Publications

2017

<Original Paper>

Takato S., Kakei Y., Mitsui M., Ishida Y., Suzuki M., Yamazaki C., Hayashi K., Ishii T., Fujioka S., Nakamura A., Soeno K., Shimada Y. (2017)
Auxin signaling through SCFTIR1/AFBs mediates feedback regulation of IAA biosynthesis
Bioscience, Biotechnology, and Biochemistry, Volume 81, Issue 5, Pages 1-7, doi:10.1080/09168451.2017.1313694<<FullText

Nakamura A., Tochio N., Fujioka S., Ito S., Kigawa T., Shimada Y., Matsuoka M., Yoshida S., Kinoshita T., Asami T., Seto H., Nakano T. (2017)
Molecular actions of two synthetic brassinosteroids, iso-carbaBL and 6-deoxoBL, which cause altered physiological activities between Arabidopsis and rice
PLoS ONE 12(4): e0174015.<<<FullText

Kakei Y., Nakamura A., Yamamoto M., Ishida Y., Yamazaki C., Sato A.,  Narukawa-Nara M., Soeno K.,  Shimada Y. (2017)
Biochemical and Chemical Biology Study of Rice OsTAR1 Revealed that Tryptophan Aminotransferase is Involved in Auxin Biosynthesis: Identification of a Potent OsTAR1 Inhibitor, Pyruvamine2031
Plant & Cell Physiology, 30 January. doi:10.1093. <<<FullText

2016

<Original Paper>

Narukawa-Nara M., Nakamura A., Kikuzato K., Kakei Y., Sato A., Mitani Y., Yamasaki-Kokudo Y., Ishii T., Hayashi KI., Asami T., Ogura T., Yoshida S., Fujioka S., Kamakura T., Kawatsu T., Tachikawa M., Soeno K., Shimada Y. (2016)
Aminooxy-naphthylpropionic acid and its derivatives are inhibitors of auxin biosynthesis targeting Trp aminotransferase: Structure-activity relationships.
The Plant Journal, May 4. doi:10.1111/tpj.13197. <<Abstract

<Review>
筧 雄介, 嶋田幸久 (2016)
AtCAST〜シロイヌナズナの発展型トランスクリプトームデータ解析ツール.
化学と生物, 54(6):371-466 <<Abstract

2015

<Original Paper>

Kakei Y., Yamazaki C., Suzuki M., Nakamura A., Sato A., Ishida Y., Kikuchi R., Higashi S., Kokudo Y., Ishii T., Soeno K., Shimada Y. (2015)
Small molecule auxin inhibitors that target YUCCA are powerful tools for studying auxin function.
The Plant Journal, doi:10.1111/tpj.13032 <<Abstract

Kakei Y., Mochida K., Sakurai T., Yoshida T., Shinozaki K., Shimada Y. (2015)
Transcriptome analysis of hormone-induced gene expression in Brachypodium distachyon.
Scientific Reports, 5:14476, doi:10.1038/srep14476 <<Abstract

Suzuki M., Yamazaki C., Mitsui M., Kakei Y., Mitani Y., Nakamura A., Ishii T., Soeno K., Shimada Y. (2015)
Transcriptional feedback regulation of YUCCA genes in response to auxin levels in Arabidopsis.
Plant Cell Reports, 34(8):1343-1352, doi:10.1007/s00299-015-1791-z <<Abstract

Kakei Y., Shimada Y. (2015)
AtCAST3.0 Update: A web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles.
Plant and Cell Physiology, (1):e7, doi:10.1093/pcp/pcu174 <<Abstract

<Book>
嶋田幸久, 菅原雅嗣 (2015)
『植物の体の中では何が起こっているのか』ベレ出版, ISBN:978-4-86064-422-2

2014

<Original Paper>

Yoshizawa E., Kaizuka M., Yamagami A., Higuchi-Takeuchi M., Matsui M., Kakei Y., Shimada Y., Sakuta M., Osada H., Asami T., Nakano T. (2014)
BPG3 is a novel chloroplast protein that involves the greening of leaves and related to brassinosteroid signaling.
Bioscience, Biotechnology, and Biochemistry, doi:10.1080/09168451.2014.885831 <<Abstract

