PhD student in the Ecology of Antibiotic Resistance and Pathogenicity

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 a driven candidate with a strong background in genomics and bioinformatics to join us for a four-year PhD project.

Information about the division and the department
Rapidly increasing antibiotic resistance necessitates innovative solutions to halt its spread. At the same time, the emergence of novel pathogenic agents, such as SARS-CoV-2 and Candida auris, highlights the importance of the environment in understanding and potentially preventing future the disease threats of the future. The work on antibiotic resistance and pathogenicity 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 and pathogenicity, and 3) building a framework to allow implementation of monitoring for antibiotic resistance and emergent pathogens. This PhD project will be involved in all of these tasks, and the distribution between them can be somewhat influenced by the interest of the recruited student. The PhD project revolves around using large-scale data-driven approaches (including machine learning, genomics and metagenomic sequence analysis) to identify risk environments and define potential novel antibiotic resistance and pathogenicity genes.

While working in the group, the student 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. The PhD student will join a productive interdisciplinary research environment at Chalmers SysBio. The project is funded by the Swedish Foundation for Strategic Research. For more information about the Bengtsson-Palme lab and SysBio, please visit these websites: https://microbiology.se and https://www.sysbio.se/

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 public sources, as well as ongoing and future experiments and sampling campaigns performed by the group and our collaborators. Furthermore, you will perform tasks related to charting pathogenicity and antimicrobial resistance in the environment at a global scale. You will increasingly be responsible for experimental planning, sample collection, data handling, writing of publications and communications of results from the project. The position will involve some degree of field work, so the candidate must be willing to travel on relatively short notice.


Qualifications
Mandatory qualifications and skills:
- A master's level degree in a relevant subject, such as genomics, systems biology, bioinformatics, molecular biology, biomedicine, or similar.
- Documented experience of bioinformatic, computational biology and genomics work.
- An ability to work independently as well as in teams and take responsibility for progress of the project.
- Fluency in spoken and written English.
- Good scientific writing skills

Meriting qualifications and skills:
- Previous work with functional annotation of genome or metagenome data
- Experience with comparative genomics
- Experience with environmental DNA
- 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)
- Previous experience with wetlab work, such as bacterial culturing, DNA extraction etc.
- Knowledge of antibiotic resistance development, pathogenicity and microbial ecology
- Specific knowledge on Pseudomonas aeruginosa genomics

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

For more information about application procedure and contact information, please visit Chalmers webpage.
See link: PhD student in the Ecology of Antibiotic Resistance and Pathogenicity


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



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