Glycolaldehyde affects the growth of and metabolic flux distribution in Synechocystis sp. PCC 6803.

Tatsumi Imada, Yoshihiro Toya, Hiroshi Shimizu

Bioscience, biotechnology, and biochemistry　2025/04/04　Research paper (scientific journal)

Modification of intracellular metabolism by expression of a C-terminal variant of phosphoribulokinase from Synechocystis sp. PCC 6803.

Hiroki Nishiguchi, Teppei Niide, Yoshihiro Toya, Hiroshi Shimizu

Bioscience, biotechnology, and biochemistry　2025/02/03　Research paper (scientific journal)

Growth inhibition by ppc deletion is rescued by isocitrate dehydrogenase mutations in Escherichia coli

Yoshihiro Toya, Tatsumi Imada, Mai Ishibashi, Yuuichi Kawamoto, Kinuka Isshiki, Atsushi Shibai, Chikara Furusawa, Hiroshi Shimizu

FEMS Microbiology Letters　2025/01/27　Research paper (scientific journal)

Identification of a novel NADPH generation reaction in the pentose phosphate pathway in Escherichia coli using mBFP

Koichiro Ueno, Shogo Sawada, Mai Ishibashi, Yoshiki Kanda, Hiroshi Shimizu, Yoshihiro Toya

Journal of Bacteriology　2024/10/10　Research paper (scientific journal)

Utilizing Ribose 1,5-Bisphosphate Isomerase and RuBisCO-Equipped Escherichia coli Nissle for Low-Carbon Footprint GABA Production

Sefli Sri Wahyu Effendi, Yoshihiro Toya, Hiroshi Shimizu, Chengfeng Xue, I-Son Ng

ACS Sustainable Chemistry & Engineering　2024/07/16　Research paper (scientific journal)

Engineering Escherichia coli for efficient glutathione production

Hiroki Mori, Misato Matsui, Takahiro Bamba, Yoshimi Hori, Sayaka Kitamura, Yoshihiro Toya, Ryota Hidese, Hisashi Yasueda, Tomohisa Hasunuma, Hiroshi Shimizu, Naoaki Taoka, Shingo Kobayashi

Metabolic Engineering　2024/07　Research paper (scientific journal)

Metabolome analysis of metabolic burden in Escherichia coli caused by overexpression of green fluorescent protein and delta-rhodopsin

Chinatsu Matsuyama, Taisuke Seike, Nobuyuki Okahashi, Teppei Niide, Kiyotaka Y. Hara, Yoko Hirono-Hara, Jun Ishii, Hiroshi Shimizu, Yoshihiro Toya, Fumio Matsuda

Journal of Bioscience and Bioengineering　2024/03　Research paper (scientific journal)

Multicolor optogenetics for regulating flux ratio of three glycolytic pathways using EL222 and CcaSR in Escherichia coli.

Hayato Akagi, Hiroshi Shimizu, Yoshihiro Toya

Biotechnology and bioengineering　2023/12/20　Research paper (scientific journal)

Effects of n-butanol production on metabolism and the photosystem in Synecococcus elongatus PCC 7942 based on metabolic flux and target proteome analyses.

Keisuke Wada, Kiyoka Uebayashi, Yoshihiro Toya, Sastia Prama Putri, Fumio Matsuda, Eiichiro Fukusaki, James C Liao, Hiroshi Shimizu

The Journal of general and applied microbiology　Vol. 69　p. 185-195　2023/03/20　Research paper (scientific journal)

Functional evaluation of non-oxidative glycolysis in Escherichia coli in the stationary phase under microaerobic conditions.

Kenta Miyoshi, Ryutaro Kawai, Teppei Niide, Yoshihiro Toya, Hiroshi Shimizu

Journal of bioscience and bioengineering　Vol. 135　No. 4　p. 291-297　2023/01/29　Research paper (scientific journal)

Effect of light fluctuations on photosynthesis and metabolic flux in Synechocystis sp. PCC 6803.

Tatsumi Imada, Chiaki Yamamoto, Masakazu Toyoshima, Yoshihiro Toya, Hiroshi Shimizu

Biotechnology progress　2023/01/26　Research paper (scientific journal)

Conversion of Mevalonate to Isoprenol Using Light Energy in Escherichia coli without Consuming Sugars for ATP Supply

Mikoto Sano, Ryo Tanaka, Kentaro Kamata, Yoko Hirono-Hara, Jun Ishii, Fumio Matsuda, Kiyotaka Y. Hara, Hiroshi Shimizu, Yoshihiro Toya

ACS Synthetic Biology　Vol. 11　No. 12　p. 3966-3972　2022/11/28　Research paper (scientific journal)

Logistic Regression-Guided Identification of Cofactor Specificity-Contributing Residues in Enzyme with Sequence Datasets Partitioned by Catalytic Properties.

Sou Sugiki, Teppei Niide, Yoshihiro Toya, Hiroshi Shimizu

ACS synthetic biology　2022/11/02　Research paper (scientific journal)

異なる炭素源を消費する2種類の大腸菌株を用いた共培養によるイソプレノール生産

村上 茉奈美, 川井 隆太郎, 三吉 健太, 芝井 厚, 前田 智也, 堀之内 貴明, 古澤 力, 戸谷 吉博, 清水 浩

日本生物工学会大会講演要旨集　Vol. 2022年　p. 225-225　2022/10

Metabolic pathway design for growth-associated phenylalanine production using synthetically designed mutualism.

Ryutaro Kawai, Yoshihiro Toya, Hiroshi Shimizu

Bioprocess and biosystems engineering　Vol. 45　No. 9　p. 1539-1546　2022/08/05　Research paper (scientific journal)

13C metabolic flux analysis clarifies distinct metabolic phenotypes of cancer cell spheroid mimicking tumor hypoxia.

Shingo Noguchi, Kenichi Wakita, Fumio Matsuda, Hiroshi Shimizu

Metabolic engineering　Vol. 73　p. 192-200　2022/07/31　Research paper (scientific journal)

Optogenetic reprogramming of carbon metabolism using light-powering microbial proton pump systems

Yoshihiro Toya, Yoko Hirono-Hara, Hidenobu Hirayama, Kentaro Kamata, Ryo Tanaka, Mikoto Sano, Sayaka Kitamura, Kensuke Otsuka, Rei Abe-Yoshizumi, Satoshi P. Tsunoda, Hiroshi Kikukawa, Hideki Kandori, Hiroshi Shimizu, Fumio Matsuda, Jun Ishii, Kiyotaka Y. Hara

Metabolic Engineering　Vol. 72　p. 227-236　2022/07　Research paper (scientific journal)

Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production.

Junya Yamamoto, Onuma Chumsakul, Yoshihiro Toya, Takuya Morimoto, Shenghao Liu, Kenta Masuda, Yasushi Kageyama, Takashi Hirasawa, Fumio Matsuda, Naotake Ogasawara, Hiroshi Shimizu, Ken-Ichi Yoshida, Taku Oshima, Shu Ishikawa

DNA research : an international journal for rapid publication of reports on genes and genomes　Vol. 29　No. 3　2022/05/24　Research paper (scientific journal)

Metabolic pathway engineering for the non-growth-associated succinate production in Escherichia coli based on flux solution space

Yoshihiro Toya, Hiroshi Shimizu

Journal of Bioscience and Bioengineering　Vol. 134　No. 1　p. 29-33　2022/05　Research paper (scientific journal)

Improvement of 2,3-butanediol production by dCas9 gene expression system in Saccharomyces cerevisiae

Keisuke Morita, Taisuke Seike, Jun Ishii, Fumio Matsuda, Hiroshi Shimizu

Journal of Bioscience and Bioengineering　Vol. 133　No. 3　p. 208-212　2022/01　Research paper (scientific journal)

Acceleration of target production in co‐culture by enhancing intermediate consumption through adaptive laboratory evolution

Ryutaro Kawai, Yoshihiro Toya, Kenta Miyoshi, Manami Murakami, Teppei Niide, Takaaki Horinouchi, Tomoya Maeda, Atsushi Shibai, Chikara Furusawa, Hiroshi Shimizu

Biotechnology and Bioengineering　Vol. 119　No. 3　p. 936-945　2021/12/28　Research paper (scientific journal)

mfapy: An open-source Python package for 13C-based metabolic flux analysis.

Fumio Matsuda, Kousuke Maeda, Takeo Taniguchi, Yuya Kondo, Futa Yatabe, Nobuyuki Okahashi, Hiroshi Shimizu

Metabolic engineering communications　Vol. 13　2021/12　Research paper (scientific journal)

Recent advances in metabolic engineering–integration of in silico design and experimental analysis of metabolic pathways

Hiroshi Shimizu, Yoshihiro Toya

Journal of Bioscience and Bioengineering　Vol. 132　No. 5　p. 429-436　2021/11　Research paper (scientific journal)

Reactor control system in bacterial co-culture based on fluorescent proteins using an Arduino-based home-made device.

Minori Kusuda, Hiroshi Shimizu, Yoshihiro Toya

Biotechnology journal　Vol. 16　No. 12　2021/09/23　Research paper (scientific journal)

Proteome analysis of response to different spectral light irradiation in Synechocystis sp. PCC 6803.

Masakazu Toyoshima, Masumi Sakata, Yoshifumi Ueno, Yoshihiro Toya, Fumio Matsuda, Seiji Akimoto, Hiroshi Shimizu

Journal of proteomics　Vol. 246　p. 104306-104306　2021/06/19　Research paper (scientific journal)

Soft-sensor development for monitoring the lysine fermentation process.

Kento Tokuyama, Yoshiki Shimodaira, Yohei Kodama, Ryuzo Matsui, Yasuhiro Kusunose, Shunsuke Fukushima, Hiroaki Nakai, Yuichiro Tsuji, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

Journal of bioscience and bioengineering　Vol. 132　No. 2　p. 183-189　2021/05/03　Research paper (scientific journal)

Treatment of RB1-intact hepatocellular carcinoma with CDK4/6 inhibitor combination therapy.

Jindan Sheng, Susumu Kohno, Nobuhiro Okada, Nobuyuki Okahashi, Kana Teranishi, Fumio Matsuda, Hiroshi Shimizu, Paing Linn, Naoko Nagatani, Minako Yamamura, Kenichi Harada, Shin-Ichi Horike, Hiroshi Inoue, Seiji Yano, Sharad Kumar, Shunsuke Kitajima, Itsuki Ajioka, Chiaki Takahashi

Hepatology (Baltimore, Md.)　Vol. 74　No. 4　p. 1971-1993　2021/04/30　Research paper (scientific journal)

Random Transfer of Ogataea polymorpha Genes into Saccharomyces cerevisiae Reveals a Complex Background of Heat Tolerance.

Taisuke Seike, Yuki Narazaki, Yoshinobu Kaneko, Hiroshi Shimizu, Fumio Matsuda

Journal of fungi (Basel, Switzerland)　Vol. 7　No. 4　p. 302-302　2021/04/15　Research paper (scientific journal)

Mutations in hik26 and slr1916 lead to high-light stress tolerance in Synechocystis sp. PCC6803.

