1. Noe Kaneko, Kumiko Hirai, Minori Oshima, Kei Yura, Mitsuharu Hattori, Nobuaki Maeda, Chiaki Ohtaka-Maruyama (2024) ADAMTS2 promotes radial migration by activating TGF-β signaling in the developing neocortex. EMBO Reports, 25, 3090-3115. doi:10.1038/s44319-024-00174-x
2. Mayu Shibata, Xingcheng Lin, Jos? N. Onuchic, Kei Yura, Ryan R. Cheng (2024) Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies. Biophysical Journal, 123 (6), 681-692. doi:10.1016/j.bpj.2024.01.028
3. Natalia Rzepecka, Yoko Ito, Kei Yura, Emi Ito, Tomohiro Uemura (2024) Identification of novel Golgi-localized putative glycosyltransferase protein in Arabidopsis thaliana. Plant Biotechnology, 41 (1), 35-44. doi:10.5511/plantbiotechnology.23.1214a
4. 由良敬、松永浩子、細川正人、和泉自泰、村松知成、福永津嵩、浜田道昭、馬場健史、竹山春子 (2024) シングルセル/微小組織マルチオミクス解析. 実験医学, 42 (2) 199-204.
5. Kohyoh Murata, Kosuke Kataoka, Ryuto Sanno, Kazuhiro Satomura, Atsushi Ogura, Toru Asahi, Kei Yura, Takeshi Suzuki (2023) Complete mitochondrial genome sequences of two ground crickets, Dianemobius fascipes nigrofasciatus and Polionemobius taprobanensis (Orthoptera: Grylloidea: trigonidiidae). Mitochondrial DNA Part B, 8 (12), 1311-1315. doi:10.1080/23802359.2023.2285400
6. Atsushi Hijikata, Tairo Oshima, Kei Yura, Yoshitaka Bessho (2023) ThermusQ: Toward the cell simulation platform for Thermus thermophilus. Journal of General and Applied Microbiology, 69(2), 59-67. doi:10.2323/jgam.2023.07.001.
7. Masatada Tamakoshi, Atsushi Hijikata, Kei Yura, Kenshiro Oshima, Hidehiro Toh, Kaoru Mitsuoka, Tairo Oshima, Yoshitaka Bessho (2023) Isolation and genomic analysis of a type IV pili-independent Thermus thermophilus phage, φMN1 from a Japanese hot spring. Journal of General and Applied Microbiology, 69(2), 117-124. doi:10.2323/jgam.2023.06.008.
8. Koyu Hon-nami, Atsushi Hijikata, Kei Yura, Yoshitaka Bessho (2023) Whole genome analyses for c-type cytochromes associated with respiratory chains in the extreme thermophile, Thermus thermophilus. Journal of General and Applied Microbiology, 69(2), 68-78. doi:10.2323/jgam.2023.06.005.
9. Saki Katagiri, Mayu Shibata, Misae Kudo, Kei Yura (2023) A trial of web-based method to teach impact of genome variation on protein structures at high school. Natural Science Report, Ochanomizu University, 73, 1-2, 13-21.
10. Naoki Nemoto, Masahiko Kawaguchi, Kei Yura, Haruo Shimada, Yoshitaka Bessho (2022) PGLN: A newly identified amino phosphoglycolipid species in Thermus thermophilus HB8. Biochemistry and Biophysics Reports, 32, 101377. doi:10.1016/j.bbrep.2022.101377.
11. Keigo Ide, Yohei Nishikawa, Toru Maruyama, Yuko Tsukada, Masato Kogawa, Hiroki Takeda, Haruka Ito, Ryota Wagatsuma, Rimi Miyaoka, Yoshikatsu Nakano, Koji Kinjo, Michihiro Ito, Masahito Hosokawa, Kei Yura, Shoichiro Suda, Haruko Takeyama (2022) Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral. Microbiome, 10, 220 doi:10.1186/s40168-022-01395-9.
12. Ryo Yokomizo, Tiago J.S. Lopes, Nagisa Takashima, Sou Hirose, Ayako Kawabata, Masataka Takenaka, Yasushi Iida, Nozomu Yanaihara, Kei Yura, Haruhiko Sago, Aikou Okamoto, Akihiro Umezawa (2022) O3C Glass-Class: A machine learning framework for prognostic prediction of ovarian clear cell carcinoma. Bioinformatics and Biology Insights, 16. doi:10.1177/11779322221134312.
13. Yohei Nishikawa, Masato Kogawa, Masahito Hosokawa, Ryota Wagatsuma, Katsuhiko Mineta, Kai Takahashi, Keigo Ide, Kei Yura, Hayedeh Behzad, Takashi Gojobori, Haruko Takeyama (2022) Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater. ISME Communications, 2, 92. doi:10.1038/s43705-022-00179-4.
