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Articles (43)
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Growth rate-coordinated transcriptome reorganization in bacteria

Matsumoto, Yuki, Murakami, Yoshie, Tsuru, Saburo, Ying, Bei-Wen, Yomo, Tetsuya

Journal:

BMC Genomics

Année:

2013

Langue:

english

Fichier:

PDF, 738 KB

english, 2013

Precise, High-throughput Analysis of Bacterial Growth

Kurokawa, Masaomi, Ying, Bei-Wen

Journal:

Journal of Visualized Experiments

Année:

2017

Langue:

english

Fichier:

PDF, 448 KB

english, 2017

Construction of Escherichia coli gene expression level perturbation collection

Akiko Kashiwagi, Takahiro Sakurai, Saburo Tsuru, Bei-Wen Ying, Kotaro Mori, Tetsuya Yomo

Journal:

Metabolic Engineering

Année:

2009

Langue:

english

Fichier:

PDF, 463 KB

english, 2009

Cell-free translation systems for protein engineering

Yoshihiro Shimizu, Yutetsu Kuruma, Bei-Wen Ying, So Umekage, Takuya Ueda

Journal:

FEBS Journal

Année:

2006

Langue:

english

Fichier:

PDF, 757 KB

english, 2006

Construction of Escherichia coli gene expression level perturbation collection

Akiko Kashiwagi, Takahiro Sakurai, Saburo Tsuru, Bei-Wen Ying, Kotaro Mori, Tetsuya Yomo

Journal:

Journal of Bioscience and Bioengineering

Année:

2009

Langue:

english

Fichier:

PDF, 70 KB

english, 2009

Refined method for the genomic integration of complex synthetic circuits

Bei-Wen Ying, Yoichiro Ito, Yoshihiro Shimizu, Tetsuya Yomo

Journal:

Journal of Bioscience and Bioengineering

Année:

2010

Langue:

english

Fichier:

PDF, 715 KB

english, 2010

Chaperone-assisted folding of a single-chain antibody in a reconstituted translation system

Bei-Wen Ying, Hideki Taguchi, Hiroshi Ueda, Takuya Ueda

Journal:

Biochemical and Biophysical Research Communications

Année:

2004

Langue:

english

Fichier:

PDF, 444 KB

english, 2004

Efficient protein selection based on ribosome display system with purified components

Hiroyuki Ohashi, Yoshihiro Shimizu, Bei-Wen Ying, Takuya Ueda

Journal:

Biochemical and Biophysical Research Communications

Année:

2007

Langue:

english

Fichier:

PDF, 221 KB

english, 2007

Multilevel comparative analysis of the contributions of genome reduction and heat shock to theEscherichia colitranscriptome

Ying, Bei-Wen, Seno, Shigeto, Kaneko, Fuyuro, Matsuda, Hideo, Yomo, Tetsuya

Journal:

BMC Genomics

Année:

2013

Langue:

english

Fichier:

PDF, 792 KB

english, 2013

A reduced genome decreases the host carrying capacity for foreign DNA

Akeno, Yuya, Ying, Bei-Wen, Tsuru, Saburo, Yomo, Tetsuya

Journal:

Microbial Cell Factories

Année:

2014

Langue:

english

Fichier:

PDF, 246 KB

english, 2014

Noisy cell growth rate leads to fluctuating protein concentration in bacteria

Tsuru, Saburo, Ichinose, Junya, Kashiwagi, Akiko, Ying, Bei-Wen, Kaneko, Kunihiko, Yomo, Tetsuya

Journal:

Physical Biology

Année:

2009

Langue:

english

Fichier:

PDF, 1.29 MB

english, 2009

Directed evolution of cell size inEscherichia coli

Yoshida, Mari, Tsuru, Saburo, Hirata, Naoko, Seno, Shigeto, Matsuda, Hideo, Ying, Bei-Wen, Yomo, Tetsuya

Journal:

BMC Evolutionary Biology

Année:

