Department of Functional Genome Informatics

73  articles.  
* There may be some overlapped articles listed due to the difference of format.

  1. Morino-Koga S, Tsuruda M, Zhao X, Oshiro S, Yokomizo T, Yamane M, Tanigawa S, Miike K, Usuki S, Yasunaga KI, Nishinakamura R, Suda T, Ogawa M: Transition of signal requirement in hematopoietic stem cell development from hemogenic endothelial cells. Proceedings of the National Academy of Sciences of the United States of America. 2024.07; 121 (31): e2404193121. ( PubMed , DOI )

  1. Mwalilino L, Yamane M, Ishiguro KI, Usuki S, Endoh M, Niwa H: The role of Zfp352 in the regulation of transient expression of 2-cell specific genes in mouse embryonic stem cells. Genes to cells : devoted to molecular & cellular mechanisms. 2023.12; 28 (12): 831-844. ( PubMed , DOI )

  2. 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 )

  3. Yasuyuki Shima, Henrik Skibbe, Yohei Sasagawa, Noriko Fujimori, Yoshimi Iwayama, Ayako Isomura-Matoba, Minoru Yano, Takumi Ichikawa, Itoshi Nikaido, Nobutaka Hattori, Tadafumi Kato: 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): ( DOI )

  4. 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 )

  5. Ogura Nao, Sasagawa Yohei, Ito Tasuku, Tameshige Toshiaki, Kawai Satomi, Sano Masaki, Doll Yuki, Iwase Akira, Kawamura Ayako, Suzuki Takamasa, Nikaido Itoshi, Sugimoto Keiko, Ikeuchi Momoko: 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 )

  6. 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 )

  7. Takada Hitomi, Sasagawa Yohei, Yoshimura Mika, Tanaka Kaori, Iwayama Yoshimi, Hayashi Tetsutaro, Isomura-Matoba Ayako, Nikaido Itoshi, Kurisaki Akira: Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis NATURE COMMUNICATIONS. 2023.06; 14 (1): 3750. ( PubMed , DOI )

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

  1. Sano H, Nakamura A, Yamane M, Niwa H, Nishimura T, Araki K, Takemoto K, Ishiguro KI, Aoki H, Kato Y, Kojima M: The polyol pathway is an evolutionarily conserved system for sensing glucose uptake. PLoS biology. 2022.06; 20 (6): e3001678. ( PubMed , DOI )

  2. 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 )

  3. 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 )

  4. Lin Chia-Wen, Septyaningtrias Dian E., Chao Hsu-Wen, Konda Mikiko, Atarashi Koji, Takeshita Kozue, Tamada Kota, Nomura Jun, Sasagawa Yohei, Tanaka Kaori, Nikaido Itoshi, Honda Kenya, McHugh Thomas J., Takumi Toru: A common epigenetic mechanism across different cellular origins underlies systemic immune dysregulation in an idiopathic autism mouse model MOLECULAR PSYCHIATRY. 2022.05; 27 (8): 3343-3354. ( PubMed , DOI )

  5. 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 )

  1. 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 )

  2. 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 )

  3. 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 )

  4. 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 )

  5. 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. ( ichushi )

  6. Naganuma H, Miike K, Ohmori T, Tanigawa S, Ichikawa T, Yamane M, Eto M, Niwa H, Kobayashi A, Nishinakamura R: Molecular detection of maturation stages in the developing kidney. Developmental biology. 2021.02; 470 62-73. ( PubMed , DOI )

  1. 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 )

  2. 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 )

  3. 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 )

  4. 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 )

  5. 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 )

  6. Takemoto K, Tani N, Takada-Horisawa Y, Fujimura S, Tanno N, Yamane M, Okamura K, Sugimoto M, Araki K, Ishiguro KI: Meiosis-Specific C19orf57/4930432K21Rik/BRME1 Modulates Localization of RAD51 and DMC1 to DSBs in Mouse Meiotic Recombination. Cell reports. 2020.05; 31 (8): 107686. ( PubMed , DOI )

