We are looking for a full-time bioinformatics PhD student to be involved in the DDLS project “Finding the prophages of Escherichia coli genomes and annotating the function of their genes using high-throughput AlphaFold”

Link to application submission page: http://lu.varbi.com/what:job/jobID:726501/ Deadline June 16th

Position title: Doctoral student in computational biology of infection Faculty of Medicine, Department of Experimental Medical Science

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

You will be based in Lund in our joint bioinformatics and experimental environment, along with the group of Vasili Hauryliuk. Together our multidisciplinary team is focused on discovering and understanding the functions of diverse microbial proteins. We have a particular interest in the discovery of new bacteriophage defence systems.

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. Read more about this DDLS subject area here: https://www.scilifelab.se/data-driven/ddls- research/ddls-epidemiology-and-biology-of-infection-ra/

Data-driven life science (DDLS) uses data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. 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 (about 290 MUSD) 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. The DDLS program has four strategic areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and biology of infection. For more information about the DDLS research school, please visit https://www.scilifelab.se/data-driven/ddls- research-school/

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

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.

How to apply:

Register and log in at the application portal here: http://lu.varbi.com/what:job/jobID:726501/

Include the following with your application:

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.

About Lund University:

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.

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 a 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.

Type of employment

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

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.

We kindly decline all sales and marketing contacts.

Type of employment First day of employment Salary
Number of positions Full-time equivalent City
County
Country
Reference number Contact

Union representative

Published
Last application date Link to ad

Temporary position According to agreement Monthly salary
1

100
Lund
Skåne län
Sweden
PA2024/1655
Gemma Atkinson, Research group leader, 046-2220000
Sofia Sönnerstedt, HR Partner, +46462229876 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
2024-05-07
2024-06-16
http://lu.varbi.com/what:job/jobID:726501/