論文・総説 - 二階堂　愛

1. Tsuyuzaki K, Ishii M, Nikaido I. Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data. BMC bioinformatics. 2023.11; 24 (1): 420. ( PubMed, DOI )

2. Shima, Y; Skibbe, H; Sasagawa, Y; Fujimori, N; Iwayama, Y; Isomura-Matoba, A; Yano, M; Ichikawa, T; Nikaido, I; Hattori, N; Kato, T. Distinctiveness and continuity in transcriptome and connectivity in the anterior-posterior axis of the paraventricular nucleus of the thalamus CELL REPORTS. 2023.10; 42 (10): 113309. ( PubMed, DOI )

3. Ogura N, Sasagawa Y, Ito T, Tameshige T, Kawai S, Sano M, Doll Y, Iwase A, Kawamura A, Suzuki T, Nikaido I, Sugimoto K, Ikeuchi M. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science advances. 2023.07; 9 (27): eadg6983. ( PubMed, DOI )

4. Takada H, Sasagawa Y, Yoshimura M, Tanaka K, Iwayama Y, Hayashi T, Isomura-Matoba A, Nikaido I, Kurisaki A. Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis. Nature communications. 2023.06; 14 (1): 3750. ( PubMed, DOI )

5. Tsuyuzaki Koki, Yamamoto Kentaro, Toyoshima Yu, Sato Hirofumi, Kanamori Manami, Teramoto Takayuki, Ishihara Takeshi, Iino Yuichi, Nikaido Itoshi. WormTensor: a clustering method for time-series whole-brain activity data from C. elegans BMC BIOINFORMATICS. 2023.06; 24 (1): 254. ( PubMed, DOI )

6. nnTensor: An R package for non-negative matrix/tensor decomposition. 2023.04; ( DOI )

7. Wibisana Johannes N., Inaba Takehiko, Shinohara Hisaaki, Yumoto Noriko, Hayashi Tetsutaro, Umeda Mana, Ebisawa Masashi, Nikaido Itoshi, Sako Yasushi, Okada Mariko. Enhanced transcriptional heterogeneity mediated by NF-kappa B super-enhancers PLOS GENETICS. 2022.06; 18 (6): e1010235. ( PubMed, DOI )

8. Herbig Maik, Isozaki Akihiro, Di Carlo Dino, Guck Jochen, Nitta Nao, Damoiseaux Robert, Kamikawaji Shogo, Suyama Eigo, Shintaku Hirofumi, Wu Angela Ruohao, Nikaido Itoshi, Goda Keisuke. Best practices for reporting throughput in biomedical research NATURE METHODS. 2022.06; 19 (6): 633-634. ( PubMed, DOI )

9. Yasuyuki Shima, Henrik Skibbe, Yohei Sasagawa, Noriko Fujimori, Itoshi Nikaido, Nobutaka Hattori, Tadafumi Kato. Distinctiveness and continuity in transcriptome and connectivity in the anterior-posterior axis of the paraventricular nucleus of thalamus bioRxiv (preprint). 2022.02; ( DOI )

10. Mishina Tappei, Tabata Namine, Hayashi Tetsutaro, Yoshimura Mika, Umeda Mana, Mori Masashi, Ikawa Yayoi, Hamada Hiroshi, Nikaido Itoshi, Kitajima Tomoya S.. Single-oocyte transcriptome analysis reveals aging-associated effects influenced by life stage and calorie restriction AGING CELL. 2021.07; e13428. ( PubMed, DOI )

11. Ishihara S, Sasagawa Y, Kameda T, Yamashita H, Umeda M, Kotomura N, Abe M, Shimono Y, Nikaido I. Local states of chromatin compaction at transcription start sites control transcription levels. Nucleic acids research. 2021.07; ( PubMed, DOI )

12. Yamada A, Hirasawa T, Nishimura K, Shimura C, Kogo N, Fukuda K, Kato M, Yokomori M, Hayashi T, Umeda M, Yoshimura M, Iwakura Y, Nikaido I, Itohara S, Shinkai Y. Derepression of inflammation-related genes link to microglia activation and neural maturation defect in a mouse model of Kleefstra syndrome. iScience. 2021.07; 24 (7): 102741. ( PubMed, DOI )

