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1

Mitochondrial genome structure and evolution in the living fossil vampire squid, Vampyroteuthis infernalis, and extant cephalopods

Shin-ichi Yokobori, Dhugal J. Lindsay, Mari Yoshida, Kotaro Tsuchiya, Akihiko Yamagishi, Tadashi Maruyama, Tairo Oshima

Journal:

Molecular Phylogenetics and Evolution

Year:

2007

Language:

english

File:

PDF, 259 KB

english, 2007

2

Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: Implications for lophotrochozoan phylogeny

Shin-ichi Yokobori, Tohru Iseto, Shuichi Asakawa, Takashi Sasaki, Nobuyoshi Shimizu, Akihiko Yamagishi, Tairo Oshima, Euichi Hirose

Journal:

Molecular Phylogenetics and Evolution

Year:

2008

Language:

english

File:

PDF, 437 KB

english, 2008

3

Mitochondrial Genome ofCiona savignyi(Urochordata, Ascidiacea, Enterogona): Comparison of Gene Arrangement and tRNA Genes withHalocynthia roretziMitochondrial Genome

Shin-ichi Yokobori, Yukari Watanabe, Tairo Oshima

Journal:

Journal of Molecular Evolution

Year:

2003

Language:

english

File:

PDF, 439 KB

english, 2003

4

Complete nucleotide sequence of the mitochondrial genome of Doliolum nationalis with implications for evolution of urochordates

Shin-ichi Yokobori, Tairo Oshima, Hiroshi Wada

Journal:

Molecular Phylogenetics and Evolution

Year:

2005

Language:

english

File:

PDF, 613 KB

english, 2005

5

The phylogenetic status of Paxillosida (Asteroidea) based on complete mitochondrial DNA sequences

Mioko Matsubara, Miéko Komatsu, Takeyoshi Araki, Shuichi Asakawa, Shin-ichi Yokobori, Kimitsuna Watanabe, Hiroshi Wada

Journal:

Molecular Phylogenetics and Evolution

Year:

2005

Language:

english

File:

PDF, 379 KB

english, 2005

6

Relationship among coelacanths, lungfishes, and tetrapods: A phylogenetic analysis based on mitochondrial cytochrome oxidase I gene sequences

Shin-ichi Yokobori, Masami Hasegawa, Takuya Ueda, Norihiro Okada, Kazuya Nishikawa, Kimitsuna Watanabe

Journal:

Journal of Molecular Evolution

Year:

1994

Language:

english

File:

PDF, 814 KB

english, 1994

7

Investigation of the Interplanetary Transfer of Microbes in the Tanpopo Mission at the Exposed Facility of the International Space Station

Kawaguchi, Yuko, Yokobori, Shin-ichi, Hashimoto, Hirofumi, Yano, Hajime, Tabata, Makoto, Kawai, Hideyuki, Yamagishi, Akihiko

Journal:

Year:

2016

Language:

english

File:

PDF, 1.01 MB

english, 2016

8

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, Shin-ichi, Shibuya, Hiroyuki, Kobayashi, Taku, Sakamoto, Masaki, Ha, Jin-Yong, Yokobori, Shin-ichi, Yamagata, Hideo, Hanazato, Takayuki

Journal:

Year:

2017

Language:

english

File:

PDF, 786 KB

english, 2017

9

Bacterial survival in response to desiccation and high humidity at above zero and subzero temperatures

Yinjie Yang, Shin-ichi Yokobori, Akihiko Yamagishi

Journal:

Advances in Space Research

Year:

2009

Language:

english

File:

PDF, 226 KB

english, 2009

10

Multiple origins of the ascidian-Prochloron symbiosis: Molecular phylogeny of photosymbiotic and non-symbiotic colonial ascidians inferred from 18S rDNA sequences

Shin-ichi Yokobori, Atsushi Kurabayashi, Brett A. Neilan, Tadashi Maruyama, Euichi Hirose

Journal:

Molecular Phylogenetics and Evolution

Year:

2006

Language:

english

File:

PDF, 911 KB

english, 2006

11

Codons AGA and AGG are read as glycine in ascidian mitochondria

Shin-ichi Yokobori, Takuya Ueda, Kimitsuna Watanabe

Journal:

Journal of Molecular Evolution

Year:

1993

Language:

english

File:

PDF, 623 KB

english, 1993

12

Gene Contents and Organization of a Mitochondrial DNA Segment of the SquidLoligo bleekeri

Junji Sasuga, Shin-ichi Yokobori, Masayuki Kaifu, Takuya Ueda, Kazuya Nishikawa, Kimitsuna Watanabe

Journal:

Journal of Molecular Evolution

Year:

1999

Language:

english

File:

PDF, 2.10 MB

english, 1999

13

The CephalopodLoligo bleekeriMitochondrial Genome: Multiplied Noncoding Regions and Transposition of tRNA Genes

Kozo Tomita, Shin-ichi Yokobori, Tairo Oshima, Takuya Ueda, Kimitsuna Watanabe

Journal:

Journal of Molecular Evolution

Year:

2002

Language:

english

File:

PDF, 746 KB

english, 2002

14

Genetic Code Variations in Mitochondria: tRNA as a Major Determinant of Genetic Code Plasticity

Shin-ichi Yokobori, Tsutomu Suzuki, Kimitsuna Watanabe

Journal:

Journal of Molecular Evolution

Year:

2001

Language:

english

File:

PDF, 803 KB

english, 2001

15

Structural analysis of the plasmid pTA1 isolated from the thermoacidophilic archaeonThermoplasma acidophilum

Kan Yamashiro, Shin-ichi Yokobori, Tairo Oshima, Akihiko Yamagishi

Journal:

Year:

2006

Language:

english

File:

PDF, 542 KB

english, 2006

16

Thermostability of ancestral mutants of Caldococcus noboribetus isocitrate dehydrogenase

Hisako Iwabata, Keiko Watanabe, Takatoshi Ohkuri, Shin-ichi Yokobori, Akihiko Yamagishi

Journal:

FEMS Microbiology Letters

Year:

2005

Language:

english

File:

PDF, 211 KB

english, 2005

17

The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus

Hiroshi Takeda, Takashi Toyooka, Yoshiho Ikeuchi, Shin-ichi Yokobori, Kan Okadome, Fuyumi Takano, Tairo Oshima, Tsutomu Suzuki, Yaeta Endo, Hiroyuki Hori

Journal:

Year:

2006

Language:

english

File:

PDF, 401 KB

english, 2006

18

A bacterial elongation factor G homologue exclusively functions in ribosome recycling in the spirochaete Borrelia burgdorferi

Takuma Suematsu, Shin-ichi Yokobori, Hiroyuki Morita, Shigeo Yoshinari, Takuya Ueda, Kiyoshi Kita, Nono Takeuchi, Yoh-ichi Watanabe

Journal:

Molecular Microbiology

Year:

2010

Language:

english

File:

PDF, 427 KB

english, 2010

19

tRNA editing in metazoans

Yokobori, Shin-ichi, Pääbo, Svante

Journal:

Year:

1995

File:

PDF, 302 KB

1995

20

Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene

Shin-ichi Yokobori, Takashi Itoh, Shigeo Yoshinari, Norimichi Nomura, Yoshihiko Sako, Akihiko Yamagishi, Tairo Oshima, Kiyoshi Kita, Yoh-ichi Watanabe

Journal:

BMC Evolutionary Biology

Year:

2009

Language:

english

File:

PDF, 944 KB

english, 2009

21

Polyadenylation creates the discriminator nucleotide of chicken mitochondrial tRNATyr

Shin-ichi Yokobori, Svante Pääbo

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 339 KB

english, 1997

22

Functional reconstitution of a crenarchaeal splicing endonuclease in vitro

Shigeo Yoshinari, Shinji Fujita, Ryoji Masui, Seiki Kuramitsu, Shin-ichi Yokobori, Kiyoshi Kita, Yoh-ichi Watanabe

