Publications

• Chikara Furusawa's google scholar citations
• Yusuke Himeoka's google scholar citations
• Saburo Tsuru's google scholar citations

Deciphering the origin of developmental stability: The role of intracellular expression variability in evolutionary conservation. Uchida Y, Tsutsumi M, Ichii S, Irie N, Furusawa C.Evol Dev. 2024 Mar;26(2):e12473. doi: 10.1111/ede.12473.

Laboratory Evolution of Antimicrobial Resistance in Bacteria to Develop Rational Treatment Strategies. Maeda T, Furusawa C.Antibiotics (Basel). 2024 Jan 18;13(1):94. doi: 10.3390/antibiotics13010094.

Evolution of hierarchy and irreversibility in theoretical cell differentiation model. Nakamura YT, Himeoka Y, Saito N, Furusawa C. PNAS Nexus. 2023 Dec 22; 3(1):pgad454. doi: 10.1093/pnasnexus/pgad454.

Prediction of cross-fitness for adaptive evolution to different environmental conditions: Consequence of phenotypic dimensional reduction. Sato TU, Furusawa C, Kaneko K. Phys. Rev. Res. 2023 5(4): 043222. doi: 10.1103/PhysRevResearch.5.043222.

Loss of function of Hog1 improves glycerol assimilation in Saccharomyces cerevisiae. Sone M, Navanopparatsakul K, Takahashi S, Furusawa C, Hirasawa T.World J Microbiol Biotechnol. 2023 Jul 21;39(10):255. doi: 10.1007/s11274-023-03696-z.

A deep learning approach for morphological feature extraction based on variational auto-encoder: an application to mandible shape. Tsutsumi M, Saito N, Koyabu D, Furusawa C. NPJ Syst Biol Appl. 2023 Jul 6;9(1):30. doi: 10.1038/s41540-023-00293-6.

Loss of function of Hog1 improves glycerol assimilation in Saccharomyces cerevisiae. Sone M, Navanopparatsakul K, Takahashi S, Furusawa C, Hirasawa T.World J Microbiol Biotechnol. 2023 Jul 21;39(10):255. doi: 10.1007/s11274-023-03696-z.

Rare-event sampling analysis uncovers the fitness landscape of the genetic code. Omachi Y, Saito N, Furusawa C. PLoS Comput Biol. 2023 Apr 17;19(4):e1011034. doi: 10.1371/journal.pcbi.

Inference of transcriptome signatures of Escherichia coli in long-term stationary phase. Takano S, Takahashi H, Yama Y, Miyazaki R, Furusawa C, Tsuru S. Sci Rep. 2023 Apr 6;13(1):5647. doi: 10.1038/s41598-023-32525-4.

Synthetic symbiosis between a cyanobacterium and a ciliate toward novel chloroplast-like endosymbiosis. Azuma Y, Tsuru S, Habuchi M, Takami R, Takano S, Yamamoto K, Hosoda K. Sci Rep. 2023 Apr 13;13(1):6104. doi: 10.1038/s41598-023-33321-w.

Stability in gene expression and body-plan development leads to evolutionary conservation. Uchida Y, Takeda H, Furusawa C, Irie N.Evodevo. 2023 Mar 14;14(1):4. doi: 10.1186/s13227-023-00208-w.

Wickerhamiella bidentis sp. nov., a novel yeast species isolated from flowers and insects in Japan. Seike T, Takekata H, Uchida Y, Sakata N, Furusawa C, Matsuda F. Int J Syst Evol Microbiol. 2023 Mar;73(3). doi: 10.1099/ijsem.0.005739.

2022

Analysis of the evolution of resistance to multiple antibiotics enables prediction of the Escherichia coli phenotype-based fitness landscape. Iwasawa J, Maeda T, Shibai A, Kotani H, Kawada M, Furusawa C.PLoS Biol. 2022 Dec 13;20(12):e3001920. doi: 10.1371/journal.pbio.3001920.

Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations. Maeda Y, Mizuuchi R, Shigenobu S, Shibai A, Kotani H, Furusawa C, Ichihashi N.RNA. 2022 Dec;28(12):1659-1667. doi: 10.1261/rna.079291.122.

Purifying selection enduringly acts on the sequence evolution of highly expressed proteins in Escherichia coli. Shibai A, Kotani H, Sakata N, Furusawa C, Tsuru S.G3 (Bethesda). 2022 Nov 4;12(11):jkac235. doi: 10.1093/g3journal/jkac235.

Single mutation makes Escherichia coli an insect mutualist. Koga R, Moriyama M, Onodera-Tanifuji N, Ishii Y, Takai H, Mizutani M, Oguchi K, Okura R, Suzuki S, Gotoh Y, Hayashi T, Seki M, Suzuki Y, Nishide Y, Hosokawa T, Wakamoto Y, Furusawa C, Fukatsu T. Nat Microbiol. 2022 Aug;7(8):1141-1150. doi: 10.1038/s41564-022-01179-9.