14. 由良　敬 (2022) 昆虫が生み出す新たな農水産資源の開発ー昆虫食ムーンショットプロジェクト. アグリバイオ, 6 (11), 8-12.
15. Ha T. T. Duong, Hirofumi Suzuki, Saki Katagiri, Mayu Shibata, Misae Arai, Kei Yura (2022) Computational study of the impact of nucleotide variations on highly conserved proteins: In the case of actin. Biophysics and Physicobiology, 19, 3190025. doi:10.2142/biophysico.bppb-v19.0025.
16. Atsuko Sato, Gina M Oba, Nathanael Aubert-Kato, Kei Yura, John Bishop (2022) Co-expression network analysis of environmental canalization in the ascidian Ciona, BMC Ecology and Evolution, 22, 53. doi:10.1186/s12862-022-02006-9.
17. 甲畑(照井)宏子、由良　敬、池田まさみ (2022) 日本語版健常者病気認知尺度:遺伝性疾患への適用の検討. 日本遺伝カウンセリング学会誌, 43 (1), 47-52.
18. Masato Kogawa, Rimi Miyaoka, Franziska Hemmerling, Masahiro Ando, Kei Yura, Keigo Ide, Yohei Nishikawa, Masahito Hosokawa, Yuji Ise, Jackson K B Cahn, Kentaro Takada, Shigeki Matsunaga, Tetsushi Mori, J?rn Piel, Haruko Takeyama (2022) Single-cell metabolite detection and genomics reveals uncultivated talented producer. PNAS nexus, 1(1), pgab007. doi:10.1093/pnasnexus/pgab007.
19. Xiaojuan Zhang, Mika Nomoto, Marta Garcia-Le?n, Naoki Takahashi, Mariko Kato, Kei Yura, Masaaki Umeda, Vicente Rubio, Yasuomi Tada, Tsuyoshi Furumoto, Takashi Aoyama, Tomohiko Tsuge (2022) CFI 25 subunit of cleavage factor I is important for maintaining the diversity of 3' UTR lengths in Arabidopsis thaliana (L.) Heynh. Plant and Cell Physiology, pcac002. doi:10.1093/pcp/pcac002.
20. Kosuke Kataoka, Yuki Togawa, Ryuto Sanno, Toru Asahi, Kei Yura (2022) Dissecting Cricket Genomes for Advancement of Entomology and Entomophagy. Biophysical Reviews, 14, 75-97. doi:10.1007/s12551-021-00924-4.
21. Shoko Miyata, Noriaki Saku, Saeko Akiyama, Palaksha Kanive Javaregowda, Kenta Ite, Nagisa Takashima, Masashi Toyoda, Kei Yura, Tohru Kimura, Hiroshi Nishina, Atsuko Nakazawa, Mureo Kasahara, Hidenori Nonaka, Tohru Kiyono, Akihiro Umezawa (2022) Puromycin-based purification of cells with high expression of the cytochrome P450 CYP3A4 gene from a patient with drug-induced liver infury (DILI). Stem Cell Research & Therapy, 13, 6. doi:10.1186/s13287-021-02680-4.
22. Gert-Jan Bekker, Masashi Yokochi, Hirofumi Suzuki, Yasuyo Ikegawa, Takeshi Iwata, Takahiro Kudo, Kei Yura, Toshimichi Fujiwara, Takeshi Kawabata, Genji Kurisu (2022) Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of 3D macromolecular structural data. Protein Science, 31, 173-186. doi:10.1002/pro.4211.
23. 由良　敬、鈴木博文、栗栖源嗣、川端　猛、木下賢吾、白井　剛、土方敦司、田之倉優 (2021) 第2章6:創薬等に役立つインターネット上のデータベース、実験医学別冊:創薬研究のための相互作用解析パーフェクト、羊土社、269-283.
24. Ryuto Sanno, Kosuke Kataoka, Shota Hayakawa, Keigo Ide, Chuong N Nguyen, Thao P Nguyen, Binh T N Le, Oanh T P Kim, Katsuhiko Mineta, Haruko Takeyama, Makio Takeda, Toshiyuki Sato, Takeshi Suzuki, Kei Yura, Toru Asahi (2021) Comparative Analysis of Mitochondrial Genomes in Gryllidea (Insecta: Orthoptera): Implications for Adaptive Evolution in Ant-loving Crickets. Genome Biology and Evolution, 13(10), evab222. doi:10.1093/gbe/evab222.
25. Kimie Date, Hiromi Sakagami, Kei Yura (2021) Regulatory properties of vitronectin and its glycosylation in collagen fibril formation and collagen degrading enzyme cathepsin K activity. Scientific Reports, 11, 12023. doi:10.1038/s41598-021-91353-6.
26. 由良　敬、鈴木丈詞、渡邉崇人、小倉　淳、朝日　透、生田和正、霜田政美、森岡伸介、佐藤秀一、中村龍平 (2021) 昆虫を活用した新たな食料生産システムの構築. JATAFFジャーナル, 9(6), 14-19.
