Original Paper (2000-)

  1. Yoshiyama T, Motohashi C, Ichihashi N, Ichii T, Yomo T.(2015) Maintenance of a translation-coupled RNA replication in dynamic micro-sized compartments under continuous stirring and flow. Chemical Engineering Journa,283(14015),10.1016/j.cej.2015.08.024,896-902
  2. Ichihashi N, Aita T, Motooka D, Nakamura S, Yomo T.(2015) Periodic pattern of genetic and fitness diversity during evolution of an artificial cell-like system. Molecular Biology and Evolution,10.1093/molbev/msv189,1-29
  3. Ying BW, Honda T, Tsuru S, Seno S, Matsuda H, Kazuta Y, Yomo T.(2015) Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages. PLOS ONE,10(8),10.1371/journal.pone.0135639,e0135639
  4. Takako Awai, Norikazu Ichihashi,Tetsuya Yomo.(2015) Activities of 20 aminoacyl-tRNA synthetases expressed in a reconstituted translation system in Escherichia coli. Biochemistry and Biophysics Reports,3,10.1016/j.bbrep.2015.08.006,140-143
  5. Usui K, Ichihashi N, Yomo T(2015) A design principle for a single-stranded RNA genome that replicates with less double-strand formation. Nucleic Acids Research,10.1093/nar/gkv742
  6. Sakatani Y, Ichihashi N, Kazuta Y, Yomo T.(2015) A transcription and translation-coupled DNA replication system using rolling-circle replication. Scientific Reports,5,(10404),10.1038/srep10404,1-9
  7. Kotaro Nishiyama, Norikazu Ichihashi, Yasuaki Kazuta, Tetsuya Yomo.(2015) Development of a reporter peptide that catalytically produces a fluorescent signal through α-complementation. Protein Science,24,(4),10.1002/pro.2667,1-16
  8. Ichihashi N, Kobori S, Yomo T.(2015) Simple identification of two causes of noise in an aptazyme system by monitoring cell-free transcription. Methods in Enzymology,550,10.1016/bs.mie.2014.10.043.93-107
  9. Yoshie Murakami,Yuki Matsumoto, Saburo Tsuru, Bei-Wen Ying,Tetsuya Yomo.(2014) Global coordination in adaptation to gene rewiring. Nucleic Acids Research,42,22,10.1093/nar/gku1366.
  10. Ishizawa Y, Ying BW, Tsuru S, Yomo T.(2014) Nutrient-dependent growth defects and mutability of mutators in Escherichia coli. Genes Cells.,10.1111/gtc.12199.
  11. Nishimura K, Tsuru S, Suzuki H, Yomo T.(2014) Stochasticity in gene expression in a cell-sized compartment. ACS Synth. Biol., 10.1021/sb500249g,1-24
  12. Uno K, Sunami T, Ichihashi N, Kazuta Y, Matsuura T, Yomo T.(2014) The Evolutionary Enhancement of Genotype-Phenotype Linkages in the Presence of Multiple Copies of Genetic Material. Chembiochem,15,10.1002/cbic.201402299,1-9
  13. Atsushi Shibai, Saburo Tsuru, Bei-Wen Ying, Daisuke Motooka, Kazuyoshi Gotoh, Shota Nakamura and Tetsuya Yomo.(2014) Mutation accumulation in bacteria exposed to UV radiation. Artificial Life 14 ,88,10.1128/JVI.01127-14,11459-114688
  14. Ryo Mizuuchi,Norikazu Ichihashi,Kimihito Usui,Yasuaki Kazuta,and Tetsuya Yomo.(2014) Adaptive Evolution of an Artificial RNA Genome to a Reduced Ribosome . ACS Synthetic Biology,10.1021/sb5000884,292-298
  15. Satoshi fujii, Tomoaki Matsuura, Takeshi Sunami, Takehiro Nishikawa, Yasuaki Kazuta, Tetsuya Yomo..(2014) Liposome display for in vitro selection and evolution of membrane proteins. Nature protocols,9,7,10.1038/nprot.2014.107,1578-1591
  16. Yasuaki Kazuta,Tomoaki Matsuura,Norikazu Ichihashi,Tetsuya Yomo.(2014) Synthesis of milligram quantities of proteins using a reconstituted in vitro protein synthesis system. Journal of Bioscience and Bioengineering,1-4
  17. Nishimura K, Matsuura T, Sunami T, Fujii S, Nishimura K, Suzuki H & Yomo T.(2014) Identification of giant unilamellar vesicles with permeability to small charged molecules. RSC Advances,4,10.1039/c4ra05332j,35224-35232
  18. Yuya Akeno, Bei-Wen Ying, Saburo Tsuru, Tetsuya Yomo.(2014) A reduced genome decreases the host carrying capacity for foreign DNA. Microbial Cell Factories 2014, 2014,13,(49),1-9
  19. Bei-Wen Ying, Saburo Tsuru, Shigeto Seno, Hideo Matsudab, Tetsuya Yomo.(2014) Gene expression scaled by distance to the genome replication site. Mol. BioSyst., 2014,10,(3),375-379
  20. Kimihito Usui, Norikazu Ichihashi, Yasuaki Kazuta, Tomoaki Matsuura, Tetsuya Yomo.(2014) Effects of ribosomes on the kinetics of Qb replication. FEBS Letters.,588,(1),117-123
  21. Yuki Matsumoto, Yoshie Murakami, Saburo Tsuru, Bei-Wen Ying, Tetsuya Yomo.(2013) Growth rate-coordinated transcriptome reorganization in bacteria. BMC Genomics 2013.,14(808),1-10
