Study Visit at the University of Helsinki: Transcriptomics and Metagenomic Research

Signe Parts, PhD student from the University of Tartu, completed a study visit at the University of Helsinki from November 30th to December 12th, 2025, with the primary aim of enhancing knowledge and gaining hands-on experience with transcriptomic methods in metagenomic research. Signe is a junior researcher and PhD candidate in medicine whose work centers on improving early detection of diabetic nephropathy by re-evaluating existing biomarkers and identifying novel prognostic connections. She specializes in bioinformatics, biomedicine, and nanomedicine, integrating these disciplines to support translational research. In addition to her academic work, Signe was a founding member of the Baltic Society of Extracellular Vesicles and is Nucleate Baltics' communications director. 

The visit focused on understanding how bioinformatic pipelines are constructed and implemented, particularly the Lazypipe pipeline developed by researchers at the University of Helsinki. In addition, the visit aimed to provide practical experience in RNA extraction, library preparation, and sequencing technologies within the context of metagenomics. 

Learning Outcomes

During the study visit, Signe gained insight into the construction and application of bioinformatic pipelines used in metagenomic research, with a particular focus on Lazypipe. Hands-on laboratory experience included RNA extraction, library preparation, and exposure to different sequencing technologies. The visit also provided an understanding of methodological differences between Nanopore and Illumina sequencing, as well as how sample preparation strategies vary depending on research objectives.

She was also introduced to current research on viral metagenomics, including the detection of complete viral and microbial genomes in sequenced materials and unexpected findings such as plant virus genomes. Additional insights included exposure to compact, portable wet-lab technologies suitable for fieldwork in diverse global settings.

Key Highlights:

• Visit to the Department of Virology, Faculty of Medicine, University of Helsinki.

• Participation in the Pathogenomics Research Group led by Dr Ravi Kant.

• Introduction to the Viral Zoonoses Research Unit.

• Meetings with Dr Teemu Smura and Dr Hanna Vauhkonen.

• Exposure to research topics ranging from vector-borne viruses to the development of diagnostic tools.

• Observation of how open science practices and collaborative research environments support the development of efficient and resource-saving tools such as the Lazypipe pipeline.

Knowledge Transfer to the University of Tartu

The study visit established the foundation for continued collaboration with Dr Ravi Kant’s research group. Knowledge gained during the visit will be applied to ongoing studies in metagenomics, particularly in exploring connections between viromes, other microorganisms, and diabetes. Practical experience from wet-lab work and bioinformatic pipeline implementation will support the conduct of high-quality research and contribute to Signe’s professional development toward a doctoral degree. The visit also provided insight into interdisciplinary One Health initiatives at the University of Helsinki, including research networks that integrate expertise across medical, biological, and computational sciences. 

As Signe said, "I will continue my studies in metagenomics to discover connections for diabetes and viromes or other microorganisms. The start of collaboration with Dr Ravi Kant's lab has been established, and there is still much to learn from their skill sets. I will apply knowledge gained from the wet lab to conducting high-quality research in pursuit of a doctoral degree."

Thank you, team of the University of Helsinki, in particular Dr Ravi Kant, for the hosting, guiding, and mentoring. This study visit supported methodological training and international research collaboration within a One Health framework.