27. Kentaro Miyazaki, Toshiyuki Moriya, Natsuko Tokito, Tairo Oshima, Kei Yura, Yoshitaka Bessho (2021) Complete Genome Sequences of Thermus thermophilus Strains HB5002 and HB5008, Isolated from Mine Hot Spring in Japan. Microbiology Resource Announcements. 10, e00272-21. doi:10.1128/MRA.00272-21.
28. Md. Mehedi Hasan, Md. Mostafizur Rahman, Kosuke Kataoka, Kei Yura, Md. Omar Faruque, Faysal Rabby Shadhen, Md Fuad Mondal (2021) Edible wild field cricket (Brachytrupes portentosus) trading in Bangladesh. Journal of Insects as Food and Feed. 7 (8), 1255-1126, doi:10.3920/JIFF2020.0163.
29. Kentaro Miyazaki, Toshiyuki Moriya, Naoki Nemoto, Tairo Oshima, Kei Yura, Yoshitaka Bessho (2021) Complete Genome Sequence of Thermus thermophilus Strain HB5018, Isolated from Mine Hot Spring in Japan. Microbiology Resource Announcements, 10, e0039-21, doi:10.1128/MRA.00039-21.
30. Keiichi Inoue, Masayuki Karasuyama, Ryoko Nakamura, Masae Konno, Daichi Yamada, Kentaro Mannen, Takashi Nagata, Yu Inatsu, Kei Yura, Oded B?j?, Hideki Kandori, Ichiro Takeuchi (2021) Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design. Communications Biology, 4, 362, doi: 10.1038/s42003-021-01878-9.
31. Saori Ogawa, Hitomi Shimidzu, Koji Fukuda, Naoki Tsunekawa, Toshiyuki Hirano, Fumitoshi Sato, Kei Yura, Tomohisa Hasunuma, Kozo Ochi, Michio Yamamoto, Wataru, Sakamoto, Kentaro Hashimoto, Hiroyuki Ogata, Tadayoshi Kanao, Michiko Nemoto, Kenji Inagaki, Takashi Tamura (2021) Multiple Mutations in RNA Polymerase β-Subunit Gene (rpoB) in Streptomyces incarnatus NRRL8089 Enhance Production of Antiviral Antibiotic Sinefungin: Modeling rif Cluster Region by Density Functional Theory. Bioscience, Biotechnology and Biochemistry, 85(5), 1275-1282. doi:10.1093/bbb/zbab011.
32. Shiori S. Aki, Kei Yura, Takashi Aoyama, Tomohiko Tsuge (2021) SAP130 and CSN1 interact and regulate male gametogenesis in Arabidopsis thaliana. Journal of Plant Research, 134(2), 279-289, doi:10.1007/s10265-021-01260-0.
33. Masa-aki Yoshida, Junichi Imoto, Yuri Kawai, Satomi Funahashi, Ryuhei Minei, Yuki Akizuki, Atsushi Ogura, Kazuhiko Nakabayashi, Kei Yura, Kazuho Ikeo (2020) Genomic and transcriptomic analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans. Marine Biotechnology. 22, 760-771, doi:10.1007/s10126-020-10001-8.
34. Mayu Shibata, Kohji Okamura, Kei Yura, Akihiro Umezawa (2020) High-precision multiclass cell classification by supervised machine learning on lectin microarray data. Regenerative Therapy, 15, 195-210, doi:10.1016/j.reth.2020.09.005.
35. Kazue Kudo, Kyoko Kojima-Aikawa, Kei Yura (2020) Past, Present and Future of Ewha-JWO-Ochanomizu Joint Symposium. Natural Science Report, Ochanomizu University, 71, Special Issue, 67-74.
36. Oanh T.P. Kim, Yuki Kagaya, Hoang S. Tran, Ryuhei Minei, Trang T.H. Tran, Ha T. T. Duong, Binh T. N. Le, Lua T. Dang, Kengo Kinoshita, Atsushi Ogura, Kei Yura. (2020) A Novel Circular ssDNA virus of Phylum Cressdnaviricota discovered in Metagenomic Data of Otter Clam (Lutraria rhynchaena). Archives of Virology, 165, 2921-2926, doi:10.1007/s00705-020-04819-9.
37. Hiroko Terui-Kohbata, Masami Ikeda, Kei Yura (2020) The reliability and validity of the Japanese version of Revised Illness Perception Questionnaires for Healthy people (IPQ-RH-J). British Journal of Cancer Research, 3(2), 384-389, doi:10.31488/bjcr.149.
38. Saki Aoto, Mayu Fushimi, Kei Yura, Kohji Okamura. (2020) Diversification of CpG-Island Promoters Revealed by Comparative Analysis Between Human and Rhesus Monkey Genomes. Mammalian Genome, doi:10.1007/s00335-020-09844-2.
