Faculty of Medicine, Department of Experimental Medical Science

Lund University was founded in 1666 and is repeatedly ranked among the world’s top 100 universities. The University has around 44 000 students and more than 8 000 staff based in Lund, Helsingborg and Malmö. We are united in our efforts to understand, explain and improve our world and the human condition.

The Faculty of Medicine is a part of Lund University, and is responsible for education and research within medicine and healthcare. Our academic programs are closely linked with the healthcare system and are firmly anchored in the faculty’s strong research tradition. Our research spans a broad field within experimental preclinical research, near-patient clinical research and health sciences research. The Faculty of Medicine, with its 1,800 employees and 2,700 students in Lund and Malmö, is a knowledge-intensive meeting place for students, teachers and researchers from all over the world.

The research group

In the Atkinson lab we are interested in making exciting discoveries about the evolution of protein function and structure. 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 Department of Experimental Medical Sciences in the Biomedical Centre (BMC) in Lund.

You can read more about our group on our lab website here: https://atkinson-lab.com/, and about the department here: https://www.medicine.lu.se/faculty-medicine-lund-university/departments/department- experimental-medical-science

One of our main research directions concerns toxin-antitoxin systems of bacteria and bacteriophages, which has led to papers in PNAS [1] and Molecular Cell [2] on toxSAS enzymes that dramatically inhibit bacterial growth though producing poisonous nucleotides, or modifying tRNA, as well as a more recent preprint on the hyper promiscuous antitoxin domain that we have named Panacea [3]. Our work on toxin- antitoxins, and their evolution, structure, function and biotechnological applications was recently supported by a generous grant from the Knut and Alice Wallenberg foundation (see https://kaw. wallenberg.org/grundforskning-djupt-inne-i-bakteriernas-arvsmassa, in Swedish). As a mechanism of defence against bacteriophages, TAs have significance for developing new biotechnological tools, as well as understanding and eventually overcoming natural barriers to phage therapy for treating antibiotic resistant infections.

We are looking for a full time PhD student to continue the lab’s high impact work, driving new directions in toxin-antitoxin system research. In our group, we strive for a supportive, respectful and stimulating working environment that promotes personal and professional development for all members.

Start date is by agreement

Job assignment

In this PhD project you will be using and developing Python tools for molecular evolutionary analyses of proteins and gene neighbourhoods, and using the results to predict novel functions. This project builds on our previous success with the FlaGs tool [4], which directly led to our high impact papers, and is being used by researchers around the world through our web server at www.webflags.se. Bioinformatic predictions that come out of this project will be verified experimentally through our collaborative network. Much of the project will focus on toxin-antitoxin systems, but you will also have opportunities to broaden your horizons to other molecular systems.

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

References

  1. Jimmy, S. et al. Proc Natl Acad Sci U S A 117, 10500-10510, (2020).
  2. Kurata, T. et al. Mol Cell 81, 3160-3170 e3169, (2021).
  3. Kurata, T. et al. bioRxiv, https://www.biorxiv.org/content/10.1101/2021.1105.1107.442387v442381, (2021).
  4. Saha, C. K. et al. Bioinformatics ∑, 1312-1314 (2021).

Qualifications
 

Required qualifications:
- Coding skills (preferably in Python)
- Background understanding of, and interest in molecular biology and evolution.
- Proficiency in spoken and written English.
   Desired qualifications:
- Experience in machine learning methods
- Experience in phylogenetic sequence analysis.
- Experience in large dataset handling.

Instructions for the application:

- A cover letter explaining your interest in the project and your previous relevant experience
- A full CV with contact details of two referees
- Bachelors and Masters certificates

Informal enquiries welcome to gemma.atkinson@med.lu.se

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 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 longer than 6 months
First day of employment By agreement
Salary Monthly salary
Number of positions 1
Working hours 100
City Lund
County Skåne län
Country Sweden
Reference number PA2021/2819
Contact
  • Gemma Atkinson, Forskargruppschef, 046-2220000
  • Sofia Sönnerstedt, Personalsamordnare, +46462229876
Union representative
  • OFR/ST:Fackförbundet ST:s kansli, 046-222 93 62
  • SACO:Saco-s-rådet vid Lunds universitet, 046-222 93 64
  • SEKO: Seko Civil, 046-222 93 66
Published 08.Sep.2021
Last application date 03.Oct.2021 11:59 PM CEST

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