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Recent publications of S. Yokobori

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2021

• "Mutation analysis of the rpoB gene in the radiation-resistant bacterium Deinococcus radiodurans R1 exposed to space"
• Fujiwara, D., Y. Kawaguchi, Y. Togashi, I. Kinoshita, J. Yatabe, I. Narumi, H. Hashimoto, S. Yokobori, & A. Yamagishi
  Astrobiology 21(12), 1494-1504 (2021) Astrobiology
• "Space Exposure of Amino Acids and Their Precursors in the Tanpopo Mission"
• Kobayashi, K., H. Mita, Y. Kebukawa, K. Nakagawa, T. Kaneko, Y. Obayashi, T. Sato, T. Yokoo, S. Minematsu, H. Fukuda, Y. Oguri, I. Yoda, S. Yoshida, K. Kanda, E. Imai, H. Yano, H. Hashimoto, S. Yokobori, & A. Yamagishi
  Astrobiology 21(12), 1479-1493 (2021) Astrobiology
• "Scientific targets of Tanpopo: Astrobiology exposure and micrometeoroid capture experiments at the Japanese Experiment Module Exposed Facility of the International Space Station"
• Yamagishi, A., S. Yokobori, K. Kobayashi, H. Mita, H. Yabuta, M. Tabata, M. Higashide, & H. Yano
  Astrobiology 21(12), 1451-1460 (2021) Astrobiology
• "Evolution of Superoxide Dismutases and Catalases in Cyanobacteria: Occurrence of the Antioxidant Enzyme Genes before the Rise of Atmospheric Oxygen"
• Harada, M., A. Akiyama, R. Furukawa, S. Yokobori, E. Tajika, & A.Yamagishi
  Journal of Molecular Evolution 89(8), 527-543 (2021) Journal of Molecular Evolution

2020

• "DNA damage and survival time course of deinococcal cell pellets during 3 years of exposure to outer space"
• Kawaguchi, Y., M. Shibuya, I. Kinoshita, J. Yatabe, I. Narumi, H. Shibata, R. Hayashi, D. Fujiwara, Y. Murano, H. Hashimoto, E. Imai, S. Kodaira, Y. Uchihori, K. Nakagawa, H. MIta, S. Yokobori, & A. Yamagishi
  Frontiers in Microbiology 11, 2050 (2020) Frontiers in Microbiology
• "Tolerance of dried cells of a terrestrial cyanobacterium, Nostoc sp. HK-01 to temperature cycles, helium-ion beams, ultraviolet radiation (172 and 254 nm), and gamma rays: Primitive analysis for space experiments"
• Tomita-Yokotani, K., S. Kimura, M. Ong, R. Ajioka, Y. Igarashi, H. Fujishiro, H. Katoh, H. Hashimoto, H. Mita, S. Yokobori, & M. Ohmori
  Eco-engineering 32, 47-53 (2020)
• "Characterization and phylogenetic position of two sympatric sister species of toxic flatworms Planocera multitentaculata and Planocera reticulata (Platyhelminthes: Acotylea)"
• Yonezawa, R., S. Itoi, Y. Igarashi, K. Yoshitake, H. Oyama, S. Kinoshita, R. Suo, S. Yokobori, H. Sugita, & S. Asakawa
  Mitochondrial DNA Part B: Resources 5, 2352-2354 (2020) Mitochondrial DNA Part B: Resources

