KOMICS

The Kazusa Metabolomics Portal

2017

Akimoto N, Ara T, Nakajima D, Suda K, Ikeda C, Takahashi S, Muneto R, Yamada M, Suzuki H, Shibata D, Sakurai N
FlavonoidSearch: A system for comprehensive flavonoid annotation by mass spectrometry
Sci Rep 2017 7: 1243
Narise T, Sakurai N, Obayashi T, Ohta H, Shibata D
Co-expressed Pathways DataBase for Tomato: a database to predict pathways relevant to a query gene
BMC Genomics 2017 18:437

2016

Yamamoto N, Kudo T, Fujiwara S, Takatsuka Y, Hirokawa Y, Tsuzuki M, Takano T, Kobayashi M, Suda K, Asamizu E, Yokoyama K, Shibata D, Tabata S, Yano K
Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae
Plant Cell Physiol 2016 57: e6
Araki T, Saga Y, Marugami M, Otaka J, Araya H, Saito K, Yamazaki M, Suzuki H, Kushiro T
Onocerin biosynthesis requires two highly dedicated triterpene cyclases in a fern Lycopodium clavatum
Chembiochem 2016 17 (4): 288-290
Hirata H, Ohnishi T, Tomida K, Ishida H, Kanda M, Sakai M, Yoshimura J, Suzuki H, Ishikawa T, Dohra H, Watanabe N
Seasonal induction of alternative principal pathway for rose flower scent
Sci Rep 2016 6: 20234
Tsukagoshi Y, Suzuki H, Seki H, Muranaka T, Ohyama K, Fujimoto Y
Ajuga Δ24-sterol reductase catalyzes the direct reductive conversion of 24-methylenecholesterol to campesterol
J Biol Chem 2016 291 (15): 8189-8198
Sakamori K, Ono N, Ihara M, Suzuki H, Matsuura H, Tanaka K, Ohta D, Kanaya S, Matsuda K
Selective regulation of pyrethrin biosynthesis by the specific blend of wound induced volatiles in Tanacetum cinerariifolium
Plant Signal Behav 2016 11 (4): e1149675
Tsukagoshi Y, Ohyama K, Seki H, Akashi T, Muranaka T, Suzuki H, Fujimoto Y
Functional characterization of CYP71D443, a cytochrome P450 catalyzing C-22 hydroxylation in the 20-hydroxyecdysone biosynthesis of Ajuga hairy roots
Phytochemistry 2016 127: 23-28
Rai A, Yamazaki M, Takahashi H, Nakamura M, Kojoma M, Suzuki H, Saito K
RNA-seq transcriptome analysis of Panax japonicus, and its comparison with other Panax species to identify potential genes involved in the saponins biosynthesis
Front Plant Sci 2016 7: 481
Hori K, Nobusawa T, Watanabe T, Madoka Y, Suzuki H, Shibata D, Shimojima M, Ohta H
Tangled evolutionary processes with commonality and diversity in plastidial glycolipid synthesis in photosynthetic organisms
Biochim Biophys Acta 2016 1861 (9 Pt B): 1294-1308
Koeduka T, Kajiyama M, Suzuki H, Furuta T, Tsuge T, Matsui K
Benzenoid biosynthesis in the flowers of Eriobotrya japonica: molecular cloning and functional characterization of p-methoxybenzoic acid carboxyl methyltransferase
Planta 2016 244 (3): 725-736
Rai A, Nakamura M, Takahashi H, Suzuki H, Saito K, Yamazaki M
High-throughput sequencing and de novo transcriptome assembly of Swertia japonica to identify genes involved in the biosynthesis of therapeutic metabolites
Plant Cell Rep 2016 35 (10): 2091-2111
Koeduka T, Kajiyama M, Furuta T, Suzuki H, Tsuge T, Matsui K
Characterization of an O-methyltransferase specific to guaiacol-type benzenoids from the flowers of loquat (Eriobotrya japonica)
J Biosci Bioeng 2016 122 (6): 679-684
Nakato J, Aoki H, Iwakura H, Suzuki H, Kanamoto R, Ohinata K
Soy-ghretropin, a novel ghrelin-releasing peptide derived from soy protein
FEBS Lett 2016 590 (16): 2681-2689
Rai A, Kamochi H, Suzuki H, Nakamura M, Takahashi H, Hatada T, Saito K, Yamazaki M
De novo transcriptome assembly and characterization of nine tissues of Lonicera japonica to identify potential candidate genes involved in chlorogenic acid, luteolosides, and secoiridoid biosynthesis pathways
J Nat Med 2016 71 (1): 1-15
Maravi DK, Kumar S, Sharma PK, Kobayashi Y, Goud VV, Sakurai N, Koyama H, Sahoo L
Ectopic expression of AtDGAT1, encoding diacylglycerol O-acyltransferase exclusively committed to TAG biosynthesis, enhances oil accumulation in seeds and leaves of Jatropha
Biotechnol Biofuels 2016 9: 226
Udomsom N, Rai A, Suzuki H, Okuyama J, Imai R, Mori T, Nakabayashi R, Saito K, Yamazaki M
Function of AP2/ERF transcription factors involved in the regulation of specialized metabolism in Ophiorrhiza pumila revealed by transcriptomics and metabolomics
Front Plant Sci 2016 7: 1861
Hashioka S, Suzuki H, Nakajima D, Miyaoka T, Wake R, Hayashida M, Horiguchi J, Andis Klegeris A
Metabolomics analysis implies noninvolvement of the kynurenine pathway neurotoxins in the interferon-β-induced neurotoxicity of adult human astrocytes Neuropsychiatry
Neuropsychiatry (London) 2017 7(2): 156-163
Fukushima A, Nakamura M, Suzuki H, Yamazaki M, Knoch E, Mori T, Umemoto N, Morita M, Hirai G, Sodeoka M, Saito K
Comparative characterization of the leaf tissue of Physalis alkekengi and Physalis peruviana using RNA-seq and metabolite profiling
Front Plant Sci 2016 7: 1883
Tamura K, Seki H, Suzuki H, Kojoma M, Saito K, Muranaka T
CYP716A179 functions as a triterpene C-28 oxidase in tissue-cultured stolons of Glycyrrhiza uralensis
Plant Cell Rep 2016 36(3): 437-445
Yamamoto N, Ara T, Sakurai N, Tsugane T, Suzuki H, Shibata D
An improved MatchedIonsFinder algorithm for refining ion feature assignments among chromatograms in liquid chromatography-mass spectrometry
Journal of Life Sciences and Technologies 2016 4 (2): 75-78

