論文

• Nagai H, Terai Y, Sugawara T, Imai H, Nishihara H, Hori M, Okada N.. Reverse evolution in RH1 for adaptation of cichlids to water depth in Lake Tanganyika, Molecular Biology and Evolution, Vol. 28, No. 6, pp. 1769-1776, June 2011.
• Okada N, Sasaki T, Shimogori T, Nishihara H.. Emergence of mammals by emergency: exaptation, Genes to Cells, Vol. 15, No. 8, pp. 801-12, Aug. 2010.
• Akasaki T, Nikaido M, Nishihara H, Tsuchiya K, Segawa S, Okada N.. Characterization of a novel SINE superfamily from invertebrates: "Ceph-SINEs" from the genomes of squids and cuttlefish, Gene, Vol. 454, No. 1-2, pp. 8-19, Apr. 2010.  公式リンク  
  
• Oliver Piskurek, Hidenori Nishihara, Norihiro Okada. 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, GENE, Vol. 441, pp. 111-118, July 2009.
• Mika Hirakawa, Hidenori Nishihara, Minoru Kanehisa, Norihiro Okada. Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes, GENE, Vol. 441, pp. 100-110, July 2009.
• Hidenori Nishihara, Shigenori Maruyama, Norihiro Okada. Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals, Proceedings of the National Academy of Sciences USA, The National Academy of Sciences of the USA, Vol. 106, No. 13, pp. 5235-5240, Mar. 2009.
• Takeshi Sasaki, Hidenori Nishihara, Mika Hirakawa, Koji Fujimura, Mikiko Tanaka, Nobuhiro Kokubo, Chiharu Kimura-Yoshida, Isao Matsuo, Kenta Sumiyama, Naruya Saitou, Tomomi Shimogori, Norihiro Okada. Possible involvement of SINEs in mammalian-specific brain formation, Proceedings of the National Academy of Sciences USA, The National Academy of Sciences of the USA, Vol. 105, No. 11, pp. 4220–4225, Mar. 2008.
• Manami Matsuura, Hidenori Nishihara, Koh Onimaru, Nobuhiro Kokubo, Shigehiro Kuraku, Norihiro Okada, Shigeru Kuratani, Mikiko Tanaka. Identification of four Engrailed genes in the Japanese lamprey, Lethenteron japonicum., Developmental Dynamics, Vol. 237, pp. 1581-1589, Mar. 2008.
• Maruo Munemasa, Masato Nikaido, Hidenori Nishihara, Stephen Donnellan, Christopher C. Austin, Norihiro Okada. Newly discovered young CORE-SINEs in marsupial genomes, Gene, Elsevier, Vol. 407, No. 1-2, pp. 176-185, Jan. 2008.  公式リンク  
  
• Hidenori Nishihara, Shuichi Kuno, Masato Nikaido, Norihiro Okada. MyrSINEs: a novel SINE family in the anteater genomes, Gene, Elsevier, Vol. 400, No. 1-2, pp. 98-103, Oct. 2007.  公式リンク  
  
• Hidenori Nishihara, Norihiro Okada, Masami Hasegawa. Rooting the eutherian tree: the power and pitfalls of phylogenomics, Genome Biology, BioMed Central, Vol. 8, No. 9, pp. R199, Sept. 2007.
• Kenji Ichiyanagi, Hidenori Nishihara, David D. Duvernell, Norihiro Okada. Acquisition of Endonuclease Specificity during Evolution of L1 Retrotransposon, Molecular Biology and Evolution, Oxford University Press, Vol. 24, No. 9, pp. 2009-2015, Sept. 2007.
• Vitaliy Matveev, Hidenori Nishihara, Norihiro Okada. 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, Molecular Biology and Evolution, Oxford University Press, Vol. 24, No. 8, pp. 1656-1666, Aug. 2007.
• Hidenori Nishihara, Arian F. A. Smit, Norihiro Okada. Functional noncoding sequences derived from SINEs in the mammalian genome, Genome Research, Cold Spring Harbor Laboratory Press, Vol. 16, No. 7, pp. 864-874, July 2006.
• Hidenori Nishihara, Masami Hasegawa, Norihiro Okada. Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions, Proceedings of the National Academy of Sciences USA, National Academy of Sciences, Vol. 103, No. 26, pp. 9929-9934, June 2006.
• Hidenori Nishihara, Yoko Satta, Masato Nikaido, J. G. M. Thewissen, Michael J. Stanhope, Norihiro Okada. A retroposon analysis of Afrotherian phylogeny, Molecular Biology and Evolution, Oxford University Press, Vol. 22, No. 9, pp. 1823-1833, Sept. 2005.  公式リンク  
  
