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1

Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor

Takayuki Tohge, Yasutaka Nishiyama, Masami Yokota Hirai, Mitsuru Yano, Jun-ichiro Nakajima, Motoko Awazuhara, Eri Inoue, Hideki Takahashi, Dayan B. Goodenowe, Masahiko Kitayama, Masaaki Noji, Mami Yam

Journal:

The Plant Journal

Year:

2005

Language:

english

File:

PDF, 393 KB

english, 2005

2

Intraspecific comparative analyses of metabolites between diploid and tetraploid Arabidopsis thaliana and Pyrus communis

Tsukaya, Hirokazu, Sawada, Yuji, Oikawa, Akira, Shiratake, Katsuhiro, Isuzugawa, Kanji, Saito, Kazuki, Hirai, Masami Yokota

Journal:

New Negatives in Plant Science

Year:

2015

Language:

english

File:

PDF, 273 KB

english, 2015

3

Metabolome-based discrimination of chrysanthemum cultivars for the efficient generation of flower color variations in mutation breeding

Sawada, Yuji, Sato, Muneo, Okamoto, Mami, Masuda, Junichi, Yamaki, Satoshi, Tamari, Mitsuo, Tanokashira, Yuki, Kishimoto, Sanae, Ohmiya, Akemi, Abe, Tomoko, Hirai, Masami Yokota

Journal:

Year:

2019

Language:

english

File:

PDF, 1.25 MB

english, 2019

4

Engineering of cyanobacteria for the photosynthetic production of limonene from CO2

Kiyota, Hiroshi, Okuda, Yukiko, Ito, Michiho, Hirai, Masami Yokota, Ikeuchi, Masahiko

Journal:

Journal of Biotechnology

Year:

2014

Language:

english

File:

PDF, 1.26 MB

english, 2014

5

The Sorghum Gene for Leaf Color Changes upon Wounding ( P ) Encodes a Flavanone 4-Reductase in the 3-Deoxyanthocyanidin Biosynthesis Pathway

Kawahigashi, Hiroyuki, Kasuga, Shigemitsu, Sawada, Yuji, Yonemaru, Jun-ichi, Ando, Tsuyu, Kanamori, Hiroyuki, Wu, Jianzhong, Mizuno, Hiroshi, Momma, Mitsuru, Fujimoto, Zui, Hirai, Masami Yokota, Matsu

Journal:

G3 Genes|Genome|Genetics

Year:

2016

Language:

english

File:

PDF, 1.61 MB

english, 2016

6

Widely targeted metabolome and transcriptome landscapes of Allium fistulosum–A. cepa chromosome addition lines revealed a flavonoid hot spot on chromosome 5A

Abdelrahman, Mostafa, Hirata, Sho, Sawada, Yuji, Hirai, Masami Yokota, Sato, Shusei, Hirakawa, Hideki, Mine, Yoko, Tanaka, Keisuke, Shigyo, Masayoshi

Journal:

Scientific Reports

Year:

2019

File:

PDF, 5.92 MB

2019

7

Effect of perforation-mediated modified atmosphere packaging on the quality and bioactive compounds of soft kale (Brassica oleracea L. convar. acephala (DC) Alef. var. sabellica L.) during storage

Boerzhijin, Surina, Makino, Yoshio, Hirai, Masami Yokota, Sotome, Itaru, Yoshimura, Masatoshi

Journal:

Food Packaging and Shelf Life

Year:

2020

File:

PDF, 1.26 MB

2020

8

Global expression profiling of sulfur-starved Arabidopsis by DNA macroarray reveals the role of O-acetyl-l-serine as a general regulator of gene expression in response to sulfur nutrition

Masami Yokota Hirai, Toru Fujiwara, Motoko Awazuhara, Tomoko Kimura, Masaaki Noji, Kazuki Saito

Journal:

The Plant Journal

Year:

2003

Language:

english

File:

PDF, 504 KB

english, 2003

9

Role ofO-acetyl-l-serine in the coordinated regulation of the expression of a soybean seed storage-protein gene by sulfur and nitrogen nutrition

Hoyeun Kim, Masami Yokota Hirai, Hiroaki Hayashi, Mitsuo Chino, Satoshi Naito, Toru Fujiwara

Journal:

Year:

1999

Language:

english

File:

PDF, 261 KB

english, 1999

10

Comparative metabolomics charts the impact of genotype-dependent methionine accumulation inArabidopsis thaliana

