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Nakai Lab (Functional In Silico Analysis)
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A bioinformatics lab that uses computers to decipher how genome information works.
AboutAbout the lab
Decoding how the genome works with computers
Nakai Lab (Functional In Silico Analysis) conducts research that uses computers to analyze the functions of genome information and gene products.
'In silico' means 'in silicon,' that is, research carried out using computers.
The lab works with experimental researchers and uses cutting-edge technologies such as next-generation sequencers to research and develop bioinformatics methods.
The lab aims to contribute to new discoveries in biology, to the understanding of the mechanisms of disease and immune response, and to regenerative medicine.
Key terms
- In silico
- A term modeled on 'in vivo' (within a living organism) and 'in vitro' (in a test tube), referring to research carried out inside a computer
- Transcription factor
- A protein that attaches to specific locations on DNA and switches nearby genes on or off
- Intrinsically disordered protein
- A protein that functions without a fixed three-dimensional structure. Its flexibly changing shape is what enables its function
NewsLab news
A doctoral student received the Osamu Gotoh Award at IIBMP2026
Prof. Nakai was elected a Fellow of the International Society for Computational Biology (ISCB)
A doctoral student received the Most Outstanding Student Publication Award from the Institute of Medical Science
A doctoral student received the Outstanding Student Publication Award from the Institute of Medical Science
The lab published a deep learning method for analyzing tissue using spatial transcriptomics
ResearchResearch themes
The lab uses computers to study the functional aspects of genome information. By investigating the mechanisms that regulate gene activity, as well as protein structures and interactions, it aims to understand the roles genes play in cells as a network of interacting genes.
*Illustrative imageGenome Informatics
The lab studies how transcription factors bind to regulatory regions on the genome to control gene expression. Its work includes modeling gene regulation, epigenetics research, and analysis of next-generation sequencing data.
*Illustrative imageComputational Proteomics
The lab uses computers to investigate protein properties from two perspectives: structure and interactions. Its work includes research on intrinsically disordered proteins, protein function prediction, and analysis of interaction networks.
*Illustrative imageDevelopment of Bioinformatics Resources
The lab develops the computational infrastructure that supports data-driven science. It makes its databases and source code publicly available so that the research community can use them.
MembersFaculty
The members of Nakai Lab are faculty, secretaries, visiting researchers, doctoral and master's students, research students, and internship students.As of 2026
- ProfessorKenta NakaiPublications ↗
- Assistant ProfessorMartin LozaPublications ↗
- Assistant ProfessorYitao Yang
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “Carbohydrate kinase 1KYH” Boghog2 / Public domain (cropped)
- Genome Informatics: “Mouse GABP ALPHA and BETA domain bound to DNA - 1AWC” Batchelor AH, Piper DE, de la Brousse FC, McKnight SL, Wolberger C / CC0 (cropped)
- Computational Proteomics: “Pp2a 2iae chainABC 1b3u chainA” Opabinia regalis / CC BY-SA 4.0 (cropped)
- Development of Bioinformatics Resources: “BalticServers data center” BalticServers.com / CC BY-SA 3.0 (cropped)
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