INFormation, INFormatics, and INFrastructure
Central activities of the CRC VirusREvolution
The Z-Project INFormation, INFormatics, and INFrastructure will provide data management, processing, and integration services to all projects of the CRC VirusREvolution and will focus on creating extensive data models of the training viruses, starting with SARS-CoV-2 and vibriophage N4. The services include (i) research data management (RDM) support, including creating and executing a data management plan, developing a common entry point for the data exchange, and training and helpdesk support for all CRC members, (ii) extending and supporting data integration for all CRC projects into the NFDI4Microbiota virus database VirJenDB, (iii) fundamental bioinformatics services providing and executing software pipelines and tools, and (iv) assistance in the FAIRification of the software tools developed in the CRC VirusREvolution. In addition, together with the respective experts, we will create comprehensive data models and facilitate access for all projects to the data gathered and generated in the CRC. Finally, based on the vibriophage N4 and the SARS-CoV-2 model systems, we aim to develop a multi-modal framework to describe the host reaction to virus infection based on standard processing and integration of transcriptomic, metabolomic, proteomic, and Raman spectroscopy data provided by A04 (Marz/ Papenfort), Z03 (Fröhlich/Höppener/Reiche), A03 (Hoffmann/Weber), B01 (Böcker/Pohnert), and C04 (Beer/Popp). To this end, we will also include the proteomics data that we will generate and evaluate in collaboration with the Proteomics Facility from the Jena University Hospital.
Overview of the Z02 INF project plan.
- WP 1: Data management strategy (Gerlach/König-Ries)
- WP 2: Semantic description and publication of research objects (König-Ries/Gerlach/Cassman)
- WP 3: Connecting CRC-specific data, tools, and visualisations within VirJenDB (Cassman)
- WP 4: Fundamental bioinformatic services (Barth)
- WP 5: Bioinformatics workflows for the model viruses (Barth/Cassman)
- WP 6: Integration of transcriptomics, metabolomics, and proteomics data of the model viruses (Barth/Cassman)
Team Members
N. N.
Research software engineer
N. N.
Postdoctoral Researcher
N. N.
Postdoctoral Researcher
Project-Specific Publications
2025
VirJenDB: a FAIR (meta) data and bioinformatics platform for all viruses Journal Article
In: Nucleic Acids Research, pp. gkaf1224, 2025.
2023
Navigating the landscape: a comprehensive review of current virus databases Journal Article
In: Viruses, vol. 15, no. 9, pp. 1834, 2023.
2021
VIDHOP, viral host prediction with deep learning Journal Article
In: Bioinformatics, vol. 37, no. 3, pp. 318–325, 2021.
BEXIS2: A FAIR-aligned data management system for biodiversity, ecology and environmental data Journal Article
In: Biodiversity Data Journal, vol. 9, pp. e72901, 2021.
Understanding experiments and research practices for reproducibility: an exploratory study Journal Article
In: PeerJ, vol. 9, pp. e11140, 2021.
Dataset search in biodiversity research: Do metadata in data repositories reflect scholarly information needs? Journal Article
In: PloS one, vol. 16, no. 3, pp. e0246099, 2021.
2020
Tissue-specific gene expression changes are associated with aging in mice Journal Article
In: Genomics, proteomics & bioinformatics, vol. 18, no. 4, pp. 430–442, 2020.
2019
Conserved aging-related signatures of senescence and inflammation in different tissues and species Journal Article
In: Aging (Albany NY), vol. 11, no. 19, pp. 8556, 2019.
2012
Oxygen minimum zones harbour novel viral communities with low diversity Journal Article
In: Environmental microbiology, vol. 14, no. 11, pp. 3043–3065, 2012.
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”Wir bringen die breite Basis mit” – Gemeinsames Plädoyer für eine enge Einbindung der Landesinitiativen für Forschungsdatenmanagement in die Nationale Forschungsdateninfrastruktur. Journal Article
In: 0000.