Dear all, there's some job openings in a great group here in Jena! See below. Best, Bas ---------- Forwarded message --------- From: Sebastian Böcker <sebastian.boecker@uni-jena.de> Date: Thu, Dec 4, 2025 at 12:03 PM Subject: job offers -- ERC advanced project BindingShadows To: Bas E. Dutilh <bedutilh@gmail.com> https://bio.informatik.uni-jena.de/mitarbeiterin-erc-bindingshadows/ The Chair for Bioinformatics, Institute of Computer Science at the Friedrich-Schiller-University Jena offers the following positions: Multiple postdocs and PhD students as research associates (Wissenschaftliche Mitarbeiterin) These positions are part of the ERC advanced project BindingShadows, funded by the European Union through the European Research Council. Liquid Chromatography Mass Spectrometry (LC-MS) is the predominant experimental techniques in untargeted metabolomics and related areas. To give a ballpark estimate: There are 2.2 million scientific studies that use mass spectrometry for the analysis of small molecules, whereas DNA sequencing is mentioned in 2.8 million studies. Our group has made substantial progress to support the annotation of small molecules: SIRIUS (Dührkop et al., Nature Methods 2019) is used by thousands of scientists submitting more than a million compound queries per day; CANOPUS (Dührkop et al., Nature Biotechnology 2021) allows to assign compound classes even for compounds that are unknown to mankind; and, the COSMIC confidence score (Hoffmann et al., Nature Biotechnology 2022) will assign a confidence to all annotations done by CSI:FingerID (Dührkop et al., PNAS 2015). The project BindingShadows will take these ideas to the next level: We will develop machine learning models that predict bioactivity (toxicity, antifungal activity etc.) as well as protein binding, solely from the mass spectral data of a small molecule, but without establishing its identity. The molecular structure of the query small molecule is unknown; it is unknown to the machine learning models, to the scientist doing the experiment, and potentially even to mankind. Elucidating the structure of the small molecule is not the focus of the project, and may be postponed until after experimental confirmation of bioactivity. Our models will not predict one particular bioactivity or protein binding, but rather tens in parallel. Evolution has, through variation and selection, optimized the structure of small molecules for tasks such as communication and warfare, and the pool of natural products is enriched with bioactive compounds. BindingShadows will allow us to harvest this information. We will then apply models at a repository scale, screening millions of tandem MS spectra in thousands of datasets for small molecules that are most likely to have bioactivity or to bind. Furthermore, we will make all methods available through the SIRIUS platform, allowing users to en passant screen for bioactive compounds. If you want to know more, watch our videos or read our papers. We offer: Challenging, interesting and highly relevant questions from machine learning, bioinformatics and computer science; an international network of cooperation partners in method development and application of our methods. Our faculty is moving into a brand new building in Oct 2026. BindindShadows will have a dedicated compute server with 10+ Hopper GPU cards, to be bought beginning of 2026. 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, computer science, chemoinformatics, or mathematics. The project combines machine learning, bioinformatics, statistics and combinatorics, so proven interest in one or more of these fields is a must. For the postdocs, we expect experience in developing machine learning models for small molecules (say, bioactivity prediction) or protein folding, or in developing computational methods for (small molecule) mass spectrometry. Introductory course level knowledge in biology and molecular biology and good programming skills are required. Willingness to visit our cooperation partners in Helsinki, München, Saarbrücken, San Diego, and Zürich is assumed. Salary is according to Entgeltgruppe 13 TV-L and between 65% and 100% (postdocs). Positions are temporary appointments; running time of the project are five years. Handicapped applicants will be given preference in case of equal qualifications. Project start is early 2026. Please send your application with the usual documents (CV, copies of certificates, publication lists, suggested contacts for references) via email and ASAP to: sekretariat.bioinformatik@uni-jena.de Friedrich-Schiller-Universität Jena Institut für Informatik Lehrstuhl für Bioinformatik Ernst-Abbe-Platz 2 07743 Jena, Germany -- Prof. Dr. Sebastian Boecker, Lehrstuhl fuer Bioinformatik Institut fuer Informatik, Friedrich-Schiller-Universitaet Jena Ernst-Abbe-Platz 2, 07743 Jena, Germany Office 3405, Phone +49 (0)3641 9-46451, Fax +49 (0)3641 9-46452 http://bio.informatik.uni-jena.de/ -- Prof. Dr. Bas E. Dutilh <http://tbb.bio.uu.nl/dutilh> Viral Ecology and Omics Group <https://www.veo.uni-jena.de/> | Metagenomics Group Microverse Cluster <https://microverse-cluster.de/en/> | Theoretical Biology and Bioinformatics <https://tbb.bio.uu.nl/> European Virus Bioinformatics Centre <http://evbc.uni-jena.de/> | Utrecht Bioinformatics Center <https://ubc.uu.nl/> Friedrich Schiller University Jena <https://www.uni-jena.de/en/> | Utrecht University <https://www.uu.nl/>