Doctoral student in bioinformatics (PA2024/339)

Updated: 3 months ago
Deadline: 05 Mar 2024

Background

We are looking for a full-time bioinformatics PhD student to be involved in the Novo Nordisk funded project: ‘Development of phage biocontrol to overcome the antiphage defense system arsenal of phytopathogenic Ralstonia solanacearum bacterium’. This is a project led by Ville Friman in the University of Helsinki, with Vasili Hauryliuk and Gemma C. Atkinson in the University of Lund as co-investigators. This position will be based in the Atkinson lab.

Due to a lack of efficient control methods, plant-pathogenic bacteria threaten safe and stable food production. This project will develop a novel biocontrol method against the plant-pathogenic bacterium Ralstonia solanacearum by employing its natural viral enemies, phages. While phages are highly pathogen-specific and safe to the environment, they can become inefficient due to the rapid development of phage resistance. This project will overcome this by identifying antiphage defence systems in R. solanacearum, and then isolating phages that can counteract these defences by escaping their recognition or by deploying their own counter-defence systems.

Description of the research group

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 is affiliated with the Lund University Virus Centre (LUVC). We strive for a supportive, respectful and stimulating working environment that promotes personal and professional development for all members.

Further information:

The Atkinson lab

https://villefrimanscience.weebly.com/

https://portal.research.lu.se/en/persons/vasili-hauryliuk

https://www.medicine.lu.se/faculty-medicine-lund-university/departments/department-experimental-medical-science

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 

Responsibilities

In this computational PhD project you will be using and developing tools for analysing bacterial genomes and predicting phage defence systems. You will work together with the other project team members in understanding and overcoming barriers to phage-based biocontrol in pathogenic bacteria. You will also be involved in the Atkinson lab’s joint effort to develop and maintain a publicly accessible bioinformatics toolbox (https://server.atkinson-lab.com/).

This collaborative project will provide valuable networking and training opportunities including research visits to Helsinki University, and you will have the opportunity to attend and present your work at international meetings.

Qualifications

The positions requires:

  • Coding skills 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 bacteriophage biology
  • Ability to conceive, execute, and complete research projects independently
  • Creativity and good group-working skills 

Desired qualifications:

  •  Experience in creating pipelines for use with high performance computing clusters
  •  Competence in large dataset handling 

How to apply

Include the following documents in your application:

  • 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 expertise 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

    For more information contact Gemma C. Atkinson [email protected]

    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§. Fulltime employment with desired start according to agreement. 



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