39. Kosuke Kataoka, Ryuhei Minei, Keigo Ide, Atsushi Ogura, Haruko Takeyama, Makio N. Takeda Suzuki, Kei Yura, Toru Asahi. (2020) The Draft Genome Dataset of the Asian Cricket Teleogryllus occipitalis for Molecular Research toward Entomophagy. Frontiers in Genetics, doi:10.3389/fgene.2020.00470.
40. Terui-Kohbata, H., Egawa, M., Yura, K., Yoshida, M. (2020) Knowledge and attitude of hereditary breast cancer among Japanese university female students. Journal of Human Genetics, doi:10.1038/s10038-020-0743-9.
41. Mitsunori Takano, Kei Yura, Taro Ueda, Kenji Yasuda (2020) Biophysics at Waseda University. Biophysical Reviews, 12, 225-232, doi:10.1007/s12551-020-00638-z.
42. Yuki Kagaya, Ryuhei Minei, Ha T. T. Duong, Binh T. N. Le, Lua T. Dang, Trang T. H. Tran, Hoa T. Nguyen, Kengo Kinoshita, Kei Yura, Atsushi Ogura, Oanh T. P. Kim (2020) Metagenome sequences from the environment of diseased otter clams, Lutraria rhynchaena, from a farm in Vietnam. Microbiology Resource Announcements, 9, e01068-19.
43. Shuntaro Chiba, Masahito Ohue, Anastasiia Gryniukova Petro Borysko, Sergey Zozulya, Nobuaki Yasuo, Ryunosuke Yoshino, Kazuyoshi Ikeda, Woong-Hee Shin, Daisuke Kihara, Mitsuo Iwadate, Hideaki Umeyama, Takaaki Ichikawa, Reiji Teramoto, Kun-Yi Hsin, Vipul Gupta, Hiroaki Kitano, Mika Sakamoto, Akiko Higuchi, Nobuaki Miura, Kei Yura, Masahiro Mochizuki, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, M. Michael Gromiha, Itsuo Nakane, Nanako Uchida, Hayase Hakariya, Modong Tan, Hironori K. Nakamura, Shogo D. Suzuki, Tomoki Ito, Masahiro Kawatani, Kentaroh Kudoh, Sakurako Takashina, Kazuki Z. Yamamoto, Yoshitaka Moriwaki, Keita Oda, Daisuke Kobayashi, Tatsuya Okuno, Shintaro Minami, George Chikenji, Philip Prathipati, Chioko Nagao, Attayeb Mohsen, Mari Ito, Kenji Mizuguchi, Teruki Honma, Takashi Ishida, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima. (2019) A prospective compound screening contest identified broader inhibitors for Sirtuin 1. Scientific Reports, 9, 19585. doi:10.1038/s41598-019-55069-y
44. Yamauchi, Y., Konno, M., Yamada, D., Yura, K., Inoue, K., Beja, O., Kandori, H. (2019) Engineered functional recovery of microbial rhodopsin without retinal-binding lysine. Photochemistry and Photobiology, 95, 1116-1121.
45. Mouhib, H., Higuchi, A., Abeln, S., Yura, K., Feenstra, K.A. (2019) Impact of pathogenic mutations of the GLUT1 glucose transporter on channel dynamics using ConsDYN enhanced sampling. F1000Research, 8, 322.
46. Sakamoto, M., Suzuki, H. Yura, K. (2019) Relationship between conformation shift and disease related variation sites in ATP-binding cassette transporter proteins. Biophysics and Physicobiology, 16, 68-79.
47. Ohtaka-Maruyama, C., Okamoto, M. Endo, K., Oshima, M., Kaneko, N., Yura, K., Okado, H., Miyata, T., Maeda, N. (2018) Synaptic transmission from subplate neurons controls radial migration of neocortical neurons. Science, 360(6386), 313-317.
48. Higuchi, A., Nonaka, N., Yura, K. (2018) iMusta4SLC: Database for the structural property and variations of solute carrier transporters. Biophysics and Physicobiology, 15, 94-103.
49. Tamura, R., Takeda, M., Sakaue, M., Yoshida, A., Ohi S., Hirano, K., Hayakawa, T., Hirohashi, N., Yura, K., Chiba, K. (2018) Starfish Apaf-1 activates effector caspase-3/9 upon apoptosis of aged eggs. Scientific Reports, 1611 (14 pages).
50. Mizutani, H., Sugawara, H., Buckle, A.M., Sangawa, T., Miyazono, K., Ohtsuka, J., Nagata, K., Shijima, T., Nosaki, S., Xu, Y., Wang, D., Hu, X., Tanokura, M., Yura, K. (2017) REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding. BMC Structural Biology, 17, 4 (8 pages).
