Adrian Egli

The Institute of Medical Microbiology at the University of Zurich is offering a PhD position focused on profiling host and pathogen transcripts using Nanopore direct RNA sequencing for rapid sepsis diagnostics. The successful candidate will join Dr. Ashley Rooney's research group, which collaborates with Prof. Adrian Egli and partners in Switzerland and internationally. The project aims to develop, validate, and optimize a metatranscriptomic RNA sequencing-based diagnostic tool for sepsis, addressing the urgent need for rapid and accurate identification of bacterial infections in clinical settings. Research activities will include optimizing sequencing workflows, bioinformatic analysis of host-pathogen interactions, and clinical validation studies. Key methods involve direct RNA sequencing from whole blood using nanopore technology, metatranscriptomic data analysis to identify pathogens and immune responses, and device development for portable diagnostics. The RADIANT-Dx consortium supports the project, aiming to deliver rapid results for treatment decisions and reduce unnecessary broad-spectrum antibiotic use. Applicants should have a background in Molecular Microbiology, Computational Biology, or related fields, with experience in RNA sequencing, nanopore technology, and bioinformatics analysis considered advantageous. Strong analytical, problem-solving, communication, and organizational skills are required, along with motivation for translational medical research. The position offers interdisciplinary training, access to high-performance computing, and the chance to contribute to impactful clinical research. To apply, candidates must send their CV and motivation letter to Dr. Ashley Rooney ([email protected]) and consult the UZH Microbiology and Immunology PhD program details at https://mim.ethz.ch. The application deadline is January 16, 2026.

The Institute of Medical Microbiology at the University of Zürich is offering a PhD position focused on the development, validation, and optimization of a metatranscriptomic RNA sequencing-based diagnostic tool for rapid sepsis diagnostics. The successful candidate will join the research group of Prof. Adrian Egli, with Dr. Ashley Rooney as Principal Investigator, and collaborate with Prof. Petra Dittrich and Dr. Andre Kahles from ETH Zürich as part of the RADIANT-Dx project consortium. This interdisciplinary project aims to address the urgent need for rapid and accurate identification of bacterial infections in clinical settings, particularly for sepsis, by developing a portable diagnostic device that utilizes real-time metatranscriptomic RNA sequencing. The research will combine expertise in molecular microbiology, computational biology, and innovative diagnostic technologies. The PhD candidate will optimize sequencing workflows, perform bioinformatic analysis of pathogen-host interactions, and participate in clinical validation studies, including proof-of-concept work at University Hospital Zurich. Key methods include direct RNA sequencing from whole blood using nanopore technology, metatranscriptomic data analysis, and device development for clinical diagnostics. Applicants should have a background in Molecular Microbiology, Computational Biology, or a related field. Experience with RNA sequencing, nanopore sequencing, and bioinformatics is advantageous. The position offers training in both wet-lab and computational techniques, access to high-performance computing, and the chance to contribute to a project with significant clinical impact. To apply, send your CV and motivation letter to Dr. Ashley Rooney ([email protected]) by January 16, 2026. For more information, consult the UZH Microbiology and Immunology PhD program details at ETH Zürich. This is an excellent opportunity for candidates interested in sepsis diagnostics, next-generation sequencing, and translational medical research.