Postdoctoral Researcher in Computational Metabolomics

Updated: about 1 month ago
Department of Chemistry
Postdoctoral Researcher in Computational Metabolomics
80-100 %

The Fenner Group at the University of Zurich is looking for a postdoctoral researcher in Computational Metabolomics to contribute to the further development of , an internationally unique resource for collecting and predicting information on the degradation of contaminants by environmental microbial consortia.
This position is part of the 2-year project enviPathPlus funded by Swiss Universities through the Open Research Data (ORD) program within action area B “Establish projects”. The aim of this action area is to foster research practices and tools to enable, facilitate and promote the sharing of research data based on ORD principles.
Your responsibilities
The successful candidate will join a team of 3-4 researchers, including bioinformaticians and data scientists, who will work together in the project enviPathPlus to link the biodegradation platform enviPath to two key research communities, i.e., systems biology and analytical chemistry. Directly linking enviPath with tools in analytical chemistry will support analytical chemists in the design, interpretation, and reporting of biodegradation experiments. Specifically, you will develop an automated workflow that predicts biotransformation products using enviPath, helps the chemists to interpret experimental data, and facilitates the upload of resulting pathways to enviPath. This includes automation of key steps such as the generation and export of suspect lists in a format that is directly compatible with MS measurement methods and transformation product identification software, automated evaluation of the identification confidence level for given MS and MS2 spectral information against a list of suspect transformation products, and the automated assembly and upload of biodegradation pathways in enviPath from the results of mass spectra matching. Additionally, the appointed person is expected to contribute to the definition of appropriate, generally applicable input and output data formats, and to the organization of an initial “scope finding” and final “dissemination” workshop.
Your profile
  • PhD in metabolomics, computational systems biology, or a related field
  • Experience in mass spectrometry and workflows for MS-based data analysis
  • Advanced programming skills, as well as proficiency in common Python libraries (e.g., pandas, numpy) and cheminformatic tools (rdkit)
  • Knowledge and/or experience in environmental chemistry is a plus
  • Excellent interpersonal skills and curiosity-driven mindset
  • Creative, proactive, and problem-solving attitude

We seek an enthusiastic individual with the ability to work both highly independently as well as in a team. In addition to relevant experience in the abovementioned activities, the candidate should have excellent project management and communication skills and be fluent in English. The candidate should have received their PhD within the last 12 months or not have more than two years of previous post-doctoral experience. Applications of senior researchers or senior post-docs will not be considered.
What we offer
Our well-funded research program combines inspiring international research environment with access to state-of-the-art scientific infrastructure. The project will be led by Kathrin Fenner, and co-led by our international enviPath partners (Dr. Jörg Wicker, University of Auckland and Tim Lorsbach ). Kathrin Fenner is professor in Environmental Chemistry at the Chemistry Department of the University of Zurich and group leader at the Department of Environmental Chemistry at Eawag. Both Eawag and the University of Zurich are located within the Zurich metropolitan area.
The University of Zurich is a modern employer and offers an excellent working environment where staff can contribute their strengths, experience and ways of thinking. We promote gender equality and are committed to staff diversity and inclusion. The compatibility of career and family is of central importance to us.
Place of work
University of Zurich Irchel, Winterthurerstrasse 190, Zürich, Switzerland
Start of employment
Employment starting date will be mutually agreed upon (preferably as soon as possible).
We ask strongly motivated candidates to submit their applications containing a motivation letter, a research summary of past accomplishments (1 page), a CV (resumé), and 1 letter of support (or the names and contact details of 2 referees) in a single pdf file by 20th February 2023.
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