Faculty of Medicine, Department of Experimental Medical Science

Lund University was founded in 1666 and is repeatedly ranked among the world’s top universities. The University has around 47 000 students and more than 8 800 staff based in Lund, Helsingborg and Malmö. We are united in our efforts to understand, explain and improve our world and the human condition.

Lund University welcomes applicants with diverse backgrounds and experiences. We regard gender equality and diversity as a strength and an asset.

Description of the workplace 

In the Atkinson lab we are interested in making discoveries about protein function and structure, with a focus on bacterial immune system components that protect against bacteriophages and other mobile genetic elements. We work mainly with bioinformatic methods, developing our own tools and taking advantage of the wealth of available genome and predicted proteome sequences. The Atkinson lab is based in the Faculty of Medicine of Lund University, in the Department of Experimental Medical Sciences (EMV) and affiliated with the Lund University Virus Centre (LUVC). You can read more about our group on our lab website here: https://atkinson-lab.com/, the department here: The Atkinson lab (atkinson-lab.com), and LUVC here Virology | Virology (lu.se)  We validate our discoveries experimentally in collaboration with the lab of Vasili Hauryliuk, with whom we have a joint team.

We are looking for a full-time bioinformatics PhD student to drive new directions in bacteria-virus interactions, applying sensitive sequence searching, high-throughput AlphaFold2 protein complex predictions, and making new computational tools of use to us and the broader scientific community.

In our group, we strive for a supportive, respectful and stimulating working environment that promotes personal and professional development for all members.

Relevant recent papers from the lab:

• Ernits, Saha et al., 2023 PNAS DOI:10.1073/pnas.2305393120
• Egorov and Atkinson 2023 Bioinformatics DOI:10.1093/bioinformatics/btad32
• Zhang et al., 2022 Nature DOI: 10.1038/s41586-022-05444-
• Kurata, Saha et al., 2022 PNAS DOI: 10.1073/pnas.2102212119
• Saha et al, 2021 Bioinformatics DOI: 10.1093/bioinformatics/btaa78
• Jimmy, Saha et al. 2020 PNAS. DOI: 10.1073/pnas.1916617117

We offer 

Lund University is a public authority which means that employees get particular benefits, generous annual leave and an advantageous occupational pension scheme. 

Read more on the University website about being a Lund University employee Work at Lund University | Lund University

Work duties and responsibilities 

In this PhD project you will be using and developing computational tools to identify and predict the function and structure of proteins and RNA.

The resulting bioinformatic predictions will be verified experimentally through our collaborative network. Much of the project will focus on toxin- and antitoxin-domain-containing systems, but you will also have opportunities to broaden your horizons to other molecular systems. You will be part of the lab’s join effort to develop and maintain a publicly accessible bioinformatics toolbox (The Atkinson Lab (atkinson-lab.com)).

You will have the opportunity to attend and present your work at international meetings.


Required qualifications 

  • Coding skills (preferably in Python)
  • Proficiency in spoken and written English
  • Experience in using and/or developing computational methods for biological discovery
  • Background understanding of, and interest in molecular biology and microbiology.
  • Emphasis will be placed on personal qualities: the position requires a structured and independent way of working, along with the ability to communicate effectively with an interdisciplinary team. 


Desired Qualifications 

  • Experience in creating pipelines for use on high performance computing clusters
  • Competence in large dataset handling
  • Previous development of web-based tools
  • Familiarity with bacteriophage biology

Further information

This is temporary position for 4 years with start date according to agreement 

How to apply

1. A cover letter (one page) with the following sections: 

        Motivation (half a page)

 Explain your interest in the project, motivation for applying, and what you hope to learn

       Eligibility and experience (half a page)

 Explain how you fulfil the eligibility and qualification requirements, describe your previous relevant experience and outline how you will contribute to the research group.

2. A CV (maximum 2 pages) with contact details of two referees 

3. Bachelors and Masters certificates 

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 employment of doctoral students is regulated in the Swedish Code of Statues 1998: 80. Only those who are or have been admitted to PhD-studies may be appointed to doctoral studentships. When an appointment to a doctoral studentship is made, the ability of the student to benefit from PhD-studies shall primarily be taken into account. In addition to devoting themselves to their studies, those appointed to doctoral studentships may be required to work with educational tasks, research and administration, in accordance with specific regulations in the ordinance.

Type of employment
Limit of tenure, four years according to HF 5 kap 7§.


Type of employment Temporary position
First day of employment According to agreement
Salary Monthly salary
Number of positions 1
Full-time equivalent 100
City Lund
County Skåne län
Country Sweden
Reference number PA2023/3164
  • Gemma Atkinson, Research group leader, 046-2220000
  • Sofia Sönnerstedt, HR Partner , +46462229876
Union representative
  • OFR/ST:Fackförbundet ST:s kansli, 046-2229362
  • SACO:Saco-s-rådet vid Lunds universitet, kansli@saco-s.lu.se
  • SEKO: Seko Civil, 046-2229366
Published 16.Oct.2023
Last application date 06.Nov.2023 11:59 PM CET

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