2019

• "Mitogenome analysis of dwarf pufferfish (Carinotetraodon travancoricus) endemic to southwest India and its implications in the phylogeny of Tetraodontidae "
• Sathyajith, C., Y. Yamanoue, S. Yokobori, S. Thampy, & V. J. Rejish Kumar
  Journal of Genetics (India) 98, 105 (2019) J. Genet.
• "Planktonic adaptive evolution to the sea surface temperature in the Neoproterozoic inferred from ancestral NDK of marine cyanobacteria. "
• Harada, M., A. Nagano, S. Yagi, R. Furukawa, S. Yokobori, & A. Yamagishi
  Earth and Planetary Science Letters 522, 98-106 (2019) ScienceDirect
• "Establishment of mesophilic-like catalytic properties on a thermophilic enzyme without the expense of its thermal stability."
• Akanuma, S., M. Bessho, H. Kimura, X.-t Zhou, R. Furukawa, S. Yokobori, & A. Yamagishi
  Scientific Reports 9: 9346 (2019) PubMed
• "Eukaryotes appearing"
• S. Yokobori, & R. Furukawa
  In: "Astrobiology: From the origins of life to the search for extraterrestrial intelligence" (Eds. A. Yamagishi, T. Kakegawa, & T. Usui.). Springer Singapore, pp. 105-121 (2019)
• "STXM-XANES analyses of Murchison meteorite powders captured by aerogel after hypervelocity impacts: A potential implication of organic matter degradation for micrometeoroid collection experiments. "
• Kebukawa, Y., K. Okudaira, H. Yabuta, S. Hasegawa, M. Tabata, Y. Furukawa, M. Ito, A. Nakato, A. L. D. Kilcoyne, K. Kobayashi, S. Yokobori, E. Imai, Y. Kawaguchi, H. Yano, & A. Yamagishi
  Geochem. J. 531, 53-67 (2019) Geochemical Journal

2018

• "Draft genome sequence of the radioresistant bacterium Deinococcus aerius TR0125, isolated from the high atmosphere above Japan. "
• Satoh, K., H. Arai, T. Sanzen, Y. Kawaguchi, H. Hayashi, S. Yokobori, A. Yamagishi, Y. Oono, & I. Narumi
  Genome Announcements 6: e00080-18 (DOI: 10.1128/genomeA.00080-18)(2017) American Society for Microbiology

2017

• "Hydroxylation of a conserved tRNA modification contributes to establishment of non-universal genetic code in echinoderm mitochondria. "
• Nagao, A., M. Ohara, K. Miyauchi, S. Yokobori, A. Yamagishi, K. Watanabe, & T. Suzuki
  Nature Struc. Mol. Biol. 4(9), 778-782 (2017) PubMed
• "Reconstructed ancestral enzymes suggest long-term cooling of Earth’s photic zone since the Archean. "
• Garcia, A. K., J. W. Schopf, S. Yokobori, S. Akanuma, A. Yamagishi
  Proc. Natl. Acad. Sci. USA 114(18), 4619-4624 (2017) PubMed
• "Diversification of mitochondrial genome of Daphnia galeata (Cladocera, Crustacea): comparison with phylogenetic consideration of the complete sequences of clones isolated from five lakes in Japan"
• Tokishita, S., H. Shibuya, T. Kobayashi, M. Sakamoto, J.-Y. Ha, S. Yokobori, H. Yamagata, & T. Hanazato
  gene 611, 38-46 (2017) PubMed
• "Updated mitochondrial phylogenomics of Pteriomorphia and Heterodonta in Bivalvia, including deep-sea chemosymbiotic Bathymodiolus mussels, vesicomyid clams, and the thyasirid clam Conchocele cf. bisecta. "
• Ozawa, M., S. Shimamura, Y. Takagi, S. Yokobori, T. Maeda, T. Maruyama & T. Yoshida
  Marine Genomics 31, 43-52 (2017) PubMed
• "Quest for ancestors of eukaryal cells based on phylogenetic analyses of aminoacyl tRNA synthetases. "
• Furukawa, R, M. Nakagawa, T. Kuroyanagi, S. Yokobori, & A. Yamagishi
  J. Mol. Evol. 84,: 51-66 (2017) PubMed