2015

Sato M, Sakurai N, Suzuki H, Shibata D, Kino K
Enzymatic carboxylation of hydroxystilbenes by the γ-resorcylic acid decarboxylase from Rhizobium radiobacter WU-0108 under reverse reaction conditions
Journal of Molecular Catalysis B: Enzymatic 2015 122: 348-352
Takahashi H, Kamakari K, Goto T, Hara H, Mohri S, Suzuki H, Shibata D, Nakata R, Inoue H, Takahashi N, Kawada T
9-oxo-10(E),12(Z),15(Z)-octadecatrienoic acid activates peroxisome proliferator-activated receptor α in hepatocytes
Lipids 2015 50 (11): 1083-1091
Hirose Y, Suda K, Liu YG, Sato S, Nakamura Y, Yokoyama K, Yamamoto N, Hanano S, Takita E, Sakurai N, Suzuki H, Nakamura Y, Kaneko T, Yano K, Tabata S, Shibata D
The Arabidopsis TAC position viewer: a high-resolution map of transformation-competent artificial chromosome (TAC) clones aligned with the Arabidopsis thaliana Columbia-0 genome
Plant J 2015 83 (6): 1114-1122
Han R, Takahashi H, Nakamura M, Bunsupa S, Yoshimoto N, Yamamoto H, Suzuki H, Shibata D, Yamazaki M, Saito K
Transcriptome analysis of nine tissues to discover genes involved in the biosynthesis of active ingredients in Sophora flavescens
Biol Pharm Bull 2015 38 (6): 876-883
Han R, Takahashi H, Nakamura M, Yoshimoto N, Suzuki H, Shibata D, Yamazaki M, Saito K
Transcriptomic landscape of Pueraria lobata demonstrates potential for phytochemical study
Front Plant Sci 2015 6:426
Suzuki M, Nakabayashi R, Ogata Y, Sakurai N, Tokimatsu T, Goto S, Suzuki M, Jasinski M, Martinoia E, Otagaki S, Matsumoto S, Saito K, Shiratake K
Multi omics in grape berry skin revealed specific induction of the stilbene synthetic pathway by ultraviolet-C irradiation
Plant Physiol 2015 168 (1): 47-59
Ara T, Enomoto M, Arita M, Ikeda C, Kera K, Yamada M, Nishioka T, Ikeda T, Nihei Y, Shibata D, Kanaya S, Sakurai N
Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses
Front Bioeng Biotechnol 2015 3:38
Kim YI, Mohri S, Hirai S, Lin S, Goto T, Ohyane C, Sakamoto T, Takahashi H, Shibata D, Takahashi N, Kawada T
Tomato extract suppresses the production of proinflammatory mediators induced by interaction between adipocytes and macrophages
Biosci Biotechnol Biochem 2015 79 (1): 82-87
Takahashi H, Hara H, Goto T, Kamakari K, Wataru N, Mohri S, Takahashi N, Suzuki H, Shibata D, Kawada T
13-oxo-9(Z),11(E),15(Z)-octadecatrienoic acid activates peroxisome proliferator-activated receptor γ in adipocytes
Lipids 2015 50 (1): 3-12
Takahashi H, Goto T, Yamazaki Y, Kamakari K, Hirata M, Suzuki H, Shibata D, Nakata R, Inoue H, Takahashi N, Kawada T
Metabolomics reveal 1-palmitoyl lysophosphatidylcholine production by peroxisome proliferator-activated receptor α
J Lipid Res 2015 56 (2): 254-265

