@book{CTT100700191,
  author = {西原秀典 and 岡田典弘},
  title = {SINEに由来するエンハンサーが寄与した哺乳類の進化},
  publisher = {農文協},
  year = 2015,
}

@book{CTT100674737,
  author = {西原秀典 and 岡田典弘},
  title = {シーラカンスゲノム中の反復配列の特徴},
  publisher = {NIS Inc.},
  year = 2014,
}

@book{CTT100724413,
  author = {田中利明 and 梶川正樹 and 西原秀典},
  title = {分子生物学},
  publisher = {},
  year = 2013,
}

@book{CTT100674720,
  author = {岡田典弘 and 西原秀典},
  title = {哺乳類 ―レトロポゾン法によって明らかになった哺乳類の進化},
  publisher = {NIS Inc.},
  year = 2013,
}

@book{CTT100643873,
  author = {西原秀典 and 丸山茂徳 and 岡田典弘},
  title = {大陸移動と哺乳類の進化},
  publisher = {NIS Inc.},
  year = 2012,
}

@article{CTT100624189,
  author = {Nagai H and Terai Y and Sugawara T and Imai H and Nishihara H and Hori M and Okada N.},
  title = {Reverse evolution in RH1 for adaptation of cichlids to water depth in Lake Tanganyika},
  journal = {Molecular Biology and Evolution},
  year = 2011,
}

@article{CTT100624188,
  author = {Okada N and Sasaki T and Shimogori T and Nishihara H.},
  title = {Emergence of mammals by emergency: exaptation},
  journal = {Genes to Cells},
  year = 2010,
}

@article{CTT100646725,
  author = {Akasaki T and Nikaido M and Nishihara H and Tsuchiya K and Segawa S and Okada N.},
  title = {Characterization of a novel SINE superfamily from invertebrates: "Ceph-SINEs" from the genomes of squids and cuttlefish},
  journal = {Gene},
  year = 2010,
}

@article{CTT100585055,
  author = {Oliver Piskurek and Hidenori Nishihara and Norihiro Okada},
  title = {The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis},
  journal = {GENE},
  year = 2009,
}

@article{CTT100585054,
  author = {Mika Hirakawa and Hidenori Nishihara and Minoru Kanehisa and Norihiro Okada},
  title = {Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes},
  journal = {GENE},
  year = 2009,
}

@article{CTT100573644,
  author = {Hidenori Nishihara and Shigenori Maruyama and Norihiro Okada},
  title = {Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = 2009,
}

@article{CTT100553869,
  author = {Takeshi Sasaki and Hidenori Nishihara and Mika Hirakawa and Koji Fujimura and Mikiko Tanaka and Nobuhiro Kokubo and Chiharu Kimura-Yoshida and Isao Matsuo and Kenta Sumiyama and Naruya Saitou and Tomomi Shimogori and Norihiro Okada},
  title = {Possible involvement of SINEs in mammalian-specific brain formation},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = 2008,
}

@article{CTT100553460,
  author = {Manami Matsuura and Hidenori Nishihara and Koh Onimaru and Nobuhiro Kokubo and Shigehiro Kuraku and Norihiro Okada and Shigeru Kuratani and Mikiko Tanaka},
  title = {Identification of four Engrailed genes in the Japanese lamprey, Lethenteron japonicum.},
  journal = {Developmental Dynamics},
  year = 2008,
}

@article{CTT100646727,
  author = {Maruo Munemasa and Masato Nikaido and Hidenori Nishihara and Stephen Donnellan and Christopher C. Austin and Norihiro Okada},
  title = {Newly discovered young CORE-SINEs in marsupial genomes},
  journal = {Gene},
  year = 2008,
}

@article{CTT100646729,
  author = {Hidenori Nishihara and Shuichi Kuno and Masato Nikaido and Norihiro Okada},
  title = {MyrSINEs: a novel SINE family in the anteater genomes},
  journal = {Gene},
  year = 2007,
}

