PhD Position: Bacterial Genomics and Metagenomics 801 views

The Applied Microbiology Research group, Department of Biomedicine, University of Basel, is inviting application for a PhD student in bacterial genomics and metagenomics.

About the position:
  • This position is part of a new Swiss National Science Foundation (SNSF)-funded research project, we aim to explore (i) the within-host evolution of multi-drug resistant bacteria in colonized patients and (ii) the patient’s environment in the hospital using a metagenomic approach.
  • The aim is to develop a new standard protocol to rapidly screen for multi-drug resistant bacteria with a high potential for application in routine clinical practice.
  • The position as a PhD student in the microbiology research laboratory involves project management, wet lab, and bioinformatics elements.
  • Specifically processing of samples from the study, DNA and RNA extraction, identification of species (e.g. with MALDI-TOF) and resistance testing (e.g. with E-Test), management of the project’s biobank, development of new PCRs, and long-read shotgun metagenomic protocols, and genomic data analysis.


  • Applicant must be enthusiastic, trained in good microbiology practice and nucleic acid extraction and manipulation.
  • Applicant must have hands-on and organizational skills, and prepared to develop new methods.
  • Experience in bioinformatic data analysis, in particular bacterial genomics, is crucial.


  • Application to be sent in one PDF file to Prof. Adrian Egli and Dr Helena Seth-Smith,  via e-mail to, Subject containing “PhD2020” including a letter of motivation, CV, certificates and recommendation letters.
—————–Quick Overview————-
Organization University of Basel
Country Switzerland
Fellowship Level Doctoral
Subject areas Microbiology
Fellowship amount Varies
Eligibility Master’s degree
Deadline 31st July 2020

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