  7. 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 )

  8. 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 )

  9. Ishiguro KI, Matsuura K, Tani N, Takeda N, Usuki S, Yamane M, Sugimoto M, Fujimura S, Hosokawa M, Chuma S, Ko MSH, Araki K, Niwa H: MEIOSIN Directs the Switch from Mitosis to Meiosis in Mammalian Germ Cells. Developmental cell. 2020.02; 52 (4): 429-445.e10. ( PubMed , DOI )

  10. 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 )

  11. Nasser H, Adhikary P, Abdel-Daim A, Noyori O, Panaampon J, Kariya R, Okada S, Ma W, Baba M, Takizawa H, Yamane M, Niwa H, Suzu S: Establishment of bone marrow-derived M-CSF receptor-dependent self-renewing macrophages. Cell death discovery. 2020; 6 63. ( PubMed , DOI )

  1. 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.

  2. 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 )

  3. 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 )

  4. 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 )

  1. 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. ( ichushi )

  2. Yamane M, Ohtsuka S, Matsuura K, Nakamura A, Niwa H: Overlapping functions of Krüppel-like factor family members: targeting multiple transcription factors to maintain the naïve pluripotency of mouse embryonic stem cells. Development (Cambridge, England). 2018.05; 145 (10): ( PubMed , DOI )

  3. 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 )

  4. 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 )

  5. 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 )

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

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

  8. 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 )

  1. 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)].

  2. Haiyang Hu, Masahiro Uesaka, Song Guo, Kotaro Shimai, Tsai-Ming Lu, Fang Li, Satoko Fujimoto, Masato Ishikawa, Shiping Liu, Yohei Sasagawa, Guojie Zhang, Shigeru Kuratani, Jr-Kai Yu, Takehiro G. Kusakabe, Philipp Khaitovich, Naoki Irie: Constrained vertebrate evolution by pleiotropic genes NATURE ECOLOGY & EVOLUTION. 2017.11; 1 (11): 1722-1730. ( DOI )

  3. 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 )

  4. 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 )

  1. Mariko Yamane, Setsuko Fujii, Satoshi Ohtsuka, Hitoshi Niwa: Zscan10 is dispensable for maintenance of pluripotency in mouse embryonic stem cells BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 2015.12; 468 (4): 826-831. ( PubMed , DOI )

  2. 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].

  3. Masaki Kinoshita, Daisuke Shimosato, Mariko Yamane, Hitoshi Niwa: Sox7 is dispensable for primitive endoderm differentiation from mouse ES cells BMC DEVELOPMENTAL BIOLOGY. 2015.10; 15 37. ( PubMed , DOI )

  4. 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 )

  5. Setsuko Fujii, Satomi Nishikawa-Torikai, Yoko Futatsugi, Yayoi Toyooka, Mariko Yamane, Satoshi Ohtsuka, Hitoshi Niwa: Nr0b1 is a negative regulator of Zscan4c in mouse embryonic stem cells SCIENTIFIC REPORTS. 2015.03; 5 9146. ( PubMed , DOI )

  6. 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 )

  1. Shunsuke Ito, Mariko Yamane, Satoshi Ohtsuka, Hitoshi Niwa: The C-terminal region of Xpc is dispensable for the transcriptional activity of Oct3/4 in mouse embryonic stem cells FEBS LETTERS. 2014.04; 588 (7): 1128-1135. ( PubMed , DOI )

  1. 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 )

  2. Masaki Shigeta, Satoshi Ohtsuka, Satomi Nishikawa-Torikai, Mariko Yamane, Setsuko Fujii, Kazuhiro Murakami, Hitoshi Niwa: Maintenance of pluripotency in mouse ES cells without Trp53 Scientific Reports. 2013.10; 3 2944. ( PubMed , DOI )