Katsunori Yoshikawa, Kenichi Ogawa, Yoshihiro Toya, Seiji Akimoto, Fumio Matsuda, Hiroshi Shimizu

Communications biology　Vol. 4　No. 1　p. 343-343　2021/03/16　Research paper (scientific journal)

Role of type I NADH dehydrogenase in Synechocystis sp. PCC 6803 under phycobilisome excited red light

Masakazu Toyoshima, Chiaki Yamamoto, Yoshifumi Ueno, Yoshihiro Toya, Seiji Akimoto, Hiroshi Shimizu

Plant Science　Vol. 304　p. 110798-110798　2021/03　Research paper (scientific journal)

Thioredoxin pathway in anabaena sp. PCC 7120: activity of NADPH-thioredoxin reductase C.

Frédéric Deschoenmaeker, Shoko Mihara, Tatsuya Niwa, Hideki Taguchi, Ken-Ichi Wakabayashi, Masakazu Toyoshima, Hiroshi Shimizu, Toru Hisabori

Journal of biochemistry　2021/02/04　Research paper (scientific journal)

Novel allosteric inhibition of phosphoribulokinase identified by ensemble kinetic modeling of Synechocystis sp. PCC 6803 metabolism.

Hiroki Nishiguchi, James Liao, Hiroshi Shimizu, Fumio Matsuda

Metabolic engineering communications　Vol. 11　2020/12　Research paper (scientific journal)

Estimation of linear and cyclic electron flows in photosynthesis based on 13C-metabolic flux analysis.

Chiaki Yamamoto, Masakazu Toyoshima, Sayaka Kitamura, Yoshifumi Ueno, Seiji Akimoto, Yoshihiro Toya, Hiroshi Shimizu

Journal of bioscience and bioengineering　Vol. 131　No. 3　p. 277-282　2020/11/20　Research paper (scientific journal)

Identification of a rate-limiting step in a metabolic pathway using the kinetic model and in vitro experiment.

Sayaka Kitamura, Hiroshi Shimizu, Yoshihiro Toya

Journal of bioscience and bioengineering　Vol. 131　No. 3　p. 271-276　2020/11/07　Research paper (scientific journal)

Assessment of Protein Content and Phosphorylation Level in Synechocystis sp. PCC 6803 under Various Growth Conditions Using Quantitative Phosphoproteomic Analysis.

Masakazu Toyoshima, Yuma Tokumaru, Fumio Matsuda, Hiroshi Shimizu

Molecules (Basel, Switzerland)　Vol. 25　No. 16　2020/08/06　Research paper (scientific journal)

Direct and quantitative analysis of altered metabolic flux distributions and cellular ATP production pathway in fumarate hydratase-diminished cells.

Shingo Noguchi, Hirokazu Ishikawa, Kenichi Wakita, Fumio Matsuda, Hiroshi Shimizu

Scientific reports　Vol. 10　No. 1　p. 13065-13065　2020/08/03　Research paper (scientific journal)

Data science-based modeling of the lysine fermentation process.

Kento Tokuyama, Yoshiki Shimodaira, Takahiro Terawaki, Yasuhiro Kusunose, Hiroaki Nakai, Yuichiro Tsuji, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

Journal of bioscience and bioengineering　Vol. 130　No. 4　p. 409-415　2020/07/21　Research paper (scientific journal)

Effects of mutations of GID protein-coding genes on malate production and enzyme expression profiles in Saccharomyces cerevisiae.

Hiroaki Negoro, Kengo Matsumura, Fumio Matsuda, Hiroshi Shimizu, Yoji Hata, Hiroki Ishida

Applied microbiology and biotechnology　Vol. 104　No. 11　p. 4971-4983　2020/06　Research paper (scientific journal)

Transcription Factor ArcA is a Flux Sensor for the Oxygen Consumption Rate in Escherichia Coli.

Naoya Nochino, Yoshihiro Toya, Hiroshi Shimizu

Biotechnology journal　Vol. 15　No. 6　2020/05/08　Research paper (scientific journal)

Comparison of metabolic profiles of yeasts based on the difference of the Crabtree positive and negative.

Makoto Imura, Katsuaki Nitta, Ryo Iwakiri, Fumio Matsuda, Hiroshi Shimizu, Eiichiro Fukusaki

Journal of bioscience and bioengineering　Vol. 129　No. 1　p. 52-58　2020/01　Research paper (scientific journal)

Flux balance analysis of cyanobacteria reveals selective use of photosynthetic electron transport components under different spectral light conditions.

Masakazu Toyoshima, Yoshihiro Toya, Hiroshi Shimizu

Photosynthesis research　Vol. 143　No. 1　p. 31-43　2020/01　Research paper (scientific journal)

Light-inducible flux control of triosephosphate isomerase on glycolysis in Escherichia coli.

Sachie Senoo, Sebastian Tommi Tandar, Sayaka Kitamura, Yoshihiro Toya, Hiroshi Shimizu

Biotechnology and bioengineering　Vol. 116　No. 12　p. 3292-3300　2019/12　Research paper (scientific journal)

High-yielding rice Takanari has superior photosynthetic response to a commercial rice Koshihikari under fluctuating light.

Shunsuke Adachi, Yu Tanaka, Atsuko Miyagi, Makoto Kashima, Ayumi Tezuka, Yoshihiro Toya, Shunzo Kobayashi, Satoshi Ohkubo, Hiroshi Shimizu, Maki Kawai-Yamada, Rowan F Sage, Atsushi J Nagano, Wataru Yamori

Journal of experimental botany　Vol. 70　No. 19　p. 5287-5297　2019/10/15　Research paper (scientific journal)

Repression of mitochondrial metabolism for cytosolic pyruvate-derived chemical production in Saccharomyces cerevisiae.

Keisuke Morita, Fumio Matsuda, Koji Okamoto, Jun Ishii, Akihiko Kondo, Hiroshi Shimizu

Microbial cell factories　Vol. 18　No. 1　p. 177-177　2019/10/15

Time-resolved analysis of short term metabolic adaptation at dark transition in Synechocystis sp. PCC 6803.

Masaharu Maruyama, Hiroki Nishiguchi, Masakazu Toyoshima, Nobuyuki Okahashi, Fumio Matsuda, Hiroshi Shimizu

Journal of bioscience and bioengineering　Vol. 128　No. 4　p. 424-428　2019/10　Research paper (scientific journal)

Prediction of Rate-Limiting Reactions for Growth-Associated Production Using a Constraint-Based Approach.

Kento Tokuyama, Yoshihiro Toya, Hiroshi Shimizu

Biotechnology journal　Vol. 14　No. 9　2019/09　Research paper (scientific journal)

Optogenetic switch for controlling the central metabolic flux of Escherichia coli.

Sebastian Tommi Tandar, Sachie Senoo, Yoshihiro Toya, Hiroshi Shimizu

Metabolic engineering　Vol. 55　p. 68-75　2019/09　Research paper (scientific journal)

クラブトリー陽性および陰性の差異に基づく酵母代謝のプロファイルの比較

井村 誠, 新田 克章, 岩切 亮, 松田 史生, 清水 浩, 福崎 英一郎

日本生物工学会大会講演要旨集　Vol. 2019年　p. 179-179　2019/08

ロドプシンを利用した大腸菌における光駆動ATP再生の物質生産への応用

田中 涼, 鎌田 健太郎, 戸谷 吉博, 松田 史生, 石井 純, 柘植 謙爾, 弘埜 陽子, 原 清敬, 清水 浩

日本生物工学会大会講演要旨集　Vol. 2019年　p. 170-170　2019/08

Theophylline-inducible riboswitch accurately regulates protein expression at low level in Escherichia coli.

Rikuto Kamiura, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

Biotechnology letters　Vol. 41　No. 6-7　p. 743-751　2019/07　Research paper (scientific journal)

Effect of precise control of flux ratio between the glycolytic pathways on mevalonate production in Escherichia coli.

Kentaro Kamata, Yoshihiro Toya, Hiroshi Shimizu

Biotechnology and bioengineering　Vol. 116　No. 5　p. 1080-1088　2019/05　Research paper (scientific journal)

Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism.

Hiroki Nishiguchi, Natsuki Hiasa, Kiyoka Uebayashi, James Liao, Hiroshi Shimizu, Fumio Matsuda

Metabolic engineering　Vol. 52　p. 273-283　2019/03

Magnesium starvation improves production of malonyl-CoA-derived metabolites in Escherichia coli.

Kento Tokuyama, Yoshihiro Toya, Fumio Matsuda, Brady F Cress, Mattheos A G Koffas, Hiroshi Shimizu

Metabolic engineering　Vol. 52　p. 215-223　2019/03　Research paper (scientific journal)

Targeted proteome analysis of microalgae under high-light conditions by optimized protein extraction of photosynthetic organisms.

Masakazu Toyoshima, Masumi Sakata, Kazuki Ohnishi, Yuma Tokumaru, Yusuke Kato, Ryutaro Tokutsu, Wataru Sakamoto, Jun Minagawa, Fumio Matsuda, Hiroshi Shimizu

Journal of bioscience and bioengineering　Vol. 127　No. 3　p. 394-402　2019/03　Research paper (scientific journal)

Fragmentation of Dicarboxylic and Tricarboxylic Acids in the Krebs Cycle Using GC-EI-MS and GC-EI-MS/MS.

Nobuyuki Okahashi, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda

Mass spectrometry (Tokyo, Japan)　Vol. 8　No. 1　2019　Research paper (scientific journal)

13C-Metabolic Flux Analysis Reveals Effect of Phenol on Central Carbon Metabolism in Escherichia coli.

Sayaka Kitamura, Yoshihiro Toya, Hiroshi Shimizu

Frontiers in microbiology　Vol. 10　p. 1010-1010　2019　Research paper (scientific journal)

Sugar phosphate analysis with baseline separation and soft ionization by gas chromatography-negative chemical ionization-mass spectrometry improves flux estimation of bidirectional reactions in cancer cells.

Nobuyuki Okahashi, Kousuke Maeda, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda

Metabolic engineering　Vol. 51　p. 43-49　2019/01　Research paper (scientific journal)

Characterization of oil-producing yeast Lipomyces starkeyi on glycerol carbon source based on metabolomics and 13C-labeling.

Yuki Maruyama, Yoshihiro Toya, Hiroshi Kurokawa, Yuka Fukano, Atsushi Sato, Hiroyasu Umemura, Kaoru Yamada, Hideaki Iwasaki, Norio Tobori, Hiroshi Shimizu

Applied microbiology and biotechnology　Vol. 102　No. 20　p. 8909-8920　2018/10　Research paper (scientific journal)

Expression of Saccharomyces cerevisiae cDNAs to enhance the growth of non-ethanol-producing S. cerevisiae strains lacking pyruvate decarboxylases.

Narazaki Y, Nomura Y, Morita K, Shimizu H, Matsuda F

Journal of bioscience and bioengineering　Vol. 126　No. 3　p. 317-321　2018/09　Research paper (scientific journal)

Metabolic flux of the oxidative pentose phosphate pathway under low light conditions in Synechocystis sp. PCC 6803.

Ueda K, Nakajima T, Yoshikawa K, Toya Y, Matsuda F, Shimizu H

Journal of bioscience and bioengineering　Vol. 126　No. 1　p. 38-43　2018/07　Research paper (scientific journal)

Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain.

