Laboratory of Molecular Bioinformatics

2026

(1) Original Papers

• Ogasawara, N., Oka, H., Tanaka, M., Gomi, K., Shimizu, M., Kato, M., Nakano, H., and Kojima, T. (2026) Genome-wide characterization of CreA-mediated transcriptional regulation in Aspergillus oryzae under carbon catabolite derepression. Biosci. Biotechnol. Biochem. 90, 99-108. [Oxford Academic]

• Ibi, D., Ishida, K., Kojima, T., Yoshida, S., Suzuki, A., Suzuki, S., Yasui, M., Shibuya, K., Nakanishi, M., Yamagami, T., Saunders, J.M., de la Fuente, Revenga, M., Gonzalez-Maeso, J., Hiramatsu, M. (2026) EGR1-mediated repression of HDAC2 regulates BDNF-dependent kindling development in a mouse model of pentylenetetrazol-induced epilepsy. Pharmacol Biochem Behav. 258, 174131. [ScienceDirect]

2025

(1) Original Papers

• Hayasaka, M., Hamajima, L., Yoshida, Y., Mori, R., Kato, H., Suzuki, H., Tsurigami, R., Kojima, T., Kato, M., and Shimizu, M. (2025) Phenanthrene degradation by a flavoprotein monooxygenase from Phanerodontia chrysosporium. Appl. Environ. Microbiol. 91, e0157424. [ASM Journals]

• Takano, C., Nakashima, K., Aoyagi, H., Kojima, T., and Kawasaki, S. (2025) Metal tolerance and recovery mechanisms of Priestia sp. Mn7 under pH 1.5. Extremophiles 29:37. [Springer]

• Dong, Y., Wainaina, C. M., Kojima, T., and Inukai, Y. (2025) OUR1/OsbZIP1-OsPIN9 regulatory module controls auxin-dependent crown root formation in rice. Front. Plant Sci. 16, 1718647. [frontiers]

(2) Books

• 牛島俊和, 中山敬一／編 羊土社 実験医学別冊 論文図表を読む作法PREMIUM: (Written in Japanese.)
  　[Editorial cooperation]
  　兒島孝明:第8章 シークエンサーなどを用いた網羅的配列解析とその応用 (249-341)
  　[Responsible sections]
  　兒島孝明, 上坂一馬: 8-2 シークエンスデータ総論①（ショートリード：illumina）(252-253),
  　兒島孝明, 上坂一馬: 8-3 シークエンスデータ総論②（ロングリード：Oxford Nanopore）(254-256),
  　兒島孝明, 上坂一馬: 8-4 シークエンスデータ総論③（ロングリード：PacBio）(257-258),
  　牛島俊和, 兒島孝明: 8-11 PCA (272-274),
  　兒島孝明: 8-12 メタジーン解析 (275-276),
  　宮本義孝, 中林一彦, 兒島孝明: 8-13 モチーフ図 (277-278),
  　兒島孝明: 8-25 Accumulation curve (308-309),
  　上坂一馬, 兒島孝明: 8-26 バルクRNA-seq (310-312),
  　兒島孝明: 8-27 MA plot（RNA-seq）(313-314),
  　上坂一馬, 兒島孝明: 9-3 細菌ゲノムアセンブリ(348-349)

2024

(1) Original Papers

• Mizutani, T., Oka, H., Goto, R., Tsurigami, T., Maruyama, J., Shimizu, M., Kato, M., Nakano, H., and Kojima, T. (2024) The Identification of a Target Gene of the Transcription Factor KojR and Elucidation of Its Role in Carbon Metabolism for Kojic Acid Biosynthesis in Aspergillus oryzae. J. Fungi 10, 113. [MDPI]

• Jia, B., Ojima-Kato, T., Kojima, T., and Nakano, H. (2024) Rapid and cost-effective epitope mapping using PURE ribosome display coupled with next-generation sequencing and bioinformatics. J. Biosci. Bioeng. 137, 321-328. [Science Direct]

• Okamoto, M., Sasaki, R., Ikeda, K.,Doi, K., Tatsumi, F., Oshima, K., Kojima, T., Mizushima, S., Ikegami, K., Yoshimura, T., Furukawa, K., Kobayashi, M., Horio, F., and Murai, A.(2024) FcRY is a Key Molecule Controlling Maternal Blood IgY Transfer to Yolks During Egg Development in Avian Species. Front. Immunol. 15, 1305587. [frontiers]

• Hosoda, A., Ito, Y., Kojima, T., Ogata Y., Haga, M., Akimoto Y., Shirasawa, M., and Kishimoto, M. (2024) Impact of electrolyzed water treatment on bacterial communities in food washing processes. Ecol. Genet. Genom. 31, 100244. [Science Direct]

• Oka, H., Kojima, T., Kato, R., Ihara, K., and Nakano, H. (2024) Construction of transcript regulation mechanism prediction models based on binding motif environment of transcription factor AoXlnR in Aspergillus oryzae. J. Bioinform. Comput. Biol. 22, 2450017. [World Scientific]

• Hosoda, A., Mabe, I., Kojima, T., Nakasu, Y., and Niizuma, Y. (2024) The ingestion of microplastics affects the diversity of the gut microbiome and testicular development in Japanese quail. Ecol. Genet. Genom. 33, 100288. [Science Direct]