Development of a device that generates a temperature gradient in a microtiter plate for microbial culture. Shibai A, Kotani H, Kawada M, Yokoi N, Furusawa C. SLAS Technol. 2022 Jul 29:S2472-6303(22)05167-6.

Distinct Survival, Growth Lag, and rRNA Degradation Kinetics during Long-Term Starvation for Carbon or Phosphate. Himeoka Y, Gummesson B, Sørensen MA, Svenningsen SL, Mitarai N.mSphere. 2022 Jun 29;7(3):e0100621.

Potential contribution of intrinsic developmental stability toward body plan conservation. Uchida Y, Shigenobu S, Takeda H, Furusawa C, Irie N. BMC Biol. 2022 Apr 11;20(1):82.

Identification of Bacterial Drug-Resistant Cells by the Convolutional Neural Network in Transmission Electron Microscope Images. Hayashi-Nishino M, Aoki K, Kishimoto A, Takeuchi Y, Fukushima A, Uchida K, Echigo T, Yagi Y, Hirose M, Iwasaki K, Shin'ya E, Washio T, Furusawa C, Nishino K. Front Microbiol. 2022 Mar 15;13:839718.

Experimental demonstration of operon formation catalyzed by insertion sequence. Kanai Y, Tsuru S, Furusawa C. Nucleic Acids Res. 2022 Feb 22;50(3):1673-1686.

Acceleration of target production in co-culture by enhancing intermediate consumption through adaptive laboratory evolution. Kawai R, Toya Y, Miyoshi K, Murakami M, Niide T, Horinouchi T, Maeda T, Shibai A, Furusawa C, Shimizu H. Biotechnol Bioeng. 2022 Mar;119(3):936-945.

Decoding gut microbiota by imaging analysis of fecal samples. Furusawa C, Tanabe K, Ishii C, Kagata N, Tomita M, Fukuda S. iScience. 2021 Nov 22;24(12):103481.

The sixth transmembrane region of a pheromone G-protein coupled receptor, Map3, is implicated in discrimination of closely related pheromones in Schizosaccharomyces pombe. Seike T, Sakata N, Shimoda C, Niki H, Furusawa C. Genetics. 2021 Dec 10;219(4):iyab150.

Mutational property of newly identified mutagen l-glutamic acid γ-hydrazide in Escherichia coli. Maeda T, Shibai A, Yokoi N, Tarusawa Y, Kawada M, Kotani H, Furusawa C. Mutat Res. 2021 Jul 21;823:111759.

Laboratory evolution of Mycobacterium on agar plates for analysis of resistance acquisition and drug sensitivity profiles. Maeda T, Kawada M, Sakata N, Kotani H, Furusawa C. Sci Rep. 2021 Jul 23;11(1):15136.

Direction and Constraint in Phenotypic Evolution: Dimension Reduction and Global Proportionality in Phenotype Fluctuation and Responses. Kaneko K, Furusawa, C. In: Crombach A. (eds) Evolutionary Systems Biology. Springer 2021, pp. 35-58.

Morphological change of coiled bacterium Spirosoma linguale with acquisition of β-lactam resistance. Maeda T, Kotani H, Furusawa C. Sci Rep. 2021 Jun 24;11(1):13278.

Elevated Sporulation Efficiency in Fission Yeast Schizosaccharomyces japonicus Strains Isolated from Drosophila. Seike T, Sakata N, Matsuda F, Furusawa C. J Fungi (Basel). 2021 Apr 29;7(5):350.

When to wake up? The optimal waking-up strategies for starvation-induced persistence. Himeoka Y, Mitarai N. PLoS Comput Biol. 2021 Feb 11;17(2):e1008655.

High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli. Maeda T, Iwasawa J, Kotani H, Sakata N, Kawada M, Horinouchi T, Sakai A, Tanabe K, Furusawa C. Nat Commun. 2020 Nov 24;11(1):5970.

Toward understanding of evolutionary constraints: experimental and theoretical approaches. Furusawa C, Irie N. Biophys Rev. 2020 Oct;12(5):1155-1161

Evolutionary Changes in DnaA-Dependent Chromosomal Replication in Cyanobacteria. Ohbayashi R, Hirooka S, Onuma R, Kanesaki Y, Hirose Y, Kobayashi Y, Fujiwara T, Furusawa C, Miyagishima SY. Front Microbiol. 2020 Apr 28;11:786.

Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis. Horinouchi T, Furusawa C. Biophys Rev. 2020 Jun;12(3):677-682.

Suppression of antibiotic resistance evolution by single-gene deletion. Horinouchi T, Maeda T, Kotani H, Furusawa C. Sci Rep. 2020 Mar 6;10(1):4178.

Complete Genome Sequence of a Radioresistant Bacterial Strain, Deinococcus grandis ATCC 43672. Shibai A, Satoh K, Kawada M, Kotani H, Narumi I, Furusawa C. Microbiol Resour Announc. 2019 Nov 7;8(45):e01226-19.