Higashide T., Narukawa M., Shimada Y., Soeno K. (2014)
Suppression of Elongation and Growth of Tomato Seedlings by Auxin Biosynthesis Inhibitors and Modeling of the Growth and Environmental Response.
Scientific Reports, doi:4:4556 :10.1038/srep04556 <<Abstract

Ishida Y., Hayashi K., Soeno K., Asami T., Nakamura S., Suzuki M., Nakamura A., Shimada Y. (2014)
Analysis of a putative auxin biosynthesis inhibitor, Indole-3-oxoethylphosphonic Acid,
in Arabidopsis.
Bioscience, Biotechnology, and Biochemistry, doi:10.1080/09168451.2014.877183 <<Abstract

2013

<Original Paper>

Mishiba K., Nagashima Y., Suzuki E., Hayashi N., Ogata Y., Shimada Y., Koizumi N. (2013)
Defects in IRE1 enhance cell death and fail to degrade mRNAs of secretory pathway proteins in the Arabidopsis unfolded protein response.
Proc. Natl. Acad. Sci. USA, doi:10.1073/pnas.1219047110 <<Abstract

Ishida Y., Nakamura A., Mitani Y., Suzuki M., Soeno K., Asami T., Shimada Y. (2013)
Comparison of indole derivatives as potential intermediates of auxin biosynthesis in Arabidopsis.
Plant Biotechnology, 30:No.2 185-190, doi:10.5511/plantbiotechnology.13.0128c <<Abstract

Sasaki E., Ogura T., Takei K., Kojima M., Kitahata N., Sakakibara H., Asami T.,  Shimada Y. (2013)
Uniconazole, a cytochrome P450 inhibitor, inhibits trans-zeatin biosynthesis in Arabidopsis,
Phytochemirstry, 87:30-38, doi:10.1016/j.phytochem.2012.11.023. <<Full Text

2012

<Original Paper>

Hayashi K., Kepinski S., Hirose M., Kuboki A., Shimada Y., Nozaki H. (2012)
Rational Design of Auxin Antagonist of the SCFTIR1 auxin receptor complex.
ACS Chemical Biology, 16;7(3):590-8, doi:10.1021/cb200404c <<Abstract

Okamoto M., Tsuboi Y., Goda H., Shimada Y., Hirayama T. (2012)
Transcriptomic analysis of double hormone treatments revealed a novel relation among ABA, SA and JA actions in Arabidopsis cultured cell Multiple hormone treatment revealed novel cooperative relationships between abscisic acid and biotic stress hormones in cultured cells.
Plant Biotech, 29:19-34, doi:10.5511/plantbiotechnology.11.1130a <<Article

2011

<Original Papers>

Stotz H. U., Sawada Y., Shimada Y., Hirai  M. Y., Sasaki E., Krischke M., Brown P. D., Saito K., Kamiya Y. (2011)
Role of camalexin, indole glucosinolates, and side chain modification of glucosinolate-derived isothiocyanates in defense of Arabidopsis against Sclerotinia sclerotiorum.
The Plant Journal, 67(1):81-93, doi:10.1111/j.1365-313X.2011.04578.x<<Abstract

Stotz H. U., Jikumaru Y., Shimada Y., Sasaki E., Stingl N., Mueller MJ, Kamiya Y. (2011)
Jasmonate-dependent and COI1-independent defense responses against Sclerotinia sclerotiorum in Arabidopsis thaliana: auxin is part of COI1-independent defense signaling.
Plant Cell Physiol, 52(11):1941-56, doi: 10.1093/pcp/pcr127 <<Abstract

Nagashima Y., Mishiba K., Suzukia E., Shimada Y, Iwata Y., Koizumi N. (2011)
Arabidopsis IRE1 catalyses unconventional splicing of bZIP60 mRNA to produce the active transcription factor.
Scientific Reports, 1:29, doi:10.1038/srep00029 <<Article

