RIKEN Center for Biosystems Dynamics Research (BDR)

2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011

2020

　

Original Papers

1. Tomoya Maeda, Junichiro Iwasawa, Hazuki Kotani, Natsue Sakata, Masako Kawada, Takaaki Horinouchi, Aki Sakai, Kumi Tanabe, Chikara Furusawa, "High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli" Nature Communications, 11, 5970 (2020)
2. Takaaki Horinouchi, Tomoya Maeda, Hazuki Kotani, Chikara Furusawa, "Suppression of antibiotic resistance evolution by single-gene deletion" Scientific reports, 10, 4178 (2020)

Reviews

1. Takaaki Horinouchi, Chikara Furusawa, "Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis" Biophysical Reviews, 12, 677-682 (2020)

2019

　

Original Papers

1. Atsushi Shibai, Katsuya Satoh, Masako Kawada, Hazuki Kotani, Issay Narumi, Chikara Furusawa, "Complete Genome Sequence of a Radioresistant Bacterial Strain, Deinococcus grandis ATCC 43672" Microbiology resource announcements, 8, 45 (2019)
2. Atsushi Shibai, Tomoya Maeda, Masako Kawada, Hazuki Kotani, Natsue Sakata, Chikara Furusawa, "Complete Genome Sequences of Three Star-Shaped Bacteria, Stella humosa, Stella vacuolata, and Stella Species ATCC 35155" Microbiology resource announcements, 8, 32 (2019)
3. Tomoya Maeda, Takaaki Horinouchi, Natsue Sakata, Aki Sakai, Chikara Furusawa, "High-throughput identification of the sensitivities of an Escherichia coli ΔrecA mutant strain to various chemical compounds" The Journal of antibiotics 72, 7, 566 (2019)
4. Tomoyuki Yamaguchi, Shunsuke Teraguchi, Chikara Furusawa, Hiroaki Machiyama, Tomonobu M Watanabe, Hideaki Fujita, Shimon Sakaguchi, Toshio Yanagida, "Theoretical modeling reveals that regulatory T cells increase T-cell interaction with antigen-presenting cells for stable immune tolerance" International immunology, dxz043 (2019)

2018

　

Original Papers

1. Chikara Furusawa, Takaaki Horinouchi, Tomoya Maeda, "Toward prediction and control of antibiotic-resistance evolution" Current opinion in biotechnology 54, 45-49 (2018)
2. Takaaki Horinouchi, Tomoya Maeda, Chikara Furusawa, "Understanding and engineering alcohol-tolerant bacteria using OMICS technology" World Journal of Microbiology and Biotechnology 34, 11, 157 (2018)
3. Takahiro Komori, Atsushi Shibai, Hiromi Saito, Yuya Akeno, Arno Germond, Takaaki Horinouchi, Chikara Furusawa, Saburo Tsuru, "Enhancement of K‐strategy evolution in histidine utilization using a container with compartments" Genes to Cells 23, 10, 893-903 (2018)
4. Kazuko Okamoto, Arno Germond, Hideaki Fujita, Chikara Furusawa, Yasushi Okada, Tomonobu M Watanabe, "Single cell analysis reveals a biophysical aspect of collective cell-state transition in embryonic stem cell differentiation" Scientific reports 8, 1, 11965 (2018)
5. Arno Germond, Taro Ichimura, Takaaki Horinouchi, Hideaki Fujita, Chikara Furusawa, Tomonobu M Watanabe, "Raman spectral signature reflects transcriptomic features of antibiotic resistance in Escherichia coli" Communications biology 1, 1, 85 (2018)
6. Kento Tokuyama, Yoshihiro Toya, Takaaki Horinouchi, Chikara Furusawa, Fumio Matsuda, Hiroshi Shimizu, "Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain" Biotechnology and bioengineering 115, 6, 1542-1551 (2018)
7. Kunihiko Kaneko, Chikara Furusawa, "Macroscopic Theory for Evolving Biological Systems Akin to Thermodynamics" Annual review of biophysics 47, 273-290 (2018)
8. Takashi Hirasawa, Masaki Saito, Katsunori Yoshikawa, Chikara Furusawa, Hiroshi Shmizu, "Integrated Analysis of the Transcriptome and Metabolome of Corynebacterium glutamicum during Penicillin‐Induced Glutamic Acid Production" Biotechnology journal 13, 5, 1700612 (2018)
9. Chikara Furusawa, Kunihiko Kaneko, "Formation of dominant mode by evolution in biological systems" Physical Review E 97, 4 (2018)

