The University of Tokyo Graduate School of Frontier Sciences Department of Computational Biology
2003 - 2007
The University of Tokyo Graduate School of Mathematical Sciences
2001 - 2003
Information Processing Society of Japan
The Molecular Biology Society of Japan
International Society for Computational Biology
Society of Evolutionary Studies, Japan
Japanese Society for Bioinformatics
Life sciences / Genetics /
Life sciences / Evolutionary biology /
Life sciences / Systems genomics /
Life sciences / Genomics /
Phylogenetic and structural insights into the origin of C-type lectin Mincle in vertebrates.
Taiki Ito, Carla Guenther, Eri Ishikawa, Takae Yabuki, Masamichi Nagae, Yoichiro Nakatani, Sho Yamasaki
Immunogenetics Vol. 77 No. 1 p. 18-18 2025/03/22 Research paper (scientific journal)
Publisher: Springer Science and Business Media LLC
Variability in non-tumor areas of colorectal cancer patients as revealed by endoscopic intestinal step biopsies.
Shoko Ikuta, Yutaka Saito, So Takata, Yoichiro Nakatani, Izumi Nagatomo, Satoshi Shiba, Yoshito Takeda, Yasushi Totoki, Sayaka Mizutani, Hironori Sunakawa, Hiroaki Ikematsu, Hiroyuki Takamaru, Atsushi Kumanogoh, Shinichi Yachida
Molecular cancer Vol. 23 No. 1 p. 249-249 2024/11/07 Research paper (scientific journal)
PCDHGC3 hypermethylation as a potential biomarker of intestinal neuroendocrine carcinomas.
Tamara Cubiella, Lucía Celada, Jaime San-Juan-Guardado, Raúl Rodríguez-Aguilar, Álvaro Suárez-Priede, María Poch, Francisco Dominguez, Iván Fernández-Vega, Pedro Montero-Pavón, Mario F Fraga, Yoichiro Nakatani, So Takata, Shinichi Yachida, Nuria Valdés, María-Dolores Chiara
The Journal of pathology Vol. 263 No. 4-5 p. 418-428 2024/08 Research paper (scientific journal)
An integrative epigenomic approach identifies ELF3 as an oncogenic regulator in ASCL1-positive neuroendocrine carcinoma.
Masafumi Horie, Hidenori Tanaka, Masami Suzuki, Yoshihiko Sato, So Takata, Erina Takai, Naoya Miyashita, Akira Saito, Yoichiro Nakatani, Shinichi Yachida
Cancer science Vol. 114 No. 6 p. 2596-2608 2023/02/24 Research paper (scientific journal)
Comprehensive Genomic Profiling of Neuroendocrine Carcinomas of the Gastrointestinal System.
Shinichi Yachida, Yasushi Totoki, Michael Noe, Yoichiro Nakatani, Masafumi Horie, Kenta Kawasaki, Hiromi Nakamura, Mihoko Saito-Adachi, Masami Suzuki, Erina Takai, Natsuko Hama, Ryota Higuchi, Seiko Hirono, Satoshi Shiba, Mamoru Kato, Eisaku Furukawa, Yasuhito Arai, Hirofumi Rokutan, Taiki Hashimoto, Shuichi Mitsunaga, Mitsuro Kanda, Hidenori Tanaka, So Takata, Ayaka Shimomura, Minoru Oshima, Wenzel M Hackeng, Tomoyuki Okumura, Keiichi Okano, Masakazu Yamamoto, Hiroki Yamaue, Chigusa Morizane, Koji Arihiro, Toru Furukawa, Toshiro Sato, Tohru Kiyono, Lodewijk A A Brosens, Laura D Wood, Ralph H Hruban, Tatsuhiro Shibata
Cancer discovery Vol. 12 No. 3 p. 692-711 2021/12/08 Research paper (scientific journal)
Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution
Yoichiro Nakatani, Prashant Shingate, Vydianathan Ravi, Nisha E. Pillai, Aravind Prasad, Aoife McLysaght, Byrappa Venkatesh
Nature Communications Vol. 12 No. 1 2021/07/23 Research paper (scientific journal)
Publisher: Springer Science and Business Media LLC
CTCF looping is established during gastrulation in medaka embryos
Ryohei Nakamura, Yuichi Motai, Masahiko Kumagai, Candice L. Wike, Haruyo Nishiyama, Yoichiro Nakatani, Neva C. Durand, Kaori Kondo, Takashi Kondo, Tatsuya Tsukahara, Atsuko Shimada, Bradley R. Cairns, Erez Lieberman Aiden, Shinichi Morishita, Hiroyuki Takeda
Genome Research Vol. 31 No. 6 p. 968-980 2021/06 Research paper (scientific journal)
Publisher: Cold Spring Harbor Laboratory
Macrosynteny analysis shows the absence of ancient whole-genome duplication in lepidopteran insects
Nakatani, Y., McLysaght, A.
