IPB Halle: Leibniz Institute of Plant Biochemistry English

IPB Newsletter | April 2025
Understanding Plants!

The IPB Video
IPB Seminar | 17.07. 2025 | 16:00

Functional genomics and gene editing for abiotic stress resilience in crops
Prof. Sanjib Kumar Panda, Central University of Rajasthan, India
Molecular Signal Processing

Prof. Dr. Steffen Abel
How plants stand their ground.
Bioorganic Chemistry

Prof. Dr. Ludger Wessjohann
The chemistry of nature - basis for active compounds for human and plant health.
Biochemistry of Plant Interactions

Prof. Dr. Tina Romeis
Interactions in, of and with plants.
Cell and Metabolic Biology

Prof. Dr. Alain Tissier
Secondary but never unimportant - the biological functions of plant secondary metabolites.
Independent Junior Research Group

Dr. Mariana Schuster

News

Over 600 guests came to the IPB on July 4 for the Long Night of Sciences to learn lots of new things and put their knowledge to the test at our science quiz course. This year, our program was aimed equally at children and…

Our 10th Leibniz Plant Biochemistry Symposium on May 7 and 8 was a great success. This year's theme was new methods and research approaches in natural product chemistry. The excellent presentations on active substances and…

Omani medicinal plant in the focus of phytochemistry
IPB scientists and partners from Dhofar University recently took a closer phytochemical look at the Omani medicinal plant Terminalia dhofarica. Terminalia is rich in…

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PhD position in (bio)chemistry (m/f/d) (14/2025)

Date: 2025-07-11 Reference Number: 14/2025

Biological-Technical Assistant (m/f/d) or Biological Laboratory Technician (m/f/d) or Chemical-Technical Assistant (m/f/d) or Chemical Laboratory Technician (m/f/d)

Date: 2025-06-27 Reference Number: 13/2025

PhD in Machine Learning for Enzyme Design (m/f/d)

Date: 2025-05-16 Reference Number: 11/2025

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Preprints

Zulfiqar, M.; Gadelha, L.; Steinbeck, C.; Sorokina, M.; Peters, K.; MAW - The reproducible Metabolome Annotation Workflow for untargeted tandem mass Spectrometry bioRxiv (2022) DOI: 10.1101/2022.10.17.512224

Mapping the chemical space of compounds to chemical structures remains a challenge in metabolomics. Despite the advancements in untargeted liquid chromatography-mass spectrometry (LC-MS) to achieve a high-throughput profile of metabolites from complex biological resources, only a small fraction of these metabolites can be annotated with confidence. Many novel computational methods and tools have been developed to enable chemical structure annotation to known and unknown compounds such as in silico generated spectra and molecular networking. Here, we present an automated and reproducible Metabolome Annotation Workflow (MAW) for untargeted metabolomics data to further facilitate and automate the complex annotation by combining tandem mass spectrometry (MS2) input data pre-processing, spectral and compound database matching with computational classification, and in silico annotation. MAW takes the LC-MS2 spectra as input and generates a list of putative candidates from spectral and compound databases. The databases are integrated via the R package Spectra and the metabolite annotation tool SIRIUS as part of the R segment of the workflow (MAW-R). The final candidate selection is performed using the cheminformatics tool RDKit in the Python segment (MAW-Py). Furthermore, each feature is assigned a chemical structure and can be imported to a chemical structure similarity network. MAW is following the FAIR (Findable, Accessible, Interoperable, Reusable) principles and has been made available as the docker images, maw-r and maw-py. The source code and documentation are available on GitHub. The performance of MAW is evaluated on two case studies. We found that MAW can improve candidate ranking by integrating spectral databases with annotation tools like SIRIUS which contributes to an efficient candidate selection procedure. The results from MAW are also reproducible and traceable, compliant with the FAIR guidelines. Taken together, MAW could greatly facilitate automated metabolite characterization in diverse fields such as clinical metabolomics and natural product discovery.

Preprints

Schreiber, T.; Tripathee, S.; Iwen, T.; Prange, A.; Vahabi, K.; Grützner, R.; Horn, C.; Marillonnet, S.; Tissier, A.; DNA double strand breaks lead to de novo transcription and translation of damage-induced long RNAs in planta bioRxiv (2022) DOI: 10.1101/2022.05.11.491484

Preprints

Illig, A.-M.; Siedhoff, N. E.; Schwaneberg, U.; Davari, M. D.; A hybrid model combining evolutionary probability and machine learning leverages data-driven protein engineering bioRxiv (2022) DOI: 10.1101/2022.06.07.495081

Preprints

Bao, Z.; Guo, Y.; Deng, Y.; Zang, J.; Zhang, J.; Ouyang, B.; Qu, X.; Bürstenbinder, K.; Wang, P.; The microtubule-associated protein SlMAP70 interacts with SlIQD21 and regulates fruit shape formation in tomato bioRxiv (2022) DOI: 10.1101/2022.08.08.503161

IPB Newsletter | April 2025

Understanding Plants!

IPB Seminar | 17.07. 2025 | 16:00

Molecular Signal Processing

Bioorganic Chemistry

Biochemistry of Plant Interactions

Cell and Metabolic Biology

Independent Junior Research Group

News

Hands-on science and a big quiz marathon at the Long Night of Sciences

Well-attended symposium

+++ News Ticker Science #182 +++ Natural Products+++

Job vacancies

PhD position in (bio)chemistry (m/f/d) (14/2025)

Biological-Technical Assistant (m/f/d) or Biological Laboratory Technician (m/f/d) or Chemical-Technical Assistant (m/f/d) or Chemical Laboratory Technician (m/f/d)

PhD in Machine Learning for Enzyme Design (m/f/d)

Publications

Advanced Search