  3. Nobuo Yoshimoto, Akiko Kida, Xu Jie, Masaya Kurokawa, Masumi Iijima, Tomoaki Niimi, Andres D. Maturana, Itoshi Nikaido, Hiroki R. Ueda, Kenji Tatematsu, Katsuyuki Tanizawa, Akihiko Kondo, Ikuo Fujii, Shun'ichi Kuroda: An automated system for high-throughput single cell-based breeding SCIENTIFIC REPORTS. 2013.02; 3 1191. ( PubMed , DOI )

  4. Tomoko Nakanishi, Rumiko Saito, Makoto Taniguchi, Haruka Oda, Atsumi Soma, Mayu Yasunaga, Mariko Yamane, Kenzo Sato: In Vivo Determination of Vitamin D Function Using Transgenic Mice Carrying a Human Osteocalcin Luciferase Reporter Gene BIOMED RESEARCH INTERNATIONAL. 2013; 2013 895706. ( PubMed , DOI )

  1. Naohiro Hori, Mariko Yamane, Kaori Kouno, Kenzo Sato: Induction of DNA Demethylation Depending on Two Sets of Sox2 and Adjacent Oct3/4 Binding Sites (Sox-Oct Motifs) within the Mouse H19/Insulin-like Growth Factor 2 (Igf2) Imprinted Control Region JOURNAL OF BIOLOGICAL CHEMISTRY. 2012.12; 287 (52): 44006-44016. ( PubMed , DOI )

  2. Yuko Okamura-Oho, Kazuro Shimokawa, Satoko Takemoto, Asami Hirakiyama, Sakiko Nakamura, Yuki Tsujimura, Masaomi Nishimura, Takeya Kasukawa, Koh-hei Masumoto, Itoshi Nikaido, Yasufumi Shigeyoshi, Hiroki R. Ueda, Gang Song, James Gee, Ryutaro Himeno, Hideo Yokota: Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space PLOS ONE. 2012.09; 7 (9): e45373. ( PubMed , DOI )

  1. Takeya Kasukawa, Koh-hei Masumoto, Itoshi Nikaido, Mamoru Nagano, Kenichiro D. Uno, Kaori Tsujino, Carina Hanashima, Yasufumi Shigeyoshi, Hiroki R. Ueda: Quantitative Expression Profile of Distinct Functional Regions in the Adult Mouse Brain PLOS ONE. 2011.08; 6 (8): e23228. ( PubMed , DOI )

  1. Yoshimi Tokuzawa, Ken Yagi, Yzumi Yamashita, Yutaka Nakachi, Itoshi Nikaido, Hidemasa Bono, Yuichi Ninomiya, Yukiko Kanesaki-Yatsuka, Masumi Akita, Hiromi Motegi, Shigeharu Wakana, Tetsuo Noda, Fred Sablitzky, Shigeki Arai, Riki Kurokawa, Toru Fukuda, Takenobu Katagiri, Christian Schoenbach, Tatsuo Suda, Yosuke Mizuno, Yasushi Okazaki: Id4, a New Candidate Gene for Senile Osteoporosis, Acts as a Molecular Switch Promoting Osteoblast Differentiation PLOS GENETICS. 2010.07; 6 (7): e1001019. ( PubMed , DOI )

  2. Keiichiro Suzuki, Fumi Ohbayashi, Itoshi Nikaido, Akihiko Okuda, Haruyoshi Takaki, Yasushi Okazaki, Kohnosuke Mitani: Integration of exogenous DNA into mouse embryonic stem cell chromosomes shows preference into genes and frequent modification at junctions CHROMOSOME RESEARCH. 2010.02; 18 (2): 191-201. ( PubMed , DOI )

  1. Yutaka Nakachi, Ken Yagi, Itoshi Nikaido, Hidemasa Bono, Mio Tonouchi, Christian Schonbach, Yasushi Okazaki: Identification of novel PPAR gamma target genes by integrated analysis of ChIP-on-chip and microarray expression data during adipocyte differentiation BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 2008.07; 372 (2): 362-366. ( DOI )

  1. Nikaido, I, C Saito, A Wakamoto, Y Tomaru, T Arakawa, Y Hayashizaki, Y Okazaki: EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes NUCLEIC ACIDS RESEARCH. 2004.01; 32 D548-D551. ( PubMed , DOI )