@article{CTT100548860,
  author = {Hidenori Nishihara and Norihiro Okada and Masami Hasegawa},
  title = {Rooting the eutherian tree: the power and pitfalls of phylogenomics},
  journal = {Genome Biology},
  year = 2007,
}

@article{CTT100548858,
  author = {Kenji Ichiyanagi and Hidenori Nishihara and David D. Duvernell and Norihiro Okada},
  title = {Acquisition of Endonuclease Specificity during Evolution of L1 Retrotransposon},
  journal = {Molecular Biology and Evolution},
  year = 2007,
}

@article{CTT100548857,
  author = {Vitaliy Matveev and Hidenori Nishihara and Norihiro Okada},
  title = {Novel SINE Families from Salmons Validate Parahucho (Salmonidae) as a Distinct Genus and Give Evidence that SINEs Can Incorporate LINE-related 3'-Tails of Other SINEs},
  journal = {Molecular Biology and Evolution},
  year = 2007,
}

@article{CTT100548855,
  author = {Hidenori Nishihara and Arian F. A. Smit and Norihiro Okada},
  title = {Functional noncoding sequences derived from SINEs in the mammalian genome},
  journal = {Genome Research},
  year = 2006,
}

@article{CTT100548856,
  author = {Hidenori Nishihara and Masami Hasegawa and Norihiro Okada},
  title = {Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = 2006,
}

@article{CTT100646743,
  author = {Hidenori Nishihara and Yoko Satta and Masato Nikaido and J. G. M. Thewissen and Michael J. Stanhope and Norihiro Okada},
  title = {A retroposon analysis of Afrotherian phylogeny},
  journal = {Molecular Biology and Evolution},
  year = 2005,
}

@article{CTT100646748,
  author = {Nikaido Masato and Nishihara Hidenori and Fukumoto Yukio and Okada Norihiro},
  title = {Ancient SINEs from African endemic mammals},
  journal = {Molecular Biology and Evolution},
  year = 2003,
}

@article{CTT100906888,
  author = {Genki Imaizumi and Kazutaka Ushio and Hidenori Nishihara and Ingo Braasch and Erika Watanabe and Shiori Kumagai and Tadaomi Furuta and Koji Matsuzaki and Michael Romero and Akira Kato and Ayumi Nagashima},
  title = {Functional divergence in solute permeability between ray-finned fish-specific paralogs of aqp10},
  journal = {Genome Biol. Evol.},
  year = 2024,
}

@article{CTT100887505,
  author = {Toya Motoshima and Ayumi Nagashima and Chihiro Ota and Haruka Oka and Kohei Hosono and Ingo Braasch and Hidenori Nishihara and Akira Kato},
  title = {Na+- Cl- cotransporter 2 is not fish-specific and is widely found in amphibians, non-avian reptiles, and select mammals},
  journal = {Physiol. Genomics},
  year = 2023,
}

@article{CTT100885789,
  author = {Teruhisa Tamaki and Takafumi Yoshida and Eri Shibata and Hidenori Nishihara and Haruki Ochi and Atsushi Kawakami},
  title = {Splashed E-box and AP-1 motifs cooperatively drive regeneration response and shape regeneration abilities},
  journal = {Biology Open},
  year = 2023,
}

@article{CTT100885788,
  author = {Qiaoyi Liang and Meng-Ching Ko and Nathaniel SR Ng and Borja Reh and Jessica GH Lee and Atsuko Yamashita and Hidenori Nishihara and Yasuka Toda and Maude W Baldwin},
  title = {T1R2-mediated sweet sensing in a lizard},
  journal = {Current Biology},
  year = 2022,
}