2014

Langue:

english

Fichier:

PDF, 1.09 MB

english, 2014

Nontuberculous mycobacterial osteomyelitis

Bi, Sheng, Hu, Fei-Shu, Yu, Hai-Ying, Xu, Kai-Jin, Zheng, Bei-Wen, Ji, Zhong-Kang, Li, Jun-Jie, Deng, Mei, Hu, Hai-Yang, Sheng, Ji-Fang

Journal:

Infectious Diseases

Année:

2015

Langue:

english

Fichier:

PDF, 775 KB

english, 2015

Bacterial Cells Carrying Synthetic Dual-Function Operon Survived Starvation

Matsumoto, Yuki, Ito, Yoichiro, Tsuru, Saburo, Ying, Bei-Wen, Yomo, Tetsuya

Journal:

Journal of Biomedicine and Biotechnology

Année:

2011

Langue:

english

Fichier:

PDF, 904 KB

english, 2011

The Escherichia coli transcriptome linked to growth fitness

Ying, Bei-Wen, Yama, Kazuma, Kitahara, Kazuki, Yomo, Tetsuya

Journal:

Genomics Data

Année:

2016

Langue:

english

Fichier:

PDF, 185 KB

english, 2016

Bacterial transcriptome reorganization in thermal adaptive evolution

Ying, Bei-Wen, Matsumoto, Yuki, Kitahara, Kazuki, Suzuki, Shingo, Ono, Naoaki, Furusawa, Chikara, Kishimoto, Toshihiko, Yomo, Tetsuya

Journal:

BMC Genomics

Année:

2015

Langue:

english

Fichier:

PDF, 1.93 MB

english, 2015

Correlation between genome reduction and bacterial growth

Kurokawa, Masaomi, Seno, Shigeto, Matsuda, Hideo, Ying, Bei-Wen

Journal:

DNA Research

Année:

2016

Langue:

english

Fichier:

PDF, 683 KB

english, 2016

Functional specialization in regulation and quality control in thermal adaptive evolution

Yama, Kazuma, Matsumoto, Yuki, Murakami, Yoshie, Seno, Shigeto, Matsuda, Hideo, Gotoh, Kazuyoshi, Motooka, Daisuke, Nakamura, Shota, Ying, Bei-Wen, Yomo, Tetsuya

Journal:

Genes to Cells

Année:

2015

Langue:

english

Fichier:

PDF, 1.15 MB

english, 2015

Nutrient-dependent growth defects and mutability of mutators in Escherichia coli

Ishizawa, Yuuka, Ying, Bei-Wen, Tsuru, Saburo, Yomo, Tetsuya

Journal:

Genes to Cells

Année:

2015

Langue:

english

Fichier:

PDF, 1.63 MB

english, 2015

A simple comparison of the extrinsic noise in gene expression between native and foreign regulations in Escherichia coli

Ying, Bei-Wen, Seno, Shigeto, Matsuda, Hideo, Yomo, Tetsuya

Journal:

Biochemical and Biophysical Research Communications

Année:

2017

Langue:

english

Fichier:

PDF, 914 KB

english, 2017

Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction

Nishimura, Issei, Kurokawa, Masaomi, Liu, Liu, Ying, Bei-Wen, Lee, Sang Yup

Journal:

mBio

Année:

2017

Langue:

english

Fichier:

PDF, 1.44 MB

english, 2017

Mutation accumulation under UV radiation in Escherichia coli

Shibai, Atsushi, Takahashi, Yusuke, Ishizawa, Yuka, Motooka, Daisuke, Nakamura, Shota, Ying, Bei-Wen, Tsuru, Saburo

Journal:

Scientific Reports

Année:

2017

Langue:

english

Fichier:

PDF, 2.21 MB

english, 2017

Biochemical and genetic characterization of a novel metallo-β-lactamase from marine bacterium Erythrobacter litoralis HTCC 2594

