2024年

• 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
• Mayu Shibata, Xingcheng Lin, José 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
• 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
• 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.

2023年

• 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
• 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.
• 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.
• 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.
• 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.

2022年

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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 (2022) Single-cell metabolite detection and genomics reveals uncultivated talented producer. PNAS nexus, 1(1), pgab007. doi:10.1093/pnasnexus/pgab007.
• 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 (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.
• 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.
• 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.
• 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.

2021年

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Keiichi Inoue, Masayuki Karasuyama, Ryoko Nakamura, Masae Konno, Daichi Yamada, Kentaro Mannen, Takashi Nagata, Yu Inatsu, Kei Yura, Oded Béjà, 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.
• 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.
• 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.

2020年

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Kagaya, Y., Minei, R., Duong, H.T.T., Le, B. T. N., Dang, L.T., Tran, T.T.H., Nguyen, H.T., Kinoshita, K., Yura, K., Ogura, A., Kim. O.T.P. (2020) Metagenome sequences from the environment of diseased otter clams, Lutraria rhynchaena, from a farm in Vietnam. Microbiology Resource Announcements, 9, e01068-19. doi:10.1128/MRA.01068-19.

2019年

• 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.
• 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.
• 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, 88, 322.
• 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.

2018年

• Ohtaka-Maruyama C., Okamoto, M., Endo, K., Oshima, M., Kaneko, N., Yura, K., Okada, H., Miyata, T., Maeda, N. (2018) Synaptic transmission from subplate neurons controls radial migration of neocortical neurons. Science, 360, 313-317.
• 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.
• 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).
• 由良　敬 (2018)　支部だより 第7回関東支部会報告と2020年大会にむけて。生物物理, 58 (5), 277-278.

2017年

• 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).
• 由良　敬 (2017)　斎藤信彦先生を偲んで。日本物理学会誌, 72 (4), 277.

2016年

• 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.
• Yokoyama S., Yura, K. (2016) Special issue: big data analyses in structural and functional genomics. Journal of Structural and Functional Genomics, 17, 67.
• 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.
• Yura, K. (2016) Obituary: Nobuhiko Saitô, a man who understood protein folding in his own way. Biophysics and Physicobiology, 13, 245-247.
• Yura, K., Wako, H. (2016) Memorial Issue for Professor Nobuhiko Saitô. Biophysics and Physicobiology, 13, 243.
• 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.
• Yura, K. (2016) Preface of Special Issue “Protein-Ligand Interactions”. Biophysics and Physicobiology, 13, 85-86.

2015年

• 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.
• 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.
• Takahashi, K., Yoshida, K., Yura, K., Ashihara, H., Sakuta, M. (2015) Biochemical Analysis of Phytolacca DOPA Dioxygenase. Natural Product Communications, 10, 717-719.
• 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.
• 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.
• 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.

2014年

• 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.
• Hayashi, K., Kawai, Y.L., Yura, K., Yoshida, M., Ogura, A., Hata, K., Nakabayashi, K., Okamura, K. (2014) Complete genome sequence of the mitochondrial DNA of the sparkling enope squid, Watasenia scintillans. Mitochondrial DNA, doi:10.3109/19401736.2014.971251.
• 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.
• Kawai, Y.L., Yura, K., Shindo, M., Kusakabe, R., Hayashi, K., Hata, K., Nakabayashi, K., Okamura, K. (2014) Complete genome sequence of the mitochondrial DNA of the river lamprey, Lethenteron japonicum. Mitochondrial DNA, doi:10.3109/19401736.2013.861432.
• Yoshida, M., Yura, K., Ogura, A. (2014) Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants. Scientific Reports 4, 4256.
• Masui, R., Takahata, Y., Inoue, M., Iio, Y., Okanishi, H., Kim, K., Nakagawa, N., Yura, K., Kuramitsu, S. (2014) Structural insights of post-translational modification sites in the proteome of Thermus thermophilus. Journal of Structural and Functional Genomics, 15(3), 137-151.
• 由良　敬(分担翻訳) (2014)　第5章　構造に基づく医薬品設計における自由エネルギー計算、「ドラッグデザイン:構造とリガンドに基づくアプローチ」(田之倉優、小島正樹　監訳)　東京化学同人、pp.65-92.

