Itoshi NIKAIDO

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, Jan 7, 2025 Peer-reviewedLast authorCorresponding author

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, Oct 23, 2024 Peer-reviewed

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, Nov 7, 2023 Peer-reviewedLast authorCorresponding author

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, Oct 18, 2023 Peer-reviewed

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, Oct 17, 2023 Peer-reviewedCorresponding author

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

Science Advances, 9(27), Jul 7, 2023 Peer-reviewed

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, Jun 29, 2023 Peer-reviewedCorresponding author

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, Jun 16, 2023 Peer-reviewedLast authorCorresponding author

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

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

Apr 26, 2023

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

Koki Tsuyuzaki, Itoshi Nikaido

Journal of Open Source Software, Apr 23, 2023 Peer-reviewedLast author

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, Mar 12, 2023 Peer-reviewed

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, Jun 1, 2022 Peer-reviewed

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, May 4, 2022 Peer-reviewed

A common epigenetic mechanism across different cellular origins underlies systemic immune dysregulation in an idiopathic autism mouse model.

Chia-Wen Lin, Dian E Septyaningtrias, Hsu-Wen Chao, Mikiko Konda, Koji Atarashi, Kozue Takeshita, Kota Tamada, Jun Nomura, Yohei Sasagawa, Kaori Tanaka …

Molecular psychiatry, 27(8) 3343-3354, May 2, 2022 Peer-reviewed

Improved MeSH analysis software tools for farm animals.

Sabrina T Amorim, Koki Tsuyuzaki, Itoshi Nikaido, Gota Morota

Animal genetics, Dec 2, 2021 Peer-reviewed

Erratum: Derepression of inflammation-related genes link to microglia activation and neural maturation defect in a mouse model of Kleefstra syndrome.

Yamada A, Hirasawa T, Nishimura K, Shimura C, Kogo N, Fukuda K, Kato M, Yokomori M, Hayashi T, Umeda M …

iScience, Oct, 2021

Derepression of inflammation-related genes link to microglia activation and neural maturation defect in a mouse model of Kleefstra syndrome.

Ayumi Yamada, Takae Hirasawa, Kayako Nishimura, Chikako Shimura, Naomi Kogo, Kei Fukuda, Madoka Kato, Masaki Yokomori, Tetsutaro Hayashi, Mana Umeda …

iScience, 24(7) 102741-102741, Jul 23, 2021 Peer-reviewed

Single-oocyte transcriptome analysis reveals aging-associated effects influenced by life stage and calorie restriction.

Tappei Mishina, Namine Tabata, Tetsutaro Hayashi, Mika Yoshimura, Mana Umeda, Masashi Mori, Yayoi Ikawa, Hiroshi Hamada, Itoshi Nikaido, Tomoya S Kitajima

Aging cell, e13428, Jul 10, 2021 Peer-reviewed

Local states of chromatin compaction at transcription start sites control transcription levels.

Satoru Ishihara, Yohei Sasagawa, Takeru Kameda, Hayato Yamashita, Mana Umeda, Naoe Kotomura, Masayuki Abe, Yohei Shimono, Itoshi Nikaido

Nucleic acids research, 49(14) 8007-8023, Jul 7, 2021 Peer-reviewedLast authorCorresponding author

Tracing the origin of hair follicle stem cells.

Ritsuko Morita, Noriko Sanzen, Hiroko Sasaki, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Takaki Yamamoto, Tatsuo Shibata, Takaya Abe, Hiroshi Kiyonari …

Nature, 594(7864) 547-552, Jun 9, 2021 Peer-reviewed

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