FSU Jena research profile – VirusREvolution

Research profile of the applicant university

Strategy and planning

The Friedrich Schiller University (FSU) Jena pursues a long-term strategy of integrating excellence in fundamental research with translational, data-driven, and interdisciplinary approaches. Its guiding vision is to address major societal challenges through innovation, collaboration, and sustainable infrastructure development. The university continuously adapts its structures to strengthen key research areas, enhance visibility, and foster cooperation with national and international partners.

a. Strategic research framework and institutional integration.

The FSU Jena’s traditional research profile is composed of three profile areas: LIGHT – optics and photonics, innovative materials and technologies; LIFE – microbiology, biodiversity and bio-geo-interactions, ageing research; and LIBERTY – change of social systems, enlightenment, romanticism, contemporary history. These profile lines form the foundation of interdisciplinary research at the FSU and are manifested in the form of many centres and clusters, which engender those collaborations. The proposed CRC VirusREvolution, combining virology, bioinformatics, and photonics, strategically anchors itself at the interface of the LIFE and LIGHT profiles, thereby strengthening the university’s long-term vision to connect life sciences, data science, and optical technologies.

The FSU has three profile areas: LIGHT, LIFE, and LIBERTY, which are interconnected with and strengthened by other non-university research institutions in Jena. Both CRC AquaDiva and CRC FungiNet have recently concluded, making the expertise and datasets generated within these consortia fully available to support the proposed CRC VirusREvolution. Their established knowledge bases and resources provide an immediate foundation for advancing the CRC’s research objectives.

For the CRC VirusREvolution strategic cooperation with local and national non-university research institutions has been established, specifically with the Leibniz Institute of Photonic Technology (Leibniz IPHT), Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz HKI), Fraunhofer Institute for Applied Optics and Precision Engineering (Frauenhofer-IOF), Leibniz Institute on Aging – Fritz-Lipmann-Institute (Leibniz FLI), Friedrich Loeffler Institute (FLI), Robert Koch Institute (RKI). This forms a cornerstone of FSU Jena’s research planning, fostering translational science and innovation.

Jena’s strategic development is further shaped by DFG-funded CRCs and research units, including CRC 1076 AquaDiva CRC 1278 PolyTarget CRC 1375 NOA CRC 1127 ChemBioSys CRC/TR 124 FungiNet TRR 234 CataLight as well as Research Units such as FOR 2179 MAD Soil FOR 2518 DynIon, and FOR 3004 SYNABS. This dense research landscape ensures long-term continuity, supporting FSU’s strategy to link basic and applied science through sustainable structures.

b. Supporting research institutions in Jena.

Besides the participating non-university research institutions, the CRC VirusREvolution benefits from close collaborations with several supporting research organisations in Jena:

• InfectoGnostics – develops innovative diagnostic platforms for infectious diseases.

• InfectControl – focuses on prevention and control strategies for microbial infections.

• InfectoOptics – applies advanced optical technologies for infection detection and monitoring.

• Max Planck Institute for Biochemistry – conducts fundamental research in molecular and cellular biology relevant to host-pathogen interactions.

• Max Planck Institute for Geoanthropology – investigates human-environment interactions with implications for pathogen transmission.

• Max Planck Institute for Chemical Ecology – studies chemical communication in ecological systems, relevant for pathogen-vector interactions.

• Fraunhofer Institute for Applied Optics and Precision Engineering (IOF) – provides photonics and imaging technologies for biomedical applications.

• German Aerospace Center (DLR) – supports advanced imaging, sensing, and analytical technologies.

• CEMSIS – specialises in sensor systems and optical measurement technologies.

• Helmholtz Institute Jena – focuses on energy- and environment-related research with broad technological expertise.

• Leibniz Zentrum für Photonik in der Infektionsforschung (LZP) – develops photonic approaches to study infectious diseases.

These partnerships are crucial, as most of the city’s scientific success stories have emerged from interactions between university groups and specialised institutes, enabling access to unique technologies, expertise, and collaborative networks.

c. Strategic alliances, infrastructure, and future planning.

The University Alliance (“Universitätsbund”) Halle-Jena-Leipzig is a long-standing strategic partnership between the Martin Luther University Halle-Wittenberg, the Friedrich Schiller University Jena, and the University of Leipzig. It promotes joint research, teaching, and infrastructure development, providing an efficient framework for collaboration and resource sharing. The proposed CRC VirusREvolution will build upon these structures, ensuring smooth cooperation across universities. Of the 32 PIs, three (P. Stadler (B02), J. Meiler (B03), C. Schoeder (B03)) are based in Leipzig, underlining the alliance’s strong integrative character. The alliance also hosts the German Centre for Integrative Biodiversity Research (iDiv), jointly run by the three universities and eight non-university partners, further exemplifying successful cooperative research structures. Shared mentoring, mobility, and equality programmes, such as the inter- university Mentoring Programme for female postdocs, joined by S. Deinhardt-Emmer (C02) and M. Marz (A04), further align with the CRC’s goals for career development and diversity.