@article{CTT100874482,
  author = {Takahiro Segawa and Takahiro Yonezawa and Hiroshi Mori and Ayako Kohno and Yuichiro Kudo and Ayumi Akiyoshi and Jiaqi Wu and Fuyuki Tokanai and Minoru Sakamoto and Naoki Kohno and Hidenori Nishihara},
  title = {Paleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan},
  journal = {Current Biology},
  year = 2022,
}

@article{CTT100875298,
  author = {Nikaido, M. and Nishihara, H. and Okada, N.},
  title = {SINEs as Credible Signs to Prove Common Ancestry in the Tree of Life: A Brief Review of Pioneering Case Studies in Retroposon Systematics},
  journal = {genes},
  year = 2022,
}

@article{CTT100874481,
  author = {Yurika Namba and Yuka W Iwasaki and Kazumichi M Nishida and Hidenori Nishihara and Tetsutaro Sumiyoshi and Mikiko C Siomi},
  title = {Maelstrom functions in the production of Siwi-piRISC capable of regulating transposons in Bombyx germ cells},
  journal = {iScience},
  year = 2022,
}

@article{CTT100874480,
  author = {Beni Lestari and Satomi Naito and Akinori Endo and Hidenori Nishihara and Akira Kato and Erika Watanabe and Kimitoshi Denda and Masayuki Komada and Toshiaki Fukushima},
  title = {Placental Mammals Acquired Functional Sequences in NRK for Regulating the CK2–PTEN–AKT Pathway and Placental Cell Proliferation},
  journal = {Molecular Biology and Evolution},
  year = 2022,
}

@article{CTT100864649,
  author = {Hidenori Nishihara and Roscoe Stanyon and Hideyuki Tanabe and Akihiko Koga},
  title = {Replacement of owl monkey centromere satellite by a newly evolved variant was a recent and rapid process},
  journal = {Genes to Cells},
  year = 2021,
}

@article{CTT100862918,
  author = {Takahiro Segawa and Takahiro Yonezawa and Hiroshi Mori and Ayumi Akiyoshi and Morten E Allentoft and Ayako Kohno and Fuyuki Tokanai and Eske Willerslev and Naoki Kohno and Hidenori Nishihara},
  title = {Ancient DNA reveals multiple origins and migration waves of extinct Japanese brown bear lineages},
  journal = {Royal Society Open Science},
  year = 2021,
}

@article{CTT100846439,
  author = {Kyoko Ishino and Hidetoshi Hasuwa and Jun Yoshimura and Yuka W Iwasaki and Hidenori Nishihara and Naomi M Seki and Takamasa Hirano and Marie Tsuchiya and Hinako Ishizaki and Harumi Masuda and Tae Kuramoto and Kuniaki Saito and Yasubumi Sakakibara and Atsushi Toyoda and Takehiko Itoh and Mikiko C Siomi and Shinichi Morishita and Haruhiko Siomi},
  title = {Hamster PIWI proteins bind to piRNAs with stage-specific size variations during oocyte maturation},
  journal = {Nucleic Acids Research},
  year = 2021,
}

@article{CTT100837207,
  author = {Nikaido, M. and Kondo, S. and Zicong Zhang and Wu, J. and Nishihara, H. and Niimura, Y. and Suzuki, S. and Touhara K. and Suzuki, Y. and Noguchi, H. and Minakuchi, Y. and Toyoda, A. and Fujiyama, A. and Sugano, S. and Yoneda, M. and Kai, C.},
  title = {Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera},
  journal = {DNA Research},
  year = 2020,
}

@article{CTT100816100,
  author = {Ratchaphol Thongchum and Hidenori Nishihara and Kornsorn Srikulnath and Hirohisa Hirai and Akihiko Koga},
  title = {The CENP-B box, a nucleotide motif involved in centromere formation, has multiple origins in New World monkeys},
  journal = {Genes & Genetic Systems},
  year = 2019,
}

