Postdoc: Algorithmic developments to automatically detect RiPP structural features

The Faculty of Science / the Institute for Biology is looking for a:

Postdoc: Algorithmic developments to automatically detect RiPP structural features from untargeted LC-MS/MS based metabolomics data

Vacancy number:15203

Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a class of microbial metabolites with high potential as antibiotics. In addition, they may well serve as plant biocontrol agents, because many of them have narrow-spectrum biological activities and exhibit low levels of toxicity. While recently several tools have been developed to facilitate the detection of RiPP pathways in microbial genomes, the automated detection of RiPP signatures in untargeted LC-MS/MS based metabolomics data is still a challenge.

The current project aims at developing algorithms for the automated detection of characteristic RiPP structural features in the microbial metabolome, identified through the characteristic MS/MS fragmentation pattern associated with them. This will facilitate the quick assessment of whether or not RiPPs are being produced by the bacteria, and the identification of the RiPP class being produced together with typical RiPP post translational modifications (PTMs). The resulting algorithms will be implemented into existing software solutions that work with metabolomics data and will facilitate integrative omics mining for RiPPs by recognizing structural features from mass spectrometry data that can also be predicted from the genome.

For this project we seek an enthusiastic postdoctoral researcher who will be appointed for a period of two years, working under the supervision of Dr. Justin van der Hooft from Wageningen University & Research, and Dr. Somayah Elsayed from Leiden University. The postdoc will be imbedded within a larger multidisciplinary NWO project, KIC Microbiome Mission, involving several public/private organizations in the Netherlands and abroad, that aims at the identification and implementations of RiPPs as potential plant biocontrol agents.

Key responsibilities

• Cataloging the different classes of RiPPs identified with LC-MS/MS so far, their structural features, and their characteristic MS/MS fragmentation patterns.
• Developing algorithms that detect the MS/MS fragmentation patterns that recognize RiPPS, and are specific to the different RiPP classes and PTMs.
• Testing the generated algorithms on both in house and publicly available MS/MS data.
• Apply the algorithms to newly generated data in the NWO KIC Microbiome Mission project, to speed up the discovery process of new RiPPs within the microbial metabolome.
• Implementing the new algorithms into existing software tools such as FERMO.

Selection Criteria

• PhD in computational metabolomics or related field.
• Strong knowledge in organic chemistry and mass spectrometry.
• Knowledge in MS-based metabolomics data analysis, and machine learning algorithms.
• Experience in peptide sequencing using MS/MS is a pré.
• Experience with programming, in particular in Python
• Proficiency in spoken and written English.
• Feels at home in a diverse, multinational environment.
• Excellent communication skills and a collaborative attitude.

Research at our faculty
The Faculty of Science is a world-class faculty where staff and students work together in a dynamic international environment. It is a faculty where personal and academic development are top priorities. Our people are committed to expand fundamental knowledge by curiosity and to look beyond the borders of their own discipline; their aim is to benefit science, and to make a contribution to addressing the major societal challenges of the future.

The research carried out at the Faculty of Science is very diverse, ranging from mathematics, information science, astronomy, physics, chemistry and bio-pharmaceutical sciences to biology and environmental sciences. The research activities are organised in eight institutes. These institutes offer eight bachelor’s and twelve master’s programmes. The faculty has grown strongly in recent years and now has more than 2300 {see https://www.universiteitleiden.nl/wiskunde-en-natuurwetenschappen} staff and almost 5000 {see https://www.universiteitleiden.nl/wiskunde-en-natuurwetenschappen} students. We are located at the heart of Leiden’s Bio Science Park, one of Europe’s biggest science parks, where university and business life come together.

For more information, see https://www.universiteitleiden.nl/en/science and https://workingat.leiden.edu/

The Institute for Biology
The research within the Institute of Biology Leiden (IBL) aims to work on the science base of biodiversity and health, which is reflected in our leading principle Harnessing Biodiversity for Health. We perform innovative curiosity-driven research to answer fundamental questions, and solutions-driven research to help solving major societal challenges. The latter include protecting nature’s biodiversity, creating sustainable biotechnology and agriculture and increasing good health. Our research focuses on four Research Themes: Bioactive Molecules, Host-Microbe Interactions, Development & Disease and Evolution & Biodiversity. Located in a thriving scientific environment with our Faculty of Sciences, Naturalis Biodiversity Centre, the Leiden University Medical Centre and the Leiden Bioscience Park, IBL offers an exciting, internationally oriented and inclusive place to work and study.

Terms and conditions
We offer a full-time, 2 year term position. Salary range from € 3.345,-- to € 5.278,-- gross per month (pay scale 10 in accordance with the Collective Labour Agreement for Dutch Universities).

Leiden University offers an attractive benefits package with additional holiday (8%) and end-of-year bonuses(8.3 %), training and career development and sabbatical leave. Our individual choices model gives you some freedom to assemble your own set of terms and conditions. Candidates from outside the

Netherlands may be eligible for a substantial tax break.
Leiden University is strongly committed to diversity within its community and especially welcomes applications from members of underrepresented groups.

Information
Enquiries can be made to Dr. Somayah Elsayed, s.elsayed@biology.leidenuniv.nl. If you have any questions about the procedure, please contact Christina Kamerman (HR@biology.leidenuniv.nl).

Applications
Applications for this vacancy can be submitted via the blue button of our online system. Please ensure that you upload the following additional documents quoting the vacancy number:

• CV
• Motivation letter

Only applications received before 1 November 2024 can be considered.