51. Masakiyo, Y., Ogura, A., Ichihara, K., Yura, K., Shimada, S. (2016) Candidate key genes for low-salinity adaptation identified by RNA-seq comparison between closely related Ulvarian species in marine and brackish waters. Algal Resources, 9(2), 61-76.
52. Gojobori, T. Ikeo, K., Katayama, Y., Kawabata, T., Kinjo, AR., Kinoshita, K., Kwon, Y., Migita, O., Mizutani, H., Muraoka, M., Nagata, K., Omori, S., Sugawara, H., Yamada, D, Yura, K. (2016) VaProS: A Database-Integration Approach for Protein/Genome Information Retrieval. Journal of Structural and Functional Genomics, 17(4), 69-81.
53. Suzuki, Y., Yura, K. (2016) Conformational shift in the closed state of GroEL induced by ATP-binding triggers a transition to the open state. Biophysics and Physicobiology, 13, 127-134.
54. Hayashi, K., Kawai, Y.L., Yura, K., Yoshida, M., Ogura, A., Hata, K., Nakabayashi, K., Okamura, K. (2016) Complete genome sequence of the mitochondrial DNA of the sparkling enope squid, Watasenia scintillans. Mitochondrial DNA, 27(3), 1842-1843.
55. Aoto, S., Yura, K. (2015) Case study on the evolution of hetero-oligomer interfaces based on the differences in paralogous proteins. Biophysics and Physicobiology, 12, 103-116.
56. Inoue, K., Urushibara, K., Kanai, M., Yura, K., Fujii, S., Hashimoto, Y., Ishigami-Yuasa, M., Mori, S., Kawachi, E., Matsumura, M., Hirano, T., Kagechika, H., Tanatani, A. (2015) Design and synthesis of 4-benzyl-1-(2H)-phthalazinone derivatives as novel androgen receptor antagonists. European Journal of Medicinal Chemistry, 102, 310-319.
57. Takahashi, K., Yoshida, K., Yura, K., Ashihara, H., Sakuta, M. (2015) Biochemical Analysis of Phytolacca DOPA Dioxygenase. Natural Product Communications, 10, 717-719.
58. Hijikata, A., Yura, K., Ohara, O., Go, M. (2015) Structural and functional analyses of Barth syndrome-causing mutations and alternative splicing in the tafazzin acyltransferase domain. Meta Gene, 4, 92-106.
59. Hori-Tanaka, Y., Yura, K., Takai-Igarashi, T., Tanaka, H. (2015) Structural classification of steroid-binding sites on proteins by coarse-grained atomic environment and its correlation with their biological function. Steroids, 96, 81-88.
60. Kamijyo, A., Yura, K., Ogura, A. (2015) Distinct evolutionary rate in the eye field transcription factors found by estimation of ancestral protein structure. Gene, 555 (2), 73-79.
61. Kawai, Y.L., Yura, K., Shindo, M., Kusakabe, R., Hayashi, K., Hata, K., Nakabayashi, K., Okamura, K. (2015) Complete genome sequence of the mitochondrial DNA of the river lamprey, Lethenteron japonicum. Mitochondrial DNA, 25(6), 863-864.
62. Kuppuraj, G., Kruise, D., Yura, K. (2014) Conformational behaviour of flavin adenine dinucleotide: Conserved stereochemistry in bound and free states. The Journal of Physical Chemistry B, 118 (47), 13486-13497.
63. Kato, Y.S., Yagi, T., Harris, S.A., Ohki, S., Yura, K., Shimizu, Y., Honda, S., Kamiya, R., Burgess, S.A., Tanokura, M. (2014) Structure of the microtubule-binding domain of flagellar dynein. Structure, 22 (11) 1628-1638.
64. Yoshida, M., Yura, K., Ogura, A. (2014) Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants. Scientific Reports, 4, 4256.
65. Masui,R., Takahata, Y., Inoue, M., Iio, Y., Okanishi, H., Kim, K., Nakagawa, N., Yura, K., Kuramitsu, S. (2013) Structural insights of post-translational modification sites in the proteome of Thermus thermophilus. Journal of Structural and Functional Genomics, 15(3), 137-151
66. Terui, H., Tachikawa, T., Kakuta, M., Nishimura, Y., Yatsuoka, T., Yamaguchi, K., Yura, K., Akagi, K. T (2013) Molecular and clinical characteristics of MSH6 germline variants detected in colorectal cancer patients. Oncology Reports, 30(6), 2909-2916.
67. Hoshina, S., Yura, K., Teranishi, H., Kiyasu, N., Tominaga, A., Kadoma, H., Nakatsuka, A., Kunichika, T., Obuse, C., Waga, S. (2013) Human Origin Recognition Complex Binds Preferentially to G-Quadruplex-Preferable RNA and Single-Stranded DNA. Journal of Biological Chemistry, 288(42), 30161-30171.