  1. Hidemasa Bono, Itoshi Nikaido, Takeya Kasukawa, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Yasushi Okazaki: Comprehensive analysis of the mouse metabolone based on the transcriptome Genome Research. 2003.06; 13 (6 B): 1345-1349. ( PubMed , DOI )

  2. L Nikaido, C Saito, Y Mizuno, M Meguro, H Bono, M Kadomura, T Kono, GA Morris, PA Lyons, M Oshimura, Y Hayashizaki, Y Okazaki: Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling GENOME RESEARCH. 2003.06; 13 (6B): 1402-1409. ( PubMed , DOI )

  3. H Bono, K Yagi, T Kasukawa, Nikaido, I, N Tominaga, R Miki, Y Mizuno, Y Tomaru, H Goto, H Nitanda, D Shimizu, H Makino, T Morita, J Fujiyama, T Sakai, T Shimoji, DA Hume, Y Hayashizaki, Y Okazaki: Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays GENOME RESEARCH. 2003.06; 13 (6B): 1318-1323. ( PubMed , DOI )

  1. Y Okazaki, M Furuno, T Kasukawa, J Adachi, H Bono, S Kondo, Nikaido, I, N Osato, R Saito, H Suzuki, Yamanaka, I, H Kiyosawa, K Yagi, Y Tomaru, Y Hasegawa, A Nogami, C Schonbach, T Gojobori, R Baldarelli, DP Hill, C Bult, DA Hume, J Quackenbush, LM Schriml, A Kanapin, H Matsuda, S Batalov, KW Beisel, JA Blake, D Bradt, Brusic, V, C Chothia, LE Corbani, S Cousins, E Dalla, TA Dragani, CF Fletcher, A Forrest, KS Frazer, T Gaasterland, M Gariboldi, C Gissi, A Godzik, J Gough, S Grimmond, S Gustincich, N Hirokawa, IJ Jackson, ED Jarvis, A Kanai, H Kawaji, Y Kawasawa, RM Kedzierski, BL King, A Konagaya, Kurochkin, IV, Y Lee, B Lenhard, PA Lyons, DR Maglott, L Maltais, L Marchionni, L McKenzie, H Miki, T Nagashima, K Numata, T Okido, WJ Pavan, G Pertea, G Pesole, N Petrovsky, R Pillai, JU Pontius, D Qi, S Ramachandran, T Ravasi, JC Reed, DJ Reed, J Reid, BZ Ring, M Ringwald, A Sandelin, C Schneider, CAM Semple, M Setou, K Shimada, R Sultana, Y Takenaka, MS Taylor, RD Teasdale, M Tomita, R Verardo, L Wagner, C Wahlestedt, Y Wang, Y Watanabe, C Wells, LG Wilming, A Wynshaw-Boris, M Yanagisawa, Yang, I, L Yang, Z Yuan, M Zavolan, Y Zhu, A Zimmer, P Carninci, N Hayatsu, T Hirozane-Kishikawa, H Konno, M Nakamura, N Sakazume, K Sato, T Shiraki, K Waki, J Kawai, K Aizawa, T Arakawa, S Fukuda, A Hara, W Hashizume, K Imotani, Y Ishii, M Itoh, Kagawa, I, A Miyazaki, K Sakai, D Sasaki, K Shibata, A Shinagawa, A Yasunishi, M Yoshino, R Waterston, ES Lander, J Rogers, E Birney, Y Hayashizaki: Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs NATURE. 2002.12; 420 (6915): 563-573. ( PubMed , DOI )

  2. Y Mizuno, Y Sotomaru, Y Katsuzawa, T Kono, M Meguro, M Oshimura, J Kawai, Y Tomaru, H Kiyosawa, Nikaido, I, H Amanuma, Y Hayashizaki, Y Okazaki: Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 2002.02; 290 (5): 1499-1505. ( PubMed , DOI )

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