2014

Mano J, Khorobrykh S, Matsui K, Iijima Y, Sakurai N, Suzuki H, Shibata D
Acrolein is formed from trienoic fatty acids in chloroplast: A targeted metabolomics approach
Plant Biotechnology 2014 31: 535–543
Ragamustari SK, Masaomi Yamamura M, Ono E, Hattori T, Suzuki S, Suzuki H, Shibata D, Umezawa T
Substrate-enantiomer selectivity of matairesinol O-methyltransferases
Plant Biotechnology 2014 31: 257–267
Miyashita T, Okamura T, Iijima Y, Suzuki H, Shibata D, Takaya Y, Tanaka H, Etoh H
(S)-3-Amino-1-ethylglutarimide from green tea (Camellia sinensis)
Studies in Science and Technology 2014 3 (1): 45-48
Reuscher S, Akiyama M, Yasuda T, Makino H, Aoki K, Shibata D, Shiratake K
The sugar transporter inventory of tomato: genome-wide identification and expression analysis
Plant Cell Physiol 2014 55 (6): 1123-1141
Sugimoto K, Matsui K, Iijima Y, Akakabe Y, Muramoto S, Ozawa R, Uefune M, Sasaki R, Alamgir KM, Akitake S, Nobuke T, Galis I, Aoki K, Shibata D, Takabayashi J
Intake and transformation to a glycoside of (Z)-3-hexenol from infested neighbors reveals a mode of plant odor reception and defense
Proc Natl Acad Sci U S A 2014 111 (19): 7144-7149
Singh DK, Calviño M, Brauer EK, Fernandez-Pozo N, Strickler S, Yalamanchili R, Suzuki H, Aoki K, Shibata D, Stratmann JW, Popescu GV, Mueller LA, Popescu SC
The tomato kinome and the tomato kinase library ORFeome: novel resources for the study of kinases and signal transduction in tomato and solanaceae species
Mol Plant Microbe Interact 2014 27 (1): 7-17
Maruyama K, Urano K, Yoshiwara K, Morishita Y, Sakurai N, Suzuki H, Kojima M, Sakakibara H, Shibata D, Saito K, Shinozaki K, Yamaguchi-Shinozaki K
Integrated analysis of the effects of cold and dehydration on rice metabolites, phytohormones, and gene transcripts
Plant Physiology 2014 64 (4): 1759-1771
Aoki Y, Takahashi S, Takayama D, Ogata Y, Sakurai N, Suzuki H, Asawatreratanakul K, Wititsuwannakul D, Wititsuwannakul R, Shibata D, Koyama T, Nakayama T
Identification of laticifer-specific genes and their promoter regions from a natural rubber producing plant Hevea brasiliensis
Plant Sci 2014 225: 1-8
Kera K, Ogata Y, Ara T, Nagashima Y, Shimada N, Sakurai N, Shibata D, Suzuki H
ShiftedIonsFinder: A standalone Java tool for finding peaks with specified mass differences by comparing mass spectra of isotope-labeled and unlabeled data sets
Plant Biotechnology 2014 31: 269-274
Sakurai N, Ara T, Enomoto M, Motegi T, Morishita Y, Kurabayashi A, Iijima Y, Ogata Y, Nakajima D, Suzuki H, Shibata D
Tools and Databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data
BioMed Research International 2014, Volume 2014: 194812

2013

Koeduka T, Suzuki S, Iijima Y, Ohnishi T, Suzuki H, Watanabe B, Shibata D, Umezawa T, Pichersky E, Hiratake J
Enhancement of production of eugenol and its glycosides in transgenic aspen plants via genetic engineering
Biochem Biophys Res Commun 2013 436 (1): 73-78
Asano T, Kobayashi K, Kashihara E, Sudo H, Sasaki R, Iijima Y, Aoki K, Shibata D, Saito K, Yamazaki M
Suppression of camptothecin biosynthetic genes results in metabolic modification of secondary products in hairy roots of Ophiorrhiza pumila
Phytochemistry 2013 91: 128-139
Nakashima A, von Reuss SH, Tasaka H, Nomura M, Mochizuki S, Iijima Y, Aoki K, Shibata D, Boland W, Takabayashi J, Matsui K
Traumatin- and dinortraumatin-containing galactolipids in Arabidopsis: their formation in tissue-disrupted leaves as counterparts of green leaf volatiles
J Biol Chem 2013 288 (36): 26078-26088
Takita E, Kohda K, Tomatsu H, Hanano S, Moriya K, Hosouchi T, Sakurai N, Suzuki H, Shinmyo A, Shibata D
Precise sequential DNA ligation on a solid substrate: solid-based rapid sequential ligation of multiple DNA molecules
DNA Research 2013 20 (6): 583-592
Takahashi H, Suzuki H, Suda K, Yamazaki Y, Takino A, Kim YI, Goto T, Iijima Y, Aoki K, Shibata D, Takahashi N, Kawada T
Long-chain free fatty acid profiling analysis by liquid chromatography-mass spectrometry in mouse treated with peroxisome proliferator-activated receptor α agonist
Biosci Biotechnol Biochem 2013 77 (11): 2288-2293
Reuscher S, Akiyama M, Mori C, Aoki K, Shibata D, Shiratake K
Genome-wide identification and expression analysis of aquaporins in tomato
PLoS One 2013 8 (11): e79052
Mannen K, Matsumoto T, Takahashi S, Yamaguchi Y, Tsukagoshi M, Sano R, Suzuki H, Sakurai N, Shibata D, Koyama T, Nakayama T
Coordinated transcriptional regulation of isopentenyl diphosphate biosynthetic pathway enzymes in plastids by phytochrome-interacting factor 5
Biochem Biophys Res Commun 2013 443 (2): 768-774
Iijima Y, Watanabe B, Sasaki R, Takenaka M, Ono H, Sakurai N, Umemoto N, Suzuki H, Shibata D, Aoki K
Steroidal glycoalkaloid profiling and structures of glycoalkaloids in wild tomato fruit
Phytochemistry 2013 95: 145-157
Kato M, Kamoi T, Sasaki R, Sakurai N, Aoki K, Shibata D, Imai S
Structures and reactions fo compounds involved in pink discolouration of onion
Food Chemistry 2013 139(1-4): 885-892
Yu X, Kikuchi A, Matsunaga E, Morishita Y, Nanto K, Sakurai N, Suzuki H, Shibata D, Shimada T, Watanabe KN
The Choline Oxidase Gene codA Confers Salt Tolerance to Transgenic Eucalyptus globulus in a Semi-Confined Condition
Molecular Biotechnology 2013 54(2): 320-330
Sakurai N, Ara T, Kanaya S, Nakamura Y, Iijima Y, Enomoto M, Motegi T, Aoki K, Suzuki H, Shibata D
Application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values
Bioinformatics 2013 29 (2): 290-291