68. Terui, H., Akagi, K., Kawame, H., Yura, K. (2013) CoDP: predicting the impact of unclassified genetic variants in MSH6 by the combination of different properties of the protein. Journal of Biomedical Science, 20, 25.
69. Takai, T., Higaki, K., Aguilar-Moncayo, M., Mena-Barragan, T., Hirano, Y., Yura, K., Yu, L., Ninomiya, Garcia-Moreno, H.M.I., Sakakibara, Y., Ohno, K., Nanba, E., Mellet, C.O., Fernandez, J.M.G., Suzuki, Y. (2013) A bicyclic 1-deoxygalactonojirimycin derivative as a novel pharmacological chaperone for GM1 gangliosidosis. Molecular Therapy, 21(3), 526-532.
70. Kobayashi, E., Yura, K., Nagai, Y. (2013) Distinct Conformation of ATP Molecule in Solution and on Protein. BIOPHYSICS, 9, 1-12.
71. Aguilar-Moncayo, M., Takai, T., Higaki, K., Mena-Barragan T., Hirano, Y., Yura, K., Li, L., Yu, Y., Ninomiya, H., Garcia-Moreno, M.I., Ishii, S., Sakakibara, Y., Ohno, K., Nanba, E., Oritz Mellet, C., Garcai Fernandez, J.M., Suzuki, Y. (2012) Tuning glycosidase inhibition through aglycone interactions: pharmacological chaperones for Fabry disease and GM1 gangliosidosis. Chem. Commun., 48, 6514-6516.
72. Hijikata, A., Yura, K., Noguti, T., Go, M. (2011) Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility. Proteins: Structure, Function, and Bioinformatics, 79(6), 1868-1877.
73. Yura, K., Hayward, S. (2009) The interwinding nature of protein-protein interfaces and its implication for protein complex formation. Bioinformatics, 25(23), 3108-3113 (open access). (Google Scholar Cited by ... )
74. Yura, K., Sulaiman, S., Hatta, Y., Shionyu, M., Go, M. (2009) RESOPS: A database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures. Plant and Cell Physiology, 50 (11), 1865-1873 (open access).
75. Yura, K., Go, M. (2008) Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles. BMC Plant Biology, 8, 79 (open access). (Google Scholar Cited by ... )
76. Yura, K., Miyata, Y., Arikawa, T., Higuchi, M., Sugita, M. (2008) Characteristics and prediction of RNA editing sites in transcripts of the moss Takakia lepidozioides chloroplast. DNA Research, 15 (5), 309-321 (open access). (Google Scholar Cited by ... )
77. Matsumoto, A., Kamata, T., Takagi, J., Iwasaki, K., Yura, K. (2008) Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal mode analysis. Biophysical Journal, 95 (6), 2895-2908. (Google Scholar Cited by ... )
78. Miyazawa, Y., Nishioka, H., Yura, K., Yamato, T. (2008) Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue. Biophysical Journal, 94 (6), 2194-2203.(Google Scholar Cited by ... )
79. Genome Information Integration Project and H-Invitational 2 consortium (Yura, K. is the 66th / 138 authors). (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research, 36, D793-D799 (open access). (Google Scholar Cited by ...)
80. Kono, H., Yuasa, T., Nishiue, S., Yura, K. (2008) coliSNP database server mapping nsSNPs on protein structures. Nucleic Acids Research, 36, D409-D413 (open access). (Google Scholar Cited by ...)
81. Gong, X., Nakamura, K., Yu, H., Yura, K., Go, N. (2007) BAAQ: An infrastructure for application integration and knowledge discovery in bioinformatics. IEEE Transactions on Information Technology in Biomedicine, 11 (4), 428-434.
82. Yura, K., Yamaguchi, A., Go, M. (2006) Coverage of whole proteome by structural genomics observed through protein homology modeling database. Journal of Structural and Functional Genomics, 7 (2), 65-76 (open access). (Google Scholar Cited by ...)
83. Kim, T.P.O., Yura, K., Go, N. (2006) Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction. Nucleic Acids Research, 34 (22), 6450-6460 (open access). (Google Scholar Cited by ...) (access status in NAR)
84. Yura, K., Shionyu, M., Hagino, K., Hijikata, A., Hirashima, Y., Nakahara, T., Eguchi, T., Shinoda, K., Yamaguchi, A., Takahashi, K., Itoh, T., Imanishi, T., Gojobori, T., Go, M. (2006) Alternative splicing in human transcriptome: functional and structural influence on proteins. Gene, 380 (2), 63-71. (Google Scholar Cited by ... )
85. Takeda, J., Suzuki, Y., Nakao, M., Barrero, R., Koyanagi, K., Jin, L., Motono, C., Hata, H., Isogai,T., Nagai, K., Otsuki, T., Kuryshev, V., Shionyu, M., Yura, K., Go, M., Thierry-Mieg, J., Thierry-Mieg, D., Wiemann, S., Nomura, N., Sugano, S., Gojobori, T., Imanishi, T. (2006) Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Research, 34 (14), 3917-3928 (open access). (Google Scholar Cited by ...)
