PhD Position - Profiling Host and Pathogen Transcripts using Nanopore
Direct RNA Sequencing for Sepsis Diagnostics – Start Date 01.03.2026
Our research group at the Institute of Medical Microbiology of the University of Zurich is
searching for a PhD candidate to contribute to the development, validation, and optimization of
a metatranscriptomic RNA sequencing-based diagnostic tool for rapid sepsis diagnostics.
Dr. Ashley Rooney (Principal Investigator) conducts research in the group of Prof. Adrian Egli,
which focuses on understanding host-pathogen interactions to develop novel diagnostic tools.
The group uses cutting-edge next-generation sequencing and bioinformatics to analyze whole
genome and metagenomic data for in-house research projects as well as in collaboration with
Swiss and international partners.
Project Background: Rapid and accurate identification of bacterial infections, particularly in
emergency departments, remains a significant challenge in clinical practice. Sepsis, a
dysregulated response to infection, is a leading cause of mortality globally, where delays in
diagnosis or inappropriate antimicrobial treatment can contribute to worse patient outcomes.
Current diagnostic methods can take 24–72 hours, often leading to unnecessary broad-spectrum
antibiotic use, antimicrobial resistance, and increased healthcare costs. The RADIANT-Dx
project consortium aims to address these issues by developing a portable diagnostic device that
utilizes real-time metatranscriptomic RNA sequencing to provide rapid and accurate results
from blood samples within hours.
Methods: The PhD candidate will work on optimizing sequencing workflows, bioinformatic
analysis of pathogen-host interactions, and clinical validation including the following:
• RNA Sequencing: Develop and optimize workflows for direct RNA sequencing from
whole blood using nanopore sequencing technology.
• Bioinformatic Analysis: Analyze metatranscriptomic data to accurately identify
bacterial pathogens, host immune responses, and their interactions.
• Validation: Conduct biological and clinical validation studies, including bacterial spike-
in models and support a proof-of-concept clinical study at the University Hospital
Zurich.
• Device Development: Collaborate in the design and testing of the portable diagnostic
device.
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Professional and personal skills:
• A background in Molecular Microbiology, Computational Biology, or a related field.
• Experience with RNA sequencing, nanopore sequencing technology, and bioinformatics
analysis (not mandatory but advantageous).
• Strong problem-solving and analytical skills.
• Ability to work both independently and collaboratively in a multidisciplinary team.
• High attention to detail and organizational skills.
• Strong writing and communication skills.
• Strong motivation to contribute to translational medical research.
What We Offer:
• A dynamic, interdisciplinary research environment combining molecular microbiology,
computational biology, and innovative diagnostics.
• The opportunity to work on cutting-edge technologies, including nanopore sequencing
and portable diagnostic devices.
• Extensive training in both wet-lab techniques and bioinformatic analysis.
• Access to high-performance computing resources for data analysis and a collaborative
research team.
• The chance to contribute to a project with high potential for clinical impact.
All interested applicants please send their CV and motivation letter to Dr. Ashley Rooney
(Principal Investigator): arooney@[Link]. Please consult the UZH Microbiology and
Immunology program for PhD program details [Link] The application deadline is
January 16 2026.