  22. Takuyo Aita, Norikazu Ichihashi, Tetsuya Yomo. (2013) Probabilistic model based error correction in a set of various mutant sequences analyzed by next-generation sequencing. Computational Biology and Chemistry.,2013(47),221-230
  23. Norikazu Ichihashi, Kimihito Usui, Yasuaki Kazuta, Takeshi Sunami, Tomoaki Matsuura, Tetsuya Yomo. (2013) Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment. Nature Communications.,4(2494),1-7
  24. Satoshi Fujii, Tomoaki Matsuura, Takeshi Sunami, Yasuaki Kazuta, Tetsuya Yomo.(2013) In vitro evolution of hemolysin using a liposome display. PNAS.,110(42),16796-16801
  25. Kimihito Usui, Norikazu Ichihashi, Yasuaki Kazuta, Tomoaki Matsuura, Tetsuya Yomo.(2013) Kinetic model of double-stranded RNA formation during long RNA replication by Qβ replicase. FEBS Letters.,2013(587),2565-2571
  26. Shungo Kobori, Norikazu Ichihashi, Yasuaki Kazuta, Tetsuya Yomo.(2013) A controllable gene expression system in liposomes that includes a positive feedback loop. Mol. BioSyst., 2013. ,9(6),1282-1285
  27. Kotaro Nishiyama, Norikazu Ichihashi, Tomoaki Matsuura, Yasuaki Kazuta, Tetsuya Yomo.(2012) α-Complementation in an artificial genome replication system in liposomes. Chembiochem. ,2012(13),2701-2706
  28. Takehiro Nishikawa, Takeshi Sunami, TomoakiMatsuura, Tetsuya Yomo.(2012) Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes. Journal of Nucleic Acids. ,2012,1-11
  29. Tomoaki Matsuura, Kazufumi Hosoda, Yasuaki Kazuta, Norikazu Ichihashi, Hiroaki Suzuki, Tetsuya Yomo.(2012) Effects of Compartment Size on the Kinetics of Intracompartmental Multimeric Protein Synthesis. ACS Synth. Biol. ,2012(1),431-437
  30. Shungo Kobori, Norikazu Ichihashi, Yasuaki Kazuta, Tomoaki Matsuura, Tetsuya Yomo.(2012) Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system:modeling of ligand-dependent and -independent expression. RNA. ,18(8),1458-1465
  31. Nishimura Koji, Matsuura Tomoaki, Nishimura Kazuya, Sunami Takeshi, Suzuki Hiroaki, Yomo Tetsuya.(2012) Cell-free protein synthesis inside giant unilamellar vesicles analyzed by flow cytometry. Langmuir. , 2012(28),8426-8432
  32. Yohsuke Bansho, Norikazu Ichihashi, Yasuaki Kazuta, Tomoaki Matsuura, Hiroaki Suzuki, Tetsuya Yomo.(2012) Importance of parasite RNA species repression for prolonged translation-coupled RNA self-replication. CHEMISTRY BIOLOGY. , 19(4),478-487
  33. Takehiro Nishikawa, Takeshi Sunami, Tomoaki Matsuura, Norikazu Ichihashi, Tetsuya Yomo.(2012) Construction of Gene Screening System Using Giant Unilamellar Liposomes and Fluorescence Activated Cell Sorter. Analytical Chemistry 2012. , 84,5017-5024
  34. YukiMatsumoto, Yoichiro Ito, Saburo Tsuru, Bei-Wen Ying, Tetsuya Yomo.(2011) Bacterial Cells Carrying Synthetic Dual-Function Operon Survived Starvation. Journal of Biomedicine and Biotechnology. , 2011,1-10
  35. Filippo Caschera, Takeshi Sunami, Tomoaki Matsuura, Hiroaki Suzuki, Martin M. Hanczyc, and Tetsuya Yomo.(2011) Programmed Vesicle Fusion Triggers Gene Expression. Langmuir. , 27(21),13082-13090
  36. Yoshihiro Shimizu, Saburo Tsuru, Yoichiro Ito, Bei-Wen Ying, Tetsuya Yomo.(2011) Stochastic Switching Induced Adaptation in a Starved Escherichia coli Population. PLoS ONE. , 6(9),e23953
  37. Tomoaki Matsuura, Kazufumi Hosoda, Norikazu Ichihashi, Yasuaki Kazuta, Tetsuya Yomo.(2011) Kinetic Analysis of -Galactosidase and -Glucuronidase Tetramerization Coupled with Protein Translation. Journal of Biological Chemistry. , 286(25),22028-22034
  38. Saburo Tsuru, Nao Yasuda, Yoshie Murakami, Junya Ushioda, Akiko Kashiwagi, Shingo Suzuki, Kotaro Mori, Bei-Wen Ying, Tetsuya Yomo.(2011) Adaption by stochastic switching of a monostable genetic circuit in Escherichia coil. Molecular Systems Biology. , 7(493),1-10
  39. Norikazu Ichihashi, Tomoaki Matsuura, Kazufumi Hosoda and Tetsuya Yomo.(2010) Identification of two forms of Q replicase with different thermal stabilities but identical RNA replication activity. The Journal of Biological Chemistry. , 285(48), 37210-37217
  40. Takeshi Sunami, Filippo Caschera, Yuuki Morita, Taro Toyota, Kazuya Nishimura,Tomoaki Matsuura, Hiroaki Suzuki, Martin M. Hanczyc, and Tetsuya Yomo (2010) Detection of Association and Fusion of Giant Vesicles Using a Fluorescence-Activated Cell Sorter. Langmuir. , 26(19), 15098-15103
  41. Takeshi Sunami, Kazufumi Hosoda, Hiroaki Suzuki, Tomoaki Matsuura, Tetsuya Yomo. (2010) Cellular compartment model for exploring the effect of the lipidic membrane on the kinetics of encapsulated biochemical reactions. Langmuir, 26(11), 8544-8551.