2016

• "Birth of Archaeal Cells—Molecular phylogenetic analyses of G1P dehydrogenase, G3P dehydrogenases, and glycerol kinase suggest derived features of archaeal membranes having G1P-polar lipids"
• Yokobori, S., Y. Nakajima, S. Akanuma, & A. Yamagishi
  Archaea Article ID 1802675 (2016) Hindawi
• "Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein"
• Hashimoto, T., D. D. Horikawa, Y. Saito, H. Kuwahara, H. Kozuka-Hata, T. Shin-I, Y. Minakuchi, K. Ohishi, A. Motoyama, T. Aizu, K. Abe, T. Horiuchi, A. Enomoto, K. Kondo, S. Tanaka, Y. Hara, S. Koshikawa, H. Sagara, T. Miura, S. Yokobori, K. Miyagawa, S. Sugano, Y. Suzuki, T. Kubo, M. Oyama, Y. Kohara, A. Fujiyama, K. Arakawa, T. Katayama, A. Toyoda, & T. Kunieda
  Nature Comm. 7, 12808 (DOI: 10.1038/ncomms12808) (2016) Nature
• "Investigation of the interplanetary transfer of microbes in the Tanpopo mission at the Exposed Facility of the International Space Station"
• Kawaguchi, Y., S.Yokobori, H. Hashimoto, H. Yano, M. Tabata, H. Kawai & A. Yamagishi
  Astrobiolgy 16, 1-14 (2016)
• "Ultralow-density double-layer silica aerogel fabrication for the intact capture of cosmic dust in low-Earth orbits"
• Tabata, M., H. Kawai, H. Yano, E. Imai, H. Hshimoto, S. Yokobori, & A. Yamagishi
  J. Sol-Gel Sci. Tech. 77(2): 325-334

2015

• "Epistasis effects of multiple ancestral-consensus amino acid substitutions on the thermal stability of glycerol kinase from Cellulomonas sp. NT3060"
• Fukuda, Y., A. Abe, T. Tamura, T. Kishimoto, A. Sogabe, S. Akanuma, S. Yokobori, A. Yamagishi, K. Imada, & K. Inagaki
  J. Biosci. Bioeng. (in press)
• "Robustness of predictions of extremely thermally stable proteins in ancient organisms"
• Akanuma, S., S. Yokobori, Y. Nakajima, M. Bessho,& A. Yamagishi
  Evol. 69(11): 2954–2962
• "Evolution of eukaryotic DNA polymerases via interaction between cells and large DNA viruses"
• Takemura, M., S. Yokobori, H. Ogata
  J. Mol. Evol. 81(1-2): 24-33
• "Ancestral amino acids substitution improved thermal stability of recombinant lignin-peroxidase from white-rot fungi, Phanerochaete chrysosporium strain UAMH 3641"
• Semba, Y., M. Ishida, S. Yokobori, A. Yamagishi
  Protein Engineer. Des. Select. 28(7): 221-230

2014

• "Fluorescence imaging of microbe-containing particles shot from a two-stage Light-gas gun into an aerogel"
• Kawaguchi, Y., T. Sugino, M. Tabata, K. Okudaira, E. Imai, H. Yano, S. Hasegawa, H. Hashimoto, H. Yabuta, K. Kobayashi, H. Kawai, H. Mita, S. Yokobori, & Yamagishi A.
  Orig. Life Evol. Biosph. (2014) doi:10.1007/s11084-014-9361-x. Springer
• "Chapter 2. How the early genetic code was established? -Inference from the analysis of extant animal mitochondrial decoding systems-"
• Watanabe, K., & S. Yokobori.
  In Chemical Biology of Nucleic Acids: Fundamentals and Clinical Applications (Eds. Erdmann VA, Markiewicz WT, Barciszewski J.) Springer-Verlag Berlin Heidelberg, pp. 25-40 (2014).
• "Arabidopsis thaliana mitochondrial EF-G1 functions in two different translational steps."
• Suematsu, T., O. Watanabe, K. Kita, & S. Yokobori, Y. Watanabe
  J. Biochem. (Tokyo) 155(2), 107-114 (2014). PubMed