Tokuyama K, Toya Y, Horinouchi T, Furusawa C, Matsuda F, Shimizu H

Biotechnology and bioengineering　Vol. 115　No. 6　p. 1542-1551　2018/06　Research paper (scientific journal)

Comparative analysis of fermentation and enzyme expression profiles among industrial Saccharomyces cerevisiae strains.

Uebayashi K, Shimizu H, Matsuda F

Applied microbiology and biotechnology　Vol. 102　No. 16　p. 7071-7081　2018/06　Research paper (scientific journal)

Transcriptome analysis of the cyanobacterium Synechocystis sp. PCC 6803 and mechanisms of photoinhibition tolerance under extreme high light conditions.

Ogawa K, Yoshikawa K, Matsuda F, Toya Y, Shimizu H

Journal of bioscience and bioengineering　Vol. 126　No. 5　p. 596-602　2018/06　Research paper (scientific journal)

Mass Spectrometry-Based Method to Study Inhibitor-Induced Metabolic Redirection in the Central Metabolism of Cancer Cells.

Araki C, Okahashi N, Maeda K, Shimizu H, Matsuda F

Mass spectrometry (Tokyo, Japan)　Vol. 7　No. 1　2018/06

A pyruvate carbon flux tugging strategy for increasing 2,3-butanediol production and reducing ethanol subgeneration in the yeast Saccharomyces cerevisiae.

Ishii J, Morita K, Ida K, Kato H, Kinoshita S, Hataya S, Shimizu H, Kondo A, Matsuda F

Biotechnology for biofuels　Vol. 11　2018/06

Integrated Analysis of the Transcriptome and Metabolome of Corynebacterium glutamicum during Penicillin-Induced Glutamic Acid Production.

Hirasawa T, Saito M, Yoshikawa K, Furusawa C, Shmizu H

Biotechnology journal　Vol. 13　No. 5　2018/05　Research paper (scientific journal)

Metabolic engineering of mevalonate-producing Escherichia coli strains based on thermodynamic analysis.

Nagai H, Masuda A, Toya Y, Matsuda F, Shimizu H

Metabolic engineering　Vol. 47　p. 1-9　2018/05　Research paper (scientific journal)

Comparative Targeted Proteomics of the Central Metabolism and Photosystems in SigE Mutant Strains of Synechocystis sp. PCC 6803.

Tokumaru Y, Uebayashi K, Toyoshima M, Osanai T, Matsuda F, Shimizu H

Molecules (Basel, Switzerland)　Vol. 23　No. 5　2018/05　Research paper (scientific journal)

¹³C-metabolic flux analysis of ethanol-assimilating Saccharomyces cerevisiae for S-adenosyl-L-methionine production.

Hayakawa K, Matsuda F, Shimizu H

Microbial cell factories　Vol. 17　No. 1　2018/05　Research paper (scientific journal)

Optimal ¹³C-labeling of glycerol carbon source for precise flux estimation in Escherichia coli.

Toya Y, Ohashi S, Shimizu H

Journal of bioscience and bioengineering　Vol. 125　No. 3　p. 301-305　2018/03　Research paper (scientific journal)

Metabolic impact of nutrient starvation in mevalonate-producing Escherichia coli

Ami Masuda, Yoshihiro Toya, Hiroshi Shimizu

BIORESOURCE TECHNOLOGY　Vol. 245　No. Pt B　p. 1634-1640　2017/12　Research paper (scientific journal)

Metabolic engineering of isopropyl alcohol-producing Escherichia coli strains with C-13-metabolic flux analysis

Nobuyuki Okahashi, Fumio Matsuda, Katsunori Yoshikawa, Tomokazu Shirai, Yoshiko Matsumoto, Mitsufumi Wada, Hiroshi Shimizu

BIOTECHNOLOGY AND BIOENGINEERING　Vol. 114　No. 12　p. 2782-2793　2017/12　Research paper (scientific journal)

Learning from quantitative data to understand central carbon metabolism.

Matsuda F, Toya Y, Shimizu H

Biotechnology advances　Vol. 35　No. 8　p. 971-980　2017/12

Identification of alcohol stress tolerance genes of Synechocystis sp PCC 6803 using adaptive laboratory evolution

Takuya Matsusako, Yoshihiro Toya, Katsunori Yoshikawa, Hiroshi Shimizu

BIOTECHNOLOGY FOR BIOFUELS　Vol. 10　2017/12　Research paper (scientific journal)

Prediction of Cross-resistance and Collateral Sensitivity by Gene Expression profiles and Genomic Mutations

Takaaki Horinouchi, Shingo Suzuki, Hazuki Kotani, Kumi Tanabe, Natsue Sakata, Hiroshi Shimizu, Chikara Furusawa

SCIENTIFIC REPORTS　Vol. 7　No. 1　2017/10　Research paper (scientific journal)

The RB-IL-6 axis controls self-renewal and endocrine therapy resistance by fine-tuning mitochondrial activity.

S Kitajima, A Yoshida, S Kohno, F Li, S Suzuki, N Nagatani, Y Nishimoto, N Sasaki, H Muranaka, Y Wan, T C Thai, N Okahashi, F Matsuda, H Shimizu, T Nishiuchi, Y Suzuki, K Tominaga, N Gotoh, M Suzuki, M E Ewen, D A Barbie, O Hirose, T Tanaka, C Takahashi

Oncogene　Vol. 36　No. 36　p. 5145-5157　2017/09/07　Research paper (scientific journal)

Heterologous expression of bacterial phosphoenol pyruvate carboxylase and Entner-Doudoroff pathway in Saccharomyces cerevisiae for improvement of isobutanol production

Keisuke Morita, Yuta Nomura, Jun Ishii, Fumio Matsuda, Akihiko Kondo, Hiroshi Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 124　No. 3　p. 263-270　2017/09　Research paper (scientific journal)

Metabolic Flux Analysis of the Synechocystis sp. PCC 6803 Delta nrtABCD Mutant Reveals a Mechanism for Metabolic Adaptation to Nitrogen-Limited Conditions (vol 58, pg 537, 2017)

Tsubasa Nakajima, Katsunori Yoshikawa, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

PLANT AND CELL PHYSIOLOGY　Vol. 58　No. 5　p. 976-976　2017/05

Metabolic engineering of Synechocystis sp PCC 6803 for enhanced ethanol production based on flux balance analysis

Katsunori Yoshikawa, Yoshihiro Toya, Hiroshi Shimizu

BIOPROCESS AND BIOSYSTEMS ENGINEERING　Vol. 40　No. 5　p. 791-796　2017/05　Research paper (scientific journal)

Metabolic Flux Analysis of the Synechocystis sp PCC 6803 Delta nrtABCD Mutant Reveals a Mechanism for Metabolic Adaptation to Nitrogen-Limited Conditions

Tsubasa Nakajima, Katsunori Yoshikawa, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

PLANT AND CELL PHYSIOLOGY　Vol. 58　No. 3　p. 537-545　2017/03　Research paper (scientific journal)

C-13-metabolic flux analysis for mevalonate-producing strain of Escherichia coli

Keisuke Wada, Yoshihiro Toya, Satomi Banno, Katsunori Yoshikawa, Fumio Matsuda, Hiroshi Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 123　No. 2　p. 177-182　2017/02　Research paper (scientific journal)

Targeted proteome analysis of single-gene deletion strains of Saccharomyces cerevisiae lacking enzymes in the central carbon metabolism

Fumio Matsuda, Syohei Kinoshita, Shunsuke Nishino, Atsumi Tomita, Hiroshi Shimizu

PLOS ONE　Vol. 12　No. 2　2017/02　Research paper (scientific journal)

Prediction of Hopeless Peptides Unlikely to be Selected for Targeted Proteome Analysis.

Matsuda F, Tomita A, Shimizu H

Mass spectrometry (Tokyo, Japan)　Vol. 6　No. 1　2017/02

Omics-integrated approach for metabolic state analysis of microbial processes

Hiroshi Shimizu, Chikara Furusawa, Takashi Hirasawa, Katsunori Yoshikawa, Yoshihiro Toya, Tomokazu Shirai, Fumio Matsuda

Applied Bioengineering: Innovations and Future Directions　p. 213-236　2017/01/01　Part of collection (book)

Metabolic Adaptation to Nutritional Stress in Human Colorectal Cancer.

Masaaki Miyo, Masamitsu Konno, Naohiro Nishida, Toshinori Sueda, Kozo Noguchi, Hidetoshi Matsui, Hugh Colvin, Koichi Kawamoto, Jun Koseki, Naotsugu Haraguchi, Junichi Nishimura, Taishi Hata, Noriko Gotoh, Fumio Matsuda, Taroh Satoh, Tsunekazu Mizushima, Hiroshi Shimizu, Yuichiro Doki, Masaki Mori, Hideshi Ishii

Scientific reports　Vol. 6　p. 38415-38415　2016/12/07　Research paper (scientific journal)

Recent advances in amino acid production by microbial cells

Takashi Hirasawa, Hiroshi Shimizu

CURRENT OPINION IN BIOTECHNOLOGY　Vol. 42　p. 133-146　2016/12

Investigation of useful carbon tracers for ¹³C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions.

Maeda K, Okahashi N, Toya Y, Matsuda F, Shimizu H

Metabolic engineering communications　Vol. 3　p. 187-195　2016/12　Research paper (scientific journal)

Combinatorial deletions of glgC and phaCE enhance ethanol production in Synechocystis sp PCC 6803

Katsunori Namakoshi, Tubasa Nakajima, Katsunori Yoshikawa, Yoshihiro Toya, Hiroshi Shimizu

JOURNAL OF BIOTECHNOLOGY　Vol. 239　p. 13-19　2016/12　Research paper (scientific journal)

Glutamic acid fermentation: Discovery of glutamic acid-producing microorganisms, analysis of the production mechanism, metabolic engineering, and industrial production process

Takashi Hirasawa, Hiroshi Shimizu

Industrial Biotechnology: Products and Processes　p. 339-360　2016/11/26　Part of collection (book)

Positive effects of proline addition on the central metabolism of wild-type and lactic acid-producing Saccharomyces cerevisiae strains

Riyanto Heru Nugroho, Katsunori Yoshikawa, Fumio Matsuda, Hiroshi Shimizu

BIOPROCESS AND BIOSYSTEMS ENGINEERING　Vol. 39　No. 11　p. 1711-1716　2016/11　Research paper (scientific journal)

GC-MS/MS survey of collision-induced dissociation of tert-butyldimethylsilyl-derivatized amino acids and its application to C-13-metabolic flux analysis of Escherichia coli central metabolism

Nobuyuki Okahashi, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda

ANALYTICAL AND BIOANALYTICAL CHEMISTRY　Vol. 408　No. 22　p. 6133-6140　2016/09　Research paper (scientific journal)

Significant association of cadaveric dura mater grafting with subpial Aβ deposition and meningeal amyloid angiopathy.

