Papers - YURA Kei

1. Identification of novel Golgi-localized putative glycosyltransferase protein in Arabidopsis thaliana

   Plant Biotechnology, , vol.41(1)(p.35 - 44), 2024.03, Natalia Rzepecka, Yoko Ito, Kei Yura, Emi Ito, Tomohiro Uemura, Original, Research paper (scientific journal), Coauthor

2. Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies

   Biophysical Journal, , vol.123(6)(p.681 - 692), 2024.01, Mayu Shibata, Xingcheng Lin, José N. Onuchic, Kei Yura, Ryan R. Chen, Original, Research paper (scientific journal), Coauthor

3. シングルセル/微小組織マルチオミクス解析

   実験医学, Yodosha, , vol.42(2)(p.199 - 204), 2024.01, 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, Survey, Research paper (scientific journal), Capital Author

4. Complete mitochondrial genome sequences of two ground crickets, Dianemobius fascipes nigrofasciatus and Polionemobius taprobanensis (Orthoptera: Grylloidea: trigonidiidae)

   Mitochondrial DNA Part B, , vol.8(12)(p.1311 - 1315), 2023.12, Kohyoh Murata, Kosuke Kataoka, Ryuto Sanno, Kazuhiro Satomura, Atsushi Ogura, Toru Asahi, Kei Yura, Takeshi Suzuki, Original, Research paper (scientific journal), Coauthor

5. ThermusQ: Toward the cell simulation platform for Thermus thermophilus

   Journal of General and Applied Microbiology, Applied Microbiology, Molecular and Cellular Biosciences Research Foundation, , vol.69(2)(p.59 - 67), 2023.09, Atsushi Hijikata, Tairo Oshima, Kei Yura, Yoshitaka Bessho, Original, Research paper (scientific journal), Coauthor

6. 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, Applied Microbiology, Molecular and Cellular Biosciences Research Foundation, , vol.69(2)(p.117 - 124), 2023.07, Masatada Tamakoshi, Atsushi Hijikata, Kei Yura, Kenshiro Oshima, Hidehiro Toh, Kaoru Mitsuoka, Tairo Oshima, Yoshitaka Bessho, Original, Research paper (scientific journal), Coauthor

7. Whole genome analyses for c-type cytochromes associated with respiratory chains in the extreme thermophile, Thermus thermophilus

   Journal of General and Applied Microbiology, Applied Microbiology, Molecular and Cellular Biosciences Research Foundation, , vol.69(2)(p.68 - 78), 2023.06, Koyu Hon-nami, Atsushi Hijikata, Kei Yura, Yoshitaka Bessho, Original, Research paper (scientific journal), Coauthor

8. A trial of web-based method to teach impact of genome variation on protein structures at high school

   Natural Science Report, Ochanomizu University, Ochanomizu University, , vol.73(1-2)(p.13 - 21), 2023.03, Saki Katagiri, Mayu Shibata, Misae Kudo, Kei Yura, Original, Research paper (scientific journal), Coauthor

9. PGLN: A newly identified amino phosphoglycolipid species in Thermus thermophilus HB8

   Biochemistry and Biophysics Reports, Elsevier B.V., , vol.32(p.101377 - ), 2022.12, Naoki Nemoto, Masahiko Kawaguchi, Kei Yura, Haruo Shimada, Yoshitaka Bessho, Original, Research paper (scientific journal), Coauthor

10. Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral

    Microbiome, Springer Nature, , vol.10(p.220 - ), 2022.12, 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, Original, Research paper (scientific journal), Coauthor

11. O3C Glass-Class: A machine learning framework for prognostic prediction of ovarian clear cell carcinoma

    Bioinformatics and Biology Insights, SAGE Journal, , vol.16(p.11779322221134312 - ), 2022.11, 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, Original, Research paper (scientific journal), Coauthor

12. Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater

    ISME Communications, Springer Nature, , vol.2(1)(p.92 - ), 2022.09, Yohei Nishikawa, Masato Kogawa, Masahito Hosokawa, Ryota Wagatsuma, Katsuhiko Mineta, Kai Takahashi, Keigo Ide, Kei Yura, Hayedeh Behzad, Takashi Gojobori, Haruko Takeyama, Original, Research paper (scientific journal), Coauthor