• Nikaido Masato, Nishihara Hidenori, Fukumoto Yukio, Okada Norihiro. Ancient SINEs from African endemic mammals, Molecular Biology and Evolution, Vol. 20, No. 4, pp. 522-527, Apr. 2003.
• Genki Imaizumi, Kazutaka Ushio, Hidenori Nishihara, Ingo Braasch, Erika Watanabe, Shiori Kumagai, Tadaomi Furuta, Koji Matsuzaki, Michael Romero, Akira Kato, Ayumi Nagashima. Functional divergence in solute permeability between ray-finned fish-specific paralogs of aqp10, Genome Biol. Evol., vol. 16, no. 1, pp. evad221, Jan. 2024.
• Toya Motoshima, Ayumi Nagashima, Chihiro Ota, Haruka Oka, Kohei Hosono, Ingo Braasch, Hidenori Nishihara, Akira Kato. Na+- Cl- cotransporter 2 is not fish-specific and is widely found in amphibians, non-avian reptiles, and select mammals, Physiol. Genomics, vol. 55, no. 3, p. 113-113, Mar. 2023.  公式リンク  
  
• Teruhisa Tamaki, Takafumi Yoshida, Eri Shibata, Hidenori Nishihara, Haruki Ochi, Atsushi Kawakami. Splashed E-box and AP-1 motifs cooperatively drive regeneration response and shape regeneration abilities, Biology Open, Vol. 12, No. 2, bio059810, Jan. 2023.
• Qiaoyi Liang, Meng-Ching Ko, Nathaniel SR Ng, Borja Reh, Jessica GH Lee, Atsuko Yamashita, Hidenori Nishihara, Yasuka Toda, Maude W Baldwin. T1R2-mediated sweet sensing in a lizard, Current Biology, Vol. 32, No. 23, pp. R1302-R1303, Dec. 2022.
• Takahiro Segawa, Takahiro Yonezawa, Hiroshi Mori, Ayako Kohno, Yuichiro Kudo, Ayumi Akiyoshi, Jiaqi Wu, Fuyuki Tokanai, Minoru Sakamoto, Naoki Kohno, Hidenori Nishihara. Paleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan, Current Biology, Vol. 32, No. 11, pp. 2494–2504, June 2022.
• Nikaido, M., Nishihara, H., Okada, N.. SINEs as Credible Signs to Prove Common Ancestry in the Tree of Life: A Brief Review of Pioneering Case Studies in Retroposon Systematics, genes, Vol. 13, No. 6, pp. 989, May 2022.
• Yurika Namba, Yuka W Iwasaki, Kazumichi M Nishida, Hidenori Nishihara, Tetsutaro Sumiyoshi, Mikiko C Siomi. Maelstrom functions in the production of Siwi-piRISC capable of regulating transposons in Bombyx germ cells, iScience, Vol. 25, No. 3, p. 103914, Mar. 2022.
• Beni Lestari, Satomi Naito, Akinori Endo, Hidenori Nishihara, Akira Kato, Erika Watanabe, Kimitoshi Denda, Masayuki Komada, Toshiaki Fukushima. Placental Mammals Acquired Functional Sequences in NRK for Regulating the CK2–PTEN–AKT Pathway and Placental Cell Proliferation, Molecular Biology and Evolution, Vol. 39, No. 2, p. msab371, Feb. 2022.
• Hidenori Nishihara, Roscoe Stanyon, Hideyuki Tanabe, Akihiko Koga. Replacement of owl monkey centromere satellite by a newly evolved variant was a recent and rapid process, Genes to Cells, Vol. 26, No. 12, pp. 979–986, Dec. 2021.
• Takahiro Segawa, Takahiro Yonezawa, Hiroshi Mori, Ayumi Akiyoshi, Morten E Allentoft, Ayako Kohno, Fuyuki Tokanai, Eske Willerslev, Naoki Kohno, Hidenori Nishihara. Ancient DNA reveals multiple origins and migration waves of extinct Japanese brown bear lineages, Royal Society Open Science, Vol. 8, No. 8, pp. 210518, Aug. 2021.
• Kyoko Ishino, Hidetoshi Hasuwa, Jun Yoshimura, Yuka W Iwasaki, Hidenori Nishihara, Naomi M Seki, Takamasa Hirano, Marie Tsuchiya, Hinako Ishizaki, Harumi Masuda, Tae Kuramoto, Kuniaki Saito, Yasubumi Sakakibara, Atsushi Toyoda, Takehiko Itoh, Mikiko C Siomi, Shinichi Morishita, Haruhiko Siomi. Hamster PIWI proteins bind to piRNAs with stage-specific size variations during oocyte maturation, Nucleic Acids Research, Vol. 49, No. 5, pp. 2700–2720, Feb. 2021.
• Nikaido, M., Kondo, S., Zicong Zhang, Wu, J., Nishihara, H., Niimura, Y., Suzuki, S., Touhara K., Suzuki, Y., Noguchi, H., Minakuchi, Y., Toyoda, A., Fujiyama, A., Sugano, S., Yoneda, M., Kai, C.. Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera, DNA Research, Vol. 27, Issue 4, Sept. 2020.
