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News

2025-03-19 - Protocol published in 実験医学

We published a protocol for using DeepSpaceDB in 実験医学 (in Japanese). [pdf]

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Research Interests

My current research is focusing on these topics:

1. finding biological insights in single-cell and spatial transcriptomics data. See this paper for an example.
2. construction of DeepSpaceDB, a database for spatial transcriptomics data
3. finding interesting genes in single-cell and spatial transcriptome data. See singleCellHaystack on GitHub and CRAN, or this and this publication.
4. analysis of large-scale gene expression data, including removal of technical biases and inference of gene regulatory networks
5. analysis of stimulus-induced changes in epigenetic markers and their effect on transcription

In addition, I have been involved in many interdisciplinary collaborations, especially involving the field of immunology.

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Teaching

Since 2017 I am teaching statistics, data analysis, bioinformatics, and R programming in Kyoto University.

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Career Summary

2022-present: Associate Professor, LiMe, Kyoto University
2017-2022: Lecturer, INFRONT (now LiMe), Kyoto University
2014-2017: Unit leader of the Immuno-Genomics Research Unit, IFReC, Osaka University
2012-2017: Specially Appointed Assistant Professor, IFReC, Osaka University
2009-2012: Post-doctoral researcher, IFReC, Osaka University
2009: Ph.D. in the field of Bioinformatics, University of Tokyo
2004: Master of Science in Molecular Biotechnology , Ghent University, Belgium
2003: Master in biochemistry, KHBO Belgium