@article{CTT100807915,
  author = {Soichiro Yamanaka and Hidenori Nishihara and Hidehiro Toh and Luis Augusto Eijy Nagai and Kosuke Hashimoto and Sung-Joon Park and Aoi Shibuya and Ana Maria Suzuki and Yujiro Tanaka and Kenta Nakai and Piero Carninci and Hiroyuki Sasaki and Haruhiko Siomi},
  title = {Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation},
  journal = {Developmental Cell},
  year = 2019,
}

@article{CTT100810760,
  author = {Hidenori Nishihara},
  title = {Retrotransposons spread potential cis-regulatory elements during mammary gland evolution},
  journal = {Nucleic Acids Research},
  year = 2019,
}

@article{CTT100807916,
  author = {Yoko Arai and Andrzej W. Cwetsch and Eva Coppola and Sara Cipriani and Hidenori Nishihara and Hiroaki Kanki and Yoann Saillour and Betty Freret-Hodara and Annie Dutriaux and Norihiro Okada and Hideyuki Okano and Colette Dehay and Jeannette Nardelli and Pierre Gressens and Tomomi Shimogori and Giuseppe D’Onofrio and Alessandra Pierani},
  title = {Evolutionary Gain of Dbx1 Expression Drives Subplate Identity in the Cerebral Cortex},
  journal = {Cell Reports},
  year = 2019,
}

@article{CTT100759520,
  author = {Hidenori Nishihara and Roscoe Stanyon and Junko Kusumi and Hirohisa Hirai and Akihiko Koga},
  title = {Evolutionary Origin of OwlRep, a Megasatellite DNA Associated with Adaptation of Owl Monkeys to Nocturnal Lifestyle},
  journal = {Genome Biology and Evolution},
  year = 2018,
}

@article{CTT100807917,
  author = {Doshun Ito and Yuta Ihara and Hidenori Nishihara and Shinji Masuda},
  title = {Phylogenetic analysis of proteins involved in the stringent response in plant cells},
  journal = {Journal of Plant Research},
  year = 2017,
}

@article{CTT100736947,
  author = {Naoko Takezaki and Hidenori Nishihara},
  title = {Support for Lungfish as the Closest Relative of Tetrapods by Using Slowly Evolving Ray-Finned Fish as the Outgroup},
  journal = {Genome Biology and Evolution},
  year = 2017,
}

@article{CTT100726732,
  author = {Hidenori Nishihara and Naoki Kobayashi and Chiharu Kimura-Yoshida and Kuo Yan and Olga Bormuth and Qiong Ding and Akiko Nakanishi and Takeshi Sasaki and Mika Hirakawa and Kenta Sumiyama and Yasuhide Furuta and Victor Tarabykin and Isao Matsuo and Norihiro Okada},
  title = {Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in the Mammalian Secondary Palate},
  journal = {PLoS Genetics},
  year = 2016,
}

@article{CTT100711024,
  author = {Takezaki N and Nishihara H},
  title = {Resolving the Phylogenetic Position of Coelacanth: The Closest Relative Is Not Always the Most Appropriate Outgroup.},
  journal = {Genome Biology and Evolution},
  year = 2016,
}

@article{CTT100711023,
  author = {Nishihara H and Plazzi F and Passamonti M and Okada N},
  title = {MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals.},
  journal = {Genome Biology and Evolution},
  year = 2016,
}

@article{CTT100700192,
  author = {Kuramoto, T. and Nishihara, H. and Watanabe, M. and Okada, N.},
  title = {Determining the Position of Storks on the Phylogenetic Tree of Waterbirds by Retroposon Insertion Analysis},
  journal = {Genome Biology and Evolution},
  year = 2015,
}