2013

• "Selection of lichens resistant to the cosmic environment – thermal cycle treatment, UV irradiation and heavy particle beam –."
• Takahashi, Y., S. Shibata, J. Yokoyama, H. Hashimoto, S. Yokobori, & A. Yamagishi
  Biol. Sci. Space 27: 9-18 (2013).
• "The possible interplanetary migration of aggregated microbes: Viability of Deinococcus spp. under the environmental conditions at ISS for exposure experiment of microbes in Tanpopo mission."
• Kawaguchi, Y., Y., Yang, K. Shiraishi, N. Kawashiri, Y. Takahashi, T. Sugino, K. Nakagawa, A. Tanigawa, H. Hashimoto, S. Yoshida, K. Kobayashi, K. Satoh, I. Narumi, S. Yokobori, & A. Yamagishi
  Orig. Life Evol. Biosph. 43(4-5), 411-428 (2013). PubMed Springer
• "Life without tRNA^Arg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes."
• Yokobori, S., A. Kitamura, H. Grosjean, & Y. Bessho
  Nucleic Acids Res. 41:6531-7543 (2013). PubMed
• "Experimental evidence for the thermophilicity of ancestral life."
• Akanuma S., Y. Nakajima, S. Yokobori, M. Kimura, N. Nemoto, T. Mase, K. Miyazono, M. Tanokura, & A. Yamagishi
  Proc. Natl. Acad. Sci. USA 110 (27), 11067-11072 (2013).
• "Chapter 12.　Comparative Genomics of Thermophilic Bacteria and Archaea."
• Akanuma, S., S. Yokobori, & A. Yamagishi
  In "Thermophilic Microbes in Environmental and Industrial Biotechnology" (Eds. Satyanarayana, T., Litterchild J., Kawarabayasi, Y.). Springer Science, pp. 331-349 (2013).
• "Decoding mechanism of non-universal genetic codes in Loligo bleekeri mitochondria."
• Ohira, T., T. Suzuki, K. Miyauchi, T. Suzuki, S. Yokobori, A. Yamagishi, & K. Watanabe
  J. Bio. Chem. 288: 7645-7652 (2013). PubMed

2012

• "Tolerance of eggs in the Tardigrade Ramazzottius varieornatus to extreme environments."
• Horikawa, D.D., A. Yamaguchi, T. Sakashita, D. Tanaka, N. Hamada, F. Yukuhiro, H. Kuwahara, T. Kunieda, M. Watanabe, Y. Nakahara, S. Wada, T. Funayama, C. Katagiri, S. Higashi, S. Yokobori, M. Kuwabara, L. J. Rothschild, T. Okuda, H. Hashimoto, & Y. Kobayashi
  Astrobiol. 12: 283-289 (2012) PubMed

2011

• "Unique characteristics of ascidian mitochondrial tRNAs - Existence of three 5-taurinometylyuridine-containing tRNAs corresponding to the non-universal genetic codes."
• Suzuki, T., K. Miyauchi, T. Suzuki, S. Yokobori, N. Shigi, A. Kondow, N. Takeuchi, A. Yamagishi, & K. Watanabe
  J. Biol. Chem. 286: 35494-35498 (2011).
• "Genetic code. Introduction (Version 2)."
• Watanabe, K., & S. Yokobori
  In: Encyclopedia of Life Science. John Wiley & Sons, Ltd., Chichester. (2011). DOI: 10.1002/9780470015902.a0000809.pub2
• "tRNA modification and genetic code variations in animal mitochondria."
• Watanabe, K., & S. Yokobori
  J. Nucleic Acids. (in press) (2011).
• "Tanpopo cosmic dust collector: silica aerogel production and bacterial DNA contamination analysis."
• Tabata, M., Y. Kawaguchi, S. Yokobori, H. Kawai, J. Takahashi, H. Yano, & A. Yamagishi.
  Biol. Sci. Space 25: 7-12 (2011).
• "Phylogeny-based design of a B-subunit of DNA gyrase and its ATPase domain using a small set of homologous amino acid sequences."
• Akanuma, S., S. Iwami, T. Yokoi, N. Nakamura, H. Watanabe, S. Yokobori, & A. Yamagishi.
  J.Mol.Biol. 412:212-225 (2011) PubMed
• "Male death resulting from hybridization between subspecies of the gypsy moth, Lymantria dispar."
• Higashiura, Y., H. Yamaguchi, M. Ishihara, N. Ono, H. Tsukagoshi, S. Yokobori, S. Tokishita, H. Yamagata, & T. Fukatsu.
  Heredity 106:603-613 (2011) PubMed