2017

　

Original Papers

1. Shingo Suzuki, Takaaki Horinouchi, Chikara Furusawa, "Acceleration and suppression of resistance development by antibiotic combinations" BMC genomics 18, 1, 328 (2017)
2. Tetsuhiro S Hatakeyama, Chikara Furusawa, "Metabolic dynamics restricted by conserved carriers: Jamming and feedback" PLoS computational biology 13, 11, e1005847 (2017)
3. Takaaki Horinouchi, Shingo Suzuki, Hazuki Kotani, Kumi Tanabe, Natsue Sakata, Hiroshi Shimizu, Chikara Furusawa, "Prediction of cross-resistance and collateral sensitivity by gene expression profiles and genomic mutations" Scientific reports 7, 1, 14009 (2017)
4. Takaaki Horinouchi, Aki Sakai, Hazuki Kotani, Kumi Tanabe, Chikara Furusawa, "Improvement of isopropanol tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies" Journal of biotechnology 255, 47-56 (2017)
5. Mari Yoshida, Sabrina Galinanes Reyes, Soichiro Tsuda, Takaaki Horinouchi, Chikara Furusawa, Leroy Cronin, "Time-programmable drug dosing allows the manipulation, suppression and reversal of antibiotic drug resistance in vitro" Nature communications 8, 15589 (2017)
6. Arno Germond, Vipin Kumar, Taro Ichimura, Jerome Moreau, Chikara Furusawa, Hideaki Fujita, Tomonobu M Watanabe, "Raman spectroscopy as a tool for ecology and evolution" Journal of The Royal Society Interface 14, 131, 20170174 (2017)
7. Hirotaka Matsumoto, Hisanori Kiryu, Chikara Furusawa, Minoru SH Ko, Shigeru BH Ko, Norio Gouda, Tetsutaro Hayashi, Itoshi Nikaido, "SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation" Bioinformatics 33, 15, 2314-2321 (2017)

2016

　

Original Papers

1. Chikara Furusawa, Tomoyuki Yamaguchi, "Robust and accurate discrimination of self/non-self antigen presentations by regulatory T cell suppression" PloS one 11, 9, e0163134 (2016)
2. Shingo Suzuki, Takaaki Horinouchi, Chikara Furusawa, "Phenotypic changes associated with the fitness cost in antibiotic resistant Escherichia coli strains" Molecular BioSystems, 12, 2 (2016)

2015

　

Original Papers

1. Katsunori Yoshikawa, Shimpei Aikawa, Yuta Kojima, Yoshihiro Toya, Chikara Furusawa, Akihiko Kondo, Hiroshi Shimizu, "Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction" PloS one, 10, 12 (2015)
2. Bei-Wen Ying, Yuki Matsumoto, Kazuki Kitahara, Shingo Suzuki, Naoaki Ono, Chikara Furusawa, Toshihiko Kishimoto, Tetsuya Yomo, "Bacterial transcriptome reorganization in thermal adaptive evolution" BMC genomics, 16, 1 (2015)
3. Takaaki Horinouchi, Shingo Suzuki, Takashi Hirasawa, Naoaki Ono, Tetsuya Yomo, Hiroshi Shimizu, Chikara Furusawa, "Phenotypic convergence in bacterial adaptive evolution to ethanol stress" BMC evolutionary biology, 15, 1 (2015)
4. Chikara Furusawa, Kunihiko Kaneko, "Global relationships in fluctuation and response in adaptive evolution" Journal of The Royal Society Interface, 12, 109 (2015)
5. Tadashi Miyamoto, Chikara Furusawa, Kunihiko Kaneko, "Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation" PLoS computational biology, 11, 8 (2015)
6. Shuichi Kajihata, Fumio Matsuda, Mika Yoshimi, Kenshi Hayakawa, Chikara Furusawa, Akihisa Kanda, Hiroshi Shimizu, "13C-based metabolic flux analysis of Saccharomyces cerevisiae with a reduced Crabtree effect" Journal of Bioscience and Bioengineering, 120, 2 (2015)
7. Kunihiko Kaneko, Chikara Furusawa, Tetsuya Yomo, "Universal Relationship in Gene-Expression Changes for Cells in Steady-Growth State" Physical Review X, 5, 011014 (2015)