Proceedings of the National Academy of Sciences of the United States of America Vol. 116 No. 6 p. 1816-1818 2019/02 Research paper (scientific journal)
Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes
Yoichiro Nakatani, Aoife McLysaght
BIOINFORMATICS Vol. 33 No. 14 p. I369-I378 2017/07 Research paper (scientific journal)
Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species
Yoichiro Nakatani, Cecilia C. Mello, Shin-ichi Hashimoto, Atsuko Shimada, Ryohei Nakamura, Tatsuya Tsukahara, Wei Qu, Jun Yoshimura, Yutaka Suzuki, Sumio Sugano, Hiroyuki Takeda, Andrew Fire, Shinichi Morishita
BMC GENOMICS Vol. 16 2015/11 Research paper (scientific journal)
Coordinated Changes in DNA Methylation in Antigen-Specific Memory CD4 T Cells
Shin-ichi Hashimoto, Katsumi Ogoshi, Atsushi Sasaki, Jun Abe, Wei Qu, Yoichiro Nakatani, Budrul Ahsan, Kenshiro Oshima, Francis H. W. Shand, Akio Ametani, Yutaka Suzuki, Shuichi Kaneko, Takashi Wada, Masahira Hattori, Sumio Sugano, Shinichi Morishita, Kouji Matsushima
JOURNAL OF IMMUNOLOGY Vol. 190 No. 8 p. 4076-4091 2013/04 Research paper (scientific journal)
Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns
Wei Qu, Shin-ichi Hashimoto, Atsuko Shimada, Yoichiro Nakatani, Kazuki Ichikawa, Taro L. Saito, Katsumi Ogoshi, Kouji Matsushima, Yutaka Suzuki, Sumio Sugano, Hiroyuki Takeda, Shinichi Morishita
GENOME RESEARCH Vol. 22 No. 8 p. 1419-1425 2012/08 Research paper (scientific journal)
Genome-wide profiling of DNA methylation in human cancer cells
Katsumi Ogoshi, Shin-ichi Hashimoto, Yoichiro Nakatani, Wei Qu, Kenshiro Oshima, Katsushi Tokunaga, Sumio Sugano, Masahira Hattori, Shinichi Morishita, Kouji Matsushima
GENOMICS Vol. 98 No. 4 p. 280-287 2011/10 Research paper (scientific journal)
Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites
Shin Sasaki, Cecilia C. Mello, Atsuko Shimada, Yoichiro Nakatani, Shin-ichi Hashimoto, Masako Ogawa, Kouji Matsushima, Sam Guoping Gu, Masahiro Kasahara, Budrul Ahsan, Atsushi Sasaki, Taro Saito, Yutaka Suzuki, Sumio Sugano, Yuji Kohara, Hiroyuki Takeda, Andrew Fire, Shinichi Morishita
SCIENCE Vol. 323 No. 5912 p. 401-404 2009/01 Research paper (scientific journal)
High-Resolution Analysis of the 5'-End Transcriptome Using a Next Generation DNA Sequencer
Shin-ichi Hashimoto, Wei Qu, Budrul Ahsan, Katsumi Ogoshi, Atsushi Sasaki, Yoichiro Nakatani, Yongjun Lee, Masako Ogawa, Akio Ametani, Yutaka Suzuki, Sumio Sugano, Clarence C. Lee, Robert C. Nutter, Shinichi Morishita, Kouji Matsushima
PLOS ONE Vol. 4 No. 1 2009/01 Research paper (scientific journal)
The genome of a lepidopteran model insect, the silkworm Bombyx mori
Qingyou Xia, Jun Wang, Zeyang Zhou, Ruiqiang Li, Wei Fan, Daojun Cheng, Tingcai Cheng, Junji Qin, Jun Duan, Hanfu Xu, Qibin Li, Ning Li, Mingwei Wang, Fangyin Dai, Chun Liu, Ying Lin, Ping Zhao, Huijie Zhang, Shiping Liu, Xingfu Zha, Chunfeng Li, Aichun Zhao, Minhui Pan, Guoqing Pan, Yihong Shen, Zhihong Gao, Zilong Wang, Genhong Wang, Zhengli Wu, Yong Hou, Chunli Chai, Quanyou Yu, Ningjia He, Ze Zhang, Songgang Li, Huanming Yang, Cheng Lu, Jian Wang, Zhonghuai Xiang, Masahiro Kasahara, Yoichiro Nakatani, Kimiko Yamamoto, Hiroaki