86. Metsugi, S., Uenoyama, A., Adan, J., Miyata, M., Yura, K., Kono, H., Go, N. (2005) Sequence analysis of the gliding protein Gli349 in Mycoplasma mobile. BIOPHYSICS, 1, 33-43 (open access). (Google Scholar Cited by ...)
87. Kim, T.P.O., Yura, K., Go, N., Harumoto, T. (2005) Newly sequenced eRF1s from ciliates: the diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions. Gene, 346, 277-286, (Erratum). (Google Scholar Cited by ...)
88. Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Koyanagi, K.O., Barrero, R.A., Tamura, T., Yamaguchi-Kabata, T., Tanino, M., Yura, K., et al. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biology, 2 (6), 0856-0875 (open access). (Google Scholar Cited by ...)
89. Kaneko, S., Ichinose, H., Fujimoto, Z., Kuno, A., Yura, K., Go, M., Mizuno, H., Kusakabe, I., Kobayashi, H. (2004) Structure and function of a family 10 beta-xylanase chimera of Streptomyces olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex. Journal of Biological Chemistry, 279 (25), 26619-26626 (open access). (Google Scholar Cited by ...)
90. Kim, T.P.O., Yura, K., Go, N., Harumoto, T. (2004) Highly divergent actins from Karyorelictean, Heterotrich and Litostome Ciliates. Journal of Eukaryotic Microbiology, 51 (2), 227-233. (Google Scholar Cited by ...)
91. Yamaguchi, A.,Iida, K., Matsui, N., Tomoda, S., Yura, K., Go, M. (2004) Het-PDB Navi. : A database for protein-small molecule interactions. Journal of Biochemistry (Tokyo) 135 (1), 79-84. (Google Scholar Cited by ...)
92. Nakamura, K., Kawabata, T., Yura, K., Go, N. (2003) Novel types of two-domain multi-copper oxidases: Possible missing links in the evolution FEBS Letters, 553 (3), 239-244. (Google Scholar Cited by ...)
93. Yamaguchi, A., Iwadate, M., Suzuki, E., Yura, K., Kawakita, S., Umeyama, H., Go, M. (2003) Enlarged FAMSBASE: 3D protein structure models of genome sequences for 41 species. Nucleic Acids Research, 31 (1), 463-468 (open access). (Google Scholar Cited by ...)
94. Ahsan M.M., Kaneko, S., Wang, Q., Yura, K., Go, M., Hayashi K. (2001) Capacity of Thermomonospora alba XylA to impart thermostability in family F/10 chimeric xylanases. Enzyme Microb. Technol., 28 (1), 8-15. (Google Scholar Cited by ...)
95. Yoshihara, S., Geng, X.X., Okamoto, S., Yura, K., Murata, T., Go M., Ohmori, M., Ikeuchi, M. (2001) Mutational analysis of genes involved in pilus structure, motility and transformation competency in the unicellular motile cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiology, 42(1), 63-73. (Google Scholar Cited by ...)
96. Kaneko, S., Iwamatsu, S., Kuno, A., Fujimoto, Z., Sato, Y., Yura, K., Go, M., Mizuno, H., Taira, K., Hasegawa, T., Kusakabe, I., Hayashi, K. (2000) Module shuffling of a family F/10 xylanase: replacement of modules M4 and M5 of the FXYN of Streptomyces olivaceoviridis E-86 with those of the Cex of Cellulomonas fimi. Protein Engineering, 13 (12), 873-879 (open access). (Google Scholar Cited by ...)
97. Kikuchi, H., Wako, H., Yura, K., Go, M., Mimuro, M. (2000) Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis. Biophysical Journal, 79 (3), 1587-1600 (open access). (Google Scholar Cited by ...)
98. Kaneko, S., Kuno, A., Fujimoto, Z., Shimizu, D., Machida, S., Sato, Y., Yura, K., Go, M., Mizuno, H., Taira, K. , Kusakabe, I. and Hayashi, K. (1999) An investigation of the nature and function of module 10 in a family F/10 xylanase FXYN of Streptomyces olivaceoviridis E-86 by module shuffling with the Cex of Cellulomonas fimi and by site-directed mutagenesis. FEBS Letters, 460 (1), 61-66. (Google Scholar Cited by ...)
99. Sato, Y., Niimura, Y., Yura, K., Go, M. (1999) Module-intron correlation and intron sliding in family F/10 xylanase genes. Gene, 238 (1), 93-101. (Google Scholar Cited by ...)