2014

　

Original Papers

1. Takaaki Horinouchi, Teruaki Minamoto, Shingo Suzuki, Hiroshi Shimizu, and Chikara Furusawa, "Development of an automated culture system for laboratory evolution"Journal of Laboratory Automation, in press
2. Kento Tokuyama, Satoshi Ohno, Katsunori Yoshikawa, Takashi Hirasawa, Shotaro Tanaka, Chikara Furusawa and Hiroshi Shimizu, "Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli"Microbial Cell Factories,13,64(2014)
3. Satoshi Oono, Hiroshi Shimizu, Chikara Furusawa, "FastPros: Screening of reaction knockout strategies for metabolic engineering" Bioinformatics, in press
4. T. Nakajima, S. Kajihata, K. Yoshikawa, F. Matsuda, C. Furusawa, T. Hirasawa, H. Shimizu, "Integrated Metabolic Flux and Omics Analysis of Synechocystis sp. PCC 6803 under Mixotrophic and Photoheterotrophic Conditions"Plant Cell Physiol, In press
5. S. Kajihata, C. Furusawa, F. Matsuda, H. Shimizu, "OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis"Biomed Res Int, In press
6. N. Okahashi, S. Kajihata, C. Furusawa, H. Shimizu, "Reliable Metabolic Flux Estimation in Escherichia coli Central Carbon Metabolism Using Intracellular Free Amino Acids"Metabolites, 4,(2),408-420
7. Yuto Yamauchi, Takashi Hirasawa, Masato Nishii, Chikara Furusawa, Hiroshi Shimizu, "Enhanced acetic acid and succinic acid production under microaerobic conditions by?Corynebacterium glutamicum?harboring?Escherichia coli?transhydrogenase gene?pntAB" The Journal of General and Applied Microbiology, 60,(3),112-118
8. T. Hirasawa, Y. Ida, C. Furusawa, H. Shimizu, "Potential of a Saccharomyces cerevisiae recombinant strain lacking ethanol and glycerol biosynthesis pathways in efficient anaerobic bioproduction. "Bioengineered, 5,(2),123-128

2013

　

Original Papers

1. Satoshi Oono, Hiroshi Shimizu, Chikara Furusawa, "FastPros: Screening of reaction knockout strategies for metabolic engineering" Bioinformatics, in press
2. Takashi Hirasawa, Katsunori Yoshikawa, Aki Ookubo, Chikara Furusawa, Hiroshi Shimizu, "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," J. Biotech., 168(2), 185-93 (2013)
3. Chikara Furusawa, Kunihiko Kaneko, "Epigenetic feedback regulation accelerates adaptation and evolution," PLoS One, 8(5), e61251 (2013)
4. Chikara Furusawa, Takaaki Horinouchi, Takashi Hirasawa, Hiroshi Shimizu, "Systems metabolic engineering: the creation of microbial cell factories by rational metabolic design and evolution," Adv. Biochem. Eng. Biotechnol., 131, 1-23 (2013)
5. Yoshihiro Ida, Takashi Hirasawa, Chikara Furusawa, Hiroshi Shimizu, "Utilization of Saccharomyces cerevisiae recombinant strain incapable of both ethanol and glycerol biosynthesis for anaerobic bioproduction," Applied Microbiology and Biotechnology, 97(11), 4811-4819 (2013)
6. Katsunori Yoshikawa, Takashi Hirasawa, Kenichi Ogawa, Yuki Hidaka, Tsubasa Nakajima, Chikara Furusawa, Hiroshi Shimizu, "Integrated transcriptomic and metabolomic analysis of the central metabolism of Synechocystis sp. PCC 6803 under different trophic conditions," Biotechnology Journal,8(5), 571-580 (2013)