13. Computational study of the impact of nucleotide variations on highly conserved proteins: In the case of actin

    Biophysics and Physicobiology, Biophysical Society of Japan, , vol.19(1)(p.e190025 - ), 2022.07, Ha T. T. Duong, Hirofumi Suzuki, Saki Katagiri, Mayu Shibata, Misae Arai, Kei Yura (, Original, Research paper (scientific journal), Coauthor

14. 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, , vol.43(1)(p.47 - 52), 2022.05, 甲畑(照井)宏子・由良　敬・池田まさみ, Original, Research paper (scientific journal), Coauthor

15. Co-expression network analysis of environmental canalization in the ascidian Ciona

    BMC Ecology and Evolution, , vol.22(p.53), 2022.04, Atsuko Sato, Gina M Oba, Nathanael Aubert-Kato, Kei Yura, John Bishop, Original, Research paper (scientific journal), Coauthor

16. Single-cell metabolite detection and genomics reveals uncultivated talented producer

    PNAS nexus, , vol.1(1)(p.pgab007), 2022.03, 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, Jörn Piel, Haruko Takeyama , Original, Research paper (scientific journal), Coauthor

17. Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of 3D macromolecular structural data

    Protein Science, , vol.31(1)(p.173 - 186), 2022.01, Gert-Jan Bekker, Masashi Yokochi, Hirofumi Suzuki, Yasuyo Ikegawa, Takeshi Iwata, Takahiro Kudo, Kei Yura, Toshimichi Fujiwara, Takeshi Kawabata, Genji Kurisu, Original, Research paper (scientific journal), Capital Author

18. 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, , vol.63(3)(p.369 - 383), 2022.01, Xiaojuan Zhang, Mika Nomoto, Marta Garcia-León, Naoki Takahashi, Mariko Kato, Kei Yura, Masaaki Umeda, Vicente Rubio, Yasuomi Tada, Tsuyoshi Furumoto, Takashi Aoyama, Tomohiko Tsuge, Original, Research paper (scientific journal), Coauthor

19. Dissecting Cricket Genomes for Advancement of Entomology and Entomophagy

    Biophysical Reviews, , vol.14(p.75 - 97), 2022.01, Kosuke Kataoka, Yuki Togawa, Ryuto Sanno, Toru Asahi, Kei Yura, Survey, Research paper (scientific journal), Coauthor

20. 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, , vol.13(p.6), 2022.01, 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, Original, Research paper (scientific journal), Coauthor

21. Comparative Analysis of Mitochondrial Genomes in Gryllidea (Insecta: Orthoptera): Implications for Adaptive Evolution in Ant-loving Crickets

    Genome Biology and Evolution, , vol.13(10)(p.evab222), 2021.09, 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, Original, Research paper (scientific journal), Coauthor

22. Regulatory properties of vitronectin and its glycosylation in collagen fibril formation and collagen degrading enzyme cathepsin K activity

    Scientific Reports, , vol.11(p.12023 - ), 2021.06, Kimie Date, Hiromi Sakagami, Kei Yura, Original, Research paper (scientific journal), Coauthor

23. 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, , vol.9(6)(p.14 - 19), 2021.06, 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, Survey, Research paper (scientific journal), Capital Author

24. Edible wild field cricket (Brachytrupes portentosus) trading in Bangladesh.

    Journal of Insects as Food and Feed, , vol.7(8)(p.1255 - 1126), 2021.06, Md. Mehedi Hasan, Md. Mostafizur Rahman, Kosuke Kataoka, Kei Yura, Md. Omar Faruque, Faysal Rabby Shadhen, Md Fuad Mondal, Original, Research paper (scientific journal), Coauthor

25. 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, , vol.85(5)(p.1275 - 1282), 2021.05, 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, Original, Research paper (scientific journal), Coauthor

26. Complete Genome Sequences of Thermus thermophilus Strains HB5002 and HB5008, Isolated from Mine Hot Spring in Japan

    Microbiology Resource Announcements, , vol.10(p.e00272-21 - ), 2021.04, Kentaro Miyazaki, Toshiyuki Moriya, Natsuko Tokito, Tairo Oshima, Kei Yura, Yoshitaka Bessho, Original, Research paper (scientific journal), Coauthor