2012

Kamimoto Y, Terasaka K, Hamamoto M, Takanashi K, Fukuda S, Shitan N, Sugiyama A, Suzuki H, Shibata D, Wang B, Pollmann S, Geisler M, Yazaki K.
Arabidopsis ABCB21 is a facultative auxin im/exporter regulated by cytoplasmic auxin concentration
Plant Cell Physiol 2012 53(12): 2090-2100
Noutoshi Y, Okazaki M, Kida T, Nishina Y, Morishita Y, Ogawa T, Suzuki H, Shibata D, Jikumaru Y, Hanada A, Kamiya Y, Shirasu K
Novel Plant Immune-Priming Compounds Identified via High-Throughput Chemical Screening Target Salicylic Acid Glucosyltransferases in Arabidopsis
Plant Cell 2012 24(9): 3795-3804
The Tomato Genome Consortium
The tomato genome sequence provides insights into fleshy fruit evolution
Nature 2012 485(7400): 635-641
Suzuki N, Uefuji H, Nishikawa T, Mukai Y, Yamashita A, Hattori M, Ogasawara N, Bamba T, Fukusaki E, Kobayashi A, Ogata Y, Sakurai N, Suzuki H, Shibata D, Nakazawa Y
Construction and analysis of EST libraries of the trans-polyisoprene producing plant, Eucommia ulmoides Oliver
Planta 2012 Jun 26 (Epub)
Asano T, Kobayashi K, Kashihara E, Sudo H, Sasaki R, Iijima Y, Aoki K, Shibata D, Saito K, Yamazaki M
Suppression of camptothecin biosynthetic genes results in metabolic modification of secondary products in hairy roots of Ophiorrhiza pumila
Phytochemistry 2012 May 29 (Epub)
Sano R, Ara T, Akimoto N, Sakurai N, Suzuki H, Fukuzawa Y, Kawamitsu Y, Ueno M, and Shibata D
Dynamic metabolic changes during fruit maturation in Jatropha curcas L.
Plant Biotechnology 2012, 29 (2): 175-178
Sakurai N, Ogata Y, Ara T, Sano R, Akimoto N, Hiruta A, Suzuki H, Kajikawa M, Widyastuti U, Suharsono S, Yokota A, Akashi K, Kikuchi J, and Shibata D
Development of KaPPA-View4 for omics studies on Jatropha and a database system KaPPA-Loader for construction of local omics databases
Plant Biotechnology 2012, 29, 131-135
Takanashi K, Takahashi H, Sakurai N, Sugiyama A, Suzuki H, Shibata D, Nakazono M, Yazaki K
Tissue-specific transcriptome analysis in nodules of Lotus japonicus
Molecular Plant-Microbe Interactions 2012, 25 (7): 869-876
Ogawa Y, Nozomu Sakurai N, Oikawa A, Suzuki H, Aoki K, Ohta D, Saito K, and Shibata D
High-throughput cryopreservation of plant cell cultures for functional genomics
Plant Cell Physiol 2012, 53 (5), 943-952
Young-il Kim, Shizuka Hirai, Tsuyoshi Goto, Chie Ohyane, Haruya Takahashi, Taneaki Tsugane, Chiaki Konishi, Takashi Fujii, Shuji Inai, Yoko Iijima, Koh Aoki, Daisuke Shibata, Nobuyuki Takahashi, and Teruo Kawada
Potent PPAR alpha Activator Derived from Tomato Juice, 13-oxo-9,11-Octadecadienoic Acid, Decreases Plasma and Hepatic Triglyceride in Obese Diabetic Mice
PLoS One 2012, 7 (2), e31317
Saga H, Ogawa T, Kai K, Suzuki H, Ogata Y, Sakurai N, Shibata D, and Ohta D
Identification and characterization of ANAC042, a transcription factor family gene involved in the regulation of camalexin biosynthesis in Arabidopsis
Mol Plant Microbe Interact 2012 25 (5) 684-696
Naoki Yamamoto, Tatsuya Suzuki, Takeshi Ara1, Nozomu Sakurai, Sayaka Shinpo, Yoshihiko Morishita, Ryosuke Sasaki, Taneaki Tsugane, Hideyuki Suzuki and Daisuke Shibata
MatchedIonsFinder: A software tool for revising alignment matrices of spectrograms from liquid chromatography-mass spectrometry
Plant Biotechnology 2012, 29 (1), 109-113
Matsunaga E, Nanto K, Oishi M, Ebinuma H, Morishita Y, Sakurai N, Suzuki H, Shibata D, and Shimada T
Agrobacterium-mediated transformation of Eucalyptus globulus using explants with shoot apex with introduction of bacterial choline oxidase gene to enhance salt tolerance
Plant Cell Rep 2012, 31 (1), 225-235