Hamaguchi T, Taniguchi Y, Sakai K, Kitamoto T, Takao M, Murayama S, Iwasaki Y, Yoshida M, Shimizu H, Kakita A, Takahashi H, Suzuki H, Naiki H, Sanjo N, Mizusawa H, Yamada M

Acta neuropathologica　Vol. 132　No. 2　p. 313-315　2016/08

Metabolome analysis of Saccharomyces cerevisiae and optimization of culture medium for S-adenosyl-L-methionine production

Kenshi Hayakawa, Fumio Matsuda, Hiroshi Shimizu

AMB EXPRESS　Vol. 6　No. 1　2016/06　Research paper (scientific journal)

(13)C-metabolic flux analysis of ethanol-assimilating saccharomyces cerevisiae for S-adenosyl-L-methionine production

K. Hayakawa, F. Matsuda, H. Shimizu

Metabolic Engineering 11　p. 635-636　2016　Research paper (international conference proceedings)

Enhancement of 1,5-diaminopentane production in a recombinant strain of Corynebacterium glutamicum by Tween 40 addition

Yuta Matsushima, Takashi Hirasawa, Hiroshi Shimizu

JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY　Vol. 62　No. 1　p. 42-45　2016　Research paper (scientific journal)

Metabolic characterization of cultured mammalian cells by mass balance analysis, tracer labeling experiments and computer-aided simulations.

Okahashi N, Kohno S, Kitajima S, Matsuda F, Takahashi C, Shimizu H

Journal of bioscience and bioengineering　Vol. 120　No. 6　p. 725-731　2015/12　Research paper (scientific journal)

Enhanced dipicolinic acid production during the stationary phase in Bacillus subtilis by blocking acetoin synthesis.

Toya Y, Hirasawa T, Ishikawa S, Chumsakul O, Morimoto T, Liu S, Masuda K, Kageyama Y, Ozaki K, Ogasawara N, Shimizu H

Bioscience, biotechnology, and biochemistry　Vol. 79　No. 12　p. 2073-2080　2015/12　Research paper (scientific journal)

Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction.

Yoshikawa K, Aikawa S, Kojima Y, Toya Y, Furusawa C, Kondo A, Shimizu H

PloS one　Vol. 10　No. 12　2015/12　Research paper (scientific journal)

(13)C-metabolic flux analysis in S-adenosyl-L-methionine production by Saccharomyces cerevisiae.

Hayakawa K, Kajihata S, Matsuda F, Shimizu H

Journal of bioscience and bioengineering　Vol. 120　No. 5　p. 532-538　2015/11　Research paper (scientific journal)

Metabolomic analysis of acid stress response in Saccharomyces cerevisiae.

Nugroho RH, Yoshikawa K, Shimizu H

Journal of bioscience and bioengineering　Vol. 120　No. 4　p. 396-404　2015/10　Research paper (scientific journal)

Absolute quantitation of glycolytic intermediates reveals thermodynamic shifts in Saccharomyces cerevisiae strains lacking PFK1 or ZWF1 genes.

Nishino S, Okahashi N, Matsuda F, Shimizu H

Journal of bioscience and bioengineering　Vol. 120　No. 3　p. 280-286　2015/09　Research paper (scientific journal)

Phenotypic convergence in bacterial adaptive evolution to ethanol stress.

Horinouchi T, Suzuki S, Hirasawa T, Ono N, Yomo T, Shimizu H, Furusawa C

BMC evolutionary biology　Vol. 15　2015/09　Research paper (scientific journal)

¹³C-based metabolic flux analysis of Saccharomyces cerevisiae with a reduced Crabtree effect.

Kajihata S, Matsuda F, Yoshimi M, Hayakawa K, Furusawa C, Kanda A, Shimizu H

Journal of bioscience and bioengineering　Vol. 120　No. 2　p. 140-144　2015/08　Research paper (scientific journal)

SSDesign: Computational metabolic pathway design based on flux variability using elementary flux modes.

Toya Y, Shiraki T, Shimizu H

Biotechnology and bioengineering　Vol. 112　No. 4　p. 759-768　2015/04　Research paper (scientific journal)

Effect of malic enzyme on ethanol production by Synechocystis sp. PCC 6803.

Yoshikawa K, Hirasawa T, Shimizu H

Journal of bioscience and bioengineering　Vol. 119　No. 1　p. 82-84　2015/01　Research paper (scientific journal)

Nano-scale liquid chromatography coupled to tandem mass spectrometry using the multiple reaction monitoring mode based quantitative platform for analyzing multiple enzymes associated with central metabolic pathways of Saccharomyces cerevisiae using ultra

Matsuda F, Ogura T, Tomita A, Hirano I, Shimizu H

Journal of bioscience and bioengineering　Vol. 119　No. 1　p. 117-120　2015/01　Research paper (scientific journal)

Development of an Automated Culture System for Laboratory Evolution

Takaaki Horinouchi, Teruaki Minamoto, Shingo Suzuki, Hiroshi Shimizu, Chikara Furusawa

JALA　Vol. 19　No. 5　p. 478-482　2014/10　Research paper (scientific journal)

Integrated Metabolic Flux and Omics Analysis of Synechocystis sp PCC 6803 under Mixotrophic and Photoheterotrophic Conditions

Tsubasa Nakajima, Shuichi Kajihata, Katsunori Yoshikawa, Fumio Matsuda, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu

PLANT AND CELL PHYSIOLOGY　Vol. 55　No. 9　p. 1605-1612　2014/09　Research paper (scientific journal)

C-13-metabolic flux analysis in heterologous cellulase production by Bacillus subtilis genome-reduced strain

Yoshihiro Toya, Takashi Hirasawa, Takuya Morimoto, Kenta Masuda, Yasushi Kageyama, Katsuya Ozaki, Naotake Ogasawara, Hiroshi Shimizu

JOURNAL OF BIOTECHNOLOGY　Vol. 179　p. 42-49　2014/06　Research paper (scientific journal)

Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli

Kento Tokuyama, Satoshi Ohno, Katsunori Yoshikawa, Takashi Hirasawa, Shotaro Tanaka, Chikara Furusawa, Hiroshi Shimizu

MICROBIAL CELL FACTORIES　Vol. 13　2014/05　Research paper (scientific journal)

Reliable Metabolic Flux Estimation in Escherichia coli Central Carbon Metabolism Using Intracellular Free Amino Acids.

Okahashi N, Kajihata S, Furusawa C, Shimizu H

Metabolites　Vol. 4　No. 2　p. 408-420　2014/05

Glutamic Acid

Takashi Hirasawa, Hiroshi Shimizu

Bioprocessing of Renewable Resources to Commodity Bioproducts　p. 473-495　2014/04/28　Part of collection (book)

FastPros: screening of reaction knockout strategies for metabolic engineering

Satoshi Ohno, Hiroshi Shimizu, Chikara Furusawa

BIOINFORMATICS　Vol. 30　No. 7　p. 981-987　2014/04　Research paper (scientific journal)

Potential of a Saccharomyces cerevisiae recombinant strain lacking ethanol and glycerol biosynthesis pathways in efficient anaerobic bioproduction

Takashi Hirasawa, Yoshihiro Ida, Chikara Furusawa, Hiroshi Shimizu

BIOENGINEERED　Vol. 5　No. 2　p. 123-128　2014/03　Research paper (scientific journal)

OpenMebius: An Open Source Software for Isotopically Nonstationary C-13-Based Metabolic Flux Analysis

Shuichi Kajihata, Chikara Furusawa, Fumio Matsuda, Hiroshi Shimizu

BIOMED RESEARCH INTERNATIONAL　Vol. 2014　2014　Research paper (scientific journal)

Enhanced acetic acid and succinic acid production under microaerobic conditions by Corynebacterium glutamicum harboring Escherichia coli transhydrogenase gene pntAB

Yuto Yamauchi, Takashi Hirasawa, Masato Nishii, Chikara Furusawa, Hiroshi Shimizu

JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY　Vol. 60　No. 3　p. 112-118　2014　Research paper (scientific journal)

Metabolic engineering of Saccharomyces cerevisiae to improve succinic acid production based on metabolic profiling

Yuma Ito, Takashi Hirasawa, Hiroshi Shimizu

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　Vol. 78　No. 1　p. 151-159　2014/01　Research paper (scientific journal)

A Vector Library for Silencing Central Carbon Metabolism Genes with Antisense RNAs in Escherichia coli

Nobutaka Nakashima, Satoshi Ohno, Katsunori Yoshikawa, Hiroshi Shimizu, Tomohiro Tamura

APPLIED AND ENVIRONMENTAL MICROBIOLOGY　Vol. 80　No. 2　p. 564-573　2014/01　Research paper (scientific journal)

Flux analysis and metabolomics for systematic metabolic engineering of microorganisms

Yoshihiro Toya, Hiroshi Shimizu

Biotechnology Advances　Vol. 31　No. 6　p. 818-826　2013/11　Research paper (scientific journal)

Flux analysis and metabolomics for systematic metabolic engineering of microorganisms.

Toya Y, Shimizu H

Biotechnology advances　Vol. 31　No. 6　p. 818-826　2013/11

ArtPathDesign: rational heterologous pathway design system for the production of nonnative metabolites.

Chatsurachai S, Furusawa C, Shimizu H

Journal of bioscience and bioengineering　Vol. 116　No. 4　p. 524-527　2013/10　Research paper (scientific journal)

Genome-wide identification of the targets for genetic manipulation to improve L-lactate production by Saccharomyces cerevisiae by using a single-gene deletion strain collection.

Hirasawa T, Takekuni M, Yoshikawa K, Ookubo A, Furusawa C, Shimizu H

Journal of biotechnology　Vol. 168　No. 2　p. 185-193　2013/10　Research paper (scientific journal)

Potential of a Saccharomyces cerevisiae recombinant strain lacking ethanol and glycerol biosynthesis pathways in efficient anaerobic bioproduction

Takashi Hirasawa, Yoshihiro Ida, Chikara Furusawa, Hiroshi Shimizu

Bioengineered　Vol. 5　No. 2　2013/09/26　Research paper (scientific journal)

Design of superior cell factories based on systems wide omics analysis

Katsunori Yoshikawa, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu

Systems Metabolic Engineering　p. 57-81　2013/08/01　Part of collection (book)

Utilization of Saccharomyces cerevisiae recombinant strain incapable of both ethanol and glycerol biosynthesis for anaerobic bioproduction.

Ida Y, Hirasawa T, Furusawa C, Shimizu H

Applied microbiology and biotechnology　Vol. 97　No. 11　p. 4811-4819　2013/06　Research paper (scientific journal)

Integrated transcriptomic and metabolomic analysis of the central metabolism of Synechocystis sp. PCC 6803 under different trophic conditions.

Yoshikawa K, Hirasawa T, Ogawa K, Hidaka Y, Nakajima T, Furusawa C, Shimizu H

Biotechnology journal　Vol. 8　No. 5　p. 571-580　2013/05　Research paper (scientific journal)

Systems metabolic engineering for the production of bio-nylon precursor.

Shimizu H

Biotechnology journal　Vol. 8　No. 5　p. 513-514　2013/05　Research paper (scientific journal)

In silico screening of triple reaction knockout Escherichia coli strains for overproduction of useful metabolites.

Ohno S, Furusawa C, Shimizu H

Journal of bioscience and bioengineering　Vol. 115　No. 2　p. 221-228　2013/02　Research paper (scientific journal)

Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.