Jiang, Xia-Wei, Cheng, Hong, Huo, Ying-Yi, Xu, Lin, Wu, Yue-Hong, Liu, Wen-Hong, Tao, Fang-Fang, Cui, Xin-Jie, Zheng, Bei-Wen

Journal:

Scientific Reports

Année:

2018

Langue:

english

Fichier:

PDF, 3.46 MB

english, 2018

2P-145 Quantitative observation of adaptive response to nutrient starvation(Cell biology,The 47th Annual Meeting of the Biophysical Society of Japan)

Matsumoto, Yuki, Ying, Bei-Wen, Ito, Yoichiro, Ichinose, Junya, Yomo, Tetsuya

Journal:

Seibutsu Butsuri

Année:

2009

Langue:

english

Fichier:

PDF, 251 KB

english, 2009

3P-282 Adaptive response to environmental changes utilizing the bistability of the lactose operon(The 46th Annual Meeting of the Biophysical Society of Japan)

Shimizu, Yoshihiro, Ying, Bei-Wen, Ito, Yoishiro, Ichinose, Junya, Yomo, Tetsuya

Journal:

Seibutsu Butsuri

Année:

2008

Langue:

english

Fichier:

PDF, 297 KB

english, 2008

3P213 Single Cell Analysis on a Synthetic Toggle Switch Sensitive to Environmental Perturbation(Cell biology,The 48th Annual Meeting of the Biophysical Society of Japan)

Matsumoto, Yuki, Ito, Yoichiro, Tsuru, Saburo, Ying, Bei-Wen, Yomo, Tetsuya

Journal:

Seibutsu Butsuri

Année:

2010

Fichier:

PDF, 239 KB

2010

3P-279 Identical regulatory mechanisms, diverse expression patterns : A study on the adaptive response to environmental changes(The 46th Annual Meeting of the Biophysical Society of Japan)

Mita, Hiromichi, Ying, Bei-Wen, Ito, Yoichiro, Yomo, Tetsuya

Journal:

Seibutsu Butsuri

Année:

2008

Langue:

english

Fichier:

PDF, 287 KB

english, 2008

3P-285 Adaptive response to leucine starvation occurred devoid of the native leu operon(The 46th Annual Meeting of the Biophysical Society of Japan)

Yasuda, Nao, Ying, Bei-Wen, Tsuru, Saburo, Suzuki, Shingo, Yomo, Tetsuya

Journal:

Seibutsu Butsuri

Année:

2008

Langue:

english

Fichier:

PDF, 297 KB

english, 2008

1P-169 Adaptive response to environmental changes utilizing the bistability of the lactose operon(Cell biology, The 47th Annual Meeting of the Biophysical Society of Japan)

Shimizu, Yoshihiro, Ying, Bei-Wen, Ichinose, Junya, Ito, Yoichiro, Yomo, Tetsuya

Journal:

Seibutsu Butsuri

Année:

2009

Langue:

english

Fichier:

PDF, 195 KB

english, 2009

2P-143 Stochastic gene expression induced population selection promotes adaptation to nutrient depletion(Cell biology,The 47th Annual Meeting of the Biophysical Society of Japan)

Tsuru, Saburo, Ying, Bei-Wen, Mori, Kotaro, Ushioda, Junya, Kashiwagi, Akiko, Yomo, Tetsuya

Journal:

Seibutsu Butsuri

Année:

2009

Langue:

english

Fichier:

PDF, 243 KB

english, 2009

Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process

Kishimoto, Toshihiko, Ying, Bei-Wen, Tsuru, Saburo, Iijima, Leo, Suzuki, Shingo, Hashimoto, Tomomi, Oyake, Ayana, Kobayashi, Hisaka, Someya, Yuki, Narisawa, Dai, Yomo, Tetsuya, Gojobori, Takashi

Journal:

PLoS Genetics

Année:

2015

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2015

Comparison of Sequence Reads Obtained from Three Next-Generation Sequencing Platforms