　

International Conference

1. Chikara Furusawa, "Oscillatory protein expression dynamics generates robust and irreversible differentiation dynamics of stem cells," 8th Asian Biophysics Association (ABA) Symposium (Jeju, Korea, May 2013)
2. Chikara Furusawa, "Oscillatory protein expression dynamics generates robust and irreversible differentiation dynamics of stem cells," iCeMS Symposium on Theoretical and Computational Biology (Kyoto, Japan, Mar. 2013)

2012

Original Papers

1. Naoaki Ono, Shingo Suzuki, Chikara Furusawa, Hiroshi Shimizu, Tetsuya Yomo, "Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays," PLoS One, 8(1), e54571 (2012)
2. Chikara Furusawa and Kunihiko Kaneko, "A dynamical-systems view of stem cell biology," Science, 338(6104), 215-217 (2012)
3. Chikara Furusawa and Kunihiko Kaneko, "Adaptation to optimal cell growth through self-organized criticality," Physical Review Letters, 108, 208103 (2012)
4. Satoshi Ohno, Chikara Furusawa and Hiroshi Shimizu, "In silico screening of triple reaction knockout Escherichia coli strains for overproduction of useful metabolites," Journal of Bioscience and Bioengineering, 115(2), 221-228 (2012)
5. Sunisa Chatsurachai, Chikara Furusawa, Hiroshi Shimizu, "An in silico platform for the design of heterologous pathways in nonnative metabolite production," BMC Bioinformatics, 13(1), 93 (2012)
6. Yuki Usui, Takashi Hirasawa, Chikara Furusawa, Tomokazu Shirai, Natsuko Yamamoto, Hirotada Mori, Hiroshi Shimizu, "Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using 13C metabolic flux analysis," Microbial Cell Factories, 11(1),87 (2012)

International Conference

1. Kazufumi Hosoda, Akihiro Asao, Shingo Suzuki, Tetsuya Yomo, "Experimental evolution of an artificial bacterial mutualism," 13th International Conference on the simulation & synthesis of living systems (Artificial life 13), (Michigan, USA, July 2012)
2. Chikara Furusawa, "Oscillatory protein expression dynamics generates robust and irreversible differentiation dynamics of stem cells," 4th International Congress on Stem Cells and Tissue Formation (Dresden, Germany, July 2012)
3. Chikara Furusawa, "Temporal oscillation in protein expressions geenrates robust differentiation dynamics of stem cells," 11th Annual Meeting of International Socienty for Stem Cell Research (Yokohama, Japan, June 2012)

Reviews

1. Chikara Furusawa, Takaaki Horinouchi, Takashi Hirasawa, Hiroshi Shimizu,"Systems metabolic engineering: the creation of microbial cell factories by rational metabolic design and evolution," Advanced Biochemical Engineering/Biotechnology, 131, 1-23 (2012)
2. Takashi Hirasawa, Jongpill Kim, Tomokazu Shirai, Chikara Furusawa, Hiroshi Shimizu, "Molecular mechanisms and metabolic engineering of glutamate overproduction in Corynebacterium glutamicum," Subcellular Biochemistry Vol. 64, Reprogramming Microbial Metabolic Pathways, 261-281 (2012)
3. Katsunori Yoshikawa, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu, "Design of Superior Cell Factories Based on Systems Wide Omics Analysis," Systems Metabolic Engineering, Chapter3, 21-81 (2012)