Sakamoto T., Kawabe A., Tokida-Segawa A., Shimizu B., Takatsuto S., Shimada Y., Fujioka S., Mizutani M. (2011)
Rice CYP734As function as multisubstrate and multifunctional enzymes in brassinosteroid catabolism.
The Plant Journal, 67(1):1-12, doi: 10.1111/j.1365-313X.2011.04567.x <<Abstract

Sasaki E., Takahashi C., Asami T., Shimada Y. (2011)
AtCAST, a tool for exploring gene expression similarities among DNA microarray experiments using networks.
Plant Cell Physiol, 52(1):169-80, doi: 10.1093/pcp/pcq185 <<Abstract

2010

<Original Papers>

Ishii T., Soeno K., Asami T., Fujioka S., Shimada Y. (2010) Arabidopsis seedlings over-accumulated indole-3-acetic acid in response to aminooxyacetic acid.
Bioscience, Biotechnology, and Biochemistry, 74(11):2345-7 <<Abstract

Soeno K., Goda H., Ishii T., Ogura T., Tachikawa T., Sasaki E., Yoshida S., Fujioka S., Asami T., Shimada Y. (2010)
Auxin-biosynthesis inhibitors, identified by genomics-based approach, provide insights into auxin biosynthesis.
Plant Cell Physiol, 51(4):524-36, doi: 10.1093/pcp/pcq032 (Rapid Paper, Editor-in-chief’s choice) <<Abstract

Matsuda F., Hirai MY., Sasaki E., Akiyama K., Yonekura-Sakakibara K., Provart NJ., Sakurai T., Shimada Y., Saito K. (2010)
AtMetExpress development: phytochemical atlas of Arabidopsis development.
PlantPhysiology, 152(2):566-78, doi: 10.1104/pp.109.148031 <<Abstract

<Book>
Sasaki E., Asami T., Shimada Y. (2010)
AtGenExpress, the first large-scale transcriptome data set in Arabidopsis: project summary and its practical applications.
Advances in genetics research. 2:197-211, NOVA, NewYork

<Review>
林謙一郎, 嶋田幸久 (2010)
植物機能制御剤の探索・創製とその生理学,化学遺伝学への応用2 オーキシン:その代謝・輸送・情報伝達経路を制御するケミカルツール.
化学と生物, 48: 485-492

2009

<Original Papers>

Mashiguchi K., Sasaki E., Shimada Y., Nagae M., Ueno K., Nakano T., Yoneyama K., Suzuki Y., Asami T. (2009)
Feedback-Regulation of Strigolactone Biosynthetic Genes and Strigolactone-Regulated Genes in Arabidopsis.
Bioscience, Biotechnology, and Biochemistry, 73(11):2460-5 <<Abstract

2008

<Original Papers>

Akiyama K., Chikayama E., Yuasa H., Shimada Y., Tohge T., Shinozaki K., Hirai M., Sakurai T., Kikuchi J., Saito K. (2008)
PRIMe: a Web site that assembles tools for metabolomics and transcriptomics.
In Silico Biology, 8(3-4):339-45 <<FullText

Goda H., Sasaki E., Akiyama K., Maruyama-Nakashita A., Nakabayashi K., Li W., Ogawa M., Yamauchi U., Preston J., Aoki K., Kiba T., Takatsuto S., Fujioka S., Asami T., Nakano T., Kato H., Mizuno T., Sakakibara H., Yamaguchi S., Nambara E., Kamiya Y., Takahashi H., Hirai MY., Sakurai T., Shinozaki K., Saito K., Yoshida S., Shimada Y. (2008)
The AtGenExpress hormone- and chemical-treatment data set: Experimental design, data evaluation, model data analysis, and data access.
The Plant Journal, 55(3):526-42, doi: 10.1111/j.0960-7412.2008.03510.x<<Abstract

<Review>
佐々木江理子, 嶋田幸久 (2008)
モデル植物の遺伝子発現データベースとホルモン研究.
バイオサイエンスとバイオインダストリー, 66(7): 352-358