13. Morita Ritsuko, Sanzen Noriko, Sasaki Hiroko, Hayashi Tetsutaro, Umeda Mana, Yoshimura Mika, Yamamoto Takaki, Shibata Tatsuo, Abe Takaya, Kiyonari Hiroshi, Furuta Yasuhide, Nikaido Itoshi, Fujiwara Hironobu. Tracing the origin of hair follicle stem cells NATURE. 2021.06; ( DOI )

14. 二階堂 愛. High-throughput Transcriptome Analysis for Building Cell Atlas(和訳中) 日本循環器学会学術集会抄録集. 2021.03; 85回 ME08-4. ( 医中誌 )

15. Sawada Tomoyo, Chater Thomas E., Sasagawa Yohei, Yoshimura Mika, Fujimori-Tonou Noriko, Tanaka Kaori, Benjamin Kynon J. M., Paquola Apua C. M., Erwin Jennifer A., Goda Yukiko, Nikaido Itoshi, Kato Tadafumi. Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids MOLECULAR PSYCHIATRY. 2020.08; 25 (11): 2695-2711. ( PubMed, DOI )

16. Mereu Elisabetta, Lafzi Atefeh, Moutinho Catia, Ziegenhain Christoph, McCarthy Davis J., Alvarez-Varela Adrian, Batlle Eduard, Sagar, Gruen Dominic, Lau Julia K., Boutet Stephane C., Sanada Chad, Ooi Aik, Jones Robert C., Kaihara Kelly, Brampton Chris, Talaga Yasha, Sasagawa Yohei, Tanaka Kaori, Hayashi Tetsutaro, Braeuning Caroline, Fischer Cornelius, Sauers Sascha, Trefzer Timo, Conrad Christian, Adiconis Xian, Nguyen Lan T., Regev Aviv, Levin Joshua Z., Parekh Swati, Janjic Aleksandar, Wange Lucas E., Bagnoli Johannes W., Enard Wolfgang, Gut Marta, Sandberg Rickard, Nikaido Itoshi, Gut Ivo, Stegle Oliver, Heyn Holger. Benchmarking single-cell RNA-sequencing protocols for cell atlas projects NATURE BIOTECHNOLOGY. 2020.06; 38 (6): 747-+. ( PubMed, DOI )

17. Michida Hiroki, Imoto Hiroaki, Shinohara Hisaaki, Yumoto Noriko, Seki Masahide, Umeda Mana, Hayashi Tetsutaro, Nikaido Itoshi, Kasukawa Takeya, Suzuki Yutaka, Okada-Hatakeyama Mariko. The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression CELL REPORTS. 2020.06; 31 (9): 107724. ( PubMed, DOI )

18. Shiozawa Seiji, Nakajima Mayutaka, Okahara Junko, Kuortaki Yoko, Kisa Fumihiko, Yoshimatsu Sho, Nakamura Mari, Koya Ikuko, Yoshimura Mika, Sasagawa Yohei, Nikaido Itoshi, Sasaki Erika, Okano Hideyuki. Primed to Naive-Like Conversion of the Common Marmoset Embryonic Stem Cells STEM CELLS AND DEVELOPMENT. 2020.06; 29 (12): 761-773. ( PubMed, DOI )

19. Ochiai Hiroshi, Hayashi Tetsutaro, Umeda Mana, Yoshimura Mika, Harada Akihito, Shimizu Yukiko, Nakano Kenta, Saitoh Noriko, Liu Zhe, Yamamoto Takashi, Okamura Tadashi, Ohkawa Yasuyuki, Kimura Hiroshi, Nikaido Itoshi. Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells SCIENCE ADVANCES. 2020.06; 6 (25): eaaz6699. ( PubMed, DOI )

20. Ozaki Haruka, Hayashi Tetsutaro, Umeda Mana, Nikaido Itoshi. Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets BMC GENOMICS. 2020.03; 21 (1): 177. ( PubMed, DOI )