PhD position: Dual RNA-seq analysis of pathogen and host

Code: 54/2017



The research department “RNA biology of bacterial infections” (RABI) of Prof. Jörg Vogel at the Helmholtz Institute for RNA-based infection research (HIRI) in Würzburg (Germany) is offering a PhD position: Dual RNA-seq analysis of pathogen and host. The Helmholtz Institute for RNA-based Infection Research (HIRI) has been established in May 2017 as a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Julius Maximilian University of Würzburg (JMU). Located on the Würzburg medical campus, it will be the first research institution worldwide to exclusively address the role of ribonucleic acids (RNAs) in infection processes. Based on these findings, the HIRI will pioneer an integrative approach to exploit the vast potential of RNAs as a diagnostic molecule, target and drug for new strategies to combat infectious diseases. (


The HIRI is recruiting a doctoral student to study bacterial infections using simultaneous RNA sequencing of pathogen and host (dual RNA-seq; see Westermann et al. (2016) Nature 529:496-501). The successful applicant will work with experienced bioinformaticians and experimentalists to construct, validate, and interpret an atlas of Salmonella gene expression as it infects a variety of eukaryotic host cells. The project will focus on the development and application of computational methods for RNA-seq time course analysis, functional interpretation, and visualization. There will be opportunities to apply the methods developed in this project to a range of host-pathogen systems studied at the HIRI, and by our national and international collaborators. Additional details on the dual RNA-seq approach can be found in Westermann, Barquist, and Vogel (2017) PLoS Pathogens 13(2):e1006033; Barquist, Westermann, and Vogel (2016) Phil. Trans. R. Soc. B 371:20160081. The successful applicant will work in the dynamic environment of the HIRI in Würzburg, which is part of the Helmholtz Centre for Infection Research.


  • Master’s Degree/Diploma in bioinformatics, microbiology, immunology, computer science, engineering, or a related field 
  • Knowledge of a scripting language (Python, Perl, etc.) and R
  • Experience with the Unix shell
  • Basic knowledge of statistics
  • Strong written and spoken English language communication skills

Desired background:

  • Previous experience in working with large-scale biological data sets, particularly RNA-seq
  • Previous experience in infection biology or bacteriology
  • Familiarity with non-coding RNA biology
  • Interest in machine learning, statistical modeling, and/or network inference


HIRI Würzburg

The Handicapped

Qualified applicants with a disability will be given preference.

Special preference toward women


Starting date

January/February, 2018

Contract time limit

Initial term 1 year, with the possibility of an extension of additional 2 years

Probation period

6 months


alike TVöD E13 (50%) with the possibility of an additional payment of 10%

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Applications accepted until  29.10.2017

Applicants are required to complete the online application form here:
Please select Application HZI Jobs and refer to the job number 54/2017.

For more details regarding the PhD project, please contact Dr. Lars Barquist via e-mail

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HZI International Graduate School

The HZI International Graduate School for Infection Research (GS-FIRE) provides an innovative structured PhD programme within the field of Infection Research.

PhD programme “Epidemiology”

The PhD programme “Epidemiology” is a three-year doctoral programme in the area of epidemiological research and is coordinated by the Department of Epidemiology of the HZI.

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