Miyako Kusano, Atsushi Fukushima, Henning Redestig, Makoto Kobayashi, Hitomi Otsuki, Hitoshi Onouchi, Satoshi Naito, Masami Yokota Hirai, Kazuki Saito

Journal:

Year:

2010

Language:

english

File:

PDF, 512 KB

english, 2010

11

Widely targeted metabolomics and coexpression analysis as tools to identify genes involved in the side-chain elongation steps of aliphatic glucosinolate biosynthesis

Doris Albinsky, Yuji Sawada, Ayuko Kuwahara, Mutsumi Nagano, Akiko Hirai, Kazuki Saito, Masami Yokota Hirai

Journal:

Year:

2010

Language:

english

File:

PDF, 364 KB

english, 2010

12

Toward genome-wide metabolotyping and elucidation of metabolic system: metabolic profiling of large-scale bioresources

Masami Yokota Hirai, Yuji Sawada, Shigehiko Kanaya, Takashi Kuromori, Masatomo Kobayashi, Romy Klausnitzer, Kosuke Hanada, Kenji Akiyama, Tetsuya Sakurai, Kazuki Saito, Kazuo Shinozaki

Journal:

Journal of Plant Research

Year:

2010

Language:

english

File:

PDF, 203 KB

english, 2010

13

A robust omics-based approach for the identification of glucosinolate biosynthetic genes

Masami Yokota Hirai

Journal:

Phytochemistry Reviews

Year:

2009

Language:

english

File:

PDF, 261 KB

english, 2009

14

A stress-inducible sulphotransferase sulphonates salicylic acid and confers pathogen resistance in Arabidopsis

DONGWON BAEK, PRASANTH PATHANGE, JUNG-SUNG CHUNG, JIAFU JIANG, LIQIONG GAO, AKIRA OIKAWA, MASAMI YOKOTA HIRAI, KAZUKI SAITO, PAUL W. PARE, HUAZHONG SHI

Journal:

Plant, Cell & Environment

Year:

2010

Language:

english

File:

PDF, 634 KB

english, 2010

15

Coordinated activation of metabolic pathways for antioxidants and defence compounds by jasmonates and their roles in stress tolerance in Arabidopsis

Yuko Sasaki-Sekimoto, Nozomi Taki, Takeshi Obayashi, Mitsuko Aono, Fuminori Matsumoto, Nozomu Sakurai, Hideyuki Suzuki, Masami Yokota Hirai, Masaaki Noji, Kazuki Saito, Tatsuru Masuda, Ken-ichiro Taka

Journal:

The Plant Journal

Year:

2005

Language:

english

File:

PDF, 886 KB

english, 2005

16

Proteomic and transcriptomic analysis of Arabidopsis seeds: molecular evidence for successive processing of seed proteins and its implication in the stress response to sulfur nutrition

Yasuhiro Higashi, Masami Yokota Hirai, Toru Fujiwara, Satoshi Naito, Masaaki Noji, Kazuki Saito

Journal:

The Plant Journal

Year:

2006

Language:

english

File:

PDF, 472 KB

english, 2006

17

WRKY6 is involved in the response to boron deficiency in Arabidopsis thaliana

Ichiro Kasajima, Yoko Ide, Masami Yokota Hirai, Toru Fujiwara

Journal:

Physiologia Plantarum

Year:

2010

Language:

english

File:

PDF, 1.04 MB

english, 2010

18

Exogenous application of 5-aminolevulinic acid increases the transcript levels of sulfur transport and assimilatory genes, sulfate uptake, and cysteine and glutathione contents in Arabidopsis thaliana

Akiko MARUYAMA-NAKASHITA, Masami Yokota HIRAI, Shigeyuki FUNADA, Shoichi FUEKI

Journal:

Soil Science & Plant Nutrition

Year:

2010

Language:

english

File:

PDF, 291 KB

english, 2010

19

Expression of Soybean Seed Storage Protein Genes in Transgenic Plants and Their Response to Sulfur Nutritional Conditions

Satoshi Naito, Masami Yokota Hirai, Kumiko Inaba-Higano, Eiji Nambara, Toru Fujiwara, Hiroaki Hayashi, Yoshibumi Komeda, Mitsuo Chino

Journal:

Journal of Plant Physiology

Year:

1995

Language:

english

File:

PDF, 1.03 MB

english, 1995

20

RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database

Yuji Sawada, Ryo Nakabayashi, Yutaka Yamada, Makoto Suzuki, Muneo Sato, Akane Sakata, Kenji Akiyama, Tetsuya Sakurai, Fumio Matsuda, Toshio Aoki, Masami Yokota Hirai, Kazuki Saito