100. Yura, K., Toh, H., Go, M. (1999) Putative mechanism of natural transformation as deduced from genome data. DNA Research, 6 (2), 75-82 (open access). (Google Scholar Cited by ...)
101. Yura, K., Shionyu, M., Kawatani, K., Go, M. (1999) Repetitive use of a phosphate-binding module in DNA polymerase beta, Oct-1 POU domain and phage repressors. Cellular and Molecular Life Sciences, 55 (3), 472-486. (Google Scholar Cited by ...)
102. Yura, K., Go, M. (1997) The homeodomain-like putative product of plastid genome: A possible role in plastid differentiation. Res. Comm. Biochem. Cell & Mol. Biol., 1 (1), 79-81. (Google Scholar Cited by ...) (publisher site)
103. Nakashima, T. Sekiguchi, T., Sunamoto, H., Yura, K., Tomoda, S., Go, M., Kere, J., Schlessinger, D., Nishimoto, T. (1994) Structure of the human CCG1 gene: relationship between the exons/introns and functional domain/modules of the protein. Gene, 141 (2), 193-200. (Google Scholar Cited by ...)
104. Koga, H., Sagara, Y., Yaoi, T., Tsujimura, M., Nakamura, K., Sekimizu, K., Makino, R., Shimada, H., Ishimura, Y., Yura, K., Go, M., Ikeguchi, M., Horiuchi, T. (1993) Essential role of the Arg112 residue of cytochrome P450cam for election transfer from reduced putidaredoxin. FEBS Letters, 331 (1-2), 109-113. (Google Scholar Cited by ...)
105. Yura, K., Tomoda, S., Go, M. (1993) Repeat of a helix-turn-helix module in DNA binding proteins. Protein Engineering, 6 (6), 621-628. (Google Scholar Cited by ...)

1. Yura, K. (2008) Prediction of Protein-RNA, Protein-Protein and Protein-Ligand Interfaces Based on Protein Sequences and 3D-Structures, in the Proceedings of International Symposium on Frontiers of Computational Science 2008 (eds. Yukio Kaneda, Masaki Sasai, Kanta Tachibana), pp.77-86.
2. Go, M., Yura, K., Shionyu, M. (2007) Contribution of computational biology and structural genomics to understand genome and transcriptome. "Proceedings of the International Symposium on Frontiers of Computational Science 2005 (ISFCS2005)", (eds. Y. Kaneda, H. Kawamura and M. Sasai), Springer, 75-80.
3. Goto, J., Yasunaga, T., Nagai, R., Matsumoto, A., Yura, K., Takagi, J., Iwasaki, K. (2006) Toward the elucidation of the pathway of integrin conformational changes. Modern Scientific Instruments, Supplementary, 65-66.
4. Iwasaki, K., Matsumoto, A., Yura, K., Goto, T., Yasunaga, T., Nagai, R., Takagi, J. (2006) The pathway of conformational changes of cell adhesion protein, integrin. Proceedings of the 16th International Microscopy Congress (IMC16), 234.
5. Ishida, H., Matsumoto, A., Tsutsumi, Y., Yura, K. (2006) Conformational analysis of the structure of riosome fit into electron microscopy density maps with normal mode analyses and molecular dynamics simulations. Proceedings of the 16th International Microscopy Congress (IMC16), 242.
6. Gong, X., Nakamura, K., Yura, K., Go, N. (2006) Toward Building Grid Applications in Bioinformatics. Proceedings of the Fourth Australasian Symposium on Grid Computing and e-Research (AusGrid 2006), 54, (eds. R. Buyya, and T. Ma) ACS, 17-23.
7. Gong, X.J., Yura, K., Go, N. (2005) A grid-based system for integrating bioinformatics applications. Proceedings of the IADIS International Conference: Applied Computing 2005, 1, 551-558. (Google Scholar Cited by ...)

1. Nagai, Y., Yura, K., Kagawa, H., Wako, H. (2012) Discretized Curvature Analysis for Ribose and Adenine Rings of ATP-Analogs Bound to Myosin, in Memoirs of Kokushikan University Center for Information Science, 33, 55-60.
2. Kinoshita, K., Kono, H., Yura, K. (2008) Prediction of molecular interactions from 3D-structures: from small ligands to large protein complexes, in Prediction of Protein Structures, Functions, and Interactions (ed. Bujnicki, J.M.), Wiley and Sons,159-186.
3. Go, M., Yura, K. (1999) Protein Folding and Genome Evolution, in "Old and New Views of Protein Folding (eds. Kuwajima, K. and Arai, M.), Elsevier, 239-248.
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6. Saito, N., Yura, K. and Fukuda, Y. (1990) Some remarks on protein folding, in "Protein Structural Analysis, Folding and Design" (ed. M. Hatano), Japan Sci. Soc. Press and Elsevier, 19-35.

Publication in Japanese

Being Acknowledged