Journal:

Biochemical and Biophysical Research Communications

Year:

2005

Language:

english

File:

PDF, 348 KB

english, 2005

23

Archaeal pre-mRNA splicing: A connection to hetero-oligomeric splicing endonuclease

Shigeo Yoshinari, Takashi Itoh, Steven J. Hallam, Edward F. DeLong, Shin-ichi Yokobori, Akihiko Yamagishi, Tairo Oshima, Kiyoshi Kita, Yoh-ichi Watanabe

Journal:

Biochemical and Biophysical Research Communications

Year:

2006

Language:

english

File:

PDF, 338 KB

english, 2006

24

Purification and characterization of pepsinogens from the gastric mucosa of African coelacanth, Latimeria chalumnae, and properties of the major pepsins

Masao Tanji, Etsuko Yakabe, Takashi Kageyama, Shin-ichi Yokobori, Masao Ichinose, Kazumasa Miki, Hisashi Ito, Kenji Takahashi

Journal:

Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology

Year:

2007

Language:

english

File:

PDF, 522 KB

english, 2007

25

Induction profile of HSP70-cognate genes by environmental pollutants in Chironomidae

Tatsuya Yoshimi, Koji Odagiri, Yutaka Hiroshige, Shin-ichi Yokobori, Yuji Takahashi, Yoshio Sugaya, Takashi Miura

Journal:

Environmental Toxicology and Pharmacology

Year:

2009

Language:

english

File:

PDF, 914 KB

english, 2009

26

Designing Thermostable Proteins: Ancestral Mutants of 3-Isopropylmalate Dehydrogenase Designed by using a Phylogenetic Tree

Keiko Watanabe, Takatoshi Ohkuri, Shin-ichi Yokobori, Akihiko Yamagishi

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 548 KB

english, 2006

27

Extremely Thermophilic Translation System in the Common Ancestor Commonote: Ancestral Mutants of Glycyl-tRNA Synthetase from the Extreme Thermophile Thermus thermophilus

Hideaki Shimizu, Shin-ichi Yokobori, Takatoshi Ohkuri, Takashi Yokogawa, Kazuya Nishikawa, Akihiko Yamagishi

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1.03 MB

english, 2007

28

Phylogeny-Based Design of a B-Subunit of DNA Gyrase and Its ATPase Domain Using a Small Set of Homologous Amino Acid Sequences

Satoshi Akanuma, Shoko Iwami, Tamaki Yokoi, Nana Nakamura, Hideaki Watanabe, Shin-ichi Yokobori, Akihiko Yamagishi

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 840 KB

english, 2011

29

Introns in protein-coding genes in Archaea

Yoh-ichi Watanabe, Shin-ichi Yokobori, Toshiro Inaba, Akihiko Yamagishi, Tairo Oshima, Yutaka Kawarabayasi, Hisasi Kikuchi, Kiyoshi Kita

Journal:

Year:

2002

Language:

english

File:

PDF, 173 KB

english, 2002

30

RNA editing in metazoan mitochondria: staying fit without sex

G.Valentin Börner, Shin-ichi Yokobori, Mario Mörl, Marion Dörner, Svante Pääbo

Journal:

Year:

1997

Language:

english

File:

PDF, 704 KB

english, 1997

31

Encyclopedia of Life Sciences || Evolution of the Genetic Code

Yokobori, Shin-ichi

Year:

2001

Language:

english

File:

PDF, 341 KB

english, 2001

32

[IEEE 2009 International Symposium on Micro-NanoMechatronics and Human Science (MHS) - Nagoya, Japan (2009.11.9-2009.11.11)] 2009 International Symposium on Micro-NanoMechatronics and Human Science - Enzymatic and crystallographic characterization of archaeal tRNA splicing endonuclease

Kitajima, Tsubasa, Hirata, Akira, Iwashita, Chikako, Yokobori, Shin-ichi, Hori, Hiroyuki