2011

Furuta K, Kubo M, Sano K, Demura T, Fukuda H, Liu YG, Shibata D, Kakimoto T
The CKH2/PKL chromatin remodeling factor negatively regulates cytokinin responses in Arabidopsis calli
Plant Cell Physiol 2011, 52 (4), 618-628
Kubo M, Furuta K, Demura T, Fukuda H, Liu YG, Shibata D, Kakimoto T
The CKH1/EER4 gene encoding a TAF12-like protein negatively regulates cytokinin sensitivity in Arabidopsis thaliana
Plant Cell Physiol 2011, 52 (4), 629-637
Nakashima A, Iijima Y, Aoki K, Shibata D, Sugimoto K, Takabayashi J, and Matsui T
Monogalactosyl diacylglycerol is a substrate for lipoxygenase: its implications for oxylipin formation directly from lipids
J. Plant Interactions 2011, 6, 93-97
Takahashi H, Kim YI, Hirai S, Goto T, Ohyane C, Tsugane T, Konishi C, Fujii T, Inai S, Iijima Y, Aoki K, Shibata D, Takahashi N, Kawada T
Comparative and stability analyses of 9- and 13-Oxo-octadecadienoic acids in various species of tomato
Biosci Biotechnol Biochem 2011, 75 (8), 1621-1624
Kim, Y-I., Hirai S., Takahashi H., Goto T., Ohyane C., Tsugane T., Konishi C., Fujii T., Inai S., Iijima Y., Aoki. K., Shibata, D., Takahashi, N., and Kawada, T
9-oxo-10(E),12(E)-Octadecadienoic acid derived from tomato is a potent PPAR alpha agonist to decrease triglyceride accumulation in mouse primary hepatocytes
Mol Nutr Food Res 2011, 55 (4), 585-593
Ogata Y, Suzuki H
Plant expressed sequence tags databases: practical uses and the improvement of their searches using network module analysis
Plant Biotechnol 2011, 28 (4), 351-360
Yamamura, M., Wada, S., Sakakibara, N., Nakatsubo, T., Suzuki, S., Hattori, T., Takeda, M., Sakurai, N., Suzuki, H., Shibata, D., Umezawa, T
Occurrence of Guaiacyl/p-Hydroxyphenyl Lignin in Arabidopsis thaliana T87 Cells
Plant Biotechnol 2011, 28 (1), 1-8
Suzuki, S., Suda, K., Sakurai, N., Ogata, Y., Hattori, T., Suzuki, H., Shibata, D., Umezawa, T
Analysis of expressed sequence tags in developing secondary xylem and shoot of Acacia mangium
J Wood Sci 2011, 57 (1), 40-46
Sakurai N, Ara T, Ogata Y, Sano R, Ohno T, Sugiyama K, Hiruta A, Yamazaki K, Yano K, Aoki K, Aharoni A, Hamada K, Yokoyama, Kawamura S, Otsuka H, Tokimatsu T, Kanehisa M, Suzuki H, Saito K and Shibata D
KaPPA-View4: A metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data
Nucleic Acids Res. 2011, 39, D677-684

2010

Ozaki S, Ogata Y, Suda K, Kurabayashi A, Suzuki T, Yamamoto N, Iijima Y, Tsugane T, Fujii T, Konishi C, Inai S, Bunsupa S, Yamazaki M, Shibata D, Aoki K
Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module
DNA Res. 2010, 17(2), 105-116
Aoki K, Yano K, Suzuki A, Kawamura S, Sakurai N, Suda K, Kurabayashi A, Suzuki T, Tsugane T, Watanabe M, Ooga K, Torii M, Narita T, Shin-I T, Kohara Y, Yamamoto N, Takahashi H, Watanabe Y, Egusa M, Kodama M, Ichinose Y, Kikuchi M, Fukushima S, Okabe A, Arie T, Sato Y, Yazawa K, Satoh S, Omura T, Ezura H, Shibata D
Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics
BMC Genomics. 2010, 11, 210
Ogata Y, Suzuki H, Sakurai N, Shibata D
CoP: a database for characterizing co-expressed gene modules with biological information in plants
Bioinformatics. 2010, 26(9), 1267-1268
Ogawa T, Ara T, Aoki K, Suzuki H and Shibata D
Transient increase in salicylic acid and its glucose conjugates after wounding in Arabidopsis leaves
Plant Biotechnology 2010, 27, 205-209
 