Abe, Brudrul Ahsan, Takaaki Daimon, Koichiro Doi, Tsuguru Fujii, Haruhiko Fujiwara, Asao Fujiyama, Ryo Futahashi, Shin Ichi Hashimoto, Jun Ishibashi, Masafumi Iwami, Keiko Kadono-Okuda, Hiroyuki Kanamori, Hiroshi Kataoka, Susumu Katsuma, Shinpei Kawaoka, Hideki Kawasaki, Yuji Kohara, Toshinori Kozaki, Reginaldo M. Kuroshu, Seigo Kuwazaki, Kouji Matsushima, Hiroshi Minami, Yukinobu Nagayasu, Tatsuro Nakagawa, Junko Narukawa, Junko Nohata, Kazuko Ohishi, Yukiteru Onor, Mizuko Osanai-Futahashi, Katsuhisa Ozaki, Wei Qu, Ladislav Roller, Shin Sasaki, Takuji Sasaki, Atsushi Seino, Masaru Shimomura, Michihiko Shimomura, Tadasu Shini, Tetsuro Shinoda, Takahiro Shiotsuki, Yoshitaka Suetsugu, Sumio Sugano, Makiko Suwa, Yutaka Suzuki, Shigeharu Takiya, Toshiki Tamura, Hiromitsu Tanaka, Yoshiaki Tanaka, Kazushige Touhara, Tomoyuki Yamada, Minoru Yamakawa, Naoki Yamanaka, Hiroshi Yoshikawa, Yang Sheng Zhong, Toru Shimada, Shinichi Morishita
Insect Biochemistry and Molecular Biology Vol. 38 No. 12 p. 1036-1045 2008/12 Research paper (scientific journal)
UTGB/medaka: Genomic resource database for medaka biology
Budrul Ahsan, Daisuke Kobayashi, Tomoyuki Yamada, Masahiro Kasahara, Shin Sasaki, Taro I. Saito, Yukinobu Nagayasu, Koichiro Doi, Yoichiro Nakatani, Wei Qu, Tomoko Jindo, Atsuko Shimada, Kiyoshi Naruse, Atsushi Toyoda, Yoko Kuroki, Asao Fujiyama, Takashi Sasaki, Atsushi Shimizu, Shuichi Asakawa, Nobuyoshi Shimizu, Shin-Ichi Hashimoto, Jun Yang, Yongjun Lee, Kouji Matsushima, Sumio Sugano, Mitsuru Sakaizumi, Takanori Narita, Kazuko Ohishi, Shinobu Haga, Fumiko Ohta, Hisayo Nomoto, Keiko Nogata, Tomomi Morishita, Tomoko Endo, Tadasu Shin-i, Hiroyuki Takeda, Yuji Kohara, Shinichi Morishita
Nucleic Acids Research Vol. 36 No. 1 p. D747-D752 2008/01 Research paper (scientific journal)
Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates
Yoichiro Nakatani, Hiroyuki Takeda, Yuji Kohara, Shinichi Morishita
GENOME RESEARCH Vol. 17 No. 9 p. 1254-1265 2007/09 Research paper (scientific journal)
The medaka draft genome and insights into vertebrate genome evolution
Masahiro Kasahara, Kiyoshi Naruse, Shin Sasaki, Yoichiro Nakatani, Wei Qu, Budrul Ahsan, Tomoyuki Yamada, Yukinobu Nagayasu, Koichiro Doi, Yasuhiro Kasai, Tomoko Jindo, Daisuke Kobayashi, Atsuko Shimada, Atsushi Toyoda, Yoko Kuroki, Asao Fujiyama, Takashi Sasaki, Atsushi Shimizu, Shuichi Asakawa, Nobuyoshi Shimizu, Shin-Ichi Hashimoto, Jun Yang, Yongjun Lee, Kouji Matsushima, Sumio Sugano, Mitsuru Sakaizumi, Takanori Narita, Kazuko Ohishi, Shinobu Haga, Fumiko Ohta, Hisayo Nomoto, Keiko Nogata, Tomomi Morishita, Tomoko Endo, Tadasu Shin-I, Hiroyuki Takeda, Shinichi Morishita, Yuji Kohara
Nature Vol. 447 No. 7145 p. 714-719 2007/06/07 Research paper (scientific journal)
Diversity of Ca2+-induced morphology revealed by morphological phenotyping of Ca2+-sensitive mutants of Saccharomyces cerevisiae
Shinsuke Ohnuki, Satoru Nogami, Hanako Kanai, Dai Hirata, Yoichiro Nakatani, Shinichi Morishita, Yoshikazu Ohya
EUKARYOTIC CELL Vol. 6 No. 5 p. 817-830 2007/05 Research paper (scientific journal)
Medaka genome sequencing and the comparative genomics of fishes
