Doctoral Researcher, Multidisciplinary Center of Excellence in Antimicrobial Resistance Research

Updated: over 1 year ago
Deadline: 24 Nov 2022

DESCRIPTION OF THE POSITION

We offer a unique opportunity for a motivated doctoral researcher to work with us in a newly established Multidisciplinary Center of Excellence in Antimicrobial Resistance Research (CoE-AMR) which is one of the units nominated by the Academy of Finland in Finnish Centers of Excellence in Research 2022-2029 call. The CoE is based at leading Finnish universities, University of Helsinki (UH) and University of Turku (UTU). The core faculty of the CoE consists of five research groups working in the fields of Infectious diseases, Microbiology, Sociology, Evolutionary biology and Bioinformatics.

The participating PIs are:

Teppo Hiltunen (UTU), Experimental Evolution Research Group, Department of Biology https://www.expevo.org

Anu Kantele (UH), Infectious Diseases, Faculty of Medicine

https://researchportal.helsinki.fi/en/persons/anu-kantele

Ville Mustonen (UH), Bioinformatics and Evolution Research Group

https://www.helsinki.fi/en/researchgroups/bioinformatics-and-evolution

Salla Sariola (UH), Faculty of Social Sciences

https://www.socialmicrobes.org/

Marko Virta (UH), Molecular Environmental Biosciences Research Group, Faculty of Agriculture and Forestry

https://www.helsinki.fi/en/researchgroups/molecular-environmental-biosciences/research/antibiotic-resistance-human-impacted-environments  

The Multidisciplinary Centre of Excellence in Antimicrobial Resistance Research will take a comprehensive approach to understanding determinants of antimicrobial resistance across scales from a “One Health” perspective that incorporates humans, animals and the environment. The researchers from different scientific disciplines will work in close collaboration in order to achieve the interdisciplinary scientific goals and targets of the CoE.

We invite applications in order to recruit a Doctoral researcher who will work together with us to realize the scientific mission of the CoE. Overall, the suitable scientific backgrounds and fields include but are not limited to Infectious diseases, Experimental evolution, Microbiology, Sociology, Evolutionary biology and Bioinformatics. Together we will do field, social, laboratory as well as computational integrative science to understand AMR. If you are motivated to work in a multidisciplinary environment and can contribute to the research mission of the unit, do not hesitate to apply even if your background is not directly in the listed areas. Fluency in English and excellent writing skills are essential.

The successful candidate will become part of a multidisciplinary team. The actual research will depend on the applicant's background. When applying, please indicate in the application cover letter a research theme/themes that is/are of your primary interest. 

Theme 1: Microbiology, experimental evolution and data science (with PI’s Virta, Mustonen and Hiltunen)

In this theme we will use environmental and experimental model systems (e.g. waste water communities and synthetic bacterial communities) combined with various data analysis methods (e.g. evolutionary theory-based inference, machine learning) to study how AMR develops in the community context and the related eco-evolutionary dynamics of community resilience against stressors. This theme is at the interface of environmental microbiology, microbial evolution, eco-evolutionary theory and data science. 

We aim to recruit a PhD researcher with a focus either A) in microbiology, experimental evolution or community ecology (experience in working with bacterial model systems is beneficial) or B) in a highly quantitative field e.g. MSc in Physics, Mathematics, Computer Science, Engineering, Statistics, Computational Biology, Bioinformatics or similar (experience in working with big biological data sets is beneficial). All candidates are required to have a burning interest in evolution. Experimental positions are in the group of Marko Virta (University of Helsinki) with close collaboration with the group of Teppo Hiltunen (University of Turku) and the data science positions at the group of Ville Mustonen (University of Helsinki) with a highly collaborative atmosphere between the groups, working on shared projects.

Theme 2: Social Science

The social science theme will investigate the role of sociological factors (social practices, livelihood practices, development infrastructures and policies) in enabling AMR evolution and colonization. We seek candidates with an interest in combining analysis of the social with the biomedical or microbiological to develop an interdisciplinary research profile that can contribute to the fulfilment of the Centre’s scientific objectives. Whilst the position for those applying under this theme is located in the Faculty of Social Science, the candidate will work in close collaboration with the disciplines across the Centre.

