Behind the Scenes of AMR Accelerator Data Management
Interview with Leonie von Berlin: COMBINE & GNA NOW
The COMBINE project continues to coordinate data management within the AMR Accelerator projects. The scientists behind this effort are determined to provide a publicly accessible platform for storing and analysing in vitro and in vivo AMR-related data resources. The recent publication of the team’s work on machine learning (ML) models for predicting antibiotic activity has highlighted the value of harmonised data as training sets for Artificial Intelligence-informed drug discovery and development. The insights from this work are now published in the Journal of Chemical Information and Modeling. One of the authors, Leonie von Berlin, shared her perspective on the AMR field, science, and passion.
What specific aspect of AMR is your research focused on?
My research focuses on ensuring that data generated within the AMR Accelerator is findable, accessible, interoperable, and reusable (FAIR). Effective collaboration across institutions and projects is crucial for advancing AMR research, but its impact depends on the availability and usability of the data. One of the biggest challenges in my work is harmonising data from different research sites. Even when standardised templates for data documentation are used, each site—and even each researcher—has their own style and formatting preferences. Additionally, many steps and decisions in the data generation process are often not well-documented, making it difficult to ensure consistency. That’s why I assess the FAIRness of data within the AMR Accelerator and work on FAIRifying it when necessary.
Transforming information from multiple sources into a coherent, standardised format that can be published, easily understood and reused by researchers worldwide is a complex task. It requires ongoing communication with individual researchers to clarify details, align formats, and ensure that the data meets FAIR principles. By making research outputs more sustainable and accessible to the wider scientific community, we enhance their value and contribute to a more effective global response to antimicrobial resistance.
Leonie von Berlin is a Data Manager & Scientist at
Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg
How do you maintain enthusiasm in your research journey?
I would say this is a very important question for any researcher and one that I struggled a lot with during my PhD at the Karolinska Institute in Stockholm. Initially, I studied Biology in Bonn, where I focused on neuroscience. During my internships in Boston and later in my PhD, I worked on understanding brain development using OMICs (omics refers to a field of study in biological sciences that ends with -omics, such as genomics, transcriptomics, proteomics, or metabolomics) tools and Python programming. After completing a short postdoc, I joined Fraunhofer ITMP in Hamburg, which led me to become part of the AMR Accelerator through COMBINE and GNA NOW projects.
What I’ve learned is that I need to see a clear link between my work and a tangible impact—even if it helps improve the life of just one person. Knowing that my efforts contribute, directly or indirectly, to reducing suffering and creating a healthier world keeps me engaged and motivated.
During my PhD in basic science, I sometimes struggled to see that connection, which made it hard to stay passionate. Within AMR Accelerator, the link is very palpable for me as we strive to prevent the spread of diseases caused by resistant microbes. The opportunity to address a pressing global health challenge inspires me to work in AMR research. By tackling antimicrobial resistance today, we can help prevent severe health consequences in the future.
Can you describe a typical day for you?
I usually start my workday between 8 and 9 AM by checking the latest publications and emails, and then creating a to-do list to structure my day. My schedule often includes various video calls for different projects, including work package meetings for COMBINE.
As I am responsible for FAIR data within the AMR Accelerator, I frequently collaborate with research sites to standardise data and ensure it is uploaded to open platforms. When I’m not in meetings, I focus on my tasks—though balancing calls and doing the work can sometimes be a challenge. Currently, I am testing the grit42 software and working on uploading COMBINE data to enhance its FAIRness.
What advice would you give other researchers or students interested in AMR research?
Learn programming and data handling next to laboratory research. Those skills will become more and more important and boost your career!
How do you think the public can contribute to the fight against AMR?
AMR is a global crisis that affects everyone, and we all have a role to play in combating it. We should use antibiotics responsibly—only when prescribed—and always complete the full course of treatment. Reducing the consumption of meat from mass animal farms can help limit antibiotic overuse, which contributes to resistance in our food and water systems. Practising good hygiene and staying up to date with vaccinations also helps prevent infections, reducing the need for antibiotics.
What interests do you have outside of your research?
In my free time, you will find me cosily snuggled up reading a book, dancing ballet, doing yoga, hiking, or, on a lazy Sunday, brunching with friends. I love the topic of psychology, and I am completing training on it soon, which will give me the chance to tackle health issues from another side.
How do you balance your professional and personal life?
I am very strict about my working hours—I don’t overwork, I avoid working in the evenings, and I keep my weekends free. When I get home, I consciously disconnect from work. However, I’ve learned that true balance isn’t just about setting time boundaries—it’s about mindset.
During my PhD, I saw colleagues staying late and working on weekends, and I often felt the internal pressure to do the same. But I made a deliberate choice to stick to my schedule, knowing that rest is essential for creativity and efficiency. It wasn’t always easy, and I had to actively resist the belief that success requires constant overworking. In the end, maintaining this balance never harmed my career—on the contrary, it’s one of the reasons I am where I am today.
Want to know more? Take a look at other publications from COMBINE:
- Fernow J, Olliver M, Couet W, et al. The AMR Accelerator: from individual organizations to efficient antibiotic development partnerships. Nature Reviews Drug Discovery 2024. Published online September 23, 2024. doi:10.1038/d41573-024-00138-9. Green Open Access available through DiVA.
- Arrazuria R, Kerscher B, Huber KE, et al. Expert workshop summary: Advancing toward a standardized murine model to evaluate treatments for antimicrobial resistance lung infections. Frontiers in Microbiology. 2022;13:988725. doi:10.3389/fmicb.2022.988725
- Arrazuria R, Kerscher B, Huber KE, et al. Variability of murine bacterial pneumonia models used to evaluate antimicrobial agents. Frontiers in Microbiology. 2022;13:988728. doi:10.3389/fmicb.2022.988728
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Bekeredjian-Ding I. Challenges for Clinical Development of Vaccines for Prevention of Hospital-Acquired Bacterial Infections. Frontiers in Immunology. 2020;11:533705. doi:10.3389/FIMMU.2020.01755