Journal:

Year:

2012

Language:

english

File:

PDF, 784 KB

english, 2012

21

INTEGRATED LC-MS/MS SYSTEM FOR PLANT METABOLOMICS

Sawada, Yuji, Hirai, Masami Yokota

Journal:

Computational and Structural Biotechnology Journal

Year:

2013

Language:

english

File:

PDF, 2.58 MB

english, 2013

22

Capillary electrophoresis-mass spectrometry reveals the distribution of carbon metabolites during nitrogen starvation in Synechocystis sp. PCC 6803

Osanai, Takashi, Oikawa, Akira, Shirai, Tomokazu, Kuwahara, Ayuko, Iijima, Hiroko, Tanaka, Kan, Ikeuchi, Masahiko, Kondo, Akihiko, Saito, Kazuki, Hirai, Masami Yokota

Journal:

Environmental Microbiology

Year:

2014

Language:

english

File:

PDF, 1.91 MB

english, 2014

23

Plant lipidomics based on hydrophilic interaction chromatography coupled to ion trap time-of-flight mass spectrometry

Yozo Okazaki, Yukiko Kamide, Masami Yokota Hirai, Kazuki Saito

Journal:

Year:

2013

Language:

english

File:

PDF, 793 KB

english, 2013

24

Pleiotropic effect of sigE over-expression on cell morphology, photosynthesis and hydrogen production in Synechocystis sp. PCC 6803

Osanai, Takashi, Kuwahara, Ayuko, Iijima, Hiroko, Toyooka, Kiminori, Sato, Mayuko, Tanaka, Kan, Ikeuchi, Masahiko, Saito, Kazuki, Hirai, Masami Yokota

Journal:

The Plant Journal

Year:

2013

Language:

english

File:

PDF, 534 KB

english, 2013

25

Frequency-dependent herbivory by a leaf beetle,Phaedon brassicae, on hairy and glabrous plants ofArabidopsis hallerisubsp.gemmifera

Sato, Yasuhiro, Kawagoe, Tetsuhiro, Sawada, Yuji, Hirai, Masami Yokota, Kudoh, Hiroshi

Journal:

Evolutionary Ecology

Year:

2014

Language:

english

File:

PDF, 509 KB

english, 2014

26

ANGUSTIFOLIA3 Signaling Coordinates Proliferation between Clonally Distinct Cells in Leaves

Kawade, Kensuke, Horiguchi, Gorou, Usami, Takeshi, Hirai, Masami Yokota, Tsukaya, Hirokazu

Journal:

Current Biology

Year:

2013

Language:

english

File:

PDF, 743 KB

english, 2013

27

Rre37 stimulates accumulation of 2-oxoglutarate and glycogen under nitrogen starvation in Synechocystis sp. PCC 6803

Joseph, Ancy, Aikawa, Shimpei, Sasaki, Kengo, Teramura, Hiroshi, Hasunuma, Tomohisa, Matsuda, Fumio, Osanai, Takashi, Hirai, Masami Yokota, Kondo, Akihiko

Journal:

Year:

2014

Language:

english

File:

PDF, 971 KB

english, 2014

28

Estimation of kinetic parameters in an S-system equation model for a metabolic reaction system using the Newton–Raphson method

Iwata, Michio, Sriyudthsak, Kansuporn, Hirai, Masami Yokota, Shiraishi, Fumihide

Journal:

Mathematical Biosciences

Year:

2014

Language:

english

File:

PDF, 1.74 MB

english, 2014

29

PENDISC: A Simple Method for Constructing a Mathematical Model from Time-Series Data of Metabolite Concentrations

Sriyudthsak, Kansuporn, Iwata, Michio, Hirai, Masami Yokota, Shiraishi, Fumihide

Journal:

Bulletin of Mathematical Biology

Year:

2014

Language:

english

File:

PDF, 1.25 MB

english, 2014

30

Combination of Liquid Chromatography–Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry with 13 C-Labeling for Chemical Assignment of Sulfur-Containing Metabolites in Onion Bulbs

Nakabayashi, Ryo, Sawada, Yuji, Yamada, Yutaka, Suzuki, Makoto, Hirai, Masami Yokota, Sakurai, Tetsuya, Saito, Kazuki

Journal:

Analytical Chemistry

Year:

2013

Language:

english

File:

PDF, 967 KB

english, 2013

31

Analysis of systemic sulfur metabolism in plants using integrated ‘-omics’ strategies

Hirai, Masami Yokota, Saito, Kazuki

Journal:

Molecular BioSystems

Year:

2008

Language:

english

File:

PDF, 3.51 MB

english, 2008

32

Wax ester and lipophilic compound profiling ofEuglena gracilisby gas chromatography-mass spectrometry: toward understanding of wax ester fermentation under hypoxia

Furuhashi, Takeshi, Ogawa, Takumi, Nakai, Rai, Nakazawa, Masami, Okazawa, Atsushi, Padermschoke, Adchara, Nishio, Kazuki, Hirai, Masami Yokota, Arita, Masanori, Ohta, Daisaku

Journal:

Year:

2015

Language:

english

File:

PDF, 1.23 MB

english, 2015

33

Metabolomic analysis reveals rewiring of S ynechocystis sp. PCC 6803 primary metabolism by ntcA overexpression

Osanai, Takashi, Oikawa, Akira, Iijima, Hiroko, Kuwahara, Ayuko, Asayama, Munehiko, Tanaka, Kan, Ikeuchi, Masahiko, Saito, Kazuki, Hirai, Masami Yokota

Journal:

Environmental Microbiology

Year:

2014

Language:

english

File:

PDF, 1.02 MB

english, 2014

34

Independent roles of methionine and O -acetyl- l -serine in the regulation of the β subunit gene of β-conglycinin

Hirai, Masami Yokota, Kim, Hoyeun, Hayashi, Hiroaki, Chino, Mitsuo, Naito, Satoshi, Fujiwara, Torn

Journal:

Soil Science & Plant Nutrition

Year:

2002

Language:

english

File:

PDF, 880 KB

english, 2002

35

Ectopic expression of myo-inositol 3-phosphate synthase induces a wide range of metabolic changes and confers salt tolerance in rice

Kusuda, Hiroki, Koga, Wataru, Kusano, Miyako, Oikawa, Akira, Saito, Kazuki, Hirai, Masami Yokota, Yoshida, Kaoru T.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.83 MB

english, 2015

36

Alteration of cyanobacterial sugar and amino acid metabolism by overexpression hik 8 , encoding a KaiC-associated histidine kinase

Osanai, Takashi, Shirai, Tomokazu, Iijima, Hiroko, Kuwahara, Ayuko, Suzuki, Iwane, Kondo, Akihiko, Hirai, Masami Yokota

Journal:

Environmental Microbiology

Year:

2015

Language:

english

File:

PDF, 1.68 MB

english, 2015

37

Elucidation of Gene-to-Gene and Metabolite-to-Gene Networks in Arabidopsis by Integration of Metabolomics and Transcriptomics

Hirai, Masami Yokota, Klein, Marion, Fujikawa, Yuuta, Yano, Mitsuru, Goodenowe, Dayan B., Yamazaki, Yasuyo, Kanaya, Shigehiko, Nakamura, Yukiko, Kitayama, Masahiko, Suzuki, Hideyuki, Sakurai, Nozomu,

Journal:

Journal of Biological Chemistry

Year:

2005

Language:

english

File:

PDF, 990 KB

english, 2005

38

Morphological and plant hormonal changes during parasitization by Cuscuta japonica on Momordica charantia

Furuhashi, Takeshi, Kojima, Mikiko, Sakakibara, Hitoshi, Fukushima, Atsushi, Hirai, Masami Yokota, Furuhashi, Katsuhisa

Journal:

Journal of Plant Interactions

Year:

2014

Language:

english

File:

PDF, 1.23 MB

english, 2014

39

One day of nitrogen starvation reveals the effect of sigE and rre37 overexpression on the expression of genes related to carbon and nitrogen metabolism in Synechocystis sp. PCC 6803

Nakaya, Yuka, Iijima, Hiroko, Takanobu, Junko, Watanabe, Atsuko, Hirai, Masami Yokota, Osanai, Takashi

Journal:

Journal of Bioscience and Bioengineering

Year:

2015

Language:

english

File:

PDF, 3.00 MB

english, 2015

40

Response of aliphatic glucosinolate biosynthesis to signaling molecules in MAM gene knockout mutants of Arabidopsis

Li, Yimeng, Tang, Xiaoyan, Hirai, Masami Yokota, Yan, Xiufeng

Journal:

Plant Biotechnology

Year:

2013

Language:

english

File:

PDF, 374 KB

english, 2013

41

A new class of plant lipid is essential for protection against phosphorus depletion

Okazaki, Yozo, Otsuki, Hitomi, Narisawa, Tomoko, Kobayashi, Makoto, Sawai, Satoru, Kamide, Yukiko, Kusano, Miyako, Aoki, Toshio, Hirai, Masami Yokota, Saito, Kazuki

Journal:

Nature Communications

Year:

2013

Language:

english

File:

PDF, 725 KB

english, 2013

42

Integrating transcriptome and target metabolome variability in doubled haploids ofAllium cepafor abiotic stress protection

Abdelrahman, Mostafa, Sawada, Yuji, Nakabayashi, Ryo, Sato, Shusei, Hirakawa, Hideki, El-Sayed, Magdi, Hirai, Masami Yokota, Saito, Kazuki, Yamauchi, Naoki, Shigyo, Masayoshi

Journal:

Molecular Breeding

Year:

2015

Language:

english

File:

PDF, 2.57 MB

english, 2015

43

Os-GIGANTEA Confers Robust Diurnal Rhythms on the Global Transcriptome of Rice in the Field

Takeshi Izawa, Motohiro Mihara, Yuji Suzuki, Meenu Gupta, Hironori Itoh, Atsushi J. Nagano, Ritsuko Motoyama, Yuji Sawada, Masahiro Yano, Masami Yokota Hirai, Amane Makino and Yoshiaki Nagamura

Journal:

Year:

2011

Language:

english

File:

PDF, 2.97 MB

english, 2011

44

Expression of a Soybean (Glycine max [L.] Merr.) Seed Storage Protein Gene in Transgenic Arabidopsis thaliana and Its Response to Nutritional Stress and to Abscisic Acid Mutations

Satoshi Naito, Masami Yokota Hirai, Mitsuo Chino and Yoshibumi Komeda

Journal:

PLANT PHYSIOLOGY

Year:

1994

Language:

english

File:

PDF, 1.16 MB

english, 1994

45

Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops

Onda, Yoshihiko, Hashimoto, Kei, Yoshida, Takuhiro, Sakurai, Tetsuya, Sawada, Yuji, Hirai, Masami Yokota, Toyooka, Kiminori, Mochida, Keiichi, Shinozaki, Kazuo

Journal:

Proceedings Biological Sciences

Year:

2015

Language:

english

File:

PDF, 1007 KB

english, 2015

46

Effects of Sulfur Nutrition on Expression of the Soybean Seed Storage Protein Genes in Transgenic Petunia

Toru Fujiwara, Masami Yokota Hirai, Mitsuo Chino, Yoshibumi Komeda and Satoshi Naito

Journal:

PLANT PHYSIOLOGY

Year:

1992

Language:

english

File:

PDF, 1.15 MB

english, 1992

47

PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems

Sriyudthsak, Kansuporn, Mejia, Ramon Francisco, Arita, Masanori, Hirai, Masami Yokota

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 1.37 MB

english, 2016

48

A Chloroplastic UDP-Glucose Pyrophosphorylase from Arabidopsis Is the Committed Enzyme for the First Step of Sulfolipid Biosynthesis

Yozo Okazaki, Mie Shimojima, Yuji Sawada, Kiminori Toyooka, Tomoko Narisawa, Keiichi Mochida, Hironori Tanaka, Fumio Matsuda, Akiko Hirai, Masami Yokota Hirai, Hiroyuki Ohta and Kazuki Saito

Journal:

Year:

2009

File:

PDF, 2.90 MB

2009

49

A Chloroplastic UDP-Glucose Pyrophosphorylase from Arabidopsis Is the Committed Enzyme for the First Step of Sulfolipid Biosynthesis

Yozo Okazaki, Mie Shimojima, Yuji Sawada, Kiminori Toyooka, Tomoko Narisawa, Keiichi Mochida, Hironori Tanaka, Fumio Matsuda, Akiko Hirai, Masami Yokota Hirai, Hiroyuki Ohta and Kazuki Saito

Journal:

Year:

2009

Language:

english

File:

PDF, 2.90 MB

english, 2009

50

Effects of different secondary metabolite profiles in plant defense syndromes on specialist and generalist herbivores

Okamura, Yu, Sawada, Yuji, Hirai, Masami Yokota, Murakami, Masashi

Journal:

Entomological Science

Year:

2016

Language:

english

File:

PDF, 393 KB

english, 2016