2010

• "Search for microbes on the Mars surface with special interest in methane-oxidizing bacteria."
• Yamagishi A., S. Yokobori, Y. Yoshimura, M. Yamashita, H. Hashimoto, T. Kubota, H. Yano, J. Haruyama, M. Tabata, K. Kobayashi, H. Honda, Y. Utsumi, T. Saiki, T. Itoh, A. Miyakawa, K. Hamase, T. Naganuma, H. Mita, K. Tonokura, S. Sasaki, & H. Miyamoto, Japan Astrobiology Mars Project (JAMP)
  Biol. Sci. Space 24: 67-82(2010)
• "The complete mitochondrial genome of Caprella scaura (Caprellidea) with a note on a unique gene order pattern and duplicated control region."
• Ito, A., M. Aoki, S. Yokobori, & H. Wada.
  Mitochondrial DNA 21: 183-190(2010) PubMed
• "Repetitive sequences in the lamprey mitochondrial DNA control region and speciation of Lethenteron."
• Okada, K., Y. Yamazaki, S. Yokobori, & H. Wada.
  Gene 465: 45-52(2010) PubMed
• "Improvement of Bacillus circulans β-amylase activity attained using the ancestral mutation method."
• Yamashiro, K., S. Yokobori, S. Koikeda, & A. Yamagishi.
  Protein Engineer. Des. Select. 23: 519-528 (2010) PubMed
• "Evolution of genetic code"
• Yokobori, S., T. Ueda, & K. Watanabe.
  In: Encyclopedia of Life Science 2010. John Wiley & Sons, Ltd., Chichester. http://www.els.net/ [DOI: 10.1002/9780470015902.a0000548.pub2]. (2010) PubMed
• "A bacterial elongation factor G homolog exclusively functions in ribosome recycling in the spirochaete Borrelia burgdorferi."
• Suematsu, T., S. Yokobori, H. Morita, S. Yoshinari, T. Ueda, K. Kita, N. Takeuchi, & Y. Watanabe
  Mol. Microbiol. 75: 1445-1454 (2010) PubMed
• "Deinococcus aetherius sp. nov., isolated from the stratosphere."
• Yang, Y., T. Itoh, S. Yokobori, S. Itahashi, H. Shimada, K. Satoh, H. Ohba, I. Narumi, & A. Yamagishi.
  Internatl. J. Syst. Evol. Microbiol. 60: 776-779(2010) PubMed

2009

• "Assessing Panspermia hypothesis by microorganisms collected from the high altitude atmosphere."
• Yang Y, Yokobori S. and Yamagishi A.
  Biol. Sci. Space. 23, 151-163 (2009) PubMed
• "Deinococcus aerius sp. nov., isolated from the high atmosphere."
• Yang, Y.-J., T. Itoh, S. Yokobori, S. Itahashi, H. Shimada, K. Satoh, H. Ohba, I. Narumi, & A. Yamagishi
  Internatl. J. Syst, Evol. Microbiol. 59: 1862-1866 (2009) PubMed
• "Gain and loss of an intron in the protein-coding gene in Archaea."
• Yokobori, S., T. Itoh, S. Yoshinari, N. Nomura, Y. Sako, A. Yamagishi, T. Oshima, K. Kita, & Y. Watanabe
  BMC Evol. Biol. 9: 198 (2009) PubMed
• "Potential speciation of morphotypes in the photosymbiotic ascidian Didemnum molle in the Ryukyu Archipelago, Japan."
• Hirose, M., S. Yokobori, & E. Hirose
  Coral Reefs 28: 119-126 (2009) PubMed
• "Induction profile of HSP70-cognate genes by environmental pollutants in Chironomidae.."
• Yoshimi, T., K. Odagiri, S. Yokobori, Y. Takahashi, Y. Sugaya, & T. Miura
  Environ. Toxic. Pharmacol. 28: 294-301 (2009) PubMed
• "Bacterial survival responses to desiccation and high humidity."
• Yang, Y.-J., S. Yokobori, & A. Yamagishi
  Adv. Space Res. (a COSPAR publ.) 43: 1285-1290 (2009) PubMed
• "TANPOPO: Astrobiology Exposure and Micrometeoroid Capture Experiments — For Understanding Survival Possibility of Microorganisms in Space."
• Yokobori, S., A. Yamagishi, Y. Yang, K. Fujisaki, Y. H. Hashimoto, H. Kawai, K. Kobayashi, H. Mita, K. Okudaira, M. Tabata, H. Yano, M. Yamashita, Y. Yoshimura, TANPOPO WG.
  Ori. Life Evol. Biosph. 39:64 (2009) PubMed
• "Significance of Organic Compounds in Interplanetary Dust Particles: Scientific Objectives of Tanpopo Mission."
• Kobayashi, K., H. Hashimoto, T. Kaneko, H. Mita, S. Nakashima, H. Naraoka, K. Okudaira, J. Takahashi, Y. Takano, A. Yamagishi, M. Yamashita, H.Yano, S. Yokobori, TANPOPO WG.
  Ori. Life Evol. Biosph. 39:4 (2009)
• "TANPOPO: Astrobiology Exposure and Micrometeoroid Capture Experiments on the KIBO, ISS."
• Mita, H., A. Yamagishi, H. Yano, K. Okudaira, K. Kobayashi, S. Yokobori, M. Tabata, H. Kawai, H. Hashimoto , TANPOPO WG.
  Ori. Life Evol. Biosph. 39: 371-372 (2009)
• "TANPOPO: Astrobiology Exposure and Micrometeoroid Capture Experiments — For Understanding Survival Possibility of Microorganisms in Space."
• Yokobori, S., A. Yamagishi, Y. Yang, K. Fujisaki, H. Hashimoto, H. Kawai, K. Kobayashi, H. Mita, K. Okudaira, M. Tabata, H. Yano, M. Yamashita, Y. Yoshimura, TANPOPO WG.
  Ori. Life Evol. Biosph. 39: 377-378 (2009) PubMed