  42. Hiroya Urabe, Norikazu Ichihashi, Tomoaki Matsuura, Kazufumi Hosoda, Yasuaki Kazuta, Hiroshi Kita, Tetsuya Yomo.(2010) Compartmentalization in a water-in-oil emulsion repressed the spontaneous amplification of RNA by Qbeta replicase. Biochemistry, 49(9), 1809-1813.
  43. Nishimura, K., Hosoi, T., Sunami, T., Toyota, T., Fujinami, M., Oguma, K., Matsuura, T., Suzuki, H., and Yomo, T. (2009) Population analysis of structural properties of giant liposomes by flow cytometry. Langmuir, 25(18), 10439-10443.
  44. Tsuru, S., Ichinose, J., Kashiwagi, A., Ying, B-W., Kaneko, K., and Yomo, T. (2009) Noisy cell growth rate leads to fluctuating protein concentration in bacteria. Physical Biology, 6 (3): 1-9.
  45. Kashiwagi, A., Sakurai, T., Tsuru, S., Ying, B-W., Mori, K., and Yomo, T. (2009) Construction of Escherichia coli gene expression level perturbation collection. Metabolic Engineering, 11 (1): 56-63.
  46. Tsukada, K., Okazaki, M., Kita, H., Inokuchi, Y., Urabe, I., and Yomo, T. (2009) Quantitative analysis of the bacteriophage Q infection cycle. Biochimica et Biophysica Acta, 1790 (1): 65-70.
  47. Takeshi Sunami, Hiroshi Kita, Kazufumi Hosoda, Tomoaki Matsuura, Hiroaki Suzuki, Tetsuya Yomo. (2009) Chapter 2 - Detection and Analysis of Protein Synthesis and RNA Replication in Giant Liposomes. In:Methods in Enzymology Volume 464, Nejat Duzgunes (ed.). Academic Press, New York, pp. 19-29.
  48. Hosoda, K., Sunami, T., Kazuta, Y., Matsuura,T., Suzuki, H., and Yomo, T. (2008) Quantitative study of the structure of multilamellar giant liposomes as a container of protein synthesis reaction. Langmuir, 24 (23): 13540-13548.
  49. Ichihashi, N., Matsuura, T., Kita, H., Hosoda, K., Sunami, T., Tsukada, K., and Yomo, T. (2008) Translation-replication balance determines the replication efficiency of the self-encoding system. ChemBioChem, 9 (18): 3023-3028.
  50. Kita, H., Matsuura, T., Sunami, T., Hosoda, K., Ichihashi, N., Tsukada, K., Urabe, I., and Yomo T. (2008) Replication of genetic information with self-encoded replicase in liposomes. ChemBioChem, 9 (15): 2403-2410.
  51. Hosoda, K., Matsuura, T., Kita, H., Ichihashi, N., Tsukada, K., Urabe, I., and Yomo, T. (2008) A novel sequence-specific RNA quantification method using nicking endonuclease, dual-labeled fluorescent DNA probe, and conformation-interchangeable oligo-DNA. RNA, 14: 584-592.
    Supplementaly Information
  52. Hosoda, K., Matsuura, T., Kita, H., Ichihashi, N., Tsukada, K., and Yomo, T. (2007) Kinetic analysis of the entire RNA amplification process by Qreplicase.J. Biol. Chem., 282 (21): 15516-15527.
  53. Sunami, T., Sato, K., Matsuura, T., Tsukada, K., Urabe, I. and Yomo, T. (2006) Femtoliter compartment in liposomes for in vitro selection of proteins. Anal. Biochem., 357: 128-136.