The International Max Planck Research School at the Max Planck Institute for Chemical Ecology in Jena is looking for PhD students. One of the projects (Project 7) is from our group on “rethinking molecular networks”. Application deadline is April 19, 2024.
Mass spectrometry (MS) is the analytical platforms of choice for high-throughput screening of small molecules and untargeted metabolomics. Molecular networks were introduced in 2012 by the group of Pieter Dorrestein, and have found widespread application in untargeted metabolomics, natural products research and related areas. Molecular networking is basically a method of visualizing your data, based on the observation that similar tandem mass spectra (MS/MS) often correspond to compounds that are structurally similar. Constructing a molecular network allows us to propagate annotations through the network, and to annotate compounds for which no reference MS/MS data are available. Since its introduction, the computational method has received a few “updates”, including Feature-Based Molecular Networks and Ion Identity Molecular Networks. Yet, the fundamental idea of using the modified cosine to compare tandem mass spectra, has basically remained unchanged at the core of the method.
In this project, we want to “rethink molecular networks”, replacing the modified cosine by other measures of similarity, including fragmentation tree similarity, the Tanimoto similarity of the predicted fingerprints, and False Discovery Rate estimates. See the project description for details.
We are searching for a qualified and motivated candidate from bioinformatics, machine learning, cheminformatics and/or computer science who want to work in this exciting, quickly evolving interdisciplinary field. Please contact Sebastian Böcker in case of questions. Payment is 0.65 positions TV-L E13.
IMPRS: https://www.ice.mpg.de/129170/imprs
MPI-CE: https://www.ice.mpg.de/
SIRIUS & CSI:FingerID: https://bio.informatik.uni-jena.de/software/sirius/
Literature: https://bio.informatik.uni-jena.de/publications/ and https://bio.informatik.uni-jena.de/textbook-algoms/
Jena is a beautiful city and wine is grown in the region:
https://www.youtube.com/watch?v=DQPafhqkabc
https://www.google.com/search?q=jena&tbm=isch
https://www.study-in.de/en/discover-germany/german-cities/jena_26976.php