| 研究実績の概要 |
I developed an advanced sequence classifier for analyzing medical metagenomes.
My classifier was tested on a mock bacterial community and on pleural effusion samples from a patient with empyema (Mitsuhashi et al., 2017). It was applied to detecting bacterial pathogens in blood samples from sepsis patients (Watanabe et al., 2018). It also continues to be used for analysis of samples from empyema patients (Shiraishi et al., in preparation). Recently my classifier is also used at Kyoto University Hospital and Kansai Medical University for rapid identification of bacterial pathogens (Kai et al., 2019; Tanaka et al., 2019). A portable application of my classifier system was successfully tested in the field application in Zambia (Nakagawa et al., under review). Also my classifier was applied to detecting viral DNA in genome sequences (Kryukov et al., 2019).
My reference sequence database, called GenomeSync, currently contains 2,906 Gbp of sequence in 234,279 genomes, making it one of the largest reference genome resources. This database is specifically designed to facilitate metagenome analyses. As part of this project I developed a new advanced sequence compression method (Kryukov et al., 2019).
My sequence classifier system for investigating medical metagenomes has shown utility in research studies, field trips and tests on medical samples. The results have been described in peer-reviewed literature. We expect that our system will be widely adopted for investigating infectious diseases using next generation sequencing.
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