Year:

2009

Language:

english

File:

PDF, 456 KB

english, 2009

33

The complete mitochondrial genome of Caprella scaura (Crustacea, Amphipoda, Caprellidea), with emphasis on the unique gene order pattern and duplicated control region

Ito, Atsushi, Aoki, Masakazu N., Yokobori, Shin-ichi, Wada, Hiroshi

Journal:

Mitochondrial DNA

Year:

2010

Language:

english

File:

PDF, 131 KB

english, 2010

34

Evolution of Eukaryotic DNA Polymerases via Interaction Between Cells and Large DNA Viruses

Takemura, Masaharu, Yokobori, Shin-ichi, Ogata, Hiroyuki

Journal:

Journal of Molecular Evolution

Year:

2015

Language:

english

File:

PDF, 1.16 MB

english, 2015

35

Transfer RNA Editing in Land Snail Mitochondria

Shin-ichi Yokobori and Svante Paabo

Journal:

Proceedings of the National Academy of Sciences

Year:

1995

File:

PDF, 814 KB

1995

36

Transfer RNA Editing in Land Snail Mitochondria

Shin-ichi Yokobori and Svante Paabo

Journal:

Proceedings of the National Academy of Sciences

Year:

1995

Language:

english

File:

PDF, 814 KB

english, 1995

37

Ultralow-density double-layer silica aerogel fabrication for the intact capture of cosmic dust in low-Earth orbits

Tabata, Makoto, Kawai, Hideyuki, Yano, Hajime, Imai, Eiichi, Hashimoto, Hirofumi, Yokobori, Shin-ichi, Yamagishi, Akihiko

Journal:

Journal of Sol-Gel Science and Technology

Year:

2016

Language:

english

File:

PDF, 986 KB

english, 2016

38

Epistasis effects of multiple ancestral-consensus amino acid substitutions on the thermal stability of glycerol kinase from Cellulomonas sp. NT3060

Fukuda, Yasuhisa, Abe, Asuka, Tamura, Takashi, Kishimoto, Takahide, Sogabe, Atsushi, Akanuma, Satoshi, Yokobori, Shin-ichi, Yamagishi, Akihiko, Imada, Katsumi, Inagaki, Kenji

Journal:

Journal of Bioscience and Bioengineering

Year:

2016

Language:

english

File:

PDF, 2.49 MB

english, 2016

39

Robustness of predictions of extremely thermally stable proteins in ancient organisms

Akanuma, Satoshi, Yokobori, Shin-ichi, Nakajima, Yoshiki, Bessho, Mizumo, Yamagishi, Akihiko

Journal:

Year:

2015

Language:

english

File:

PDF, 449 KB

english, 2015

40

Updated mitochondrial phylogeny of Pteriomorph and Heterodont Bivalvia, including deep-sea chemosymbiotic Bathymodiolus mussels, vesicomyid clams and the thyasirid clam Conchocele cf. bisecta

Ozawa, Genki, Shimamura, Shigeru, Takaki, Yoshihiro, Yokobori, Shin-ichi, Ohara, Yasuhiko, Takishita, Kiyotaka, Maruyama, Tadashi, Fujikura, Katsunori, Yoshida, Takao

Journal:

Marine Genomics

Year:

2016

Language:

english

File:

PDF, 1.49 MB

english, 2016

41

Quest for Ancestors of Eukaryal Cells Based on Phylogenetic Analyses of Aminoacyl-tRNA Synthetases

Furukawa, Ryutaro, Nakagawa, Mizuho, Kuroyanagi, Takuya, Yokobori, Shin-ichi, Yamagishi, Akihiko

Journal:

Journal of Molecular Evolution

Year:

2017

Language:

english

File:

PDF, 1.12 MB

english, 2017

42

Development of mechanical space thermometer for the Tanpopo mission

HASHIMOTO, Hirofumi, IMAI, Eiichi, YANO, Hajime, WATANABE, Hideyuki, YOKOBORI, Shin-ichi, YAMAGISHI, Akihiko

