Name
FUKUNAGA, Tsukasa
Degree
Ph.D. in Science
Status
Associate Professor
HP (URL)
https://sites.google.com/site/fukunagatsu/
Monthly Spotlight
[Monthly Spotlight] is focusing on a researcher to introduce his/her research.
Development of software for estimating the function of function-unknown genes
Research Topic
Estimation of biological functions of function-unknown genes based on machine learning approaches
More than 15 years have passed since the human genome, all genetic information of human, was determined, but the functions of many human genes are still unknown. Currently, the genomes of many species in addition to the human have been determined, and these genomes also contain many function-unknown genes. Revealing the functions of the function-unknown genes is an important research topic in modern genome biology, but there are so many genes that it is impossible to experimentally reveal the functions of all genes. Therefore, estimation of gene function based on the computer science is an essential method. My research interest is development of the software for practical and accurate gene function estimation using machine learning, sequence analysis, and statistical models.
Education and Academic Employment
2011.3 B.S., Department of Bioinformatics and Systems Biology, Faculty of Science, The University of Tokyo
2016.3 Ph.D., Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo
2016.4-2017.9 JSPS Research Fellow, Faculty of Science and Engineering, Waseda University
2017.10-2021.3 Research Associate, Department of Computer Science, Graduate School of Information Science and Technologies, The University of Tokyo.
2021.4- Assistant Professor, Waseda Institute for Advanced Studies, Waseda University
Fields of Research Interests
Bioinformatics, functional non-coding RNA, genome evolution, probabilistic model, machine learning
Academic Publications
・Koichi Mori, Haruka Ozaki and Tsukasa Fukunaga*. “MotiMul: A significant discriminative sequence motif discovery algorithm with multiple testing correction.” IEEE BIBM, 186-193, (2020)
・Shion Hosoda, Suguru Nishijima, Tsukasa Fukunaga, Masahira Hattori and Michiaki Hamada*. “Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation.” Microbiome, 8, 95, (2020)
・Hangchuan Shi, Yin Sun, Miao He, Xiong Yang, Michiaki Hamada, Tsukasa Fukunaga, Xiaoping Zhang* and Chawnshang Chang*. “Targeting the TR4 nuclear receptor-mediated lncTASR/AXL signaling with Tretinoin increases the Sunitnib sensitivity to better suppress the RCC progression.” Oncogene, 39, 530-545, (2020)
・Tsukasa Fukunaga#, Junichi Iwakiri#, Yukiteru Ono and Michiaki Hamada*. “LncRRIsearch: a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data.” Frontiers in Genetics, 10, 462, (2019)
・Tsukasa Fukunaga*and Michiaki Hamada*. “RIblast: An ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach.” Bioinformatics, 33, 2658-2665., (2017)
・Tsukasa Fukunaga* and Wataru Iwasaki*. “Inactivity periods and postural change speed can explain atypical postural change patterns of Caenorhabditis elegans mutants.” BMC Bioinformatics, 18, 46. (2017)
・Masaki Miya*, Yukuto Sato, Tsukasa Fukunaga, Tetsuya Sado, Jan Yde Poulsen, Keiichi Sato, Toshifumi Minamoto, Satoshi Yamamoto, Hiroki Yamanaka, Hitoshi Araki, Michio Kondo, and Wataru Iwasaki. “MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of >230 subtropical marine species.” Royal Society Open Science, 2, 150088. (2015)
・Tsukasa Fukunaga*, Shoko Kubota, Shoji Oda, and Wataru Iwasaki*. “GroupTracker: Video Tracking System for Multiple Animals under Severe Occlusion.” Computational Biology and Chemistry, 57, 39-45. (2015)
・Tsukasa Fukunaga*, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki, and Hisanori Kiryu. “CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data.” Genome Biology, 15, R16. (2014)
・Wataru Iwasaki*, Tsukasa Fukunaga, Ryota Isagozawa, Koichiro Yamada, Yasunobu Maeda, Takashi P. Satoh, Tetsuya Sado, Kohji Mabuchi, Hirohiko Takeshima, Masaki Miya, and Mutsumi Nishida*. “MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline.” Molecular Biology and Evolution, 30, 2531-2540. (2013)
Other Interests
Chorus, Japanese chess, Bouldering
Affiliated Academic Organizations
Japanese Society for Bioinformatics
Awards
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