@article{CTT100810845,
  author = {Brawand D and Wagner CE and Li YI and Malinsky M and Keller I and Fan S and Simakov O and Ng AY and Lim ZW and Bezault E and Turner-Maier J and Johnson J and Alcazar R and Noh HJ and Russell P and Aken B and Alfoldi J and Amemiya C and Azzouzi N and Baroiller JF and Barloy-Hubler F and Berlin A and Bloomquist R and Carleton KL and Conte MA and D'Cotta H and Eshel O and Gaffney L and Galibert F and Gante HF and Gnerre S and Greuter L and Guyon R and Haddad NS and Haerty W and Harris RM and Hofmann HA and Hourlier T and Hulata G and Jaffe DB and Lara M and Lee AP and MacCallum I and Mwaiko S and Nikaido M and Nishihara H and Ozouf-Costaz C and Penman DJ and Przybylski D and Rakotomanga M and Renn SC and Ribeiro FJ and Ron M and Salzburger W and Sanchez-Pulido L and Santos ME and Searle S and Sharpe T and Swofford R and Tan FJ and Williams L and Young S and Yin S and Okada N and Kocher TD and Miska EA and Lander ES and Venkatesh B and Fernald RD and Meyer A and Ponting CP and Streelman JT and Lindblad-Toh K and Seehausen O and Di Palma F},
  title = {The genomic substrate for adaptive radiation in African cichlid fish},
  journal = {Nature},
  year = 2014,
}

@article{CTT100673542,
  author = {Kawashima Y and Nishihara H and Akasaki T and Nikaido M and Tsuchiya K and Segawa S and Okada N.},
  title = {The complete mitochondrial genomes of deep-sea squid (Bathyteuthis abyssicola), bob-tail squid (Semirossia patagonica) and four giant cuttlefish (Sepia apama, S. latimanus, S. lycidas and S. pharanois), and their application to the phylogenetic analysis of Decapodiformes.},
  journal = {Mol. Phylogenet. Evol.},
  year = 2013,
}

@article{CTT100643868,
  author = {Akiko Nakanishi and Naoki Kobayashi and Asuka Suzuki-Hirano and Hidenori Nishihara and Takeshi Sasaki and Mika Hirakawa and Kenta Sumiyama and Tomomi Shimogori and Norihiro Okada},
  title = {A SINE-Derived Element Constitutes a Unique Modular Enhancer for Mammalian Diencephalic Fgf8},
  journal = {PLoS ONE},
  year = 2012,
}

@article{CTT100646724,
  author = {Koichiro Higasa and Masato Nikaido and Taro L. Saito and Jun Yoshimura and Yutaka Suzuki and Hikoyu Suzuki and Hidenori Nishihara and Mitsuto Aibara and Benjamin P. Ngatunga and Hassan W.J. Kalombo and Sumio Sugano and Shinichi Morishita and Norihiro Okada},
  title = {Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths},
  journal = {Gene},
  year = 2012,
}

@article{CTT100634238,
  author = {Yuichi Yuzawa and Hidenori Nishihara and Tsuyoshi Haraguchi and Shinji Masuda and Mie Shimojima and Atsushi Shimoyama and Hideya Yuasa and Norihiro Okada and Hiroyuki Ohta},
  title = {Phylogeny of Galactolipid Synthase Homologs Together with Their Enzymatic Analyses Revealed A Possible Origin and Divergence Time for Photosynthetic Membrane Biogenesis},
  journal = {DNA Research},
  year = 2012,
}

@article{CTT100633245,
  author = {Kensuke Tashiro and Anne Teissier and Naoki Kobayashi and Akiko Nakanishi and Takeshi Sasaki and Kuo Yan and Victor Tarabykin and Lisa Vigier and Kenta Sumiyama and Mika Hirakawa and Hidenori Nishihara and Alessandra Pierani and Norihiro Okada},
  title = {A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons},
  journal = {PLoS ONE},
  year = 2011,
}

@article{CTT100633244,
  author = {Kohta Yoshida and Yohey Terai and Shinji Mizoiri and Mitsuto Aibara and Hidenori Nishihara and Masakatsu Watanabe and Asato Kuroiwa and Hirohisa Hirai and Yuriko Hirai and Yoichi Matsuda and Norihiro Okada},
  title = {B Chromosomes Have a Functional Effect on Female Sex Determination in Lake Victoria Cichlid Fishes},
  journal = {PLoS Genetics},
  year = 2011,
}