Ono N, Suzuki S, Furusawa C, Shimizu H, Yomo T

PloS one　Vol. 8　No. 1　2013/01　Research paper (scientific journal)

Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using C-13 metabolic flux analysis

Yuki Usui, Takashi Hirasawa, Chikara Furusawa, Tomokazu Shirai, Natsuko Yamamoto, Hirotada Mori, Hiroshi Shimizu

MICROBIAL CELL FACTORIES　Vol. 11　2012/06　Research paper (scientific journal)

An in silico platform for the design of heterologous pathways in nonnative metabolite production

Sunisa Chatsurachai, Chikara Furusawa, Hiroshi Shimizu

BMC BIOINFORMATICS　Vol. 13　2012/05　Research paper (scientific journal)

Understanding the mechanism of heat stress tolerance caused by high trehalose accumulation in Saccharomyces cerevisiae using DNA microarray

Siraje Arif Mahmud, Takashi Hirasawa, Chikara Furusawa, Katsunori Yoshikawa, Hiroshi Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 113　No. 4　p. 526-528　2012/04　Research paper (scientific journal)

Stable disruption of ethanol production by deletion of the genes encoding alcohol dehydrogenase isozymes in Saccharomyces cerevisiae

Yoshihiro Ida, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 113　No. 2　p. 192-195　2012/02　Research paper (scientific journal)

Systems metabolic engineering: the creation of microbial cell factories by rational metabolic design and evolution.

Furusawa C, Horinouchi T, Hirasawa T, Shimizu H

Advances in biochemical engineering/biotechnology　Vol. 131　p. 1-23　2012/02　Research paper (scientific journal)

Metabolic engineering innovation and developmentintegration of omics research and analysis of metabolism

Shimizu, H., Furusawa, C., Hirasawa, Katsunori, Y., Ono, N., Yoshihiro, T., Satoru, S.

Seibutsu-kogaku Kaishi　Vol. 90　No. 10　2012　Research paper (scientific journal)

Fluctuation-driven adaptation and symbiosis in cellular dynamics

Chikara Furusawa, Kota Ijichi, Hiroshi Shimizu

Lecture Notes of the Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering　Vol. 87　p. 238-248　2012　Research paper (international conference proceedings)

Molecular mechanisms and metabolic engineering of glutamate overproduction in Corynebacterium glutamicum.

Hirasawa T, Kim J, Shirai T, Furusawa C, Shimizu H

Sub-cellular biochemistry　Vol. 64　p. 261-281　2012　Research paper (scientific journal)

Improving protein secretion of a transglutaminase-secreting Corynebacterium glutamicum recombinant strain on the basis of C-13 metabolic flux analysis

Motoki Umakoshi, Takashi Hirasawa, Chikara Furusawa, Yasuhiro Takenaka, Yoshimi Kikuchi, Hiroshi Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 112　No. 6　p. 595-601　2011/12　Research paper (scientific journal)

Evaluating C-13 enrichment data of free amino acids for precise metabolic flux analysis

Eiji Mori, Chikara Furusawa, Shuichi Kajihata, Tomokazu Shirai, Hiroshi Shimizu

BIOTECHNOLOGY JOURNAL　Vol. 6　No. 11　p. 1377-1387　2011/11　Research paper (scientific journal)

Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp PCC6803

Katsunori Yoshikawa, Yuta Kojima, Tsubasa Nakajima, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　Vol. 92　No. 2　p. 347-358　2011/10　Research paper (scientific journal)

Engineering strategy of yeast metabolism for higher alcohol production

Fumio Matsuda, Chikara Furusawa, Takashi Kondo, Jun Ishii, Hiroshi Shimizu, Akihiko Kondo

MICROBIAL CELL FACTORIES　Vol. 10　2011/09　Research paper (scientific journal)

Investigation of phosphorylation status of OdhI protein during penicillin- and Tween 40-triggered glutamate overproduction by Corynebacterium glutamicum

Jongpill Kim, Takashi Hirasawa, Masaki Saito, Chikara Furusawa, Hiroshi Shimizu

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　Vol. 91　No. 1　p. 143-151　2011/07　Research paper (scientific journal)

Comprehensive phenotypic analysis of single-gene deletion and overexpression strains of Saccharomyces cerevisiae

Katsunori Yoshikawa, Tadamasa Tanaka, Yoshihiro Ida, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu

YEAST　Vol. 28　No. 5　p. 349-361　2011/05　Research paper (scientific journal)

1E1312 P71 Whole genome resequencing of experimentally evolved Escherichia coli using a next generation sequencer(Genome biology, Bioinformatics,The 49th Annual Meeting of the Biophysical Society of Japan)

Ono Naoaki, Horinouchi Takaaki, Tamaoka Kuniyasu, Suzuki Shingo, Hirasawa Takashi, Furusawa Chikara, Yomo Tetsuya, Shimizu Hiroshi

Seibutsu Butsuri　Vol. 51　2011

3N1112 Multi-omics analysis of evolved Escherichia coli strains under ethanol stress revealed slow adaptation dynamics(Protein : Measurement & Analysis, Origin of life & Evolution,The 49th Annual Meeting of the Biophysical Society of Japan)

Horinouchi Takaaki, Suzuki Shingo, Ono Naoaki, Tamaoka Kuniyasu, Hirasawa Takashi, Yomo Tetsuya, Shimizu Hiroshi, Furusawa Chikara

Seibutsu Butsuri　Vol. 51　2011

Genome-wide expression analysis of Saccharomyces pastorianus orthologous genes using oligonucleotide microarrays.

Horinouchi T, Yoshikawa K, Kawaide R, Furusawa C, Nakao Y, Hirasawa T, Shimizu H

Journal of bioscience and bioengineering　Vol. 110　No. 5　p. 602-607　2010/11　Research paper (scientific journal)

Genome-wide expression analysis of Saccharomyces pastorianus orthologous genes using oligonucleotide microarrays.

Horinouchi T, Yoshikawa K, Kawaide R, Furusawa C, Nakao Y, Hirasawa T, Shimizu H

Journal of bioscience and bioengineering　Vol. 110　No. 5　p. 602-607　2010/11　Research paper (scientific journal)

Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress.

Horinouchi T, Tamaoka K, Furusawa C, Ono N, Suzuki S, Hirasawa T, Yomo T, Shimizu H

BMC genomics　Vol. 11　2010/10/01　Research paper (scientific journal)

Saccharomyces cerevisiae and DNA microarray analyses: what did we learn from it for a better understanding and exploitation of yeast biotechnology?

Hirasawa T, Furusawa C, Shimizu H

Applied microbiology and biotechnology　Vol. 87　No. 2　p. 391-400　2010/06

Requirement of de novo synthesis of the OdhI protein in penicillin-induced glutamate production by Corynebacterium glutamicum.

Kim J, Fukuda H, Hirasawa T, Nagahisa K, Nagai K, Wachi M, Shimizu H

Applied microbiology and biotechnology　Vol. 86　No. 3　p. 911-920　2010/04　Research paper (scientific journal)

Differential importance of trehalose accumulation in Saccharomyces cerevisiae in response to various environmental stresses.

Mahmud SA, Hirasawa T, Shimizu H

Journal of bioscience and bioengineering　Vol. 109　No. 3　p. 262-266　2010/03　Research paper (scientific journal)

Differential importance of trehalose accumulation in Saccharomyces cerevisiae in response to various environmental stresses.

Mahmud SA, Hirasawa T, Shimizu H

Journal of bioscience and bioengineering　Vol. 109　No. 3　p. 262-266　2010/03　Research paper (scientific journal)

1P284 1H1255 Environmental adaptation over multiple time scales : comprehensive expression/mutation analysis of evolved E. coli under ethanol stress(Origin of life & Evolution,Oral Presentations,The 48th Annual Meeting of the Biophysical Society of Japan)

Horinouchi Takaaki, Tamaoka Kuniyasu, Furusawa Chikara, Ono Naoaki, Suzuki Shingo, Hirasawa Takashi, Yomo Tetsuya, Shimizu Hiroshi

Seibutsu Butsuri　Vol. 50　No. 2　2010

Relationship between noise characteristics in protein expressions and regulatory structures of amino acid biosynthesis pathways

Yamada T, Ou J, Furusawa C, Hirasawa T, Yomo T, Shimizu H

Iet Systems Biology　Vol. 4　No. 1　p. 82-89　2010　Research paper (scientific journal)

Investigating the effectiveness of DNA microarray analysis for identifying the genes involved in l-lactate production by Saccharomyces cerevisiae.

Hirasawa T, Ookubo A, Yoshikawa K, Nagahisa K, Furusawa C, Sawai H, Shimizu H

Applied microbiology and biotechnology　Vol. 84　No. 6　p. 1149-1159　2009/10　Research paper (scientific journal)

Analysis of stochasticity in promoter activation by using a dual-fluorescence reporter system.

Ou J, Furusawa C, Yomo T, Shimizu H

Bio Systems　Vol. 97　No. 3　p. 160-164　2009/09　Research paper (scientific journal)

Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum.

Shinfuku Y, Sorpitiporn N, Sono M, Furusawa C, Hirasawa T, Shimizu H

Microbial cell factories　Vol. 8　2009/08/03　Research paper (scientific journal)

Analysis of adaptation to high ethanol concentration in Saccharomyces cerevisiae using DNA microarray.

Dinh TN, Nagahisa K, Yoshikawa K, Hirasawa T, Furusawa C, Shimizu H

Bioprocess and biosystems engineering　Vol. 32　No. 5　p. 681-688　2009/08　Research paper (scientific journal)

Proteomic analysis of responses to osmotic stress in laboratory and sake-brewing strains of Saccharomyces cerevisiae

Takashi Hirasawa, Kazuyuki Yamada, Keisuke Nagahisa, Thai Nho Dinh, Chikara Furusawa, Yoshio Katakura, Suteaki Shioya, Hiroshi Shimizu

PROCESS BIOCHEMISTRY　Vol. 44　No. 6　p. 647-653　2009/06　Research paper (scientific journal)

Analysis of metabolic network based on conservation of molecular structure.

Hogiri T, Furusawa C, Shinfuku Y, Ono N, Shimizu H

Bio Systems　Vol. 95　No. 3　p. 175-178　2009/03　Research paper (scientific journal)

Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stress in Saccharomyces cerevisiae.

Yoshikawa K, Tanaka T, Furusawa C, Nagahisa K, Hirasawa T, Shimizu H

FEMS yeast research　Vol. 9　No. 1　p. 32-44　2009/02　Research paper (scientific journal)

3P-227 Development of resequcencing algorithm for next generation sequencer based on mate-pair distance(Genome biology:Genome analysis,The 47th Annual Meeting of the Biophysical Society of Japan)

Ono Naoaki, Suzuki Shingo, Furusawa Shingo, Shimizu Hiroshi, Yomo Tetsuya

Seibutsu Butsuri　Vol. 49　2009

Effect of odhA overexpression and odhA antisense RNA expression on Tween-40-triggered glutamate production by Corynebacterium glutamicum.