Kiyoshi Naruse, Yoichiro Nakatani, Wei Qu, Masahiro Kasahara, Shin Sasaki, Tomoyuki Yamada, Ahsan Budrul, Koichiro Doi, Yukinobu Nagayasu, Shin-ichi Hashimoto, Takanori Narita, Yoko Kuroki, Atsushi Toyoda, Tomoko Jindo, Daisuke Kobayashi, Tadasu Shin-I, Yusuke Takehana, Keita Tanaka, Mitsuru Sakaizumi, Yuji Kohara, Asao Fujiyama, Shin-ichi Morishita, Hiroyuki Takeda
ZOOLOGICAL SCIENCE Vol. 22 No. 12 p. 1378-1379 2005/12
Draft genome sequence of medaka (Orizias latides) and its usetip ful applications
Masahiro Kasahara, Shin Sasaki, Yoichiro Nakatani, Wei Qu, Ahsan Budrul, Tomoyuki Yamada, Yukinobu Nagayasu, Koichiro Doi, Kiyoshi Naruse, Takanori Narita, Tadasu Shin-I, Tomoko Jindo, Shin-ichi Hashimoto, Koji Matsushima, Yoko Kuroki, Asao Fujiyama, Hiroyuki Takeda, Shinichi Morishita, Yuji Kohara
ZOOLOGICAL SCIENCE Vol. 22 No. 12 p. 1395-1396 2005/12
Medaka genome sequencing and the vertebrate genome evolution
Kiyoshi Naruse, Yoichiro Nakatani, Wei Qu, Masahiro Kasahara, Shin Sasaki, Tomoyuki Yamada, Ahsan Budrul, Koichiro Doi, Yukinobu Nagayasu, Shin-ichi Hashimoto, Takanori Narita, Yoko Kuroki, Atsushi Toyoda, Tomoko Jindo, Daisuke Kobayashi, Tadasu Shin-I, Yuji Kohara, Asao Fujiyama, Shin-ichi Morishita, Hiroyuki Takeda
ZOOLOGICAL SCIENCE Vol. 22 No. 12 p. 1511-1512 2005/12
High-dimensional and large-scale phenotyping of yeast mutants
Y Ohya, J Sese, M Yukawa, F Sano, Y Nakatani, TL Saito, A Saka, T Fukuda, S Ishihara, S Oka, G Suzuki, M Watanabe, A Hirata, M Ohtani, H Sawai, N Fraysse, JP Latge, JM Francois, M Aebi, S Tanaka, S Muramatsu, H Araki, K Sonoike, S Nogami, S Morishita
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Vol. 102 No. 52 p. 19015-19020 2005/12 Research paper (scientific journal)
Data mining tools for the Saccharomyces cerevisiae morphological database
TL Saito, J Sese, Y Nakatani, F Sano, M Yukawa, Y Ohya, S Morishita
NUCLEIC ACIDS RESEARCH Vol. 33 No. Web Server issue p. W753-W757 2005/07 Research paper (scientific journal)
超高速シーケンサーとバイオインフォマティクス エピゲネティック薬剤処理大腸癌細胞におけるゲノムワイドな遺伝子発現解析とDNAメチル化解析(Genome-wide gene expression and DNA methylation profiling in a colon cancer cell line treated with epigenetic drugs)
橋本 真一, 曲 薇, アーサン・バドルル, 生越 克己, 中谷 洋一郎, 佐々木 惇, 鈴木 穣, 菅野 純夫, 森下 真一, 松島 綱治
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 Vol. 81回・31回 p. 3S8-5 2008/11
Publisher: (公社)日本生化学会超高速シーケンサーとバイオインフォマティクス クロマチン構造は遺伝的変異の主要因の1つである(Chromatin structure as a major determinant of natural genetic variation)
森下 真一, 佐々木 伸, Mello Cecilia, 島田 敦子, 中谷 洋一郎, 橋本 真一, Ogawa Masako, 松島 綱治, Gu Sam Guoping, 笠原 雅弘, Ahsan Budrul, 佐々木 惇, 斉藤 太郎, 鈴木 穣, 菅野 純夫, 小原 雄治, 武田 洋幸, Fire Andrew
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 Vol. 81回・31回 p. 3S8-8 2008/11
Publisher: (公社)日本生化学会次世代シーケンサーを用いたゲノムワイドなDNAメチル化様式の解析
生越克己, 橋本真一, 中谷洋一郎, 小川雅子, 森下真一, 松島綱治
生化学 2008
生物の進化・多様性をもたらしたゲノム情報解明へ 2.メダカゲノム解析に基づく脊椎動物ゲノム進化の推定
中谷洋一郎, 森下真一
実験医学 Vol. 25 No. 2 p. 232-240 2007/02/01
ゲノムから読み解く生命システム--比較ゲノムからのアプローチ(最終回)比較ゲノムを支える情報学:脊椎動物ゲノム進化を推定するロジック
森下 真一, 中谷 洋一郎
細胞工学 Vol. 25 No. 8 p. 956-962 2006/08
Publisher: 秀潤社
Life system understood from genome. Approach from comparison genome (final). Informatics supporting comparison genome: Logic to deduce the evolution of vertebrate genome.
