Yokobayashi Lab

発表論文

  • Nomura Y, Yokobayashi Y, RNA ligase ribozymes with a small catalytic core. Sci Rep 2023; 13: 8584. (PubMed / Journal (Open Access))

  • Fukunaga K, Dhamodharan V, Miyahira N, Nomura Y, Mustafina K, Oosumi Y, Takayama K, Kanai A, Yokobayashi Y, Small-Molecule Aptamer for Regulating RNA functions in Mammalian Cells and Animals. J Am Chem Soc 2023; 145: 7820-7828. (PubMed / Journal (Open Access)) (OIST press release)

  • Hauf S, Yokobayashi Y, Chemical control of phase separation in DNA solutions. Chem Commun 2023; 59: 3751-3754. (PubMed / Journal (Open Access))

  • Rotrattanadumrong R, Yokobayashi Y, Experimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning. Nat Commun 2022; 13: 4847. (PubMed / Journal (Open Access))

  • Hauf S, Rotrattanadumrong R, Yokobayashi Y, Analysis of the Sequence Preference of Saporin by Deep Sequencing. ACS Chem Biol 2022; 17: 2619-2630. (PubMed / Journal (Open Access))

  • Baeken MW, Yokobayashi Y, Identification of an ERN1 target site within EGFP mRNA. J Cell Biochem 2022; 123: 1298-1305. (PubMed / Journal (Open Access))

  • Bhat D, Hauf S., Plessy C, Yokobayashi Y, Pigolotti S. Speed variations of bacterial replisomes. eLife 2022; 11: e75884. (PubMed / Journal (Open Access))

  • Tabuchi T, Yokobayashi Y. High-throughput screening of cell-free riboswitches by fluorescence-activated droplet sorting. Nucleic Acids Res 2022; 50: 3535-3550. (PubMed / Journal (Open Access))

  • Sontakke VA, Yokobayashi Y. Programmable Macroscopic Self-Assembly of DNA-Decorated Hydrogels. J Am Chem Soc 2022; 144: 2149-2155. (PubMed / Journal (Open Access)) (Nature Resarch Highlight)

  • Diaz Arenas C, Ardaševa A, Miller J, Mikheyev AS, Yokobayashi Y. Ribozyme Mutagenic Evolution: Mechanisms of Survival. Orig Life Evol Biosph 2022; 51: 321-339. (PubMed / Journal)

  • Kim N, Yokobayashi Y. Novel RNA Viral Vectors for Chemically Regulated Gene Expression in Embryonic Stem Cells. ACS Synth Biol 2021; 10: 2959-2967. (PubMed / Journal)

  • Mustafina K, Nomura Y, Rotrattanadumrong R, Yokobayashi Y. Circularly-Permuted Pistol Ribozyme: A Synthetic Ribozyme Scaffold for Mammalian Riboswitches. ACS Synth Biol 2021; 10: 2040-2048. (PubMed / Journal)

  • Tabuchi T, Yokobayashi Y. Cell-free riboswitches. RSC Chem Biol 2021; 2: 1430-1440. (PubMed / Journal (Open Access))

  • Fukunaga K, Yokobayashi Y. Directed evolution of orthogonal RNA-RBP pairs through library-vs-library in vitro selection. Nucleic Acids Res 2022; 50: 601-616. (Selected as a "Breakthrough Article". Cover picture.) (PubMed / Journal (Open Access))

  • Nomura Y, Yokobayashi Y. Aptazyme-Based Riboswitches and Logic Gates in Mammalian Cells. Methods Mol Biol 2021; 2323: 213-220. (PubMed / Journal)

  • 横林 洋平, 「セルフリーシステムにおける人工リボスイッチの構築」, 生物工学会誌 2020; 98, 655-658. (Journal (Open Access))

  • Yokobayashi Y. High-Throughput Analysis and Engineering of Ribozymes and Deoxyribozymes by Sequencing. Acc Chem Res 2020; 53: 2903-2912. (PubMed / Journal (Open Access))

  • Danielson E, Sontakke VA, Porkovich AJ, Wang Z, Kumar P, Ziadi Z, Yokobayashi Y, Sowwan M. Graphene Based Field-Effect Transistor Biosensors Functionalized Using Gas-Phase Synthesized Gold Nanoparticles. Sens Actuators B Chem 2020; 320, 128432. (PubMed / Journal (Open Access))

  • Mustafina K, Fukunaga K, Yokobayashi Y. Design of Mammalian ON-Riboswitches Based on Tandemly Fused Aptamer and Ribozyme. ACS Synth Biol 2020; 9: 19-25. (PubMed / Journal (Open Access))

  • Dwidar M, Yokobayashi Y. Development of a histamine aptasensor for food safety monitoring. Sci Rep 2019; 9: 16659.(PubMed / Journal (Open Access))

  • Danielson E, Dhamodharan V, Porkovich A, Kumar P, Jian N, Ziadi Z, Grammatikopoulos P, Sontakke VA, Yokobayashi Y, Sowwan M. Gas-Phase Synthesis for Label-Free Biosensors: Zinc-Oxide Nanowires Functionalized with Gold Nanoparticles. Sci Rep 2019; 9: 17370. (PubMed / Journal (Open Access))

