Doctoral student in computational biology of infection (PA2024/1655)

Description of the workplace and research topic

We are looking for a full-time bioinformatics PhD student to work in the Data-driven life science (DDLS) area “Data driven epidemiology and biology of infection.” In the lab of Gemma Atkinson in Lund University, Department of Experimental Medical Science. The project’s co-investigator is Andrea Fossati, Karolinska Institute, Stockholm. Specifically, the project will be on finding the prophages of Escherichia coli genomes and annotating the function of their genes using high-throughput AlphaFold.

For more information about the Atkinson lab, visit https://atkinson-lab.com/

More information about DDLS:

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. 

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

During 2024 the DDLS Research School will be launched with the recruitment of 20 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.   For more information, please see:https://www.scilifelab.se/data-driven/ddls-research-school/

Duties and responsibilities

The project will involve pipeline development for large scale comparative sequence and structural analyses of bacterial and bacteriophage genomes and proteomes.

Expertise: Required

• 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

Expertise: Desirable:

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

Of considerable importance is how the applicant, through their experience and competence, is judged to have the ability to pass the doctoral program.

We offer

Lund University is a public authority which means that employees get particular benefits, generous annual leave and an advantageous occupational pension scheme. As doctoral student you are both admitted as a student and an employee which gives additional benefits. Read more about being admitted and employed at university website. Read more ab out being employed at Lund university Work with us.

About the employment

For regulations concerning employment of doctoral students etc, see the Higher Education Ordinance, Chapter 5.

Other information

The salary is set by a salary ladder connected to every faculty.

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 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

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§.