2013年

• 由良　敬, 高井美智留 (分担執筆)(2013) 「進化分子工学─高速分子進化によるタンパク質・核酸の開発─」第4 章　タンパク質進化の機構.株式会社エヌ・ティー・エス。
• Terui, H., Tachikawa, T., Kakuta, M., Nishimura, Y., Yatsuoka, T., Yamaguchi, K., Yura, K., Akagi, K. (2013) Molecular and clinical characteristics of MSH6 germline variants detected in colorectal cancer patients. Oncology Reports, 30(6), 2909-2916.
• 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.
• 倭　剛久、由良　敬 (2013) 分子動力学とデータベースによる統合解析、 生化学, 85(8), 646-655.
• 由良　敬 (2013) 【翻訳】天然変性タンパク質、 パリティ, 28(06), 45-47
• 川井優里、板垣　舞、芳須公美、竹田宏美、由良　敬 (2013) 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, 23(2), 199-204.
• 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 (13 pages).
• 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.
• Kobayashi, E., Yura, K., Nagai, Y. (2013) Distinct Conformation of ATP Molecule in Solution and on Protein. BIOPHYSICS, 9, 1-12.

2012年

• 由良　敬. (分担翻訳)(2012) 「ヘンダーソン生物学用語辞典」 (生物学用語辞典編集員会)　オーム社.
• 由良　敬. (2012) 巻頭言:境界にいることを楽しもう. 生物物理 52(3), 123.
• 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.
• 由良　敬. (2012) 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 66 (3), 237-239.
• Nagai, Y., Yura, K., Kagawa, H., Wako, H. (2012) Discretized Curvature Analysis for Ribose and Adenine Rings of ATP-Analogs Bound to Myosin, Memoirs of Kokushikan University Center for Information Science, 33, 55-60.

2011年

• 由良　敬. (2011) 埋め草「タンパク質立体構造散歩」の経緯. 生物物理 51(3), 144-145.
• 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.

2010年

• 由良　敬.(分担執筆) (2010) 「タンパク質の立体構造入門:基礎から構造バイオインフォマティクスへ」(藤博幸　編集)第1章 タンパク質構造の基礎、講談社 pp. 1-17.
• 由良　敬. (2010) 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, 48(1), 43-50.

2009年

• Yura, K., Hayward, S.. (2009) The interwinding nature of protein-protein interfaces and its implication for protein complex formation. Bioinformatics, 25(23), 3108-3113.
• 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.
• 由良　敬、郷　通子. (2009) 陸上植物オルガネラのRNA編集の役割. 生物物理, 49(5), 244-245.
• 由良　敬、塩生真史、藤　博幸. (2009) 構造バイオインフォマティクス. 蛋白質 核酸 酵素 (PNE) , 増刊号『融合発展する構造生物学とケミカルバイオロジーの最前線』, 54(12), 1535-1541.
• 倭　剛久、西岡宏任、由良　敬. (2009) 理論計算+生命情報学で初めて見出された機能性残基 -DNA補修酵素の場合―. 生物物理, 49(4), 196-197.
• Kinoshita, K., Kono, H., Yura, K. (2009) 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, pp 159-186.

2008年

• 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.
• 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.
• 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.
• 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.
• 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, 2194-2203.
• Genome Information Integration Project and H-Invitational 2 consortium (Yura, K. is the 75th / 136 authors) (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research, 36, D793-D799.
• Kono, H., Yuasa, T., Nishiue, S., Yura, K. (2008) coliSNP database server mapping nsSNPs on protein structures. Nucleic Acids Research, 36, D409-D413.
• 由良　敬. (2008) 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, 128 (11), 1547-1555.