27. Complete Genome Sequence of Thermus thermophilus Strain HB5018, Isolated from Mine Hot Spring in Japan

    Microbiology Resource Announcements, , vol.10(p.e0039-21 - ), 2021.03, Kentaro Miyazaki, Toshiyuki Moriya, Naoki Nemoto, Tairo Oshima, Kei Yura, Yoshitaka Bessho, Original, Research paper (scientific journal), Coauthor

28. Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design

    Communications Biology, , vol.4(p.362 - ), 2021.03, Keiichi Inoue, Masayuki Karasuyama, Ryoko Nakamura, Masae Konno, Daichi Yamada, Kentaro Mannen, Takashi Nagata, Yu Inatsu, Kei Yura, Oded Béjà, Hideki Kandori, Ichiro Takeuchi, Original, Research paper (scientific journal), Coauthor

29. SAP130 and CSN1 interact and regulate male gametogenesis in Arabidopsis thaliana

    Journal of Plant Research, , vol.134(2)(p.279 - 289), 2021.03, Shiori S. Aki, Kei Yura, Takashi Aoyama, Tomohiko Tsuge, Original, Research paper (scientific journal), Coauthor

30. Genomic and transcriptomic analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans

    Marine Biotechnology, , vol.22(p.760 - 771), 2020.12, Masa-aki Yoshida, Junichi Imoto, Yuri Kawai, Satomi Funahashi, Ryuhei Minei, Yuki Akizuki, Atsushi Ogura, Kazuhiko Nakabayashi, Kei Yura, Kazuho Ikeo, Original, Research paper (scientific journal), Coauthor

31. High-precision multiclass cell classification by supervised machine learning on lectin microarray data

    Regenerative Therapy, , vol.15(p.195 - 210), 2020.12, Mayu Shibata, Kohji Okamura, Kei Yura, Akihiro Umezawa, Original, Research paper (scientific journal), Coauthor

32. A Novel Circular ssDNA virus of Phylum Cressdnaviricota discovered in Metagenomic Data of Otter Clam (Lutraria rhynchaena)

    Archives of Virology, , vol.165(p.2921 - 2926), 2020.12, 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, Original, Research paper (scientific journal), Coauthor

33. Past, Present and Future of Ewha-JWO-Ochanomizu Joint Symposium

    Natural Science Report, Ochanomizu University, , vol.71(Special Issue)(p.67 - 74), 2020.10, Kazue Kudo, Kyoko Kojima-Aikawa, Kei Yura, Survey, Research paper (bulletin of university, research institution), Single Author

34. Diversification of CpG-Island Promoters Revealed by Comparative Analysis Between Human and Rhesus Monkey Genomes

    Mammalian Genome, , vol.31(p.240 - 251), 2020.07, Saki Aoto, Mayu Fushimi, Kei Yura, Kohji Okamura, Original, Research paper (scientific journal), Coauthor

35. The Draft Genome Dataset of the Asian Cricket Teleogryllus occipitalis for Molecular Research toward Entomophagy

    Frontiers in Genetics, , vol.11(p.470), 2020.05, Kosuke Kataoka, Ryuhei Minei, Keigo Ide, Atsushi Ogura, Haruko Takeyama, Makio N. Takeda Suzuki, Kei Yura, Toru Asahi, Original, Research paper (scientific journal), Coauthor

36. The reliability and validity of the Japanese version of Revised Illness Perception Questionnaires for Healthy people (IPQ-RH-J)

    British Journal of Cancer Research, , vol.3(2)(p.384 - 389), 2020.04, Hiroko Terui-Kohbata, Masami Ikeda, Kei Yura , Original, Research paper (scientific journal), Coauthor

37. Biophysics at Waseda University

    Biophysical Reviews, , vol.12(p.225 - 232), 2020.03, Mitsunori Takano, Kei Yura, Taro Ueda, Kenji Yasuda, Survey, Research paper (scientific journal), Coauthor

38. REFOLDdb: a new and sustainable gateway to experimental protocaols for protein refolding

    BMC Structural Biology, , vol.17(p.4 - ), 2017.05, 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., Original, Research paper (scientific journal), Coauthor