Suzuki, Shingo, Ono, Naoaki, Furusawa, Chikara, Ying, Bei-Wen, Yomo, Tetsuya, Bereswill, Stefan

Journal:

PLoS ONE

Année:

2011

Langue:

english

Fichier:

PDF, 187 KB

english, 2011

Stochastic Switching Induced Adaptation in a Starved Escherichia coli Population

Shimizu, Yoshihiro, Tsuru, Saburo, Ito, Yoichiro, Ying, Bei-Wen, Yomo, Tetsuya, Kudla, Grzegorz

Journal:

PLoS ONE

Année:

2011

Langue:

english

Fichier:

PDF, 497 KB

english, 2011

Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages

Ying, Bei-Wen, Honda, Tomoya, Tsuru, Saburo, Seno, Shigeto, Matsuda, Hideo, Kazuta, Yasuaki, Yomo, Tetsuya, Suen, Garret

Journal:

PLoS ONE

Année:

2015

Langue:

english

Fichier:

PDF, 1.11 MB

english, 2015

3TA4-10 Phenotypic fluctuation induced biological adaptation(The 47th Annual Meeting of the Biophysical Society of Japan)

Ying, Bei-Wen, Ito, Yoichiro, Shimizu, Yoshihiro, Matsumoto, Yuki, Ichinose, Junya, Tsuru, Saburo, Yomo, Tetsuya

Journal:

Seibutsu Butsuri

Année:

2009

Langue:

english

Fichier:

PDF, 456 KB

english, 2009

A decay effect of the growth rate associated with genome reduction in Escherichia coli

Tsuchiya, Kouhei, Cao, Yang-Yang, Kurokawa, Masaomi, Ashino, Kazuha, Yomo, Tetsuya, Ying, Bei-Wen

Journal:

BMC Microbiology

Année:

2018

Langue:

english

Fichier:

PDF, 1.65 MB

english, 2018

Gene Expression Order Attributed to Genome Reduction and the Steady Cellular State in Escherichia coli

Ying, Bei-Wen, Yama, Kazuma

Journal:

Frontiers in Microbiology

Année:

2018

Langue:

english

Fichier:

PDF, 1015 KB

english, 2018

Predicting the decision making chemicals used for bacterial growth

Ashino, Kazuha, Sugano, Kenta, Amagasa, Toshiyuki, Ying, Bei-Wen

Journal:

Scientific Reports

Année:

2019

Langue:

english

Fichier:

PDF, 3.69 MB

english, 2019

Experimental Challenges for Reduced Genomes: The Cell Model Escherichia coli

Kurokawa, Masaomi, Ying, Bei-Wen

Journal:

Microorganisms

Année:

2019

Langue:

english

Fichier:

PDF, 855 KB

english, 2019

Experimental Challenges for Reduced Genomes: The Cell Model Escherichia coli

Kurokawa, Masaomi, Ying, Bei-Wen

Journal:

Microorganisms

Année:

2019

Fichier:

PDF, 855 KB

2019

Clustering of Bacterial Growth Dynamics in Response to Growth Media by Dynamic Time Warping

Cao, Yang-Yang, Yomo, Tetsuya, Ying, Bei-Wen

Journal:

Microorganisms

Année:

2020

Fichier:

PDF, 1.39 MB

2020

The highly conserved chromosomal periodicity ofÂ transcriptomes and the correlation ofÂ itsÂ amplitude with the growth rate inÂ Escherichia coli

Nagai, Motoki, Kurokawa, Masaomi, Ying, Bei-Wen

Journal:

DNA Research

Année:

2020

Fichier:

PDF, 467 KB

2020

Correlated chromosomal periodicities according to the growth rate and gene expression

Liu, Liu, Kurokawa, Masaomi, Nagai, Motoki, Seno, Shigeto, Ying, Bei-Wen

Journal:

Scientific Reports

Année:

2020

Fichier:

PDF, 4.43 MB

2020