  • Nomura Y, Yokobayashi Y. Systematic minimization of RNA ligase ribozyme through large-scale design-synthesis-sequence cycles. Nucleic Acids Res 2019; 47: 8950-8960. (PubMed / Journal (Open Access))

  • Takahashi K, Yokobayashi Y. Reversible Gene Regulation in Mammalian Cells Using Riboswitch-Engineered Vesicular Stomatitis Virus Vector. ACS Synth Biol 2019; 8: 1976-1982. (PubMed / Journal (Open Access))

  • Saito H, Yokobayashi Y. Editorial overview: Mammalian synthetic biology: from devices to multicellular systems. Curr Opin Chem Biol 2019; 52: 1-2. (PubMed / Journal) (An editorial for the annual Synthetic Biology section by the coeditors)

  • Yokobayashi Y. Aptamer-based and aptazyme-based riboswitches in mammalian cells. Curr Opin Chem Biol 2019; 52: 72-78. (PubMed / Journal (Open Access))

  • Dwidar M, Seike Y, Kobori S, Whitaker C, Matsuura T, Yokobayashi Y. Programmable Artificial Cells Using Histamine-Responsive Synthetic Riboswitch. J Am Chem Soc 2019; 141: 11103-11114. (PubMed / Journal (Open Access)) (Media coverage (Japanese): Nikkei Shimbun, Nikkei Biotech)

  • Kobori S, Nomura Y, Yokobayashi Y. Self-powered RNA nanomachine driven by metastable structure. Nucleic Acids Res 2019; 47: 6007-6014. (PubMed / Journal (Open Access))

  • Yokobayashi Y. Applications of high-throughput sequencing to analyze and engineer ribozymes. Methods 2019; 161: 41-45. (PubMed / Journal (Open Access))

  • Dwidar M, Yokobayashi Y. Riboswitch Signal Amplification by Controlling Plasmid Copy Number. ACS Synth Biol 2019; 8: 245-250.(PubMed / Journal (Open Access))

  • Dhamodharan V, Nomura Y, Dwidar M, Yokobayashi Y. Optochemical control of gene expression by photocaged guanine and riboswitches. Chem Commun 2018; 54: 6181-6183. (PubMed / Journal (Open Access))

  • Yokobayashi Y. Small Molecule‐Responsive RNA Switches (Bacteria): Important Element of Programming Gene Expression in Response to Environmental Signals in Bacteria. in Synthetic Biology: Parts, Devices and Applications pp181-188, eds: Smolke C, Lee SY, Nielsen J, Stephanopoulos G, 2018; Wiley-VCH (book chapter) (Book)

  • Pozzo T, Akter F, Nomura Y, Louie AY, Yokobayashi Y. A Firefly Luciferase Mutant with Enhanced Activity and Thermostability. ACS Omega 2018; 3: 2628-2633. (PubMed / Journal (Open Access))

  • Kobori S, Yokobayashi Y. Analyzing and Tuning Ribozyme Activity by Deep Sequencing to Modulate Gene Expression Level in Mammalian Cells. ACS Synth Biol 2018; 7: 371-376. (PubMed / Journal (Open Access))

  • Nomura Y, Chien H-C, Yokobayashi Y. Direct screening for ribozyme activity in mammalian cells. Chem Commun 2017; 53: 12540-12543. (PubMed / Journal (Open Access))

  • Dhamodharan V, Kobori S, Yokobayashi Y. Large Scale Mutational and Kinetic Analysis of a Self-Hydrolyzing Deoxyribozyme. ACS Chem Biol 2017; 12: 2940-2945.(PubMed / Journal (Open Access))

  • Dwidar M, Yokobayashi Y. Controlling Bdellovibrio bacteriovorus Gene Expression and Predation Using Synthetic Riboswitches. ACS Synth Biol 2017; 6: 2035-2041. (PubMed / Journal (Open Access))

  • Kobori S, Takahashi K, Yokobayashi Y. Deep Sequencing Analysis of Aptazyme Variants Based on a Pistol Ribozyme. ACS Synth Biol 2017; 6: 1283–1288. (PubMed / Journal (Open Access))

  • Kobori S, Yokobayashi Y. High-throughput Mutational Analysis of a Twister Ribozyme. Angew Chem Int Ed 2016; 55: 10354-10357. (PubMed / Journal (Open Access))

  • 横林 洋平, 「RNAによる遺伝子発現制御デバイス」, 生物工学会誌 2016; 94, 190-193. (Journal (Open Access))

  • Nomura Y, Yokobayashi Y. Aptazyme-Based Riboswitches and Logic Gates in Mammalian Cells. Methods Mol Biol 2015; 1316: 141-148. (PubMed / Journal)

  • Kobori S, Nomura Y, Miu A, Yokobayashi Y. High-throughput assay and engineering of self-cleaving ribozymes by sequencing. Nucleic Acids Res 2015; 43: e85. (PubMed / Journal (Open Access))