39. Candidate key genes for low-salinity adaptation identified by RNA-seq comparison between closely related Ulvarian species in marine and brackish waters

    Algal Resources, , vol.9(2)(p.61 - 76), 2017.04, Masakiyo, Y., Ogura, A., Ichihara, K., Yura, K., Shimada, S., Original, Research paper (scientific journal), Coauthor

40. 斎藤信彦先生を偲んで

    日本物理学会誌, , vol.72(4)(p.277), 2017.04, Yura, K., Survey, Research paper (other academic), Capital Author

41. Special issue: big data analyses in structural and functional genomics

    Journal of Structural and Functional Genomics, , vol.17(p.67), 2017.01, Yokoyama, S., Yura, K., Survey, Research paper (conference, symposium, etc.), Capital Author

42. VaProS: A Database-Integration Approach for Protein/Genome Information Retrieval

    Journal of Structural and Functional Genomics, , vol.17(4)(p.69 - 81), 2016.12, 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., Original, Research paper (scientific journal), Coauthor

43. Obituary: Nobuhiko Saitô, a man who understood protein folding in his own way

    Biophysics and Physicobiology, , vol.13(p.245 - 247), 2016.11, Yura, K., Original, Research paper (scientific journal), Capital Author

44. Memorial Issue for Professor Nobuhiko Saitô

    Biophysics and Physicobiology, , vol.13(p.243), 2016.11, Yura, K., Wako, H., Survey, Research paper (conference, symposium, etc.), Capital Author

45. Preface of Special Issue "Protein-Ligand Interactions"

    Biophysics and Physicobiology, , vol.13(p.85 - 86), 2016.07, Yura, K., Survey, Research paper (conference, symposium, etc.), Capital Author

46. Conformational shift in the closed state of GroEL induced by ATP-binding triggers a transition to the open state

    Biophysics and Physicobiology, , vol.13(p.127 - 134), 2016.07, Suzuki, Y., Yura, K., Original, Research paper (scientific journal), Coauthor

47. Case study on the evolution of hetero-oligomer interfaces based on the differences in paralogous proteins

    Biophysics and Physicobiology, , vol.12(p.103 - 116), 2015.12, Aoto, S., Yura, K., Original, Research paper (scientific journal), Coauthor

48. Design and synthesis of 4-benzyl-1-(2H)-phthalazinone derivatives as novel androgen receptor antagonists

    European Journal of Medicinal Chemistry, , vol.102(p.310 - 319), 2015.09, 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., Original, Research paper (scientific journal), Coauthor

49. Biochemical Analysis of Phytolacca DOPA Dioxygenase.

    Natural Product Communications, , vol.10(5)(p.717 - 719), 2015.05, Takahashi, K., Yoshida, K., Yura, K., Ashihara, H., Sakuta, M., Original, Research paper (scientific journal), Coauthor

50. Structural classification of steroid-binding sites on proteins by coarse-grained atomic environment and its correlation with their biological function.

    Steroids, , vol.96(p.81 - 88), 2015.04, Hori-Tanaka, Y., Yura, K., Takai-Igarashi, T., Tanaka, H., Original, Research paper (scientific journal), Coauthor

51. Structural and functional analyses of Barth syndrome-causing mutations and alternative splicing in the tafazzin acyltransferase domain.

    Meta Gene, , vol.4(p.92 - 106), 2015.04, Hijikata, A., Yura, K., Ohara, O., Go, M., Original, Research paper (scientific journal), Coauthor

52. Conformational behaviour of flavin adenine dinucleotide: Conserved stereochemistry in bound and free states.

    The Journal of Physical Chemistry B, , vol.118(47)(p.13486 - 13497), 2014.11, Kuppuraj, G., Kruise, D., Yura, K., Original, Research paper (scientific journal), Coauthor

53. Structure of the microtubule-binding domain of flagellar dynein

    Structure, , vol.22(11)(p.1628 - 1638), 2014.11, Kato, Y.S., Yagi, T., Harris, S.A., Ohki, S., Yura, K., Shimizu, Y., Honda, S., Kamiya, R., Burgess, S.A., Tanokura, M., Original, Research paper (scientific journal), Coauthor

54. Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants

    Scientific Reports, , vol.4(p.4256 - ), 2014.03, Masa-aki Yoshida, Kei Yura, Atsushi Ogura, Original, Research paper (scientific journal), Coauthor

55. Structural insights of post-translational modification sites in the proteome of Thermus thermophilus

    Journal of Structural and Functional Genomics, , vol.15(3)(p.137 - 151), 2014.01, Masui,R., Takahata, Y., Inoue, M., Iio, Y., Okanishi, H., Kim, K., Nakagawa, N., Yura, K., Kuramitsu, S., Original, Research paper (scientific journal), Coauthor

56. Complete genome sequence of the mitochondrial DNA of the river lamprey, Lethenteron japonicum

    Mitochondrial DNA, , vol.doi:10.3109/19401736.2013.861432(doi:10.3109/19401736.2013.861432)(p.doi:10.3109/19401736.2013.861432), 2014.01, Kawai, Y.L., Yura, K., Shindo, M., Kusakabe, R., Hayashi, K., Hata, K., Nakabayashi, K., Okamura, K., Original, Research paper (scientific journal), Coauthor

57. Molecular and clinical characteristics of MSH6 germline variants detected in colorectal cancer patients

    Oncology Reports, , vol.30(6)(p.2909 - 2916), 2013.10, Terui, H., Tachikawa, T., Kakuta, M., Nishimura, Y., Yatsuoka, T., Yamaguchi, K., Yura, K., Akagi, K., Original, Research paper (scientific journal), Coauthor

58. Human Origin Recognition Complex Binds Preferentially to G-Quadruplex-Preferable RNA and Single-Stranded DNA.

    Journal of Biological Chemistry, , vol.288(42)(p.30161 - 30171), 2013.09, Hoshina, S., Yura, K., Teranishi, H., Kiyasu, N., Tominaga, A., Kadoma, H., Nakatsuka, A., Kunichika, T., Obuse, C., Waga, S., Original, Research paper (scientific journal), Coauthor

59. 分子動力学とデータベースによる統合解析

    生化学, , vol.85(8)(p.646 - 655), 2013.08, 倭　剛久、由良　敬, Survey, Research paper (scientific journal), Capital Author

60. 数学・理科教育教材の開発に向けての取組み

    情報知識学会誌, , vol.23(2)(p.199 - 204), 2013.05, 川井優里、板垣　舞、芳須公美、竹田宏美、由良　敬, Original, Research paper (bulletin of university, research institution), Coauthor

61. CoDP: Predicting the Impact of Unclassified Genetic Variants in MSH6 by the Combination of Different Properties of the Protein

    Journal of Biomedical Science, , vol.20(p.25 - ), 2013.05, Terui, H., Akagi, K., Kawame, H., Yura, K., Original, Research paper (scientific journal), Capital Author

62. A bicyclic 1-deoxygalactonojirimycin derivative as a novel pharmacological chaperone for GM1 gangliosidosis

    Molecular Therapy, , vol.21(3)(p.526 - 532), 2013.03, 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., Original, Research paper (scientific journal), Coauthor

63. Distinct Conformation of ATP Molecule in Solution and on Protein

    BIOPHYSICS, , vol.9(p.1 - 12), 2013.01, Kobayashi, E., Yura, K., Nagai, Y., Original, Research paper (scientific journal), Capital Author

64. RNAの塩基配列はDNAの塩基配列と完全に一致するのか？

    生物の科学 遺伝, , vol.66(3)(p.237 - 239), 2012.05, 由良　敬, Survey, Research paper (scientific journal), Single Author

65. Tuning glycosidase inhibition through aglycone interactions: pharmacological chaperones for Fabry disease and GM1 gangliosidosis

    Chem. Commun., , vol.48(p.6514 - 6516), 2012.05, 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., Original, Research paper (scientific journal), Coauthor

66. 巻頭言：境界にいることを楽しもう

    生物物理, , vol.52(3)(p.123), 2012.02, 由良　敬, Letters, Research paper (scientific journal), Single Author

67. 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, , vol.79(6)(p.1868 - 1877), 2011.06, Hijikata, A., Yura, K., Noguti, T., Go, M., Original, Research paper (scientific journal), Capital Author