2008

• "UV-resistant Bacteria isolated at high altitude."
• Yang,Y.-J., S.Itahashi, S.Yokobori, A.Yamagishi
  Biol. Sci. Space 22: 18-25 (2008)
• "Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: Implications for lophotrochozoan phylogeny."
• Yokobori, S., T. Iseto, S. Asakawa, T. Sasaki, N. Shimizu, A. Yamagishi, T. Oshima, E. Hirose
  Mol. Phylogen. Evol. 47: 612-628 (2008) PubMed
• "TANPOPO: astrobiology exposure and micrometeoroid capture experiments."
• Yamagishi, A., H. Yano, K. Kobayashi, K. Kobayashi, S. Yokobori, M. Tabata, H. Kawai, M. Yamashita, H. Hashimoto, H. Naraoka, & H. Mita
  International Symposium on Space Technology and Science (ISTS) Web Paper Archives. 2008-k-05 (2008) PubMed
• "Investigation of cultivable microorganisms in the stratosphere collected by using a balloon in 2005."
• Yang, Y.-J., S. Yokobori, J. Kawaguchi, T. Yamagami, I. Iijima, N. Izutsu, H. Fuke, Y. Saitoh, S. Matsuzaka, M. Namiki, S. Ohta, M. Toriumi, K. Yamada, M. Seo, & A. Yamagishi
  JAXA-RR-08-001: 35-42 (2008) PubMed

2007

• "Mitochondrial genome structure and evolution in the living fossil vampire squid, Vampyroteuthis infernalis, and extant cephalopods."
• Yokobori S, Lindsay DJ, Yoshida M, Tsuchiya K, Yamagishi A, Maruyama T, Oshima T.
  Mol Phylogenet Evol. 44(2):898-910 (2007) PubMed
• "Extremely Thermophilic Translation System in the Common Ancestor Commonote: Ancestral Mutants of Glycyl-tRNA Synthetase from the Extreme Thermophile Thermus thermophilus."
• Shimizu H, Yokobori S, Ohkuri T, Yokogawa T, Nishikawa K, Yamagishi A.
  J Mol Biol. 369(4):1060-9 (2007) PubMed
• "Purification and characterization of pepsinogens from the gastric mucosa of African coelacanth, Latimeria chalumnae, and properties of the major pepsins."
• Tanji, M., E. Yakabe, T. Kageyama, S. Yokobori, M. Ichinose, K. Miki, H. Ito, & K. Takahashi
  Comparative Biochem. Physiol. 146(3):412-20. (2007) pubmed
• “An actin homolog of the archaeon Thermoplasma acidophilum that retains the ancient trait of eukaryotic actin.”
• Hara, F., K. Yamashiro, N. Nemoto, Y. Ohta, S. Yokobori, T. Yasunaga, S. Hisanaga & A. Yamagishi
  J. Bacteol. 189: 2039-2045 (2007) pubmed