Kim J, Hirasawa T, Sato Y, Nagahisa K, Furusawa C, Shimizu H

Applied microbiology and biotechnology　Vol. 81　No. 6　p. 1097-1106　2009/01　Research paper (scientific journal)

Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays.

Furusawa C, Ono N, Suzuki S, Agata T, Shimizu H, Yomo T

Bioinformatics (Oxford, England)　Vol. 25　No. 1　p. 36-41　2009/01/01　Research paper (scientific journal)

Effect of trehalose accumulation on response to saline stress in Saccharomyces cerevisiae.

Mahmud SA, Nagahisa K, Hirasawa T, Yoshikawa K, Ashitani K, Shimizu H

Yeast (Chichester, England)　Vol. 26　No. 1　p. 17-30　2009/01　Research paper (scientific journal)

Genome-wide analysis of the effects of location and number of stress response elements on gene expression in Saccharomyces cerevisiae.

Yoshikawa K, Furusawa C, Hirasawa T, Shimizu H

Journal of bioscience and bioengineering　Vol. 106　No. 5　p. 507-510　2008/11　Research paper (scientific journal)

Improvement of L-lactate production by CYB2 gene disruption in a recombinant Saccharomyces cerevisiae strain under low pH condition.

Ookubo A, Hirasawa T, Yoshikawa K, Nagahisa K, Furusawa C, Shimizu H

Bioscience, biotechnology, and biochemistry　Vol. 72　No. 11　p. 3063-3066　2008/11　Research paper (scientific journal)

Genome-wide analysis of the effects of location and number of stress response elements on gene expression in Saccharomyces cerevisiae.

Yoshikawa K, Furusawa C, Hirasawa T, Shimizu H

Journal of bioscience and bioengineering　Vol. 106　No. 5　p. 507-510　2008/11　Research paper (scientific journal)

Comprehensive phenotypic analysis of yeast under ethanol stress condition

Katsunori Yoshikawa, Tadamasa Tanaka, Chikara Furusawa, Keisuke Nagahisa, Takashi Hirasawa, Hiroshi Shimizu

JOURNAL OF BIOTECHNOLOGY　Vol. 136　p. S111-S111　2008/10

Beer volatile compounds and their application to low-malt beer fermentation.

Kobayashi M, Shimizu H, Shioya S

Journal of bioscience and bioengineering　Vol. 106　No. 4　p. 317-323　2008/10

Beer volatile compounds and their application to low-malt beer fermentation.

Kobayashi M, Shimizu H, Shioya S

Journal of bioscience and bioengineering　Vol. 106　No. 4　p. 317-323　2008/10

Adaptation of Saccharomyces cerevisiae cells to high ethanol concentration and changes in fatty acid composition of membrane and cell size.

Dinh TN, Nagahisa K, Hirasawa T, Furusawa C, Shimizu H

PloS one　Vol. 3　No. 7　2008/07/09　Research paper (scientific journal)

An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays.

Ono N, Suzuki S, Furusawa C, Agata T, Kashiwagi A, Shimizu H, Yomo T

Bioinformatics (Oxford, England)　Vol. 24　No. 10　p. 1278-1285　2008/05/01　Research paper (scientific journal)

Dynamic change in promoter activation during lysine biosynthesis in Escherichia coli cells.

Ou J, Yamada T, Nagahisa K, Hirasawa T, Furusawa C, Yomo T, Shimizu H

Molecular bioSystems　Vol. 4　No. 2　p. 128-134　2008/02　Research paper (scientific journal)

Metabolic flux balance analysis of an industrially useful microorganism corynebacerium glutamicum by a genome-scale reconstructed model

Hiroshi Shimizu, Yohei Shinfuku, Masahiro Sono, Chikara Furusawa, Takashi Hirasawa

3rd International ICST Conference on Bio-Inspired Models of Network, Information and Computing Systems, BIONETICS 2008　2008　Research paper (international conference proceedings)

Quantitative expression analysis using oligonucleotide microarrays based on a physico-chemical model

Naoaki Ono, Shingo Suzuki, Chikara Furusawa, Hiroshi Shimizu, Tetsuya Yomo

3rd International ICST Conference on Bio-Inspired Models of Network, Information and Computing Systems, BIONETICS 2008　2008　Research paper (international conference proceedings)

1P-283 Genome wide mutation detection of Eschericia Coli using resequencing microarrays(The 46th Annual Meeting of the Biophysical Society of Japan)

ONO Naoaki, SUZUKI Shingo, FURUSAWA Chikara, SHIMIZU Hiroshi, YOMO Tetsuya

Seibutsu Butsuri　Vol. 48　2008

1P-296 A dynamic adaptive model of cell population for the emergence of complex ecosystem(The 46th Annual Meeting of the Biophysical Society of Japan)

Ijichi Kota, Furusawa Chikara, Ono Naoaki, Shimizu Hiroshi

Seibutsu Butsuri　Vol. 48　2008

Distinct roles of two anaplerotic pathways in glutamate production induced by biotin limitation in Corynebacterium glutamicum

Sato, H, Orishimo, K, Shirai, T, Hirasawa, T, Nagahisa, K, Shimizu, H, Wachi, M

J. Biosci. Biotechnol.　Vol. 106　No. 1　p. 51-58　2008　Research paper (scientific journal)

Analysis of fluctuation in protein abundance without promoter regulation based on Escherichia coli continuous culture

Tadashi Yamada, Chikara Furusawa, Keisuke Nagahisa, Akiko Kashiwagi, Tetsuya Yomo, Hiroshi Shimizu

BIOSYSTEMS　Vol. 90　No. 3　p. 614-622　2007/11　Research paper (scientific journal)

Identification of target genes conferring ethanol stress tolerance to Saccharomyces cerevisiae based on DNA microarray data analysis.

Hirasawa T, Yoshikawa K, Nakakura Y, Nagahisa K, Furusawa C, Katakura Y, Shimizu H, Shioya S

Journal of biotechnology　Vol. 131　No. 1　p. 34-44　2007/08/01　Research paper (scientific journal)

Study on roles of anaplerotic pathways in glutamate overproduction of Corynebacterium glutamicum by metabolic flux analysis.

Shirai T, Fujimura K, Furusawa C, Nagahisa K, Shioya S, Shimizu H

Microbial cell factories　Vol. 6　2007/06/02　Research paper (scientific journal)

Analysis of hemin effect on lactate reduction in Lactococcus lactis

Machiko Nagayasu, Agustin Krisna Wardani, Keisuke Nagahisa, Hiroshi Shimizu, Suteaki Shioya

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 103　No. 6　p. 529-534　2007/06　Research paper (scientific journal)

Physiological analysis of yeast cells by flow cytometry during serial-repitching of low-malt beer fermentation.

Kobayashi M, Shimizu H, Shioya S

Journal of bioscience and bioengineering　Vol. 103　No. 5　p. 451-456　2007/05　Research paper (scientific journal)

Extracting the hidden features in saline osmotic tolerance in Saccharomyces cerevisiae from DNA microarray data using the self-organizing map: biosynthesis of amino acids

Gaurav Pandey, Katsunori Yoshikawa, Takashi Hirasawa, Keisuke Nagahisa, Yoshio Katakura, Chikara Furusawa, Hiroshi Shimizu, Suteaki Shioya

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　Vol. 75　No. 2　p. 415-426　2007/05　Research paper (scientific journal)

Physiological analysis of yeast cells by flow cytometry during serial-repitching of low-malt beer fermentation.

Kobayashi M, Shimizu H, Shioya S

Journal of bioscience and bioengineering　Vol. 103　No. 5　p. 451-456　2007/05　Research paper (scientific journal)

Kinetic modeling of kefiran production in mixed culture of Lactobacillus kefiranofaciens and Saccharomyces cerevisiae

Benjamas Cheirsilp, Hiroshi Shimizu, Suteaki Shioya

PROCESS BIOCHEMISTRY　Vol. 42　No. 4　p. 570-579　2007/04　Research paper (scientific journal)

Inverse metabolic engineering by integration of multiple omics analyses

Hiroshi Shimizu, Takashi Hirasawa, Katsunori Yoshikawa, Yuki Nakakura, Keisuke Nagahisa, Chikara Furusawa, Yoshio Katakura, Suteaki Shioya

IFAC Proceedings Volumes (IFAC-PapersOnline)　Vol. 10　p. 19-24　2007　Research paper (international conference proceedings)

Production of glutamate and glutamate-related amino acids: Molecular mechanism analysis and metabolic engineering

Hiroshi Shimizu, Takashi Hirasawa

Microbiology Monograph　Vol. 5　p. 1-38　2007

Characterization and enzymatic degradation of microbial copolyester P(3HB-co-3HV)s produced by metabolic reaction model-based system

Suchada Chanprateep, Hiroshi Shimizu, Suteaki Shioya

POLYMER DEGRADATION AND STABILITY　Vol. 91　No. 12　p. 2941-2950　2006/12　Research paper (scientific journal)

Comparison of transcriptional responses to osmotic stresses induced by NaCl and sorbitol additions in Saccharomyces cerevisiae using DNA microarray.

Hirasawa T, Ashitani K, Yoshikawa K, Nagahisa K, Furusawa C, Katakura Y, Shimizu H, Shioya S

Journal of bioscience and bioengineering　Vol. 102　No. 6　p. 568-571　2006/12　Research paper (scientific journal)

Simultaneous control of apparent extract and volatile compounds concentrations in low-malt beer fermentation.

Kobayashi M, Nagahisa K, Shimizu H, Shioya S

Applied microbiology and biotechnology　Vol. 73　No. 3　p. 549-558　2006/12　Research paper (scientific journal)

Comparison of transcriptional responses to osmotic stresses induced by NaCl and sorbitol additions in Saccharomyces cerevisiae using DNA microarray.

Hirasawa T, Ashitani K, Yoshikawa K, Nagahisa K, Furusawa C, Katakura Y, Shimizu H, Shioya S

Journal of bioscience and bioengineering　Vol. 102　No. 6　p. 568-571　2006/12　Research paper (scientific journal)

Precise metabolic flux analysis of coryneform bacteria by gas chromatography-mass spectrometry and verification by nuclear magnetic resonance.

Shirai T, Matsuzaki K, Kuzumoto M, Nagahisa K, Furusawa C, Shioya S, Shimizu H

Journal of bioscience and bioengineering　Vol. 102　No. 5　p. 413-424　2006/11　Research paper (scientific journal)

Precise metabolic flux analysis of coryneform bacteria by gas chromatography-mass spectrometry and verification by nuclear magnetic resonance.

Shirai T, Matsuzaki K, Kuzumoto M, Nagahisa K, Furusawa C, Shioya S, Shimizu H

Journal of bioscience and bioengineering　Vol. 102　No. 5　p. 413-424　2006/11　Research paper (scientific journal)

Computational prediction of impact of rerouting the carbon flux in metabolic pathway on cell growth and nisin production by Lactococcus lactis

AK Wardani, S Egawa, K Nagahisa, H Shimizu, S Shioya

BIOCHEMICAL ENGINEERING JOURNAL　Vol. 28　No. 3　p. 220-230　2006/03　Research paper (scientific journal)

Robustness of cascade pH and dissolved oxygen control in symbiotic nisin production process system of Lactococcus lactis and Kluyveromyces marxianus.