68. 埋め草「タンパク質立体構造散歩」の経緯

    生物物理, , vol.51(3)(p.144 - 145), 2011.06, 由良敬, Survey, Research paper (scientific journal), Single Author

69. タンパク質の構造から機能を推定する：構造バイオインフォマティクス

    化学と生物, , vol.48(1)(p.43 - 50), 2010.01, 由良　敬, Survey, Research paper (scientific journal), Single Author

70. 構造バイオインフォマティクス

    蛋白質核酸酵素, , vol.54(12)(p.1535 - 1541), 2009.12, 由良　敬、塩生真史、藤　博幸, Survey, Research paper (scientific journal), Capital Author

71. RESOPS: A database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures.

    Plant and Cell Physiology, , vol.50(11)(p.1865 - 1873), 2009.12, Yura, K., Sulaiman, S., Hatta, Y., Shionyu, M., Go, M., Original, Research paper (scientific journal), Capital Author

72. The interwinding nature of protein-protein interfaces and its implication for protein complex formation.

    Bioinformatics, , vol.25(23)(p.3108 - 3113), 2009.12, Yura, K., Hayward, S., Original, Research paper (scientific journal), Capital Author

73. 陸上植物オルガネラのRNA編集の役割

    生物物理, , vol.49(5)(p.244 - 245), 2009.10, 由良　敬、郷　通子, Survey, Research paper (scientific journal), Capital Author

74. 理論計算＋生命情報学で初めて見出された活性部位の機能性残基 －ＤＮＡ補修酵素の場合―

    生物物理, , vol.49(4)(p.196 - 197), 2009.08, 倭　剛久、西岡宏任、由良　敬, Survey, Research paper (scientific journal), Coauthor

75. タンパク質の立体構造に基づく相互作用構造の推定

    薬学雑誌, , vol.128(11)(p.1547 - 1555), 2008.12, 由良　敬, Survey, Research paper (scientific journal), Single Author

76. Characteristics and prediction of RNA editing sites in transcripts of the moss Takakia lepidozioides chloroplast

    DNA Research, , vol.15(5)(p.309 - 321), 2008.12, Yura, K., Miyata, Y., Arikawa, T., Higuchi, M., Sugita, M., Original, Research paper (scientific journal), Capital Author

77. Prediction of Protein-RNA, Protein-Protein and Protein-Ligand Interfaces Based on Protein Sequences and 3D-Structures

    Proceedings of International Symposium on FCS2008, (p.77 - 86), 2008.11, Yura, K., Survey, Research paper (bulletin of university, research institution), Single Author

78. Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal mode analysis

    Biophysical Journal, , vol.95(6)(p.2895 - 2908), 2008.09, Matsumoto, A., Kamata, T., Takagi, J., Iwasaki, K., Yura, K., Original, Research paper (scientific journal), Coauthor

79. Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles

    BMC Plant Biology, , vol.8(p.79 - ), 2008.07, Yura, K., Go, M., Original, Research paper (scientific journal), Capital Author

80. Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue

    Biophysical Journal, , vol.94(6)(p.2194 - 2203), 2008.03, Miyazawa, Y., Nishioka, H., Yura, K., Yamato, T., Original, Research paper (scientific journal), Coauthor

81. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

    Nucleic Acids Research, , vol.36(DataBase Issue)(p.D793 - D799), 2008.01, Genome Information Integration Project and H-Invitational 2 consortium, Original, Research paper (scientific journal), Coauthor

82. coliSNP database server mapping nsSNPs on protein structures

    Nucleic Acids Research, , vol.36(DataBase Issue)(p.D409 - D413), 2008.01, Kono, H., Yuasa, T., Nishiue, S., Yura, K., Original, Research paper (scientific journal), Coauthor

83. BAAQ: An infrastructure for application integration and knowledge discovery in bioinformatics

    IEEE Transactions on Information Technology in Biomedicine, , vol.11(4)(p.428 - 434), 2007.07, Gong, X., Nakamura, K., Yu, H., Yura, K. Go, N., Original, Research paper (scientific journal), Coauthor

