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 Doctoral student in bioinformatics

Lunds universitet, Sweden

Job Information

Organisation/Company
Lunds universitet


Department
Faculty of Medicine, Department of Experimental Medical Science


Research Field
Medical sciences » Other


Researcher Profile
First Stage Researcher (R1)


Country
Sweden


Application Deadline
5 Mar 2024 – 22:59 (UTC)


Type of Contract
Temporary
Job Status
Full-time


Is the job funded through the EU Research Framework Programme?
Not funded by an EU programme
Is the Job related to staff position within a Research Infrastructure?
No

Offer Description

Background

The Faculty of Medicine, Department of Experimental Medical Science are currently seeking a full-time bioinformatics PhD student to participate in the Novo Nordisk-funded project titled: ‘Development of phage biocontrol to overcome the antiphage defense system arsenal of phytopathogenic Ralstonia solanacearum bacterium’. This project, spearheaded by Ville Friman at the University of Helsinki, with co-investigators Vasili Hauryliuk and Gemma C. Atkinson at the University of Lund, will be based in the Atkinson lab.

Due to the absence of efficient control methods, plant-pathogenic bacteria pose a significant threat to safe and consistent food production. This project aims to devise an innovative biocontrol approach against the plant-pathogenic bacterium Ralstonia solanacearum by harnessing its natural viral adversaries, phages.

While phages are highly specific to pathogens and environmentally safe, their efficacy can be compromised by the rapid emergence of phage resistance. To address this challenge, this project will identify antiphage defense systems in R. solanacearum and subsequently isolate phages capable of circumventing these defenses either by evading recognition or by deploying their own counter-defense mechanisms.

Description of the research group

In the Atkinson laboratory, their primary interest lies in unraveling the intricacies of protein function and structure, particularly focusing on components of bacterial immune systems that defend against bacteriophages and other mobile genetic elements.

The research primarily revolves around bioinformatic methodologies, where they not only develop their own tools but also capitalize on the extensive repository of genome and predicted proteome sequences available.

Situated within Lund University’s Faculty of Medicine, the lab is housed within the Department of Experimental Medical Sciences (EMV) and maintains an affiliation with the Lund University Virus Centre (LUVC). They are committed to fostering a supportive, respectful, and intellectually stimulating work environment that fosters the personal and professional growth of all our 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

The 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

3Bachelors and Masters certificates

For more information contact Gemma C. Atkinson 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§. Fulltime employment with desired start according to agreement. 
Requirements
Research FieldMedical sciencesEducation LevelMaster Degree or equivalent
Research FieldMedical sciencesYears of Research ExperienceNone
Additional Information
Work Location(s)
Number of offers available1Company/InstituteLunds universitetCountrySwedenCityLundGeofield

Where to apply
Website
https://lu.varbi.com/en/what:job/jobID:698175/type:job/where:39/apply:1

Contact
City
Lund
Website
http://www.lunduniversity.lu.se/about/work-at-lund-university

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