2006

• "Thermostable proteins designed by using phylogenetic trees."
• Yamagishi, A., K. Watanabe, H. Shimizu, T. Ohkuri, and Yokobori, S.
  In Proceedings of the International Symposium on Extremophiles and Their Applications 2005. (2006)
• “The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus: a purine36G37 sequence in tRNA is recognized by the enzyme.”
• Takeda, H., T. Yokooka, Y. Ikeuchi, S. Yokobori, K. Okadome, F. Takano, T. Oshima, T. Suzuki, Y. Endo, & H. Hori
  Genes to Cells 11: 1353-1365 (2006) pubmed
• “Structural analysis of the plasmid pTA1 isolated from the thermoacidophilic archaeon Thermoplasma acidophilum.”
• Yamashiro, K., S. Yokobori, T. Oshima, & A. Yamagishi
  Extremophiles 10: 327-335 (2006) pubmed
• “Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease.”
• Yoshinari, S., T. Itoh, S. J. Hallam, E. F. Delong, S. Yokobori, A. Yamagishi, T. Oshima, K. Kita, & Y. Watanabe
  Biochem. Biophys. Res. Com. 346: 1024-1032 (2006) pubmed
• “Multiple origins of the ascidian-Prochloron symbiosis: Molecular phylogeny of photosymbiotic and non-symbiotic colonial ascidians inferred from 18S rDNA sequences.”
• Yokobori, S., A. Kurabayashi, B. A. Neilan, T. Maruyama, & E. Hirose
  Mol. Phylogen. Evol. 40: 8-19 (2006) pubmed
• “Designing thermostable proteins: Ancestral mutants of 3-isopropylmalate dehydrogenase designed by using a phylogenetic tree.”
• Watanabe, K., T. Ohkuri, S. Yokobori, & A. Yamagishi
  J. Mol. Biol. 355: 664-674 (2006) pubmed

2005

• “Functional reconstitution of a crenarchaeal splicing endonuclease in vitro.”
• Yoshinari, S., S. Fujita, R. Masui, S. Kuramitsu, S. Yokobori, K. Kita, & Y. Watanabe
  Biochem. Biophys. Res. Com. 334: 1254-1259 (2005) pubmed
• “Splicing endonuclease of an archaeon Sulfolobus tokodaii strain 7 requires two gene products to exhibit its activity.”
• Yoshinari, S., S. Fujita, R. Masui, S. Kuramitsu, S. Yokobori, K. Kita, Y. Watanabe
  Nucleic Acids Symp. Ser. 49: 103-104
• “The phylogenetic status of Paxillosida (Asteroidea) based on complete mitochondrial DNA sequences.”
• Matsubara, M., M. Komatsu, T. Araki, S. Asakawa, S. Yokobori, K. Watanabe, & H. Wada
  Mol. Phylogenet. Evol. 36: 598-605 (2005) pubmed
• “Thermostability of ancestral mutants of Caldococcus noboribetus isocitrate dehydrogenase.”
• Iwabata, H., K. Watanabe, T. Ohkuri, S. Yokobori, & A. Yamagishi
  FEMS Microbiol. Lett. 243: 393-398 (2005) pubmed
• “Complete nucleotide sequence of the mitochondrial genome of Doliolum nationalis with implications for evolution of urochordates.”
• Yokobori, S., T. Oshima, & H. Wada
  Mol. Phylogenet. Evol. 34: 273-283 (2005) pubmed

2004

• "Strand specific nucleotide composition bias as the driving force of reassignment of AGR codons in metazoan mitochondria."
• Yokobori, S., K. Watanabe, & T. Oshima
  Endocytobiosis Cell Res. 15: 366-370 (2004) PubMed
• “Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes.”
• Yokobori, S., N. Fukuda, M. Nakamura, T. Aoyama, & T. Oshima
  Mol. Biol. Evol. 21: 2034-2046 (2004) pubmed

2003

• “Mitochondrial genome of Ciona savignyi (Urochordata, Ascidiacea, Enterogona): comparison of gene arrangement and tRNA genes with Halocynthia roretzi mitochondrial genome.”
• Yokobori, S., Y. Watanabe, & T. Oshima
  J. Mol. Evol. 57: 574-587 (2003) pubmed

