PhD student in Data Driven Antibiotic Resistance Research

Antibiotic resistance is one of the most severe threats to human health globally. The Bengtsson-Palme lab is using data driven approaches to find solutions and interventions to prevent the development of antibiotic resistance. We are looking for an aspiring student with a background in bioinformatics, computational biology or programming, with an interest in solving biological problems, to join us for a four-year PhD project.

Information about the project
Rapidly increasing antibiotic resistance necessitates innovative solutions to halt its spread. The work on preventing antibiotic resistance in the Bengtsson-Palme lab is focused on: 1) understanding and limiting spread of antibiotic resistance through the environment, 2) identifying genes involved in antibiotic resistance, 3) defining the conditions that select for antibiotic resistance in different settings, and 4) building a framework to allow implementation of monitoring for antibiotic resistance in the environment. This PhD project will be involved in all of these tasks, and the distribution between them can be somewhat influenced by your interest. The PhD project revolves around using large-scale data-driven approaches (including machine learning and metagenomic sequence analysis) to identify risk environments, define potential novel antibiotic resistance genes, and building a platform for AMR monitoring data.

The project is financed by the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) so you will participate in a national research school on data-driven life science. While working in the group, you will interact with other lab members with expertise in microbiology, bioinformatics and large-scale data analysis. Close collaborations exist with partners in Gothenburg and nationally, as well as with international partners, for example in the EMBARK program (http://antimicrobialresistance.eu). You will join a productive interdisciplinary research environment at Chalmers SysBio. For more information about the Bengtsson-Palme lab and SysBio, please visit these websites: https://microbiology.se and https://www.sysbio.se/. The details of the departmental research activities may be found here.

Major responsibilities
As a PhD student, your major responsibility will be to pursue your own doctoral studies. You will be expected to analyze and interpret large-scale data from ongoing and future experiments and sampling campaigns performed by the group and our collaborators. Furthermore, you will perform tasks related to charting antimicrobial resistance in the environment at a global scale. You will also increasingly be responsible for experimental planning, sample collection, data handling, writing of publications and communications of results from the project. You will also be expected to participate in the SciLifeLab national research school on data-driven life science. The position generally also includes teaching on Chalmers' undergraduate level or performing other duties corresponding to 20 per cent of working hours.

Qualifications
To qualify as a PhD student, you must have a master's level degree corresponding to at least 240 higher education credits in a relevant field, such as bioinformatics, molecular biology, biomedicine, statistics, computational sciences, or similar.

Mandatory qualifications and skills:
- Documented experience of bioinformatic, computational biology or programming work.
- An ability to work independently as well as in teams and take responsibility for progress in the project.
- Fluency in spoken and written English.
- Good scientific writing skills.

Meritorious qualifications and skills:
- Previous work with taxonomic and functional annotation of genome and metagenome data, as well as knowledge of biological databases.
- Experience of working with data analysis in R and programming (for example in a scripting language such as Perl or Python).
- Experience with building web sites and user interfaces.
- Previous experience with wetlab work, such as bacterial culturing, DNA extraction etc.
- Knowledge of antibiotic resistance development, machine learning, and microbial ecology.

If Swedish is not your native language, Chalmers offers Swedish courses.

Contract terms
Full-time temporary employment. The position is limited to a maximum of 4 years.

We offer
Chalmers offers a cultivating and inspiring working environment in the coastal city of Gothenburg. 
Read more about working at Chalmers and our benefits for employees.

Chalmers aims to actively improve our gender balance. We work broadly with equality projects, for example the GENIE Initiative on gender equality for excellence. Equality and diversity are substantial foundations in all activities at Chalmers.

Learn more and apply on Chalmers website: https://www.chalmers.se/en/about-chalmers/Working-at-Chalmers/Vacancies/Pages/default.aspx?rmpage=job&rmjob=10513&rmlang=UK

Application deadline: June 5, 2022

For questions, please contact:
Assistant professor Johan Bengtsson-Palme, Systems and Synthetic Biology
Email: johan.bengtsson.palme@chalmers.se

*** Chalmers declines to consider all offers of further announcement publishing or other types of support for the recruiting process in connection with this position. *** 
   



Chalmers University of Technology conducts research and education in engineering sciences, architecture, technology-related mathematical sciences, natural and nautical sciences, working in close collaboration with industry and society. The strategy for scientific excellence focuses on our six Areas of Advance; Energy, Health Engineering, Information and Communication Technology, Materials Science, Production and Transport. The aim is to make an active contribution to a sustainable future using the basic sciences as a foundation and innovation and entrepreneurship as the central driving forces. Chalmers has around 11,000 students and 3,000 employees. New knowledge and improved technology have characterised Chalmers since its foundation in 1829, completely in accordance with the will of William Chalmers and his motto: Avancez!