@article{CTT100673545,
  author = {Okada N and Nikaido M and Nishihara H.},
  title = {Phylogenomics and its Future: Devoted to M Hasegawa.},
  journal = {GENE},
  year = 2009,
}

@inproceedings{CTT100887733,
  author = {永嶌鮎美 and 元島登哉 and 太田地洋 and Ingo Braasch and 西原秀典 and 加藤明},
  title = {脊椎動物におけるslc12a10遺伝子の発現と偽遺伝子化の解析．},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100887728,
  author = {Ayumi Nagashima and Toya Motoshima and Chihiro Ota and Ingo Braasch and Hidenori Nishihara and Akira Kato},
  title = {Evolution and pseudogenization of slc12a10 gene in vertebrate animals.},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100875548,
  author = {BENI Lestari and 内藤 聡美 and 遠藤 彬則 and 西原 秀典 and 加藤 明 and 渡邊 恵理香 and 傳田 公紀 and 駒田 雅之 and 福嶋 俊明},
  title = {Comparative Phylogenetic Analysis and Molecular Characterization Reveal Eutherian-Specific Role of NRK in Regulating Placenta Development},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100853904,
  author = {Yuko Sato and Nguyen Thi Bich Ngoc and Haruka Oda and Tetsuya Handa and Hidenori Nishihara and Akihito Harada and Yasuyuki Ohkawa and Hiroshi Kimura},
  title = {Spatiotemporal dynamics of histone modifications during zebrafish zygotic genome activation},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100810865,
  author = {樋口拓人 and 西原秀典 and 梶谷嶺 and 豊田敦 and 伊藤武彦 and 岡田典弘 and 二階堂雅人},
  title = {東アフリカ産淡水魚シクリッドゲノムにおける祖先多型遺伝子座の起源},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100810872,
  author = {樋口拓人 and 西原秀典 and 梶谷嶺 and 豊田敦 and 伊藤武彦 and 岡田典弘 and 二階堂雅人},
  title = {ゲノムワイドなSINE 挿入解析から東アフリカ産シクリッドにおける祖先多型の持続性を解明する},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100810880,
  author = {樋口拓人 and 西原秀典 and 梶谷嶺 and 伊藤武彦 and 二階堂雅人},
  title = {東アフリカシクリッドゲノムにおける祖先多型遺伝子座の起源},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100810886,
  author = {樋口拓人 and 西原秀典 and 梶谷嶺 and 伊藤武彦 and 二階堂雅人},
  title = {東アフリカ産シクリッド全ゲノムを対象にした祖先多型遺伝子座の網羅的探索},
  booktitle = {},
  year = 2018,
}

@inproceedings{CTT100673675,
  author = {Nikaido M and Nishihara H and Fukumoto Y and Okada N.},
  title = {Ancient SINEs from African endemic mammals.},
  booktitle = {},
  year = 2002,
}

@misc{CTT100570015,
  author = {Hidenori Nishihara and Norihiro Okada},
  title = {Retroposons: Genetic Footprints on the Evolutionary Paths of Life},
  year = 2008,
}

@misc{CTT100816099,
  author = {Hidenori Nishihara},
  title = {Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring and morphological innovation},
  year = 2019,
}

@misc{CTT100594308,
  author = {Hidenori Nishihara},
  title = {レトロポゾンを指標とした、哺乳類における高次分類群間の系統関係に関する研究},
  year = 2005,
}



@phdthesis{CTT100594308,
  author = {Hidenori Nishihara},
  title = {レトロポゾンを指標とした、哺乳類における高次分類群間の系統関係に関する研究},
  school = {東京工業大学},
  year = 2005,
}