• Ratchaphol Thongchum, Hidenori Nishihara, Kornsorn Srikulnath, Hirohisa Hirai, Akihiko Koga. The CENP-B box, a nucleotide motif involved in centromere formation, has multiple origins in New World monkeys, Genes & Genetic Systems, Vol. 94, No. 6, pp. 301-306, Dec. 2019.
• Soichiro Yamanaka, Hidenori Nishihara, Hidehiro Toh, Luis Augusto Eijy Nagai, Kosuke Hashimoto, Sung-Joon Park, Aoi Shibuya, Ana Maria Suzuki, Yujiro Tanaka, Kenta Nakai, Piero Carninci, Hiroyuki Sasaki, Haruhiko Siomi. Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation, Developmental Cell, Vol. 51, No. 1, pp. 21-34, Oct. 2019.
• Hidenori Nishihara. Retrotransposons spread potential cis-regulatory elements during mammary gland evolution, Nucleic Acids Research, Vol. 47, No. 22, pp. 11551-11562, Oct. 2019.
• Yoko Arai, Andrzej W. Cwetsch, Eva Coppola, Sara Cipriani, Hidenori Nishihara, Hiroaki Kanki, Yoann Saillour, Betty Freret-Hodara, Annie Dutriaux, Norihiro Okada, Hideyuki Okano, Colette Dehay, Jeannette Nardelli, Pierre Gressens, Tomomi Shimogori, Giuseppe D’Onofrio, Alessandra Pierani. Evolutionary Gain of Dbx1 Expression Drives Subplate Identity in the Cerebral Cortex, Cell Reports, Vol. 29, No. 3, pp. 645-658, Oct. 2019.
• Hidenori Nishihara, Roscoe Stanyon, Junko Kusumi, Hirohisa Hirai, Akihiko Koga. Evolutionary Origin of OwlRep, a Megasatellite DNA Associated with Adaptation of Owl Monkeys to Nocturnal Lifestyle, Genome Biology and Evolution, Vol. 10, No. 1, pp. 157–165, Jan. 2018.
• Doshun Ito, Yuta Ihara, Hidenori Nishihara, Shinji Masuda. Phylogenetic analysis of proteins involved in the stringent response in plant cells, Journal of Plant Research, Vol. 130, No. 4, pp. 625–634, July 2017.
• Naoko Takezaki, Hidenori Nishihara. Support for Lungfish as the Closest Relative of Tetrapods by Using Slowly Evolving Ray-Finned Fish as the Outgroup, Genome Biology and Evolution, Vol. 9, No. 1, pp. 93-101, Jan. 2017.
• Hidenori Nishihara, Naoki Kobayashi, Chiharu Kimura-Yoshida, Kuo Yan, Olga Bormuth, Qiong Ding, Akiko Nakanishi, Takeshi Sasaki, Mika Hirakawa, Kenta Sumiyama, Yasuhide Furuta, Victor Tarabykin, Isao Matsuo, Norihiro Okada. Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in the Mammalian Secondary Palate, PLoS Genetics, Vol. 12, No. 10, e1006380, Oct. 2016.
• Takezaki N, Nishihara H. Resolving the Phylogenetic Position of Coelacanth: The Closest Relative Is Not Always the Most Appropriate Outgroup., Genome Biology and Evolution, Vol. 8, No. 4, pp. 1208-1221, Apr. 2016.
• Nishihara H, Plazzi F, Passamonti M, Okada N. MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals., Genome Biology and Evolution, Vol. 8, No. 3, pp. 528-539, Mar. 2016.
• Kuramoto, T., Nishihara, H., Watanabe, M., Okada, N.. Determining the Position of Storks on the Phylogenetic Tree of Waterbirds by Retroposon Insertion Analysis, Genome Biology and Evolution, Vol. 7, No. 12, pp. 3180-3189, Nov. 2015.
• Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alfoldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SC, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F. The genomic substrate for adaptive radiation in African cichlid fish, Nature, Vol. 513, No. 7518, pp. 375-381, Sept. 2014.
• Kawashima Y, Nishihara H, Akasaki T, Nikaido M, Tsuchiya K, Segawa S, Okada N.. 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., Mol. Phylogenet. Evol., Vol. 69, 980–993, 2013.
• Akiko Nakanishi, Naoki Kobayashi, Asuka Suzuki-Hirano, Hidenori Nishihara, Takeshi Sasaki, Mika Hirakawa, Kenta Sumiyama, Tomomi Shimogori, Norihiro Okada. A SINE-Derived Element Constitutes a Unique Modular Enhancer for Mammalian Diencephalic Fgf8, PLoS ONE, Vol. 7, No. 8, p. e43785, Aug. 2012.
• Koichiro Higasa, Masato Nikaido, Taro L. Saito, Jun Yoshimura, Yutaka Suzuki, Hikoyu Suzuki, Hidenori Nishihara, Mitsuto Aibara, Benjamin P. Ngatunga, Hassan W.J. Kalombo, Sumio Sugano, Shinichi Morishita, Norihiro Okada. Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths, Gene, Vol. 505, No. 2, pp. 324-332, June 2012.  公式リンク  
  