森下真一, 中谷洋一郎
細胞工学 Vol. 25 No. 8 p. 956-961 2006/07/22
mRNAと形態変化を絶対定量化するためのバイオインフォマティクス
森下真一, 相馬温彦, 山田智之, 斉藤太郎, 中谷洋一郎, 瀬々潤, 相垣敏郎, 伊藤隆司, 大矢禎一, 松原謙一
日本分子生物学会年会講演要旨集 Vol. 28th 2005/11/25
メダカのゲノム進化解析
中谷洋一郎, 成瀬清, QU Wei, 笠原雅弘, 佐々木伸, 永安佑希允, BUDRUL Ahsan, 山田智之, 土井晃一郎, 成田貴則, 新井理, 橋本真一, 藤山秋佐夫, 小原雄治, 武田洋幸, 森下真一
日本分子生物学会年会講演要旨集 Vol. 28th 2005/11/25
出芽酵母におけるカルシウム依存的形態変化の解析
大貫慎輔, 関谷瑞穂, 野上識, 中谷洋一郎, 森下真一, 大矢禎一
日本分子生物学会年会講演要旨集 Vol. 28th 2005/11/25
出芽酵母のフェノミクス・プロテオミクス大相関図
池西淳, 渡辺街香, 岡さとみ, 湯川格史, 佐野(熊谷)史, 斉藤太郎, 中谷洋一郎, 瀬々潤, 園池公毅
日本分子生物学会年会プログラム・講演要旨集 Vol. 27th 2004/11/25
出芽酵母における細胞形態情報の網羅的・定量的解析
佐野史, 湯川格史, 池西淳, 岡さとみ, 渡辺街香, 阪彩香, 渡辺大輔, 園池公毅, 中谷洋一郎
日本分子生物学会年会プログラム・講演要旨集 Vol. 27th 2004/11/25
出芽酵母の細胞形態情報に基づく遺伝子の機能予想
岡さとみ, 池西淳, 園池公毅, 荒木弘之, 中谷洋一郎, 瀬々潤, 森下真一, 湯川格史, 佐野(熊谷)史
日本分子生物学会年会プログラム・講演要旨集 Vol. 27th 2004/11/25
祖先ゲノム再構成による5億年前の初期脊椎動物ゲノム進化の解明
中谷洋一郎
第15回 OUバイオインフォマティス センターセミナー 2024/07
Phylogenetic and structural insights into the origin of C-type lectin Mincle in vertebrates
Ito Taiki, Guenther Carla, Ishikawa Eri, Yabuki Takae, Nagae Masamichi, Nakatani Yoichiro, Yamasaki Sho
Immunogenetics Vol. 77 No. 1 2025/03/22
Variability in non-tumor areas of colorectal cancer patients as revealed by endoscopic intestinal step biopsies
Ikuta Shoko, Saito Yutaka, Takata So, Nakatani Yoichiro, Nagatomo Izumi, Shiba Satoshi, Takeda Yoshito, Totoki Yasushi, Mizutani Sayaka, Sunakawa Hironori, Ikematsu Hiroaki, Takamaru Hiroyuki, Kumanogoh Atsushi, Yachida Shinichi
Molecular Cancer Vol. 23 2024/11/07