  • Akter F, Yokobayashi Y. RNA Signal Amplifier Circuit with Integrated Fluorescence Output. ACS Synth Biol 2015; 4: 655-658. (PubMed / Journal)

  • Nomura Y, Yokobayashi Y. Dual Genetic Selection of Synthetic Riboswitches in Escherichia coli. Methods Mol Biol 2014; 1111: 131-140. (PubMed / Journal)

  • Sharma V, Yokobayashi Y. In Vivo Screening of Artificial Small RNAs for Silencing Endogenous Genes in Escherichia coli. Methods Mol Biol 2013; 1073: 75-84. (PubMed / Journal)

  • Nomura Y, Zhou L, Miu A, Yokobayashi Y. Controlling Mammalian Gene Expression by Allosteric Hepatitis Delta Virus Ribozymes. ACS Synth Biol 2013; 2: 684-689. (PubMed / Journal (Open Access))

  • Sharma V, Sakai Y, Smythe KA, Yokobayashi Y. Knockdown of recA gene expression by artificial small RNAs in Escherichia coli. Biochem Biophys Res Commun 2013; 430: 256-259 (PubMed / Journal)

  • Nomura Y, Kumar D, Yokobayashi Y. Synthetic mammalian riboswitches based on guanine aptazyme. Chem Commun 2012; 48: 7215-7217. (PubMed / Journal)

  • Sharma V, Yamamura A, Yokobayashi Y. Engineering Artificial Small RNAs for Conditional Gene Silencing in Escherichia coli. ACS Synth Biol 2012; 1: 6-13. (PubMed / Journal)

  • Muranaka N, Sharma V, Yokobayashi Y. Enzymatic Probing Analysis of an Engineered Riboswitch Reveals Multiple OFF Conformations. Nucleosides, Nucleotides and Nucleic Acids 2011; 30: 696-705 (PubMed / Journal)

  • Kumar D, Kim SH, Yokobayashi Y. Combinatorially Inducible RNA Interference Triggered by Chemically Modified Oligonucleotides. J Am Chem Soc 2011; 133: 2783-2788. (PubMed / Journal)

  • Nomura Y, Sharma V, Yamamura A, Yokobayashi Y. Selection of silk-binding peptides by phage display. Biotechnol Lett 2011; 33: 1069-1073. (PubMed / Journal (Open Access))

  • Muranaka N, Yokobayashi Y. A synthetic riboswitch with chemical band-pass response. Chem Commun 2010; 46: 6825-6827. (PubMed / Journal)

  • Muranaka N, Yokobayashi Y. Posttranscriptional Signal Integration of Engineered Riboswitches Yields Band-Pass Output. Angew Chem Int Ed 2010; 49: 4653-4655. (PubMed / Journal)

  • Tuleuova N, Jones CN, Yan J, Ramanculov E, Yokobayashi Y, Revzin A. Development of an Aptamer Beacon for Detection of Interferon-Gamma. Anal Chem 2010; 82: 1851-1857. (PubMed / Journal)

  • Kumar D, An CI, Yokobayashi Y. Conditional RNA Interference Mediated by Allosteric Ribozyme. J Am Chem Soc 2009; 131: 13906-13907. (PubMed / Journal / Free Download)

  • Muranaka N, Abe K, Yokobayashi Y. Mechanism-Guided Library Design and Dual Genetic Selection of Synthetic OFF Riboswitches. ChemBioChem 2009; 10: 2375-2381. (PubMed / Journal)

  • Muranaka N, Sharma V, Nomura Y, Yokobayashi Y. An efficient platform for genetic selection and screening of gene switches in Escherichia coli. Nucleic Acids Res 2009; 37: e39. (PubMed / Journal).

  • Muranaka N, Sharma V, Nomura Y, Yokobayashi Y. An efficient design strategy for whole-cell and cell-free biosensors based on engineered riboswitches. Anal Lett 2009; 42: 108-122. (Journal)

  • Sharma V, Nomura Y, Yokobayashi Y. Engineering complex riboswitch regulation by dual genetic selection. J Am Chem Soc 2008; 130: 16310-16315. (PubMed / Journal)

  • Tuleuova N, An CI, Ramanculov E, Revzin A, Yokobayashi Y. Modulating endogenous gene expression of mammalian cells via RNA-small molecule interaction. Biochem Biophys Res Commun 2008; 376: 169-173. (PubMed / Journal)

  • Nomura Y, Yokobayashi Y. Reengineering a natural riboswitch by dual genetic selection. J Am Chem Soc 2007; 129: 13814-13815. (PubMed / Journal)

  • Yoshida W, Yokobayashi Y. Photonic boolean logic gates based on DNA aptamers. Chem Commun 2007; 195-197. (PubMed / Journal / Commentary )

  • Nomura Y, Yokobayashi Y. Dual selection of a genetic switch by a single selection marker. BioSystems 2007; 90: 115-120. (PubMed / Journal)

  • An CI, Trinh VB, Yokobayashi Y. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA 2006; 12: 710-716. (PubMed / Journal / Commentary )

    2005年以前の発表論文

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