The University Alliance Halle-Jena-Leipzig, est. 1995

d. FSU Jena’s excellence strategy.

The FSU was successful within the German Excellence strategy in 2019 and 2025 with the Cluster of Excellence EXC 2051 “Balance of the Microverse”. The vision of this cluster is to investigate the dynamic balance of microbial communities from the molecular to the ecosystem level. The cluster combines the expertise of the profile areas LIFE and LIGHT in microbiology, infection biology, ecology, clinical medicine, optics/photonics, materials science, and bioinformatics at the FSU, the Jena University Hospital, and eight non- university research institutes, see Fig. 12. The cluster builds on the Graduate School Jena School for Microbial Communication (JSMC), which was established in 2006 and funded until 2018 as a DFG excellence graduate school, is now funded by the Carl Zeiss foundation and from 2026 by the Free State of Thuringia. Eight PIs of VirusREvolution (B. Dutilh (A01), C. Eggeling (C01, C03), T. Figge (C03), K. Küsel (A01), M. Marz (A04), K. Papenfort (A04), G. Pohnert (B01), J. Popp (C04)) are also core members of the 25 PIs of Cluster of Excellence EXC 2051. The focus on virus tool development is unique for the CRC VirusREvolution and complements the research of the “Balance of the Microverse” perfectly, see Fig. 12. The CRC VirusREvolution thus adds substantially to the research activity in Jena by combining virology, bioinformatic, and photonic approaches. This is not only limited to analytical method development but rather spans the entire range from experimental design to multiomics data evaluation.

The Cluster of Excellence “Balance of the Microverse” has been funded by the DFG since 2019 and renewed 2025 (EXC 2051) with a focus on microbial communities. It is embedded in the profile areas LIFE (with CRC 1127 ChemBioSys, CRC 1076 AquaDiva, and CRC/TR 124 FungiNet) and LIGHT (CRC 1375 NOA, CRC 1278 PolyTarget, and TRR 234 CataLight). Although CRC AquaDiva and FungiNet have recently concluded, their expertise and datasets are fully available to support the proposed CRC VirusREvolution.

e. FSU Jena’s participation in NFDI consortia.

As part of its long-term strategy to strengthen data-driven research and open science, FSU Jena actively participates in multiple consortia within the NFDI initiative. These contributions align with the university’s institutional goal to embed FAIR data principles, promote interoperability, and foster sustainable digital research infrastructures across disciplines.

CRC VirusREvolution PIs play leading roles in several NFDI consortia: N. Cassman (Z02) and M. Marz (A04) are contributing to NFDI4Microbiota by developing the virus database VirJenDB; T. Figge (C03) is involved in NFDI4Bioimage, focusing on standardised image-based data workflows; and B. König-Ries (Z02) participates in NFDI4Biodiversity, supporting biodiversity and ecological data integration. In addition, multiple FSU researchers contribute to NFDI4Chem, coordinated by C. Steinbeck at FSU Jena, which establishes tools and standards for chemical and metabolomics data.

f. Infrastructure and digital innovation form the second pillar of the university’s strategic planning.

FSU Jena strategically invests in cutting-edge infrastructure to strengthen the interface between basic and translational research. The Center for Translational Medicine (CeTraMed) and the ThIMEDOP Innovation Centre exemplify this strategy. These facilities combine photonic, biomedical, and clinical expertise, creating a seamless pipeline from discovery to application in diagnostics, therapy, and prevention. The centres connect technological excellence in optics and photonics with the clinical strengths of the Jena University Hospital, particularly in infection and ageing research. Two PIs of the CRC VirusREvolution (C. Eggeling (C01, C03) and J. Popp (C04)) are directly involved in the EFRE-funded ThIMEDOP project, ensuring a close link between methodological innovation and clinical implementation. The SEPTomics platform provides integrated multiomics capabilities – including proteomics, metabolomics, and lipidomics – directly supporting experimental and translational research. Several CRC VirusREvolution PIs (G. Pohnert (B01), C. Eggeling (C01, C03), T. Figge (C03)) utilise SEPTomics for virus and microbiome studies, enabling comprehensive molecular profiling.

