Mitarbeiterin für Projekt Retention order prediction

Join the team!

The Chair for Bioinformatics, Institute of Computer Science at the Friedrich-Schiller-University Jena offers the following position:

PhD student as research associates (Wissenschaftliche Mitarbeiterin)

The position is part of the project on Retention time/order prediction, funded by the Deutsche Forschungsgemeinschaft.

Topic of research: Liquid Chromatography Mass Spectrometry (LC-MS) is one of predominant experimental analysis techniques for detecting and identifying small molecules such as metabolites. Our group has recently made much progress to support the identification of small molecules: CSI:FingerID (Dührkop et al., PNAS 2015) is currently the best-performing method for this task (see independent & blind CASMI contests), and SIRIUS (Dührkop et al., Nature Methods 2019) is used by thousands of scientists from more than 50 countries and six continents. Unfortunately, the orthogonal information provided by the retention time of molecules in the chromatography column is currently impossible to use for identification: Different from the mass of a molecule, its retention time is not a physical property but rather an interaction between the molecule and the chromatography column. The objective of this project is to develop computational methods for transferable retention time prediction, to integrate these methods into CSI:FingerID, and to bring identification rates of CSI:FingerID to the next level. See here why we are confident that we can “pull this off”.

See here for a beautiful introduction to this field of research, here for some background information on natural products research, and here and here for related research questions (all in German).

We offer: Challenging and interesting questions from different areas of machine learning and computer science, a network of cooperation partners in method development and application of our methods.

We are looking for: Applicants for this project must have or be about to obtain a Master’s degree or a qualification equivalent to the German Diploma in bioinformatics, chemoinformatics, computer science, or mathematics. The project combines algorithmics, combinatorics and machine learning, so proven interest in one or more of these fields is a must. Introductory course level knowledge in biology and molecular biology and good programming skills are required. Willingness to visit our cooperation partners in München, Helsinki and San Diego is also required.

Salary is according to Entgeltgruppe 13 TV-L (65%). Positions are temporary appointments. Handicapped applicants will be given preference in case of equal qualifications.

Please send your application with the usual documents (CV, copies of certificates) via email and ASAP to:

Friedrich-Schiller-Universität Jena
Institut für Informatik
Lehrstuhl für Bioinformatik
Ernst-Abbe-Platz 2
07743 Jena, Germany