• Yuichi Yuzawa, Hidenori Nishihara, Tsuyoshi Haraguchi, Shinji Masuda, Mie Shimojima, Atsushi Shimoyama, Hideya Yuasa, Norihiro Okada, Hiroyuki Ohta. Phylogeny of Galactolipid Synthase Homologs Together with Their Enzymatic Analyses Revealed A Possible Origin and Divergence Time for Photosynthetic Membrane Biogenesis, DNA Research, 19, (1), 91-102, Feb. 2012.
• Kensuke Tashiro, Anne Teissier, Naoki Kobayashi, Akiko Nakanishi, Takeshi Sasaki, Kuo Yan, Victor Tarabykin, Lisa Vigier, Kenta Sumiyama, Mika Hirakawa, Hidenori Nishihara, Alessandra Pierani, Norihiro Okada. A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons, PLoS ONE, Vol. 6, No. 12, pp. e28497, Dec. 2011.
• Kohta Yoshida, Yohey Terai, Shinji Mizoiri, Mitsuto Aibara, Hidenori Nishihara, Masakatsu Watanabe, Asato Kuroiwa, Hirohisa Hirai, Yuriko Hirai, Yoichi Matsuda, Norihiro Okada. B Chromosomes Have a Functional Effect on Female Sex Determination in Lake Victoria Cichlid Fishes, PLoS Genetics, Vol. 7, No. 8, pp. e1002203, Aug. 2011.
• Okada N, Nikaido M, Nishihara H.. Phylogenomics and its Future: Devoted to M Hasegawa., GENE, Vol. 441, 1–192, 2009.

著書

• 西原秀典, 岡田典弘. SINEに由来するエンハンサーが寄与した哺乳類の進化, 生物科学, 農文協, Vol. 67, No. 1, pp. 2-9, Dec. 2015.
• 西原秀典, 岡田典弘. シーラカンスゲノム中の反復配列の特徴, 生物の科学 遺伝, NIS Inc., Vol. 68, No. 3, pp. 267-273, May 2014.
• 田中利明, 梶川正樹, 西原秀典. 分子生物学, 生命科学基礎実験第一・第二テキスト, Apr. 2013.
• 岡田典弘, 西原秀典. 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, 生物の科学 遺伝, NIS Inc., Vol. 67, No. 2, pp. 119-126, Mar. 2013.
• 西原秀典, 丸山茂徳, 岡田典弘. 大陸移動と哺乳類の進化, 生物の科学 遺伝, NIS Inc., Vol. 66, No. 5, pp. 531-537, Sept. 2012.