For the theme 2, we are looking for candidates with different profiles and offer the candidates the possibility to select one of the following three profiles. Please make clear which profile within Theme 2 you are applying for in your application letter.

Profile 1: Biomedical Research with Sociology

We invite applicants with a background in either sociology or biomedical/global health research (or both) interested in developing methods for integrating sociological and biomedical data. Experience in clinical microbiology laboratory research and field research are highly advantageous. A candidate with this profile will work in close collaboration with Anu Kantele’s group.

Profile 2: Animals and Veterinary Practices

We invite applicants with an interest in multispecies approaches to examine the social relations of livestock production, the environment, and AMR evolution. A candidate with this profile will work in close collaboration with Marko Virta’s group.

Profile 3: Integrative Data Analysis

We invite applicants with an interest in machine learning or digital anthropology to design novel methods for combining ethnographic data with computational and machine learning technologies for integrative data analysis. A candidate with this profile will work in close collaboration with Ville Mustonen’s group.

Theme 3: The clinical infectious diseases and microbiology theme

The clinical infectious diseases and microbiology theme consists of infectious diseases, and clinical microbiology. The research focuses on clinically relevant resistant intestinal bacteria and AMR genetic elements. It explores transmission to humans and human intestinal colonization. The tasks may include interaction with the participants, collecting their samples, sampling of participants’ environments, bacterial isolation and culturing, identification of pathogens, and genetic, metagenomic and metatranscriptomic analyses.

We now seek applicants with experience in work in clinical microbiology laboratory or research in clinical microbiology. The work will mainly take place in Finland but may include field work in our study sites in Asia and Africa. Accordingly, experience in clinical microbiology laboratory work and in field work are highly advantageous. The position is mostly based at Anu Kantele’s laboratory in the Faculty of Medicine but the work will also include a close collaboration with the other groups of the CoE.

REQUIREMENTS

We are looking for a highly motivated doctoral researcher with:

  • MD or MSc. Degree in relevant field. Since the unit is multidisciplinary, many fields are suitable.
  • Excellent communication and writing skills
  • Ability to work both independently and as part of a multidisciplinary research environment
  • Some themes may require that candidates be prepared to undertake fieldwork in Asian and/or West Africa.

HOW TO APPLY

Applications must enclose the following documents in a single pdf file in either English or Finnish:

1) Letter of motivation, including a brief introduction of your background (covering the requirement points above) (max 600 words)

2) Academic CV

3) Copy of your MSc certificate and transcript of courses

4) Names and e-mail addresses of two referees.

External applicants, please submit your application using the University of Helsinki Recruitment System via the provided link (Apply Now button).

Applicants who have a helsinki.fi -username and a valid employment contract, a grant researcher’s contract or a visiting researcher’s contract at the University of Helsinki are requested to leave their application by using the employee login.

Deadline for application 24.11.2022 at 23.59 EET.

Tentative starting date is 1.1.2023.

We welcome applicants from a variety of gender identities, and linguistic and cultural backgrounds.

FURTHER INFORMATION

Further information can be obtained by email from the PIs mentioned in the description of the positions:  Teppo Hiltunen (teppo.hiltunen(at)utu.fi), Anu Kantele (anu.kantele(at)helsinki.fi), Ville Mustonen (v.mustonen(at)helsinki.fi), Andrea Butcher (andrea.butcher(at)helsinki.fi) or Marko Virta (marko.virta(at)helsinki.fi)

For further information on the recruitment process and recruitment system please contact HR Coordinator (sari.aaltonen(at)helsinki.fi) or HR Specialist Mirkka Juntunen (mirkka.juntunen(at)helsinki.fi)

The University of Helsinki (UH) is an international scientific community of 40,000 students and researchers. It is one of the leading multidisciplinary research universities in Europe and ranks among the top 100 international universities in the world. We are an equal opportunity employer and offer an attractive and diverse workplace in an inspiring environment with a variety of development opportunities and benefits. https://www.helsinki.fi/en

The University of Turku (UTU) is a world-class multidisciplinary research university of 20,000 students which offers interesting challenges and a unique vantage point to national and international research and education. https://www.utu.fi/en



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