論文・総説 - 二階堂　愛

21. Matsumoto H, Hayashi T, Ozaki H, Tsuyuzaki K, Umeda M, Iida T, Nakamura M, Okano H, Nikaido I. An NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data. NAR genomics and bioinformatics. 2020.03; 2 (1): lqz020. ( PubMed, DOI )

22. Tsuyuzaki Koki, Sato Hiroyuki, Sato Kenta, Nikaido Itoshi. Benchmarking principal component analysis for large-scale single-cell RNA-sequencing GENOME BIOLOGY. 2020.01; 21 (1): 9. ( PubMed, DOI )

23. Okumura Akinori, Hayashi Tetsutaro, Ebisawa Masashi, Yoshimura Mika, Sasagawa Yohei, Nikaido Itoshi, Umesono Yoshihiko, Mochii Makoto. Cell type-specific transcriptome analysis unveils secreted signaling molecule genes expressed in apical epithelial cap during appendage regeneration DEVELOPMENT GROWTH & DIFFERENTIATION. 2019.12; 61 (9): 447-456. ( PubMed, DOI )

24. Hirotaka Matsumoto, Tetsutaro Hayashi, Haruka Ozaki, Koki Tsuyuzaki, Mana Umeda, Tsuyoshi Iida, Masaya Nakamura, Hideyuki Okano, Itoshi Nikaido. A NMF based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq NAR Genomics and Bioinformatics. 2019.12; 2 (1): lqz020.

25. Sato Kenta, Tsuyuzaki Koki, Shimizu Kentaro, Nikaido Itoshi. CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing GENOME BIOLOGY. 2019.02; 20 (1): 31. ( PubMed, DOI )

26. Sasagawa Yohei, Hayashi Tetsutaro, Nikaido Itoshi. Strategies for Converting RNA to Amplifiable cDNA for Single-Cell RNA Sequencing Methods SINGLE MOLECULE AND SINGLE CELL SEQUENCING. 2019; 1129 1-17. ( PubMed, DOI )

27. 加藤 忠史, 澤田 知世, チェイター・トーマス , 笹川 洋平, 芳村 美佳, 藤森 典子, 田中 かおり, 合田 裕紀子, 二階堂 愛. iPS細胞を用いた精神・神経疾患研究の現状:創薬への期待　統合失調感情障害双極型に関して不一致な一卵性双生児におけるiPS細胞由来神経細胞および脳オーガノイドの表現型差異(Current status of research on neuropsychiatric disorders using iPS cells: potentiol for drug development　Phenotypic discordance of iPS cells-derived neurons/cerebral organoids between monozygotic twins discordant for schizoaffective bipolar disorder) 日本臨床精神神経薬理学会・日本神経精神薬理学会合同年会プログラム・抄録集. 2018.11; 28回・48回 124. ( 医中誌 )

28. Sasagawa Yohei, Danno Hiroki, Takada Hitomi, Ebisawa Masashi, Tanaka Kaori, Hayashi Tetsutaro, Kurisaki Akira, Nikaido Itoshi. Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads GENOME BIOLOGY. 2018.03; 19 (1): 29. ( PubMed, DOI )

29. Hayashi Tetsutaro, Ozaki Haruka, Sasagawa Yohei, Umeda Mana, Danno Hiroki, Nikaido Itoshi. Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs NATURE COMMUNICATIONS. 2018.02; 9 (1): 619. ( PubMed, DOI )

30. Chai MuhChyi, Sanosaka Tsukasa, Okuno Hironobu, Zhou Zhi, Koya Ikuko, Banno Satoe, Andoh-Noda Tomoko, Tabata Yoshikuni, Shimamura Rieko, Hayashi Tetsutaro, Ebisawa Masashi, Sasagawa Yohei, Nikaido Itoshi, Okano Hideyuki, Kohyama Jun. Chromatin remodeler CHD7 regulates the stem cell identity of human neural progenitors GENES & DEVELOPMENT. 2018.01; 32 (2): 165-180. ( PubMed, DOI )

31. Kobayashi Hideki, Nagahama Takahiko, Arai Wataru, Sasagawa Yohei, Umeda Mana, Hayashi Tetsutaro, Nikaido Itoshi, Watanabe Hiromi, Oguri Kazumasa, Kitazato Hiroshi, Fujioka Kantaro, Kido Yukari, Takami Hideto. Polysaccharide hydrolase of the hadal zone amphipods Hirondellea gigas BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY. 2018; 82 (7): 1123-1133. ( PubMed, DOI )

32. Tsuyuzaki K, Nikaido I. Biological Systems as Heterogeneous Information Networks: A Mini-review and Perspectives HeteroNAM’18. WSDM2018. 2018;

33. Tsuyuzaki K, Nikaido I. Biological Systems as Heterogeneous Information Networks: A Mini-review and Perspectives HeteroNAM’18. WSDM2018. 2018;

34. 森田 梨津子, 三千 典子, 林 哲太郎, 梅田 茉奈, 芳村 美佳, 二階堂 愛, 阿部 高也, 清成 寛, 古田 泰秀, 藤原 裕展. 毛包幹細胞の起源と誘導メカニズムの解明 生命科学系学会合同年次大会. 2017.12; 2017年度 [4P2T16-0817)].

35. Matsumoto Hirotaka, Kiryu Hisanori, Furusawa Chikara, Ko Minoru S. H., Ko Shigeru B. H., Gouda Norio, Hayashi Tetsutaro, Nikaido Itoshi. SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation BIOINFORMATICS. 2017.08; 33 (15): 2314-2321. ( PubMed, DOI )

36. Sasagawa Yohei, Nikaido Itoshi, Hayashi Tetsutaro, Danno Hiroki, Uno Kenichiro D., Imai Takeshi, Ueda Hiroki R.. Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity (vol 14, R31, 2013) GENOME BIOLOGY. 2017.01; 18 (1): 9. ( PubMed, DOI )

37. 小杉 孝嗣, 笹川 洋平, 渡辺 直子, 二階堂 愛. 転写ネットワーク変化を網羅的に同定するシークエンス技術の開発 日本生化学会大会・日本分子生物学会年会合同大会講演要旨集. 2015.12; 88回・38回 [3P0819].

38. G. Morota, F. Penagaricano, J. L. Petersen, D. C. Ciobanu, K. Tsuyuzaki, I. Nikaido. An application of MeSH enrichment analysis in livestock ANIMAL GENETICS. 2015.08; 46 (4): 381-387. ( PubMed, DOI )

39. Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido. MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis BMC BIOINFORMATICS. 2015.02; 16 45. ( PubMed, DOI )

40. Kenjiro Adachi, Itoshi Nikaido, Hiroshi Ohta, Satoshi Ohtsuka, Hiroki Ura, Mitsutaka Kadota, Teruhiko Wakayama, Hiroki R. Ueda, Hitoshi Niwa. Context-Dependent Wiring of Sox2 Regulatory Networks for Self-Renewal of Embryonic and Trophoblast Stem Cells MOLECULAR CELL. 2013.11; 52 (3): 380-392. ( PubMed, DOI )