国内会議発表 (査読有り)

• BENI Lestari, 内藤 聡美, 遠藤 彬則, 西原 秀典, 加藤 明, 渡邊 恵理香, 傳田 公紀, 駒田 雅之, 福嶋 俊明. Comparative Phylogenetic Analysis and Molecular Characterization Reveal Eutherian-Specific Role of NRK in Regulating Placenta Development, 日本分子生物学会年会, Dec. 2021.

国際会議発表 (査読なし・不明)

• Ayumi Nagashima, Toya Motoshima, Chihiro Ota, Ingo Braasch, Hidenori Nishihara, Akira Kato. Evolution and pseudogenization of slc12a10 gene in vertebrate animals., 17th TOIN International Symposium on Biomedical Engineering, Nov. 2022.
• Nikaido M, Nishihara H, Fukumoto Y, Okada N.. Ancient SINEs from African endemic mammals., S.M.B.E., June 2002.

国内会議発表 (査読なし・不明)

• 永嶌 鮎美, 潮 和敬, 今泉 元岐, 西原 秀典, 古田 忠臣, Ingo Braasch, 松崎 浩二, Michael F. Romero, 加藤 明. 条鰭類アクアポリン10パラログの輸送基質選択における機能分岐, 日本農芸化学会2024年度大会（創立100周年記念大会）, Mar. 2024.
• 永嶌鮎美, 潮和敬, 今泉元岐, 西原秀典, 古田忠臣, Ingo Braasch, 松崎浩二, Michael F. Romero, 加藤明. 魚類におけるホウ酸輸送からアクアグリセロポリンの基質選択機構へ, 第46回日本分子生物学会年会, Dec. 2023.
• 永嶌鮎美, 今泉元岐, 潮和敬, 西原秀典, 古田忠臣, Ingo Braasch, 渡邊恵理香, 熊谷詩織, 秋元仁, 松崎浩二, Michael F. Romero, 加藤明. 条鰭類Aqp10パラログの尿素およびホウ酸輸送における進化的な活性の減弱, 第46回日本分子生物学会年会, Dec. 2023.
• 太田地洋, 元島登哉, 永嶌鮎美, Ingo Braasch, 西原秀典, 加藤明. 脊椎動物におけるslc12a10遺伝子の進化, 第17回トランスポーター研究会年会, May 2023.
• 永嶌鮎美, 元島登哉, 太田地洋, Ingo Braasch, 西原秀典, 加藤明. 脊椎動物におけるslc12a10遺伝子の発現と偽遺伝子化の解析, 第45回日本分子生物学会年会, Dec. 2022.
• Yuko Sato, Nguyen Thi Bich Ngoc, Haruka Oda, Tetsuya Handa, Hidenori Nishihara, Akihito Harada, Yasuyuki Ohkawa, Hiroshi Kimura. Spatiotemporal dynamics of histone modifications during zebrafish zygotic genome activation, 第43回日本分子生物学会年会, Dec. 2020.
• 樋口拓人, 西原秀典, 梶谷嶺, 豊田敦, 伊藤武彦, 岡田典弘, 二階堂雅人. 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, 日本動物学会第90回大会, Sept. 2019.
• 樋口拓人, 西原秀典, 梶谷嶺, 豊田敦, 伊藤武彦, 岡田典弘, 二階堂雅人. 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, 日本進化学会第21回大会, Aug. 2019.
• 樋口拓人, 西原秀典, 梶谷嶺, 伊藤武彦, 二階堂雅人. 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, 第１回遺伝学会分科会, Mar. 2019.
• 樋口拓人, 西原秀典, 梶谷嶺, 伊藤武彦, 二階堂雅人. 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, 日本進化学会第20回大会, Aug. 2018.

その他の論文・著書など

• Hidenori Nishihara, Norihiro Okada. Retroposons: Genetic Footprints on the Evolutionary Paths of Life, Methods in Molecular Biology -Phylogenomics-, Humana Press, Vol. 422, pp. 201-225, July 2008.
• Hidenori Nishihara. Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring and morphological innovation, Genes & Genetic Systems, Vol. 94, No. 6, pp. 269-281, Dec. 2019.

学位論文

• 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,  本文,  Doctor of Science,  Tokyo Institute of Technology,  2005/09/--, 

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