Naoto Kubota

A computational biologist

  1. ??? (in prep)
    Naoto Kubota, et al.

  2. Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size
    Lin Lin, Jingrong Zhao, Naoto Kubota, Zhelin Li, Yi-Li Lam, Lauren P. Nguyen, Lu Yang, Sheela P. Pokharel, Steven M. Blue, Brian A. Yee, Renee Chen, Gene W. Yeo, Chun-Wei Chen, Liang Chen, Sika Zheng
    Neuron 2024. https://doi.org/10.1016/j.neuron.2024.04.006

  3. Diurnal changes in bacterial settlement on the Peyer’s patch and surrounding mucosa in the rat ileum and its effect against the intestinal immune system
    Youhei Mantani, Nanami Sakata, Naoto Kubota, Asaka Shimada, Satoki Nakanishi, Toshifumi Yokoyama, Nobuhiko Hoshi
    Cell Tissue Res 393, 83–95, 2023.

  4. Mapping of promoter usage QTL using RNA-seq data reveals their contributions to complex traits
    Naoto Kubota, Mikita Suyama
    PLoS Comput. Biol. 18(8): e1010436. 2022.

    • We proposed a new method for identifying genomic loci associated with promoter activities, called promoter usage quantitative trait loci (puQTL), using conventional RNA-seq data.

  5. The microRNA cluster C19MC confers differentiation potential into trophoblast lineages upon human pluripotent stem cells
    Norio Kobayashi, Hiroaki Okae, Hitoshi Hiura, Naoto Kubota, Eri H. Kobayashi, Shun Shibata, Akira Oike, Takeshi Hori, Chie Kikutake, Hirotaka Hamada, Hirokazu Kaji, Mikita Suyama, Marie-Line Bortolin-Cavaillé, Jérôme Cavaillé, Takahiro Arima
    Nat. Commun. 13, 3071, 2022.

  6. Functional variants in hematopoietic transcription factor footprints and their roles in the risk of immune system diseases
    Naoto Kubota, Mikita Suyama
    bioRxiv 2021.03.22.436360; doi: https://doi.org/10.1101/2021.03.22.436360

    • We integrated hematopoietic transcription factor (TF) footprints datasets generated by ENCODE project with multiple quantitative trait locus (QTL) datasets (eQTL, caQTL, bQTL, and hQTL) and investigated the associations of functional variants and immune system disease risk.

  7. An integrated analysis of public genomic data unveils a possible functional mechanism of psoriasis risk via a long-range ERRFI1 enhancer
    Naoto Kubota, Mikita Suyama
    BMC Med. Genomics 13, 8, 2020.

    • We developed a pipeline by integrating publicly available datasets provided by GWAS Catalog, FANTOM5, GTEx, SNP2TFBS, and DeepBlue to to survey psoriasis-associated functional variants that might affect protein functions or gene expression levels.

  8. Identification of reference genes for quantitative PCR analyses in developing mouse gonads
    Toshifumi Yokoyama, Takuya Omotehara, Tetsushi Hirano, Naoto Kubota, Shogo Yanai, Chinatsu Hasegawa, Tadashi Takada, Youhei Mantani, Nobuhiko Hoshi
    J. Vet. Med. Sci. 80, 1534–1539, 2018.

  9. Identification of a candidate enhancer for DMRT3 involved in spastic cerebral palsy pathogenesis
    Naoto Kubota, Toshifumi Yokoyama, Nobuhiko Hoshi, Mikita Suyama
    Biochem. Biophys. Res. Commun. 496, 133–139, 2018.

    • We identified a candidate enhancer of DMRT3 gene, which works as a locomotion coordinator in horses and mice, in a genomic deletion of spastic cerebral palsy patients.

  10. NOAEL-dose of a neonicotinoid pesticide, clothianidin, acutely induce anxiety-related behavior with human-audible vocalizations in male mice in a novel environment
    Tetsushi Hirano, Shogo Yanai, Tadashi Takada, Naoki Yoneda, Takuya Omotehara, Naoto Kubota, Kiichi Minami, Anzu Yamamoto, Youhei Mantani, Toshifumi Yokoyama, Hiroshi Kitagawa, Nobuhiko Hoshi
    Toxicol. Lett. 282, 57–63, 2018.

  11. Prenatal and early postnatal NOAEL-dose clothianidin exposure leads to a reduction of germ cells in juvenile male mice
    Shogo Yanai, Tetsushi Hirano, Takuya Omotehara, Tadashi Takada, Naoki Yoneda, Naoto Kubota, Anzu Yamamoto, Youhei Mantani, Toshifumi Yokoyama, Hiroshi Kitagawa, Nobuhiko Hoshi
    J. Vet. Med. Sci. 79, 1196–1203, 2017.

  12. Ontogenic and morphological study of gonadal formation in genetically-modified sex reversal XY(POS) mice
    Yuria Umemura, Ryosuke Miyamato, Rie Hashimoto, Kyoko Kinoshita, Takuya Omotehara, Daichi Nagahara, Tetsushi Hirano, Naoto Kubota, Kiichi Minami, Shogo Yanai, Natsumi Masuda, Hideto Yuasa, Youhei Mantani, Eiko Matsuo, Toshifumi Yokoyama, Hiroshi Kitagawa, Nobuhiko Hoshi
    J. Vet. Med. Sci. 77, 1587–1598, 2016.

  13. The combined effect of clothianidin and environmental stress on the behavioral and reproductive function in male mice
    Tetsushi Hirano, Shogo Yanai, Takuya Omotehara, Rie Hashimoto, Yuria Umemura, Naoto Kubota, Kiichi Minami, Daichi Nagahara, Eiko Matsuo, Yoshiko Aihara, Ryota Shinohara, Tomoyuki Furuyashiki, Youhei Mantani, Toshifumi Yokoyama, Hiroshi Kitagawa, Nobuhiko Hoshi
    J. Vet. Med. Sci. 77, 1207–1215, 2015.

  14. Immunohistochemical analysis of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxicity on the developmental dentate gyrus and hippocampal fimbria in fetal mice
    Yoshihiro Kobayashi, Tetsushi Hirano, Takuya Omotehara, Rie Hashimoto, Yuria Umemura, Hideto Yuasa, Natsumi Masuda, Naoto Kubota, Kiichi Minami, Shogo Yanai, Mitsuko Ishihara-Sugano, Youhei Mantani, Toshifumi Yokoyama, Hiroshi Kitagawa, Nobuhiko Hoshi
    J. Vet. Med. Sci. 77, 1355–1361, 2015.