2002

• “The cephalopod Loligo bleekeri mitochondrial genome: multiplied noncoding regions and transposition of tRNA genes.”
• Tomita, K., S. Yokobori, T. Oshima, T. Ueda, & K. Watanabe
  J. Mol. Evol. 54: 486-500 (2002) pubmed
• “Introns in protein-coding genes in Archaea.”
• Watanabe, Y., S. Yokobori, T. Inaba, A. Yamagishi, T. Oshima, Y. Kawarabayasi, H. Kikuchi, & K. Kita
  FEBS letters 501: 27-30 (2002) pubmed

2001

• “Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity.”
• Yokobori, S., T. Suzuki, & K. Watanabe
  J. Mol. Evol. 53: 314-326 (2001) pubmed

1999

• “Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata).”
• Yokobori, S., T. Ueda, G. Feldmaier-Fuchs, S. Pääbo, R. Ueshima, A. Kondow, K. Nishikawa, & K. Watanabe
  Genetics 153: 1851-1862 (1999) pubmed
• “Gene contents and organization of a mitochondrial DNA segment of the squid Loligo bleekeri.”
• Sasuga, J., S. Yokobori, M. Kaifu, T. Ueda, K. Nishikawa, & K. Watanabe
  J. Mol. Evol. 48: 692-702 (1999) pubmed
• “An extra tRNAGly(U*CU) found in ascidian mitochondria responsible for decoding non-universal codons AGA/AGG as glycine.”
• Kondow, A., T. Suzuki, S. Yokobori, T. Ueda, & K. Watanabe
  Nucleic Acids Res. 27: 2554-2559 (1999) pubmed

1998

• “The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria.”
• Castresana, J., G. Feldmaier-Fuchs, S. Yokobori, N. Satoh, & S. Pääbo
  Genetics 150: 1115-1123 (1998) pubmed
• “Ascidian mitochondrial tRNAMet possessing unique structural characteristics.”
• Kondow, A., S. Yokobori, T. Ueda, & K. Watanabe
  Nucleosides Nucleotides 17: 531-539 (1998) pubmed

1997

• “RNA editing in metazoan mitochondria: staying fit without sex.”
• Börner, G. V., S. Yokobori, M. Mörl, M. Dörner & S. Pääbo
  FEBS lett. 409: 320-324 (1997) pubmed

1996

• “Primary sequence of ascidian mitochondrial glycine tRNA translating non-universal codons AGR (R: A, G)”
• Kondo, A., S. Yokobori, T. Ueda, K. Watanabe
  Nucleic Acids Symp. Ser. 35: 279-280
• “Evolution of pulmonate gastropod mitochondrial genomes: comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures.”
• Yamazaki, N., R. Ueshima, J. A. Terrett, S. Yokobori, M. Kaifu, A. Segawa, T. Kobayashi T, K. Numachi, T. Ueda, K. Nishikawa, K. Watanabe, R. H. Thomas
  Genetics 145: 749-758 (1996) pubmed
• “Polyadenylation creates discriminator base of the chicken mitochondrial tRNATyr.”
• Yokobori, S. & S. Pääbo
  J. Mol. Biol. 265: 95-99 (1996) pubmed

1995

• “tRNA editing in metazoans.”
• Yokobori, S. & S. Pääbo
  Nature 377: 490 (1995) pubmed
• “Transfer RNA editing in land snail mitochondria.”
• Yokobori, S. & S. Pääbo
  Proc. Natl. Acad. Sci. USA 92: 10432-10435 (1995) pubmed

1994

• “Relationship among coelacanths, lungfishes, and tetrapods: a phylogenetic analysis based on mitochondrial cytochrome oxidase I gene sequences.”
• Yokobori, S., M. Hasegawa, T. Ueda, N. Okada, K. Nishikawa & K. Watanabe
  J. Mol. Evol. 38: 602-609 (1994) pubmed

1993

• “Codons AGA and AGG are read as glycine in ascidian mitochondria.”
• Yokobori, S., T. Ueda & K. Watanabe
  J. Mol. Evol. 36: 1-8 (1993) pubmed

1990

• “Genetic code of a squid mitochondria.”
• Shimayama T., J. Sasuga, H. Himeno, S. Yokobori, T. Ueda & K. Watanabe
  Nucleic Acids Symp. Ser. 22: 77-78