84. Toward the elucidation of the pathway of integrin conformational changes

    Modern Scientific Instruments, , vol.Supplementary(p.65 - 66), 2006.12, Goto, J., Yasunaga, T., Nagai, R., Matsumoto, A., Yura, K., Takagi, J., Iwasaki, K., Original, Research paper (scientific journal), Coauthor

85. Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction

    Nucleic Acids Research, , vol.34(22)(p.6450 - 6460), 2006.11, Kim, T.P.O., Yura, K., Go, N., Original, Research paper (scientific journal), Coauthor

86. Alternative splicing in human transcriptome: functional and structural influence on proteins

    Gene, , vol.380(2)(p.63 - 71), 2006.10, 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., Original, Research paper (scientific journal), Capital Author

87. 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, , vol.34(14)(p.3917 - 3928), 2006.08, 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., Original, Research paper (scientific journal), Coauthor

88. Coverage of whole proteome by structural genomics observed through protein homology modeling database

    Journal of Structural and Functional Genomics, , vol.7(2)(p.65 - 76), 2006.06, Yura, K., Yamaguchi, A., Go, M., Original, Research paper (scientific journal), Capital Author

89. 全ゲノムを対象とした蛋白質立体構造データベースの公開

    蛋白質核酸酵素, , vol.50(p.2301), 2005.12, 由良　敬、山口晶太、郷　通子, Survey, Research paper (scientific journal), Capital Author

90. Contribution of computational biology and structural genomics to understand genome and transcriptome

    Proc. of the Inter. Symp. on Frontiers of Comp. Sci., (p.75 - 80), 2005.11, Go, M., Yura, K., Shionyu, M., Survey, Research paper (bulletin of university, research institution), Coauthor

91. A grid-based system for integrating bioinformatics applications

    Proc. IADIS Inter. Conf.: Applied Computing 2005, , vol.1(p.551 - 558), 2005.10, Gong, X.J., Yura, K., Go, N., Original, Research paper (bulletin of university, research institution), Coauthor

92. Sequence analysis of the gliding protein Gli349 in Mycoplasma mobile

    BIOPHYSICS, , vol.1(p.33 - 43), 2005.05, Metsugi, S., Uenoyama, A., Adan, J., Miyata, M., Yura, K., Kono, H., Go, N., Original, Research paper (scientific journal), Coauthor

93. Newly sequenced eRF1s from ciliates: the diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions

    Gene, , vol.346(p.277 - 286), 2005.02, Kim, T.P.O., Yura, K., Go, N., Harumoto, T., Original, Research paper (scientific journal), Coauthor

94. タンパク質のフォールディング:自己組織化と遺伝子のスプライシング

    Bionics, , vol.2(1)(p.38 - 43), 2005.01, 郷　通子、由良　敬, Survey, Research paper (scientific journal), Coauthor

95. Integrative annotation of 21,037 human genes validated by full-length cDNA clones

    PLoS Biology, , 2004.06, 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., Original, Research paper (scientific journal), Coauthor

96. Structure and function of a family 10 beta-xylanase chimera of Streptomyces olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex

    Journal of Biological Chemistry, , 2004.06, Kaneko, S., Ichinose, H., Fujimoto, Z., Kuno, A., Yura, K., Go, M., Mizuno, H., Kusakabe, I., Kobayashi, H., Original, Research paper (scientific journal), Coauthor

97. Highly divergent actins from Karyorelictean, Heterotrich and Litostome Ciliates

    Journal of Eukaryotic Microbiology, , 2004.03, Kim, T.P.O., Yura, K., Go, N., Harumoto, T., Original, Research paper (scientific journal), Coauthor

98. Het-PDB Navi. : A database for protein-small molecule interactions

    Journal of Biochemistry (Tokyo), , 2004.01, Yamaguchi, A.,Iida, K., Matsui, N., Tomoda, S., Yura, K., Go, M., Original, Research paper (scientific journal), Coauthor

99. Novel types of two-domain multi-copper oxidases: Possible missing links in the evolution

    FEBS Letters, , 2003.10, Nakamura, K., Kawabata, T., Yura, K., Go, N., Original, Research paper (scientific journal), Coauthor

100. バイオインフォマティクスが追い求めるもの

     名古屋大学情報連携基盤センターニュース, , 2003.05, 由良　敬, Survey, Research paper (bulletin of university, research institution), Single Author