Wardani AK, Egawa S, Nagahisa K, Shimizu H, Shioya S

Journal of bioscience and bioengineering　Vol. 101　No. 3　p. 274-276　2006/03　Research paper (scientific journal)

Robustness of cascade pH and dissolved oxygen control in symbiotic nisin production process system of Lactococcus lactis and Kluyveromyces marxianus.

Wardani AK, Egawa S, Nagahisa K, Shimizu H, Shioya S

Journal of bioscience and bioengineering　Vol. 101　No. 3　p. 274-276　2006/03　Research paper (scientific journal)

2P480 Relationship between Evolutionary Dynamics and Preservation of Molecular Structures in Metabolic Network(50. Non-equilibrium and complex system,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Hogiri Tomoharu, Ono Naoaki, Furusawa Chikara, Shimizu Hiroshi

Seibutsu Butsuri　Vol. 46　No. 2　2006

1P402 Heterogeneity of cell population in continuous culture of Escherichia coli(16. Cell-cell communication,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Sadamitsu Makoto, Furusawa Chikara, Kashiwagi Akiko, Yomo Tetsuya, Shimizu Hiroshi

Seibutsu Butsuri　Vol. 46　No. 2　2006

Microbial interaction in a symbiotic bioprocess of lactic acid bacterium and diary yeast

Hiroshi Shimizu, Sunao Egawa, Agustin K. Wardani, Keisuke Nagahisa, Suteaki Shioya

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)　Vol. 3853　p. 93-106　2006　Research paper (international conference proceedings)

Analysis of fluctuation in gene expression based on continuous culture system

Tadashi Yamada, Makoto Sadamitsu, Keisuke Nagahisa, Akiko Kashiwagi, Chikara Furusawa, Tetsuya Yomo, Hiroshi Shimizu

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)　Vol. 3853　p. 113-127　2006　Research paper (international conference proceedings)

Application of a mathematical model and Differential Evolution algorithm approach to optimization of bacteriocin production by Lactococcus lactis C7

Sompop Moonchai, Weeranuch Madlhoo, Kanidtha Jariyachavalit, Hiroshi Shimizu, Suteaki Shioya, Somchai Chauvatcharin

Bioprocess and Biosystems Engineering　Vol. 28　No. 1　p. 15-26　2005/12　Research paper (scientific journal)

Comparative analysis of transcriptional responses to saline stress in the laboratory and brewing strains of Saccharomyces cerevisiae with DNA microarray.

Hirasawa T, Nakakura Y, Yoshikawa K, Ashitani K, Nagahisa K, Furusawa C, Katakura Y, Shimizu H, Shioya S

Appl Microbiol Biotechnol.　Vol. 70　No. 3　p. 346-357　2005/11　Research paper (scientific journal)

Development of Co-Culture Systems of Lactic Acid Bacteria and Yeasts of Bioproduction

SHIMIZU Hiroshi, CHEIRSILP Benjamas, SHIOYA Suteaki

Japanese Journal of Lactic Acid Bacteria　Vol. 16　No. 1　p. 2-10　2005/06/01

Comparative study of flux redistribution of metabolic pathway in glutamate production by two coryneform bacteria

T Shirai, A Nakato, N Izutani, K Nagahisa, S Shioya, E Kimura, Y Kawarabayasi, A Yamagishi, T Gojobori, H Shimizu

METABOLIC ENGINEERING　Vol. 7　No. 2　p. 59-69　2005/03　Research paper (scientific journal)

On-line estimation and control of apparent extract concentration in low-malt beer fermentation

Michiko Kobayashi, Toshinari Hiroshima, Keisuke Nagahisa, Hiroshi Shimizu, Suteaki Shioya

Journal of the Institute of Brewing　Vol. 111　No. 2　p. 128-136　2005　Research paper (scientific journal)

DNA microarray analysis on Saccharomyces cerevisiae under high carbon dioxide concentration in fermentation process

Nagahisa K, Nakajima T, Yoshikawa K, Hirasawa T, Katakura Y, Furusawa C, Shioya S, Shimizu H

Biotechnology and Bioprocess Engineering　Vol. 10　No. 5　p. 451-461　2005　Research paper (scientific journal)

Gene network analysis by a self-organizing map and an artificial neural network

Jihua Huang, Hiroshi Shimizu, Suteaki Shioya

IFAC Proceedings Volumes (IFAC-PapersOnline)　Vol. 37　No. 3　p. 275-280　2004　Research paper (international conference proceedings)

Simultaneous control of apparent extract and volatile compounds concentrations in beer fermentation

Suteaki Shioya, Michiko Kobayashi, Toshinari Hiroshima, Hiroshi Shimizu

IFAC Proceedings Volumes (IFAC-PapersOnline)　Vol. 37　No. 3　p. 451-456　2004　Research paper (international conference proceedings)

Analysis of Cell Population Dynamics in Continuous Culture of Escherichia coli

Yamada Tadashi, Maeoka Kouhei, Kashiwagi Akiko, Nagahisa Keisuke, Furusawa Chikara, Shioya Suteaki, Yomo Tetsuya, Shimizu Hiroshi

Asian Pacific Confederation of Chemical Engineering congress program and abstracts　Vol. 2004　p. 809-809　2004

Analysis of DNA Microarray Data using Self-Organizing Map and Hierarchical Clustering

Yoshikawa Katsunori, Pandey Gaurav, Hirasawa Takashi, Katakura Yoshio, Nagahisa Keisuke, Furusawa Chikara, Shioya Suteaki, Shimizu Hiroshi

Asian Pacific Confederation of Chemical Engineering congress program and abstracts　Vol. 2004　p. 778-778　2004

Simultaneous Control of Apparent Extract and Volatile Compounds Concentrations in a Beer Brewing Process

Kobayashi Michiko, Nagahisa Keisuke, Shimizu Hiroshi, Shioya Suteaki

Asian Pacific Confederation of Chemical Engineering congress program and abstracts　Vol. 2004　p. 787-787　2004

Metabolic Flux Analysis in Two Kinds of Coryneform Bacteria with GC-MS and NMR

Shirai Tomokazu, Kuzumoto Masanori, Matsuzaki Kunihiro, Satou Yoshiyasu, Nagahisa Keisuke, Furusawa Chikara, Shimizu Hiroshi, Shioya Suteaki

Asian Pacific Confederation of Chemical Engineering congress program and abstracts　Vol. 2004　p. 775-775　2004

Metabolic Systems Analysis at a Key Branch Point of Glutamate Production by Coryneform Bacteria

Shimizu Hiroshi, Shirai Tomokazu, Kuzumoto Masanori, Hirasawa Takashi, Katakura Yoshio, Nagahisa Keisuke, Furusawa Chikara, Shioya Suteaki

Asian Pacific Confederation of Chemical Engineering congress program and abstracts　Vol. 2004　p. 423-423　2004

Rational Design of Metabolic Pathway Improvement based on DNA Microarray Data in Yeast

Hirasawa Takashi, Nakakura Yuki, Hui Zhao, Nagahisa Keisuke, Katakura Yoshio, Shimizu Hiroshi, Shioya Suteaki

Asian Pacific Confederation of Chemical Engineering congress program and abstracts　Vol. 2004　p. 422-422　2004

Metabolic Pathway Recruiting through Modeling of Saccharomyces cerevisiae based on Genomics for Industrial Application

Shioya Suteaki, Shimizu Hiroshi, Hirasawa Takashi, Nagahisa Keisuke, Katakura Yoshio, Furusawa Chikara

Asian Pacific Confederation of Chemical Engineering congress program and abstracts　Vol. 2004　p. 416-416　2004

Analysis of Adaptation of Yeast Cells to a High Osmotic Pressure Stress based on Proteomics

Nagahisa Keisuke, Yamada Kazuyuki, Nakakura Yuki, Hirasawa Takashi, Katakura Yoshio, Shimizu Hiroshi, Shioya Suteaki

Asian Pacific Confederation of Chemical Engineering congress program and abstracts　Vol. 2004　p. 431-431　2004

Analysis of responses of complex bionetworks to changes in environmental conditions

H Shimizu, T Hirasawa, K Nagahisa, S Shioya

BIOLOGICALLY INSPIRED APPROACHES TO ADVANCED INFORMATION TECHNOLOGY　Vol. 3141　p. 13-27　2004　Research paper (scientific journal)

Interactions between Lactobacillus kefiranofaciens and Saccharomyces cerevisiae in mixed culture for kefiran production.

Cheirsilp B, Shoji H, Shimizu H, Shioya S

Journal of bioscience and bioengineering　Vol. 96　No. 3　p. 279-284　2003/12　Research paper (scientific journal)

Clustering gene expression pattern and extracting relationship in gene network based on artificial neural networks.

Huang J, Shimizu H, Shioya S

Journal of bioscience and bioengineering　Vol. 96　No. 5　p. 421-428　2003/12　Research paper (scientific journal)

Nonisothermal crystallization kinetics of biodegradable random poly(3-hydroxybutyrate-co-3-hydroxyvalerate) and block one

Suchada Chanprateep, Kensuke Kikuya, Hiroshi Shimizu, Shuhei Seki, Seiichi Tagawa, Suteaki Shioya

Journal of Chemical Engineering of Japan　Vol. 36　No. 6　p. 639-646　2003/06　Research paper (scientific journal)

Effects of the changes in enzyme activities on metabolic flux redistribution around the 2-oxoglutarate branch in glutamate production by Corynebacterium glutamicum

H Shimizu, H Tanaka, A Nakato, K Nagahisa, E Kimura, S Shioya

BIOPROCESS AND BIOSYSTEMS ENGINEERING　Vol. 25　No. 5　p. 291-298　2003/03　Research paper (scientific journal)

Enhanced kefiran production by mixed culture of Lactobacillus kefiranofaciens and Saccharomyces cerevisiae

B Cheirsilp, H Shimizu, S Shioya

JOURNAL OF BIOTECHNOLOGY　Vol. 100　No. 1　p. 43-53　2003/01　Research paper (scientific journal)

Metabolic engineering - Integrating methodologies of molecular breeding and bioprocess systems engineering

H Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 94　No. 6　p. 563-573　2002/12

Classification of fermentation performance by multivariate analysis based on mean hypothesis testing

JH Huang, H Nanami, A Kanda, H Shimizu, S Shioya

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 94　No. 3　p. 251-257　2002/09　Research paper (scientific journal)

Data preprocessing and output evaluation of an autoassociative neural network model for online fault detection in virginiamycin production

JH Huang, H Shimizu, S Shioya

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 94　No. 1　p. 70-77　2002/07　Research paper (scientific journal)

Model predictive controller for biodegradable polyhydroxyalkanoate production in fed-batch culture

S Chanprateep, K Kikuya, H Shimizu, S Shioya

JOURNAL OF BIOTECHNOLOGY　Vol. 95　No. 2　p. 157-169　2002/05　Research paper (scientific journal)

Effect of carbon and nitrogen additions on consumption activity of apparent extract of yeast cells in a brewing process

Hiroshi Shimizu, Seiichi Mizuno, Toshinari Hiroshima, Suteaki Shioya

Journal of the American Society of Brewing Chemists　Vol. 60　No. 4　p. 163-169　2002　Research paper (scientific journal)

