms and databases in the context of bioinformatics.

The position at the Department of Molecular Biology at Umeå University is temporary for four years to start immediately or as agreed. The student will be enrolled in the Umeå University Technical Faculty PhD school for Molecular Biology, as well as the national DDLS PhD school for Data driven epidemiology and biology of infection. However, we do not expect applicants to have a molecular biology background.

The PhD student will participate in activities provided by the Department of Molecular Biology, the Laboratory for Molecular Infection Medicine Sweden (MIMS), and the Umeå Centre for Microbial Research (UCMR). Furthermore, the student will take part in Data-driven Life Science (DDLS) national activities and have access to the Wallenberg AI, Autonomous Systems and Software Program (WASP). This enables interaction with researchers from different research fields and access to various scientific and technical expertise.

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 over 12 years from the Knut and Alice Wallenberg (KAW) Foundation.

In 2026 the DDLS Research School will be expanded with the recruitment of 25 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 the DDLS research school.

Description of tasks

Our group develops new single-cell multiomic methods to characterize microbial genomes, resulting in vast (terabyte-petabyte) amounts of data. Using this technology, we aim to characterize complex bacterial communities across different environments, to be stored for deeper analysis and visualization in a Microbial Cell Atlas. This position aims to develop key software components to enable this mission. The results of this project will be used to track new pathogens, combat antimicrobial resistance and biological threats, and find new enzymes of broad interest (e.g., CRISPR gene editing). It will also reduce environmental impact of bioinformatics and promote safe computing standards.

Our software is built primarily in Rust, with R and Python parts to support bioinformaticians. Our web frontend is also developed in Rust (web assembly) – all to support fast computing and handling of complex single-cell data. The software is designed from the ground up for a new type of data (single-cell whole-genome sequencing/metagenomics), and how to best analyze the data is an open research problem. Analysis covers preprocessing, assembly of DNA fragments into complete genomes, imputation of missing data, filtering of bad data, prediction of the meaning of the DNA in individual cells, compression for archiving, indexing and visualization. Our hardware encompasses CPU and GPU-nodes, and software will be designed for both multithreading and horizontal scaling.

The PhD student will become part of an interdisciplinary team of researchers and engineers, covering chemistry, microbiology, computing science, mathematics and data science. As a major team effort, the PhD student is not expected to carry out all tasks, but rather identify and tackle suitable subproblems. Experience of a statically typed programming language is however a must. We encourage independent thinking, from problem definition to solution, and projects are flexible.

A person who is employed as a PhD student shall primarily devote his-/or herself to his/her own education. The project and research environment will give the dedicated student the opportunity to train as a first-class researcher.

Qualifications

We envision applicants to come primarily from computing science, but anyone with equivalent experience or skill set is welcome to apply.

Applicants must hold a University degree equivalent to a European University Master degree or completed course requirements of at least 240 credit points, of which at least 60 credit points should be at second-cycle level. (clarification: it appears that a US undergrad might be enough to fulfill this criterion but it’s something we need to investigate further if someone applies)

To fulfil the general entry requirements, the applicant must have qualifications equivalent to either a completed degree at advanced level (second-cycle), or completed course requirements of at least 240 ECTS, including at least 60 ECTS at advanced level, or has otherwise acquired essentially equivalent knowledge within Sweden or abroad. The faculty board may, in the case of a specific applicant, consent to an exemption from the general entry requirements if there are special reasons to do so. (Higher Education Ordinance, Chapter 7, Section 39).

To meet the specific entry requirements for doctoral education in molecular biology, the applicant must have completed higher education studies comprising at least 90 credits in a relevant subject area. As this project is focused on algorithmic development, the relevant subject area can be interpreted widely.

The requirements for prior knowledge as described above are also considered to be met by those who have otherwise acquired essentially equivalent knowledge.

You must be proficient in both oral and written communication in English.

The candidate is required to:

  • Have experience of a statically typed language
  • Have knowledge of algorithm design and common data structures
  • Have significant experience of programming or computing science

It is merit if the candidate has:

  • Experience of Rust
  • Experience of web development and dynamic websites
  • Basic knowledge of mathematics (e.g. linear algebra, probability, statistics, stochastic processes)
  • Experience of developing code in larger projects
  • Any knowledge of biology
  • While we don’t expect applicants to know biology, applicants are expected to learn a sufficient amount during the course of the PhD, as to be able to effectively communicate with others, and formulate solutions to bioinformatics problems in terms of algorithms. The PhD course package will be adapted to the needs of the student.

It is to lesser extent a merit if the candidate has:

  • Experience of R and Python
  • Experience of machine learning (ideally with the PyTorch framework)
  • Experience of bioinformatics (especially of de novo assembly, single-cell analysis, and microbial bioinformatics)

You should be highly motivated and able to work productively in a team as well as independently. Excellent communication skills for interacting effectively with senior colleagues and peers are required. Great emphasis will be placed on personal suitability.

As an employee with us, you contribute to fostering an inclusive culture and a positive work environment. This involves communicating effectively across differences, demonstrating a collaborative spirit and the ability to work well with others. You maintain openness and a welcoming attitude, showing respect, compassion, and empathy. You engage with and support colleagues from diverse backgrounds and perspectives, and promote a healthy work-life balance for both yourself and others.

Basis of assessment

The evaluation of the ability and potential to assimilate the education is mainly based on:

  1. Knowledge and skills relevant to doctoral studies within the research area,

  2. The ability to formulate and solve scientific questions.

  3. Skills in written and oral communication in English.

  4. Other experience relevant to doctoral studies, such as professional experience.

Good collaborative skills, drive and independent work ability are considered positive merits.

A selection will be made among qualified applicants on the basis of their qualifications and their ability to benefit from studies at the doctoral level. After the selection of the suitable candidate, the process for the admission to doctoral studies will commence. An admission decision will be taken by the prefect.

About the employment

The position is intended to result in a doctoral degree and is limited to four years full time. If part-time teaching (max. 20%) can be offered, the employment period can be extended.

Start date 1 September 2026, or as agreed.

Wage placement takes place according to the established salary ladder for doctoral student employment.

According to the Higher Education Ordinance (Chapter 12, Section 2), the decision on employment cannot be appealed.

The PhD will result in a title of “PhD in Molecular Biology”, awarded by Umeå university, Faculty of Science and Technology

About Umeå University, Faculty of Science and Technology

Umeå University is one of Sweden’s largest higher education institutions with over 41,500 students and about 4,600 employees. The University offers a diversity of high-quality education and world-leading research in several fields. Notably, the groundbreaking discovery of the CRISPR-Cas9 gene-editing tool, which was awarded the Nobel Prize in Chemistry, was made here. At Umeå University, everything is close. Our cohesive campuses make it easy to meet, work together and exchange knowledge, which promotes a dynamic and open culture.

The ongoing societal transformation and large green investments in northern Sweden create enormous opportunities and complex challenges. For Umeå University, conducting research about – and in the middle of – a society in transition is key. We also take pride in delivering education to enable regions to expand quickly and sustainably. In fact, the future is made here.

Are you interested in learning more? Read about Umeå University as a workplace