Journal:

Transactions of the JSME (in Japanese)

Year:

2016

Language:

english

File:

PDF, 2.10 MB

english, 2016

43

Reconstructed ancestral enzymes suggest long-term cooling of Earth’s photic zone since the Archean

Garcia, Amanda K., Schopf, J. William, Yokobori, Shin-ichi, Akanuma, Satoshi, Yamagishi, Akihiko

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 1.02 MB

english, 2017

44

Hydroxylation of a conserved tRNA modification establishes non-universal genetic code in echinoderm mitochondria

Nagao, Asuteka, Ohara, Mitsuhiro, Miyauchi, Kenjyo, Yokobori, Shin-ichi, Yamagishi, Akihiko, Watanabe, Kimitsuna, Suzuki, Tsutomu

Journal:

Nature Structural and Molecular Biology

Year:

2017

Language:

english

File:

PDF, 2.09 MB

english, 2017

45

Draft Genome Sequence of the Radioresistant Bacterium Deinococcus aerius TR0125, Isolated from the High Atmosphere above Japan

Satoh, Katsuya, Arai, Hiroki, Sanzen, Toshihiko, Kawaguchi, Yuko, Hayashi, Hidenori, Yokobori, Shin-ichi, Yamagishi, Akihiko, Oono, Yutaka, Narumi, Issay

Journal:

Genome Announcements

Year:

2018

Language:

english

File:

PDF, 123 KB

english, 2018

46

3P276 Hyperthermophilic translation system in the last common ancestor : ancestral mutants of Thermus thermophilus glycyl-tRNA synthetase(Proteins- protein engineering, and evolutionary engineering,Poster Presentations)

Shimizu, Hideaki, Hane, Kohei, Yokobori, Shin-ichi, Yamagishi, Akihiko

Journal:

Seibutsu Butsuri

Year:

2007

Language:

english

File:

PDF, 240 KB

english, 2007

47

1P-075 Stability difference between resurrected Archaeal and Bacterial ancestors of nucleoside diphosphate kinase(Protein:Engineering, The 47th Annual Meeting of the Biophysical Society of Japan)

Kobayashi, Ami, Akanuma, Satoshi, Nemoto, Naoki, Kimura, Mitsuo, Yokobori, Shin-ichi, Yamagishi, Akihiko

Journal:

Seibutsu Butsuri

Year:

2009

Language:

english

File:

PDF, 243 KB

english, 2009

48

3P257 Empirical estimation of the environmental temperature of the last universal common ancestor(20. Origin of life & Evolution,Poster)

Akanuma, Satoshi, Nakajima, Yoshiki, Yokobori, Shin-ichi, Yamagishi, Akihiko

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 694 KB

english, 2013

49

1P075 Elucidation of the protein sequence-stability relationship by comparing designed ancestral proteins with reduced neutral mutations(Protein:Property,The 48th Annual Meeting of the Biophysical Society of Japan)

Akanuma, Satoshi, Yamaguchi, Minako, Kobayashi, Ami, Yokobori, Shin-ichi, Yamagishi, Akihiko

Journal:

Seibutsu Butsuri

Year:

2010

Language:

english

File:

PDF, 234 KB

english, 2010

50

Tanpopo: Astrobiology Exposure and Micrometeoroid Capture Experiments— Proposed Experiments at the Exposure Facility of ISS-JEM

YAMAGISHI, Akihiko, YOKOBORI, Shin-ichi, HASHIMOTO, Hirofumi, YANO, Hajime, HIGASHIDE, Masumi, TABATA, Makoto, IMAI, Eiichi, YABUTA, Hikaru, KOBAYASHI, Kensei, KAWAI, Hideyuki

Journal:

Transactions of the Japan society for Aeronautical and space sciences Aerospace Technology Japan

Year:

2014

Language:

english

File:

PDF, 1.71 MB

english, 2014

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