Complete Genome Sequences of Three Star-Shaped Bacteria, Stella humosa, Stella vacuolata, and Stella Species ATCC 35155. Shibai A, Maeda T, Kawada M, Kotani H, Sakata N, Furusawa C. Microbiol Resour Announc. 2019 Aug 8;8(32):e00719-19.

Theoretical modeling reveals that regulatory T cells increase T-cell interaction with antigen-presenting cells for stable immune tolerance. Yamaguchi T, Teraguchi S, Furusawa C, Machiyama H, Watanabe TM, Fujita H, Sakaguchi S, Yanagida T. Int Immunol. 2019 Oct 16;31(11):743-753.

High-throughput identification of the sensitivities of an Escherichia coli ΔrecA mutant strain to various chemical compounds. Maeda T, Horinouchi T, Sakata N, Sakai A, Furusawa C. J Antibiot (Tokyo). 2019 Jul;72(7):566-573.

Development of an Automated UV Irradiation Device for Microbial Cell Culture. Shibai A, Tsuru S, Yomo T. SLAS Technol. 2019 Jun;24(3):342-348.

Understanding and engineering alcohol-tolerant bacteria using OMICS technology. Horinouchi T, Maeda T, Furusawa C. World J Microbiol Biotechnol. 2018 Oct 19;34(11):157.

Raman spectral signature reflects transcriptomic features of antibiotic resistance in Escherichia coli. Germond A, Ichimura T, Horinouchi T, Fujita H, Furusawa C, Watanabe TM. Commun Biol. 2018 Jul 2;1:85.

Enhancement of K-strategy evolution in histidine utilization using a container with compartments. Komori T, Shibai A, Saito H, Akeno Y, Germond A, Horinouchi T, Furusawa C, Tsuru S. Genes Cells. 2018 Oct;23(10):893-903.

Single cell analysis reveals a biophysical aspect of collective cell-state transition in embryonic stem cell differentiation. Okamoto K, Germond A, Fujita H, Furusawa C, Okada Y, Watanabe TM. Sci Rep. 2018 Aug 10;8(1):11965.

Macroscopic Theory for Evolving Biological Systems Akin to Thermodynamics. Kaneko K, Furusawa C. Annu Rev Biophys. 2018 May 20;47:273-290.

Formation of dominant mode by evolution in biological systems. Furusawa C, Kaneko K. Phys Rev E. 2018 Apr;97(4-1):042410.

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. Biotechnol Bioeng. 2018 Jun;115(6):1542-1551.

Toward prediction and control of antibiotic-resistance evolution. Furusawa C, Horinouchi T, Maeda T. Curr Opin Biotechnol. 2018 Dec;54:45-49.

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. Biotechnol J. 2018 May;13(5):e1700612.

Metabolic dynamics restricted by conserved carriers: Jamming and feedback. Hatakeyama TS, Furusawa C. PLoS Comput Biol. 2017 Nov 7;13(11):e1005847.

Mutation accumulation under UV radiation in Escherichia coli. Shibai A, Takahashi Y, Ishizawa Y, Motooka D, Nakamura S, Ying BW, Tsuru S. Sci Rep. 2017 Nov 6;7(1):14531.

Prediction of Cross-resistance and Collateral Sensitivity by Gene Expression profiles and Genomic Mutations. Horinouchi T, Suzuki S, Kotani H, Tanabe K, Sakata N, Shimizu H, Furusawa C. Sci Rep. 2017 Oct 25;7(1):14009.

Improvement of isopropanol tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies. Horinouchi T, Sakai A, Kotani H, Tanabe K, Furusawa C. J Biotechnol. 2017 Aug 10;255:47-56.

Time-programmable drug dosing allows the manipulation, suppression and reversal of antibiotic drug resistance in vitro. Yoshida M, Reyes SG, Tsuda S, Horinouchi T, Furusawa C, Cronin L. Nat Commun. 2017 Jun 8;8:15589.

Raman spectroscopy as a tool for ecology and evolution. Germond A, Kumar V, Ichimura T, Moreau J, Furusawa C, Fujita H, Watanabe TM. J R Soc Interface. 2017 Jun;14(131):20170174.

Acceleration and suppression of resistance development by antibiotic combinations. Suzuki S, Horinouchi T, Furusawa C. BMC Genomics. 2017 Apr 26;18(1):328.

[Analysis of Drug Resistance Using Experimental Evolution]. Furusawa C. Yakugaku Zasshi. 2017;137(4):373-376.

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. Matsumoto H, Kiryu H, Furusawa C, Ko MSH, Ko SBH, Gouda N, Hayashi T, Nikaido I. Bioinformatics. 2017 Aug 1;33(15):2314-2321.

Expression Profiling of Antibiotic-Resistant Bacteria Obtained by Laboratory Evolution. Suzuki S, Horinouchi T, Furusawa C. Methods Mol Biol. 2017;1520:263-279.

Density-Dependent Recycling Promotes the Long-Term Survival of Bacterial Populations during Periods of Starvation. Takano S, Pawlowska BJ, Gudelj I, Yomo T, Tsuru S. mBio. 2017 Feb 7;8(1):e02336-16.