二階堂愛 (Itoshi NIKAIDO) - 論文

Heme acts as a metabolic brake on erebosis in the Drosophila gut.

Motohiro Morikawa, Tetsutaro Hayashi, Yuko Ikegawa, Tomomi Takano, Kazuya Wata, Hirohisa Kyogoku, Mariko Kuse, Mika Yoshimura, Hiroshi Nishida, Rahul Parit …

PLoS biology 24(8) e3003942 2026年8月19日査読有り

GenPerturb: sequence-grounded interpretation of perturbation transcriptomes using pretrained genomic models

Takuya Shihashi, Itoshi Nikaido

2026年7月3日

Cycling persister clones with elevated NR2F1-mediated cholesterol biosynthesis cause chemotherapy resistance

Hajime Sato, Taku Sato, Yohei Sasagawa, Ryoko Seki, Shicheng Zhang, Hiroshi Haeno, Daisuke Hishikawa, Mashito Sakai, Kenta Hata, Itoshi Nikaido …

2026年6月10日

Genomic characterization of sub-populations in human pluripotent stem cell-derived retinal progenitor cells driving retinal lamination.

Yasuaki Iwama, Tomohiro Masuda, Mika Yoshimura, Mikiya Watanabe, Yoko Ohigashi, Martin Friedlander, Kohji Nishida, Masayo Takahashi, Itoshi Nikaido, Michiko Mandai

Stem cell reports 21(4) 102831-102831 2026年4月14日査読有り

scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase.

Rawin Poonperm, Taiki Yoneda, Taito Imada, Saori Takahashi, Takako Ichinose, Hisashi Miura, Tetsutaro Hayashi, Mariko Kuse, Mika Yoshimura, Koji Nagao …

Nature communications 16(1) 10902-10902 2025年12月15日査読有り責任著者

MitoDelta: identifying mitochondrial DNA deletions at cell-type resolution from single-cell RNA sequencing data.

Haruko Nakagawa, Yasuyuki Shima, Yohei Sasagawa, Itoshi Nikaido

BMC genomics 26(1) 810-810 2025年9月25日査読有り最終著者責任著者

Elucidation of the mechanism of byproduct DNA synthesis in whole-transcript amplification by poly-A tagging and development of its specific suppression

Yohei Sasagawa, Yoshimi Iwayama, Minoru Yano, Itoshi Nikaido

2025年8月19日

The Effect of Multi-task Learning on the Prediction of Neoantigen–MHC Class II Binding

Kazuhiro Ikkyu, Itoshi Nikaido

IEEE Transactions on Computational Biology and Bioinformatics 1-12 2025年1月7日査読有り最終著者責任著者

Transcriptomic signatures of WNT-driven pathways and granulosa cell-oocyte interactions during primordial follicle activation

Hinako M. Takase, Tappei Mishina, Tetsutaro Hayashi, Mika Yoshimura, Mariko Kuse, Itoshi Nikaido, Tomoya S. Kitajima

PLOS ONE 2024年10月23日査読有り

Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data.

Koki Tsuyuzaki, Manabu Ishii, Itoshi Nikaido

BMC bioinformatics 24(1) 420-420 2023年11月7日査読有り最終著者責任著者

Distinctiveness and continuity in transcriptome and connectivity in the anterior-posterior axis of the paraventricular nucleus of the thalamus.

Yasuyuki Shima, Henrik Skibbe, Yohei Sasagawa, Noriko Fujimori, Yoshimi Iwayama, Ayako Isomura-Matoba, Minoru Yano, Takumi Ichikawa, Itoshi Nikaido, Nobutaka Hattori …

Cell reports 42(10) 113309-113309 2023年10月18日査読有り

Author Correction: Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis

Hitomi Takada, Yohei Sasagawa, Mika Yoshimura, Kaori Tanaka, Yoshimi Iwayama, Tetsutaro Hayashi, Ayako Isomura-Matoba, Itoshi Nikaido, Akira Kurisaki

Nature Communications 2023年10月17日査読有り責任著者

Nao Ogura, Yohei Sasagawa, Tasuku Ito, Toshiaki Tameshige, Satomi Kawai, Masaki Sano, Yuki Doll, Akira Iwase, Ayako Kawamura, Takamasa Suzuki …

Science Advances 9(27) 2023年7月7日査読有り

Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis.

Hitomi Takada, Yohei Sasagawa, Mika Yoshimura, Kaori Tanaka, Yoshimi Iwayama, Tetsutaro Hayashi, Ayako Isomura-Matoba, Itoshi Nikaido, Akira Kurisaki

Nature communications 14(1) 3750-3750 2023年6月29日査読有り責任著者

WormTensor: a clustering method for time-series whole-brain activity data from C. elegans.

Koki Tsuyuzaki, Kentaro Yamamoto, Yu Toyoshima, Hirofumi Sato, Manami Kanamori, Takayuki Teramoto, Takeshi Ishihara, Yuichi Iino, Itoshi Nikaido

BMC bioinformatics 24(1) 254-254 2023年6月16日査読有り最終著者責任著者

A centrifugation-based method for high-throughput biomaterial separation using magnetic microbeads

Hiroki Sugishita, Kazunori Hojo, Tetsutaro Hayashi, Itoshi Nikaido, Yukiko Gotoh

2023年4月26日

nnTensor: An R package for non-negative matrix/tensor decomposition

Koki Tsuyuzaki, Itoshi Nikaido

Journal of Open Source Software 2023年4月23日査読有り最終著者

Maternal epigenetic factors in embryonic and postnatal development.

Hiromi Nishimura, Yayoi Ikawa, Eriko Kajikawa, Natsumi Shimizu-Mizuno, Sylvain Hiver, Namine Tabata-Okamoto, Masashi Mori, Tomoya Kitajima, Tetsutaro Hayashi, Mika Yoshimura …

Genes to cells : devoted to molecular & cellular mechanisms 2023年3月12日査読有り

Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers.

Johannes N Wibisana, Takehiko Inaba, Hisaaki Shinohara, Noriko Yumoto, Tetsutaro Hayashi, Mana Umeda, Masashi Ebisawa, Itoshi Nikaido, Yasushi Sako, Mariko Okada

PLoS genetics 18(6) e1010235 2022年6月1日査読有り

Best practices for reporting throughput in biomedical research.

Maik Herbig, Akihiro Isozaki, Dino Di Carlo, Jochen Guck, Nao Nitta, Robert Damoiseaux, Shogo Kamikawaji, Eigo Suyama, Hirofumi Shintaku, Angela Ruohao Wu …

Nature methods 19(6) 633-634 2022年5月4日査読有り

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