Kim YI, Hirai S, Takahashi H, Goto T, Ohyane C, Tsugane T, Konishi C, Fujii T, Inai S, Iijima Y, Aoki K, Shibata D, Takahashi N, Kawada T
9-oxo-10(E),12(E)-octadecadienoic acid derived from tomato is a potent PPAR α agonist to decrease triglyceride accumulation in mouse primary hepatocytes
Mol Nutr Food Res. 2010, 55 (4), 585-593
Yin YG, Tominaga T, Iijima Y, Aoki K, Shibata D, Ashihara H, Nishimura S, Ezura H, Matsukura C
Metabolic alterations in organic acids and gamma-aminobutyric acid in developing tomato (Solanum lycopersicum L.) fruits
Plant Cell Physiol. 2010, 51(8), 1300-1314
Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y, Tanaka K, Tanaka S, Aoshima K, Oda Y, Kakazu Y, Kusano M, Tohge T, Matsuda F, Sawada Y, Hirai MY, Nakanishi H, Ikeda K, Akimoto N, Maoka T, Takahashi H, Ara T, Sakurai N, Suzuki H, Shibata D, Neumann S, Iida T, Tanaka K, Funatsu K, Matsuura F, Soga T, Taguchi R, Saito K, Nishioka T
MassBank: a public repository for sharing mass spectral data for life sciences
J Mass Spectrom. 2010, 45(7), 703-714
Ohta D, Kanaya S, Suzuki H
Application of Fourier-transform ion cyclotron resonance mass spectrometry to metabolic profiling and metabolite identification
Current Opinion in Biotechnology 2010, 21, 35-44
Yamamura M, Hattori T, Suzuki S, Shibata D, Umezawa T
Microscale alkaline nitrobenzene oxidation for high-throughput determination of lignin aromatic components
Plant Biotechnology 2010, 27 (4), 305-310
Nakamura N, Fukuchi-Mizutani M, Fukui Y, Ishiguro K, Suzuki K, Suzuki H, Okazaki K, Shibata D, Tanaka Y
Gerenation of pink flower varieties from blue Torenia hybrida by redirecting the flavonoid biosynthetic pathway from delphinidin to pelargonidin
Plant Biotechnology 2010, 27 (5), 375-383
Aono E, Baba T, Ara T, Nishi T, Nakamichi T, Inamoto E, Toyonaga H, Hasegawa M, Takai Y, Okumura Y, Baba M, Tomita M, Kato C, Oshima T, Nakasone K, Mori H
Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments
Molecular BioSystems 2010, 6, 1216-1226
Hamada K, Hongo K, Suwabe K, Shimizu A, Nagayama T, Abe R, Kikuchi S, Yamamoto N, Fujii T, Yokoyama K, Tsuchida H, Sano K, Mochizuki T, Oki N, Horiuchi Y, Fujita M, Watanabe M, Matsuoka M, Kurata N, Yano K
OryzaExpress: an integrated database of gene expression networks and omics annotations in rice
Plant Cell Physiology 2010, 52 (2), 220-229
Yoshida K, Iwasaka R, Shimada N, Ayabe S, Aoki T, Sakuta M
Transcriptional control of the dihydroflavonol 4-reductase multigene family in Lotus japonicus
Journal of Plant Research 2010, 123, 801-805

2009

Ogata Y, Sakurai N, Suzuki H, Aoki K, Saito K, Shibata D
The prediction of local modular structures in a co-expression network based on gene expression datasets
Genome Inform. 2009, 23(1), 117-127
Sawaki Y, Iuchi S, Kobayashi Y, Kobayashi Y, Ikka T, Sakurai N, Fujita M, Shinozaki K, Shibata D, Kobayashi M, Koyama H
STOP1 regulates multiple genes that protect arabidopsis from proton and aluminum toxicities
Plant Physiol. 2009 150(1):281-94
Zhao CR, Ikka T, Sawaki Y, Kobayashi Y, Suzuki Y, Hibino T, Sato S, Sakurai N, Shibata D, Koyama H
Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in Arabidopsis thaliana
BMC Plant Biol. 2009, 9, 32
Fujisawa M, Takita E, Harada H, Sakurai N, Suzuki H, Ohyama K, Shibata D, Misawa N
Pathway engineering of Brassica napus seeds using multiple key enzyme genes involved in ketocarotenoid formation
J Exp Bot. 2009, 60(4), 1319-1332
Ogata Y, Sakurai N, Aoki K, Suzuki H, Okazaki K, Saito K, Shibata D
KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes
Plant Cell Physiol. 2009, 50(1), 173-177
Maruyama K, Takeda M, Kidokoro S, Yamada K, Sakuma Y, Urano K, Fujita M, Yoshiwara K, Matsukura S, Morishita Y, Sasaki R, Suzuki H, Saito K, Shibata D, Shinozaki K, Yamaguchi-Shinozaki K
Metabolic pathways involved in cold acclimation identified by integrated analysis of metabolites and transcripts regulated by DREB1A and DREB2A
Plant Physiol. 2009, 150(4), 1972-1980
Urano K, Maruyama K, Ogata Y, Morishita Y, Takeda M, Sakurai N, Suzuki H, Saito K, Shibata D, Kobayashi M, Yamaguchi-Shinozaki K, Shinozaki K
Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics
Plant J. 2009, 57(6), 1065-1078
Iijima Y, Fujiwara Y, Tokita T, Ikeda T, Nohara T, Aoki K, Shibata D
Involvement of ethylene in the accumulation of esculeoside A during fruit ripening of tomato (Solanum lycopersicum)
J Agric Food Chem. 2009, 57(8), 3247-3252
Ogata Y, Suzuki H, Shibata D
A database for poplar gene co-expression analysis for systematic understanding of biological processes, including stress responses
J Wood Sci. 2009, 55(6), 395-400
Ara T, Sakurai N, Tange Y, Morishita Y, Suzuki H, Aoki K, Saito K and Shibata D
Improvement of the quantitative differential metabolome pipeline for gas chromatography-mass spectrometry data by automated reliable peak selection
Plant Biotechnology 2009, 26, 445-449
Ogata Y, Suzuki H, Shibata D
A gene co-expression database for understanding biological processes in soybean
Plant Biotechnology 2009, 26, 503-507
Ogata Y, Sakurai N, Aoki K, Suzuki H, Okazaki K, Saito K, Shibata D
KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes
Plant Cell Physiol. 2009, 50(1):173-177