(2) Book Reviews

• 兒島孝明 (2024) プログラミングはもう怖くない？～ChatGPTとバイオインフォマティクスの接点～ 生物工学会誌 バイオミディア 102, 473 (Written in Japanese.) [J-STAGE]

2023

(1) Original Papers

• Ojima-Kato, T., Yuma Nishikawa, Y., Furukawa, Y., Kojima, T., and Nakano, H. (2023) Nascent MSKIK Peptide Cancels Ribosomal Stalling by Arrest Peptides in Escherichia coli. J. Biol. Chem. 299, 104676. [ScienceDirect]

• Morita, S., Shibata, F.T., Nishiyama, T., Kobayashi, Y., Yamaguchi, K., Toga, K., Ohde, T., Gotoh, H., Kojima, T., Weber, N.J. Salvemini, M., Bino, T., Mase, M., Nakata, M., Mori, T., Mori, S., Cornette, R., Sakura, K., Lavine, C.L., Emlen, J.D. Niimi, T. and Shigenobu, S. (2023) The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation. Sci. Rep. 13, 8735. [nature]

• Mase, K., Mizuno, H., Nakamichi, N., Suzuki, T., Kojima, T., Kamiya, S., Takeuchi, T., Kondo, C., Yamashita, H., Sakaoka, S., Morikami, A., and Tsukagoshi, H. (2023) AtMYB50 regulates root cell elongation by upregulating PECTIN METHYLESTERASE INHIBITOR 8 in Arabidopsis thaliana. PLoS One 18, e0285241.[PLOS ONE]

(2) Reviews

• Takaaki Kojima (2023) Practical know-how for large-scale DNA sequence analysis. Scientific Reports of the Faculty of Agriculture, Meijo University 59, 47−54. (Written in Japanese.) [Scientific Reports of the Faculty of Agriculture, Meijo University]

(3) Books

• 岡大椰, 兒島孝明, 中野秀雄 技術情報協会 タンパク質の構造解析手法とIn silicoスクリーニングへの応用事例 第4章 第1節 バイオインフォマティクスの今後の展望 (Joint authorship) (Written in Japanese.)

2022

(1) Original Papers

• Kawai, T., Shibata, K., Akahoshi, R., Nishiuchi, S., Takahashi, H., Nakazono, M., Kojima, T., Nosaka-Takahashi, M., Sato, Y., Toyoda, A., Lucob-Agustin, N., Kano-Nakata, M., Suralta, R. R., Niones, J. M., Chen, Y., Siddique, K. H. M., Yamauchi, A., and Inukai, Y. (2022) WUSCHEL-related homeobox family genes in rice control lateral root primordium size. Proc Natl Acad Sci U S A. 119, e2101846119. [PNAS]

• Nomura, R., Tsuzuki, S., Kojima, T., Nagasawa, M.,Sato, Y., Uefune, M., Baba, Y. Hayashi, T., Nakano, H., Kato, M., and Shimizu, M. (2022) Administration of Aspergillus oryzae suppresses DSS-induced colitis. Food Chem: Mol. Sci. 4, 100063. [Science Direct]

• Uchida, S., Kojima, T., and Sugino, T. (2022) Frequency and Clinicopathological Characteristics of Patients With KRAS/BRAF Double-Mutant Colorectal Cancer: An In Silico StudyFrequency and Clinicopathological Characteristics of Patients With KRAS/BRAF Double-Mutant Colorectal Cancer: An In Silico Study. Pathol. Oncol. Res. 28, 1610206. [Pathol. Oncol. Res.]

• Kawai, T., Akahoshi, R., Shelley, I. J., Kojima, T., Sato, M., Tsuji, H., and Inukai, Y. (2022) Auxin Distribution in Lateral Root Primordium Development Affects the Size and Lateral Root Diameter of Rice. Front. Plant Sci. 13, 834378. [frontiers]

• Damnjanović, J., Odake, N., Fan, J., Camagna, M., Jia, B., Kojima, T., Nemoto, N., Hitomi, K., and Nakano, H. (2022) Comprehensive analysis of transglutaminase substrate preference by cDNA display coupled with next-generation sequencing and bioinformatics. Sci. Rep. 12, 13578. [nature]

(2) Reviews

• Uesaka, K., Oka, H., Kato, R., Kanie, K., Kojima, T., Tsugawa, H., Toda, Y., and Horinouchi, T. (2022) Bioinformatics in bioscience and bioengineering: Recent advances, applications, and perspectives. J. Biosci. Bioeng. 134, 363-373. [Science Direct]

(3) Books

• 牛島俊和, 中山敬一／編 羊土社 実験医学別冊 論文図表を読む作法: (Written in Japanese.)
  　[Editorial cooperation]
  　兒島孝明:第7章 NGSなどを用いた網羅的解析 (191-258)
  　[Responsible sections]
  　牛島俊和, 兒島孝明: 7-7 PCA (206-208),
  　兒島孝明: 7-8 メタジーン解析 (209-210),
  　宮本義孝, 中林一彦, 兒島孝明: 7-9 モチーフ図 (211-212),
  　兒島孝明: 7-18 Accumulation curve (236-237),
  　兒島孝明: 7-19 MA plot（RNA-seq）(238-239)