101. Enlarged FAMSBASE: 3D protein structure models of genome sequences for 41 species

     Nucleic Acids Research, , 2003.01, Yamaguchi, A., Iwadate, M., Suzuki, E., Yura, K., Kawakita, S., Umeyama, H., Go, M., Original, Research paper (scientific journal), Coauthor

102. モジュールに基づくゲノム機能予測

     蛋白質核酸酵素増刊「構造プロテオミクス」, , 2002.07, Yura, K., Go, M., Survey, Research paper (scientific journal), Capital Author

103. ジンクフィンガードメイン

     生体の科学：モチーフ・ドメインリスト, , 2001.09, 由良　敬、郷　通子, Survey, Research paper (scientific journal), Capital Author

104. POUドメイン

     生体の科学：モチーフ・ドメインリスト, , 2001.09, 由良　敬、郷　通子, Original, Research paper (scientific journal), Capital Author

105. Capacity of Thermomonospora alba XylA to impart thermostability in family F/10 chimeric xylanases

     Enzyme and Microbial Technology, , 2001.01, Ahsan M.M., Kaneko, S., Wang, Q., Yura, K., Go, M., Hayashi K., Original, Research paper (scientific journal), Coauthor

106. Mutational analysis of genes involved in pilus structure, motility and transformation competency in the unicellular motile cyanobacterium Synechocystis sp. PCC 6803

     Plant Cell Physiology, , 2001.01, Yoshihara, S., Geng, X.X., Okamoto, S., Yura, K., Murata, T., Go M., Ohmori, M., Ikeuchi, M., Original, Research paper (scientific journal), Coauthor

107. 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, , 2000.12, Kaneko, S., Iwamatsu, S., Kuno, A., Fujimoto, Z., Sato, Y., Yura, K., Go, M., Mizuno, H., Taira, K., Hasegawa, T., Kusakabe, I., Hayashi, K., Original, Research paper (scientific journal), Coauthor

108. Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis

     Biophysical Journal, , 2000.09, Kikuchi, H., Wako, H., Yura, K., Go, M., Mimuro, M., Original, Research paper (scientific journal), Coauthor

109. 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, , 1999.10, 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., Original, Research paper (scientific journal), Coauthor

110. Module-intron correlation and intron sliding in family F/10 xylanase genes

     Gene, , 1999.09, Sato, Y., Niimura, Y., Yura, K., Go, M., Original, Research paper (scientific journal), Coauthor

111. Putative mechanism of natural transformation as deduced from genome data

     DNA Research, , 1999.04, Yura, K., Toh, H., Go, M., Original, Research paper (scientific journal), Capital Author

112. Repetitive use of a phosphate-binding module in DNA polymerase beta, Oct-1 POU domain and phage repressors

     Cellular and Molecular Life Sciences, , 1999.03, Yura, K., Shionyu, M., Kawatani, K., Go, M., Original, Research paper (scientific journal), Capital Author

113. DNA塩基配列を用いたfastDNAmlによる進化系統樹の推定

     名古屋大学大型計算機センターニュース, , 1997.05, 由良　敬、篠田和紀、井本剛史、郷　通子, Survey, Research paper (bulletin of university, research institution), Capital Author

114. The homeodomain-like putative product of plastid genome: A possible role in plastid differentiation

     Res. Comm. Biochem. Cell & Mol. Biol., , 1997.01, Yura, K., Go, M., Original, Research paper (scientific journal), Capital Author

115. Structure of the human CCG1 gene: relationship between the exons/introns and functional domain/modules of the protein

     Gene, , 1994.04, Nakashima, T. Sekiguchi, T., Sunamoto, H., Yura, K., Tomoda, S., Go, M., Kere, J., Schlessinger, D., Nishimoto, T., Original, Research paper (scientific journal), Coauthor

116. Essential role of the Arg112 residue of cytochrome P450cam for election transfer from reduced putidaredoxin

     FEBS Letters, , 1993.09, 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., Original, Research paper (scientific journal), Coauthor

117. Repeat of a helix-turn-helix module in DNA binding proteins

     Protein Engineering, , 1993.08, Yura, K., Tomoda, S., Go, M., Original, Research paper (scientific journal), Capital Author