2008

Iijima Y, Suda K, Suzuki K, Aoki K, Shibata D
Metabolite profiling of chalcones and flavanones in tomato fruit
J. Japan. Soc. Hortic. Sci. 2008, 77(1) 94-102
Komaki H, Fudou R, Iizuka T, Nakajima D, Okazaki K, Shibata D, Ojika M, Harayama S
PCR detection of type I polyketide synthase genes in myxobacteria
Appl Environ Microbiol. 2008, 74(17), 5571-5574
Akihiro T, Koike S, Tani R, Tominaga T, Watanabe S, Iijima Y, Aoki K, Shibata D, Ashihara H, Matsukura C, Akama K, Fujimura T, Ezura H
Biochemical mechanism on GABA accumulation during fruit development in tomato
Plant Cell Physiol. 2008, 49(9), 1378-1389
Matsukura C, Aoki K, Fukuda N, Mizoguchi T, Asamizu E, Saito T, Shibata D, Ezura H
Comprehensive resources for tomato functional genomics based on the miniature model tomato micro-tom
Curr Genomics. 2008, 9(7), 436-443
Sano R, Suzuki H, Ogawa Y, Dansako T, Sakurai N, Okazaki K, Aoki K, Saito K and Shibata D
Suppression of carotenoid synthesis in transgenic Arabidopsis cultured cells over-expressing the AHL29/SOB3 gene
Plant Biotechnology 2008, 25(6), 573-578
Sano R, Ogata Y, Suzuki H, Ogawa Y, Dansako T, Sakurai N, Okazaki K, Aoki K, Saito K, and Shibata D
Over-expression of transcription associated factor genes co-expressed with genes of the mevalonate pathway, upstream of isoprenoid biosynthesis, in Arabidopsis cultured cells
Plant Biotechnology 2008, 25(6), 583-588
Nakamura Y, Kanaya S, Sakurai N, Iijima Y, Aoki K, Okazaki K, Suzuki H, Kitayama M, and Shibata D
A tool for high-throughput prediction of molecular formulas and identification of isotopic peaks from large-scale mass spectrometry data
Plant Biotechnology 2008, 25(4), 377-380
Ogawa Y, Suzuki H, Sakurai N, Aoki K, Saito K, Shibata D
Cryopreservation and metabolic profiling analysis of Arabidopsis T87 suspension-cultured cells
Cryo Letters. 2008, 29(5):427-436
Suzuki H, Sasaki R, Ogata Y, Nakamura Y, Sakurai N, Kitajima M, Takayama H, Kanaya S, Aoki K, Shibata D, Saito K
Metabolic profiling of flavonoids in Lotus japonicus using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry
Phytochemistry. 2008, 69(1):99-111
Iijima Y, Nakamura Y, Ogata Y, Tanaka K, Sakurai N, Suda K, Suzuki T, Suzuki H, Okazaki K, Kanaya S, Aoki K and Shibata D
Metabolite annotations based on the integration of mass spectral information
Plant J. 2008, 54(5), 949-962
Ogawa Y, Dansako T, Yano K, Sakurai N, Suzuki H, Aoki K, Noji M, Saito K, Shibata D
Efficient and high-throughput vector construction and Agrobacterium-mediated transformation of Arabidopsis thalianaliana suspension-cultured cells for functional genomics
Plant Cell Physiol. 2008 49(2), 242-250