Complementary to these translational facilities, the Abbe Center of Photonics (ACP) serves as a key academic hub for optics and photonics research. Through joint projects with the Fraunhofer Institute for Applied Optics and Precision Engineering, the Helmholtz Institute Jena, and the Leibniz Institute of Photonic Technology, ACP provides access to state-of-the-art photonic platforms. Four CRC VirusREvolution PIs (V. Deckert (C02), C. Eggeling (C01, C03), J. Popp (C04), M. Schmidt (C01)) are leading members of the ACP, ensuring that photonic tool development remains tightly integrated with the university’s long-term innovation strategy.

The Jena Center for Soft Matter (JCSM) provides a complementary interdisciplinary environment linking chemistry, biology, and physics with materials science. Its activities foster the translation of molecular and nanoscale principles into biological and biomedical applications. Eight PIs of CRC VirusREvolution (S. Böcker (B01), V. Deckert (C02), C. Eggeling (C01, C03), T. Figge (C03), S. Höppener (Z03), P. Jordan (B02), G. Pohnert (B01), J. Popp (C04)) are JCSM members, reflecting the strategic importance of material-based and structural approaches for life science innovation.

The Jena Center for Bioinformatics (JCB) is the university’s key platform for computational biology and systems bioinformatics. It connects theoretical and experimental groups across medicine, biology, and biotechnology, promoting algorithmic and data-driven research. Six CRC VirusREvolution PIs (S. Böcker (B01), B. Dutilh (A01), P. Dittrich (B04), T. Figge (C03), S. Hoffmann (A03), M. Marz (A04)) are JCB members, thereby linking the CRC’s bioinformatic research directly to FSU’s digital transformation strategy. The FSU Jena maintains a centralised Bioinformatics Core Facility (BiC), led by E. Barth (Z02), which provides essential support for computational analysis, data management, and high-performance computing across the life sciences. The facility enables seamless integration of experimental and multiomics data, supports reproducible workflows, and offers training for researchers at all career stages. Several CRC VirusREvolution PIs (e.g. B. Dutilh (A01), K. Küsel (A01), M. Marz (A04)) regularly utilise and contribute to BiC services, ensuring that computational and bioinformatic strategies are closely aligned with the CRC’s research goals. The APPEAL (Antivirus Pandemic Preparedness EuropeAn pLatform) initiative, coordinated at FSU Jena’s partner institution Jena University Hospital, provides a European framework for antiviral drug discovery and pandemic preparedness. Focusing on host-cell mechanisms and broad-spectrum antiviral strategies, APPEAL spans computational modelling, high-throughput screening, advanced 3D human-relevant models, animal studies, and pilot clinical validation.

Digital infrastructure and open-science initiatives are coordinated through the DigLeben consortium, which has established sustainable structures for digitalisation in the life sciences, and through FDM Thüringen, coordinated by CRC PI R. Gerlach (Z02), providing state-wide support for research data management. Together, these initiatives ensure compliance with FAIR data principles and embed digital innovation deeply into FSU’s institutional planning. In this context, the Michael Stifel Center Jena (MSCJ), with CRC PI B. König-Ries (Z02) as the spokesperson, plays an important role in establishing data science and computational modelling as strategic pillars of interdisciplinary research at FSU, whose legacy continues within newer digital initiatives.

Founded by the RKI, FLI, and, among others, the FSU Jena, a particularly relevant initiative for the CRC VirusREvolution is DiaMETA-net, a german network of research groups from different institutions, that have come together to work in the field of infectious medicine and employ new sequencing technologies (next-generation sequencing, NGS) as part of diagnostic workflows. The network is organised in an interdisciplinary manner, and its research areas span human and veterinary medicine as well as parasitology, microbiology, and virology. By linking complementary expertise of untargeted analyses based on metagenomics, it is possible to capture the genetic information present in a sample, assign them taxonomically, and thereby detect (new) pathogens whose genetic material may share only moderate similarity with known agents. Founding members include CRC PI M. Marz (A04) and M. Beer (C04).

g. European Virus Bioinformatics Center (EVBC) – the perfect partner for the CRC VirusREvolution.

A particularly relevant initiative for the CRC VirusREvolution is the European Virus Bioinformatics Center (EVBC), founded and coordinated at FSU Jena by CRC PI M. Marz (A04). The EVBC unites more than 250 researchers from over 100 institutions worldwide with the goal of advancing computational methods for virus research. It serves as a strategic networking and knowledge-exchange hub between virologists, bioinformaticians, and photonics researchers, fostering tool development, data integration, and standardisation of analytical workflows. Established explicitly as a preparatory step toward a comprehensive collaborative research structure, the EVBC laid the conceptual and organisational foundation for the CRC VirusREvolution by connecting key European partners and aligning research priorities in virus bioinformatics.