2011

Original Papers

1. Narito Suzuki, Chikara Furusawa, Kunihiko Kaneko, "Oscillatory protein expression dynamics endows stem cells with robust differentiation potential," PLoS One, 6(11), e27232 (2011)
2. Eiji Mori, Chikara Furusawa, Shuichi Kajihata, Tomokazu Shirai and Hiroshi Shimizu, "Evaluating ¹³C enrichment data of free amino acids for precise metabolic flux analysis," Biotechnology journal, 6(11), 1377-1378 (2011)
3. Katsunori Yoshikawa, Yuta Kojima, Tsubasa Nakajima, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu, "Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp. PCC6803," Applied Microbiology and Biotechnology, 92(2), 347-358 (2011)
4. Motoki Umakoshi, Takashi Hirasawa, Chikara Furusawa, Yasuhiro Takenaka, Yoshimi Kikuchi, Hiroshi Shimizu, "Improving protein secretion of a transglutaminase-secreting Corynebacterium glutamicum recombinant strain on the basis of ¹³C metabolic flux analysis," Journal of Bioscience and Bioengineering, 112(6), 595-601 (2011)
5. Fumio Matsuda, Chikara Furusawa, Takashi Kondo, Jun Ishii, Hiroshi Shimizu, Akihiko Kondo, "Engineering strategy of yeast metabolism for higher alcohol production," Microbial Cell Factories, 10(1), 70 (2011)
6. Jongpill Kim, Takashi Hirasawa, Masaki Saito, Chikara Furusawa, Hiroshi Shimizu, "Investigation of phosphorylation status of OdhI protein during penicillin- and Tween 40-triggered glutamate overproduction by Corynebacterium glutamicum," Applied Microbiology and Biotechnology, 91(1), 143-151 (2011)
7. Saburo Tsuru, Nao Yasuda, Yoshie Murakami, Junya Ushioda, Akiko Kashiwagi, Shingo Suzuki, Kotaro Mori, Bei-Wen Ying, Tetsuya Yomo, "Adaptation by stochastic switching of a monostable genetic circuit in Escherichia coli," Molecular Systems Biology, 7, 493 (2011)
8. Shingo Suzuki, Naoaki Ono, Chikara Furusawa, Bei-Wen Ying, Tetsuya Yomo, "Comparison of sequence reads obtained from three next-generation sequencing platforms," PLoS One, 6(5), e19534 (2011)

International Conference

1. Takaaki Horinouchi, Shingo Suzuki, Naoaki Ono, Kuniyasu Tamaoka, Takashi Hirasawa, Tetsuya Yomo, Hiroshi Shimizu, Chikara Furusawa "Comprehensive analysis of evolution dynamics in Escherichia coli from parallel experimental evolutions under ethanol stress condition," International Symposium on SYNTHESIZING LIFE AND BIOLOGICAL SYSTEMS (Osaka, Japan, Oct. 2011)
2. Kazufumi Hosoda, Akihiro Asao, Shingo Suzuki, Tetsuya Yomo, "Synthesizing symbiosis," International Symposium on SYNTHESIZING LIFE AND BIOLOGICAL SYSTEMS (Osaka, Japan, Oct. 2011)
3. Chikara Furusawa, Takaaki Horinouchi, Shingo Suzuki, Naoaki Ono, Kuniyasu Tamaoka, Takashi Hirasawa, Tetsuya Yomo, and Hiroshi Shimizu, "Genome-Wide resequencing and expression analyses of evolved Escherichia coli strains under ethanol stress," Society for Molecular Biology and Evolution(SMBE2011) (Kyoto, Japan, Juiy 2011)
4. Naoaki Ono, Chikara Furusawa, Takaaki Horinouchi, Kuniyasu Tamaoka, Shingo Suzuki, Takashi Hirasawa, Tetsuya Yomo, Hiroshi Shimizu, "Genome-Wide Mutational and Expression Analyses of Evolved Escherichia coli Strains under Ethanol Stress," Asian Congress on Biotechnology (ACB-2011) (Shanghai, China,May 2011)