Roles of glucose and acetate as carbon sources in L-histidine production with Brevibacterium flavum FERM1564 revealed by metabolic flux analysis

Hiroshi Shimizu, Nobuyuki Shimizu, Suteaki Shioya

Biotechnology and Bioprocess Engineering　Vol. 7　No. 3　p. 171-177　2002　Research paper (scientific journal)

Importance of carbon source feeding and pH control strategies for maximum kojic acid production from sago starch by Aspergillus flavus

Mohamad Rosfarizan, Ariff Arbakariya, Mohd Ali Hassan, Mohamed Ismail Abdul Karim, Shimizu Hiroshi, Shioya Suteaki

Journal of Bioscience and Bioengineering　Vol. 94　No. 2　p. 99-105　2002　Research paper (scientific journal)

Metabolic control analysis in glutamate synthetic pathway: Experimental sensitivity analysis at a key branch point

H Shimizu, H Tanaka, A Nakato, K Nagahisa, S Shioya

BIOLOGICAL SYSTEMS ENGINEERING　Vol. 830　p. 39-52　2002　Research paper (scientific journal)

Modelling and optimization of environmental conditions for kefiran production by Lactobacillus kefiranofaciens

B Cheirsilp, H Shimizu, S Shioya

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　Vol. 57　No. 5-6　p. 639-646　2001/12　Research paper (scientific journal)

Multivariable control of alcohol concentrations in the production of polyhydroxyalkanoates (PHAs) by Paracoccus denitrificans

S Chanprateep, N Abe, H Shimizu, T Yamane, S Shioya

BIOTECHNOLOGY AND BIOENGINEERING　Vol. 74　No. 2　p. 116-124　2001/07　Research paper (scientific journal)

Maximizing yellow pigment production in fed-batch culture of Monascus sp.

Somchai Krairak, Kouji Yamamura, Ryoichi Irie, Mikio Nakajima, Hiroshi Shimizu, Patoomporn Chim-Anage, Busaba Yongsmith, Suteaki Shioya

Journal of Bioscience and Bioengineering　Vol. 90　No. 4　p. 363-367　2000　Research paper (scientific journal)

Mining of biological data II: Assessing data structure and class homogeneity by cluster analysis

Roy T. Kamimura, Silvio Bicciato, Hiroshi Shimizu, Joe Alford, Gregory Stephanopoulos

Metabolic Engineering　Vol. 2　No. 3　p. 228-238　2000　Research paper (scientific journal)

Mining of biological data I: Identifying discriminating features via mean hypothesis testing

Roy T. Kamimura, Silvio Bicciato, Hiroshi Shimizu, Joe Alford, Gregory Stephanopoulos

Metabolic Engineering　Vol. 2　No. 3　p. 218-227　2000　Research paper (scientific journal)

A Maximum Production Strategy of Lysine Based on a Simplified Model Derived from a Metabolic Reaction Network

Hiroshi Shimizu, Noboru Takiguchi, Hisaya Tanaka, Suteaki Shioya

METABOLIC ENGINEERING　Vol. 1　No. 4　p. 299-308　1999/10　Research paper (scientific journal)

Nisin production by a mixed-culture system consisting of Lactococcus lactis and Kluyveromyces marxianus

H Shimizu, T Mizuguchi, E Tanaka, S Shioya

APPLIED AND ENVIRONMENTAL MICROBIOLOGY　Vol. 65　No. 7　p. 3134-3141　1999/07　Research paper (scientific journal)

On-line monitoring of fungal cell concentration by dielectric spectroscopy

S. Krairak, K. Yamamura, M. Nakajima, H. Shimizu, S. Shioya

Journal of Biotechnology　Vol. 69　No. 2-3　p. 115-123　1999/04/15　Research paper (scientific journal)

Maximum production strategy for biodegradable copolymer P(HB-co-HV) in fed-batch culture of Alcaligenes eutrophus

H Shimizu, Y Kozaki, H Kodama, S Shioya

BIOTECHNOLOGY AND BIOENGINEERING　Vol. 62　No. 5　p. 518-525　1999/03　Research paper (scientific journal)

Optimization of agitation and aeration conditions for maximum virginiamycin production

S Shioya, M Morikawa, Y Kajihara, H Shimizu

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　Vol. 51　No. 2　p. 164-169　1999/02　Research paper (scientific journal)

Feeding strategy of required components by metabolic engineering approach in a lysine production process

N Takiguchi, N Fukui, N Shimizu, H Shimizu, S Shioya

COMPUTER APPLICATIONS IN BIOTECHNOLOGY 1998　p. 375-380　1998　Research paper (international conference proceedings)

Bioprocess fault detection by nonlinear multivariate analysis: Application of an artificial autoassociative neural network and wavelet filter bank

Hiroshi Shimizu, Kouichi Yasuoka, Keiji Uchiyama, Suteaki Shioya

Biotechnology Progress　Vol. 14　No. 1　p. 79-87　1998/01　Research paper (scientific journal)

Method of Corynebacterium glutamicum fermentation time extension with high lysine production rate by leucine addition

Noboru Takiguchi, Naoki Fukui, Nobuyuki Shimizu, Hiroshi Shimizu, Suteaki Shioya

Journal of Fermentation and Bioengineering　Vol. 86　No. 2　p. 180-184　1998　Research paper (scientific journal)

An on-line physiological state recognition system for the lysine fermentation process based on a metabolic reaction model

N Takiguchi, H Shimizu, S Shioya

BIOTECHNOLOGY AND BIOENGINEERING　Vol. 55　No. 1　p. 170-181　1997/07　Research paper (scientific journal)

On-line fault diagnosis for optimal rice α-amylase production process of a temperature-sensitive mutant of Saccharomyces cerevisiae by an autoassociative neural network

Hiroshi Shimizu, Kouichi Yasuoka, Keiji Uchiyama, Suteaki Shioya

Journal of Fermentation and Bioengineering　Vol. 83　No. 5　p. 435-442　1997　Research paper (scientific journal)

On-line recognition of physiological state in a yeast fed-batch culture

H Shimizu, K Miura, S Shioya, K Suga

JOURNAL OF PROCESS CONTROL　Vol. 6　No. 6　p. 373-378　1996/12　Research paper (scientific journal)

Maximum virginiamycin production by optimization of cultivation conditions in batch culture with autoregulator addition

YK Yang, M Morikawa, H Shimizu, S Shioya, K Suga, T Nihira, Y Yamada

BIOTECHNOLOGY AND BIOENGINEERING　Vol. 49　No. 4　p. 437-444　1996/02　Research paper (scientific journal)

Comparison of estimation techniques for a time-dependent parameter in a metabolic reaction model

Hiroshi Shimizu, Keigo Miura, Noboru Takiguchi, Suteaki Shioya

Journal of Fermentation and Bioengineering　Vol. 81　No. 4　p. 363-365　1996　Research paper (scientific journal)

Mole fraction control of poly(3-hydroxybutyric-co-3-hydroxyvaleric) acid in fed-batch culture of Alcaligenes eutrophus

Yoshiyuki Ishihara, Hiroshi Shimizu, Suteaki Shioya

Journal of Fermentation and Bioengineering　Vol. 81　No. 5　p. 422-428　1996　Research paper (scientific journal)

Image analysis of mycelial morphology in virginiamycin production by batch culture of Streptomyces virginiae

YK Yang, M Morikawa, H Shimizu, S Shioya, K Suga, T Nihira, Y Yamada

JOURNAL OF FERMENTATION AND BIOENGINEERING　Vol. 81　No. 1　p. 7-12　1996　Research paper (scientific journal)

OPTIMUM AUTOREGULATOR ADDITION STRATEGY FOR MAXIMUM VIRGINIAMYCIN PRODUCTION IN BATCH CULTURE OF STREPTOMYCES-VIRGINIAE

YK YANG, H SHIMIZU, S SHIOYA, K SUGA, T NIHIRA, Y YAMADA

BIOTECHNOLOGY AND BIOENGINEERING　Vol. 46　No. 5　p. 437-442　1995/06　Research paper (scientific journal)

FUZZY CONTROL OF ETHANOL CONCENTRATION AND ITS APPLICATION TO MAXIMUM GLUTATHIONE PRODUCTION IN YEAST FED-BATCH CULTURE

CG ALFAFARA, K MIURA, H SHIMIZU, S SHIOYA, K SUGA, K SUZUKI

BIOTECHNOLOGY AND BIOENGINEERING　Vol. 41　No. 4　p. 493-501　1993/02　Research paper (scientific journal)

KINETIC-STUDY OF POLY-D(-)-3-HYDROXYBUTYRIC ACID (PHB) PRODUCTION AND ITS MOLECULAR-WEIGHT DISTRIBUTION CONTROL IN A FED-BATCH CULTURE OF ALCALIGENES-EUTROPHUS

H SHIMIZU, S TAMURA, S SHIOYA, K SUGA

JOURNAL OF FERMENTATION AND BIOENGINEERING　Vol. 76　No. 6　p. 465-469　1993　Research paper (scientific journal)

CYSTEINE ADDITION STRATEGY FOR MAXIMUM GLUTATHIONE PRODUCTION IN FED-BATCH CULTURE OF SACCHAROMYCES-CEREVISIAE

C ALFAFARA, K MIURA, H SHIMIZU, S SHIOYA, K SUGA

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　Vol. 37　No. 2　p. 141-146　1992/05　Research paper (scientific journal)

Fuzzy control of ethanol concentration and its application to glutathione production in yeast fed-batch culture

H. Shimizu, K. Miura, C. G. Alfafara, S. Shioya, K. Suga, K. Suzuki

IFAC Symposia Series　No. 10　p. 433-436　1992　Research paper (international conference proceedings)

OPTIMAL PRODUCTION OF GLUTATHIONE BY CONTROLLING THE SPECIFIC GROWTH-RATE OF YEAST IN FED-BATCH CULTURE

H SHIMIZU, K ARAKI, S SHIOYA, K SUGA

BIOTECHNOLOGY AND BIOENGINEERING　Vol. 38　No. 2　p. 196-205　1991/06　Research paper (scientific journal)

MEASUREMENT OF ENZYME REACTION-RATES USING ADVANCED PH CONTROL-SYSTEM - APPLICATION OF REPETITIVE PF SYSTEM

H SHIMIZU, E SADA, S SHIOYA, K SUGA

BIOTECHNOLOGY AND BIOENGINEERING　Vol. 34　No. 6　p. 794-803　1989/09　Research paper (scientific journal)

PROFILE CONTROL OF THE SPECIFIC GROWTH-RATE IN FED-BATCH EXPERIMENTS

H SHIMIZU, S SHIOYA, K SUGA, T TAKAMATSU

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　Vol. 30　No. 3　p. 276-282　1989/03　Research paper (scientific journal)

An algorithmic approach to constructing the on‐line estimation system for the specific growth rate

Hiroshi Shimizu, Takeichiro Takamatsu, Suteaki Shioya, Ken‐Ichi Suga

Biotechnology and Bioengineering　Vol. 33　No. 3　p. 354-364　1989　Research paper (scientific journal)