2007

Yano K, Aoki K, Shibata D
Genome databases for tomato
Plant Biotechnol. 2007 24, 17-25
Watanabe S, Mizoguchi T, Aoki K, Kubo Y, Mori H, Imanishi S, Yamazaki Y, Shibata D, Ezura H
Ethylmethanesulfonate (EMS) mutagenesis of Solanum lycopersicum cv. Micro-Tom for large-scale mutant screens
Plant Biotechnol. 2007 24: 33-38
Omura T, Watanabe S, Iijima Y, Aoki K, Shibata D, Ezura H
Molecular and genetic characterization of transgenic tomato expressing 3-hydroxy-3-methylglutaryl coenzyme A reductase
Plant Biotechnol. 2007 24: 107-116
Shimamura M, Akashi T, Sakurai N, Suzuki H, Saito K, Shibata D, Ayabe S, Aoki T
2-Hydroxyisoflavanone dehydratase is a critical determinant of isoflavone productivity in hairy root cultures of Lotus japonicus
Plant Cell Physiol. 2007 48, 1652-1657
Fujiwara Y, Kiyota N, Hori M, Matsushita S, Iijima Y, Aoki K, Shibata D, Takeya M, Ikeda T, Nohara T, Nagai R
Esculeogenin A, a New Tomato Sapogenol, Ameliorates Hyperlipidemia and Atherosclerosis in ApoE-Deficient Mice by Inhibiting ACAT
Arterioscler Thromb. Vasc. Biol., 2007 27(11) 2400-2406
Ishida T, Hattori S, Sano R, Inoue K, Shirano Y, Hayashi H, Shibata D, Sato S, Kato T, Tabata S, Okada K, Wada T
Arabidopsis TRANSPARENT TESTA GLABRA2 is directly regulated by R2R3 MYB transcription factors and is involved in regulation of GLABRA2 transcription in epidermal differentiation
Plant Cell, 2007 19, 2531-2543
Nakamura Y, Kimura A, Saga S, Oikawa A, Shinbo Y, Kai K, Sakurai N, Suzuki H, Kitayama M, Shibata D, Kanaya S, Ohta D
Differential metabolomics unraveling light/dark regulation of metabolic activities in Arabidopsis cell culture
Planta 2007 227, 57-66
Ikka T, Kobayashi Y, Iuchi S, Sakurai N, Shibata D, Kobayashi M, Koyama H
Natural variation of Arabidopsis thaliana reveals that aluminum resistance and proton resistance are controlled by different genetic factors
Theor. Appl. Genet. 2007 115, 709-719
Hirai MY, Sugiyama K, Sawada Y, Tohge T, Obayashi T, Suzuki A, Araki R, Sakurai N, Suzuki H, Aoki K, Goda H, Nishizawa OI, Shibata D, Saito K
Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis
Proc Natl Acad Sci USA. 2007 104(15):6478-83
Sakakibara N, Nakatsubo T, Suzuki S, Shibata D, Shimada M, Umezawa T
Metabolic analysis of the cinnamate/monolignol pathway in Carthamus tinctorius seeds by a stable-isotope-dilution method
Org Biomol Chem. 2007 5(5):802-15
Aoki K, Ogata Y, Shibata D
Approaches for extracting practical information from gene co-expression networks in plant biology
Plant Cell Physiol. 2007 48(3):381-390

2006

Oikawa A, Nakamura Y, Ogura T, Kimura A, Suzuki H, Sakurai N, Shinbo Y, Shibata D, Kanaya S, Ohta D
Clarification of pathway-specific inhibition by Fourier transform ion cyclotron resonance/mass spectrometry-based metabolic phenotyping studies
Plant Physiol. 2006 142 (2):398-413
Morikawa T, Mizutani M, Aoki N, Watanabe B, Saga H, Saito S, Oikawa A, Suzuki H, Sakurai N, Shibata D, Wadano A, Sakata K, Ohta D
Cytochrome P450 CYP710A encodes the sterol C-22 desaturase in Arabidopsis and tomato
Plant Cell. 2006 18(4):1008-22
Sawai S, Akashi T, Sakurai N, Suzuki H, Shibata D, Ayabe S, Aoki T
Plant lanosterol synthase: divergence of the sterol and triterpene biosynthetic pathways in eukaryotes
Plant Cell Physiol. 2006 47(5):673-7

2005

Sasaki-Sekimoto Y, Taki N, Obayashi T, Aono M, Matsumoto F, Sakurai N, Suzuki H, Hirai MY, Noji M, Saito K, Masuda T, Takamiya K, Shibata D, Ohta H
Coordinated activation of metabolic pathways for antioxidants and defence compounds by jasmonates and their roles in stress tolerance in Arabidopsis
Plant J. 2005 44(4):653-68
Taki N, Sasaki-Sekimoto Y, Obayashi T, Kikuta A, Kobayashi K, Ainai T, Yagi K, Sakurai N, Suzuki H, Masuda T, Takamiya K, Shibata D, Kobayashi Y, Ohta H
12-oxo-phytodienoic acid triggers expression of a distinct set of genes and plays a role in wound-induced gene expression in Arabidopsis
Plant Physiol. 2005 139(3):1268-83
Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama T, Umezawa T, Misawa N, Saito K, Shibata D
KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps
Plant Physiol. 2005 138(3):1289-300
Hirai MY, Klein M, Fujikawa Y, Yano M, Goodenowe DB, Yamazaki Y, Kanaya S, Nakamura Y, Kitayama M, Suzuki H, Sakurai N, Shibata D, Tokuhisa J, Reichelt M, Gershenzon J, Papenbrock J, Saito K
Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics
J Biol Chem. 2005 280(27):25590-5