活動概要 > 研究報告(2011~2015)

活動概要

研究報告(2011~2015)

2015
  1. Ushida, K., S. Tsuchida, Y. Ogura, A. Toyoda and F. Maruyama (2015). Domestication and cereal feeding developed domestic pig-type intestinal microbiota in animals of suidae. Anim Sci J.
  2. Urushihara, H., H. Kuwayama, K. Fukuhara, T. Itoh, H. Kagoshima, I. T. Shin, A. Toyoda, K. Ohishi, T. Taniguchi, H. Noguchi, Y. Kuroki, T. Hata, K. Uchi, K. Mohri, J. S. King, R. H. Insall, Y. Kohara and A. Fujiyama (2015). Comparative genome and transcriptome analyses of the social amoeba Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation. BMC Genomics 16: 80.
  3. Uchimura, A., M. Higuchi, Y. Minakuchi, M. Ohno, A. Toyoda, A. Fujiyama, I. Miura, S. Wakana, J. Nishino and T. Yagi (2015). Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice. Genome Res 25(8): 1125-1134.
  4. Tanaka, S., J. Tanaka, Y. Miwa, D. D. Horikawa, T. Katayama, K. Arakawa, A. Toyoda, T. Kubo and T. Kunieda (2015). Novel mitochondria-targeted heat-soluble proteins identified in the anhydrobiotic tardigrade improve osmotic tolerance of human cells. PLoS One 10(2): e0118272.
  5. Shenton, M. R., H. Ohyanagi, Z. X. Wang, A. Toyoda, A. Fujiyama, T. Nagata, Q. Feng, B. Han and N. Kurata (2015). Rapid turnover of antimicrobial-type cysteine-rich protein genes in closely related Oryza genomes. Mol Genet Genomics 290(5): 1753-1770.
  6. Sato, K., Y. Kuroki, W. Kumita, A. Fujiyama, A. Toyoda, J. Kawai, A. Iriki, E. Sasaki, H. Okano and Y. Sakakibara (2015). Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis. Sci Rep 5: 16894.
  7. Perpelescu, M., T. Hori, A. Toyoda, S. Misu, N. Monma, K. Ikeo, C. Obuse, A. Fujiyama and T. Fukagawa (2015). HJURP is involved in the expansion of centromeric chromatin. Mol Biol Cell 26(15): 2742-2754.
  8. Perkins, L. A., L. Holderbaum, R. Tao, Y. Hu, R. Sopko, K. McCall, D. Yang-Zhou, I. Flockhart, R. Binari, H. S. Shim, A. Miller, A. Housden, M. Foos, S. Randkelv, C. Kelley, P. Namgyal, C. Villalta, L. P. Liu, X. Jiang, Q. Huan-Huan, X. Wang, A. Fujiyama, A. Toyoda, K. Ayers, A. Blum, B. Czech, R. Neumuller, D. Yan, A. Cavallaro, K. Hibbard, D. Hall, L. Cooley, G. J. Hannon, R. Lehmann, A. Parks, S. E. Mohr, R. Ueda, S. Kondo, J. Q. Ni and N. Perrimon (2015). The Transgenic RNAi Project at Harvard Medical School: Resources and Validation. Genetics 201(3): 843-852.
  9. Kubota, S., T. Iwasaki, K. Hanada, A. J. Nagano, A. Fujiyama, A. Toyoda, S. Sugano, Y. Suzuki, K. Hikosaka, M. Ito and S. Morinaga (2015). A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species. PLoS Genet 11(7): e1005361.
  10. Kubota, S., T. Iwasaki, K. Hanada, A. J. Nagano, A. Fujiyama, A. Toyoda, S. Sugano, Y. Suzuki, K. Hikosaka, M. Ito and S. Morinaga (2015). Correction: A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species. PLoS Genet 11(9): e1005488.
  11. Kato, H., N. Ogawa, Y. Ohtsubo, K. Oshima, A. Toyoda, H. Mori, Y. Nagata, K. Kurokawa, M. Hattori, A. Fujiyama and M. Tsuda (2015). Complete Genome Sequence of a Phenanthrene Degrader, Mycobacterium sp. Strain EPa45 (NBRC 110737), Isolated from a Phenanthrene-Degrading Consortium. Genome Announc 3(4).
  12. Kato, H., H. Mori, F. Maruyama, A. Toyoda, K. Oshima, R. Endo, G. Fuchu, M. Miyakoshi, A. Dozono, Y. Ohtsubo, Y. Nagata, M. Hattori, A. Fujiyama, K. Kurokawa and M. Tsuda (2015). Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. DNA Res 22(6): 413-424.
  13. Izutsu, M., A. Toyoda, A. Fujiyama, K. Agata and N. Fuse (2015). Dynamics of Dark-Fly Genome Under Environmental Selections. G3 (Bethesda) 6(2): 365-376.
  14. Ito, T., Y. Tarutani, T. K. To, M. Kassam, E. Duvernois-Berthet, S. Cortijo, K. Takashima, H. Saze, A. Toyoda, A. Fujiyama, V. Colot and T. Kakutani (2015). Genome-wide negative feedback drives transgenerational DNA methylation dynamics in Arabidopsis. PLoS Genet 11(4): e1005154.
  15. An, Y., A. Toyoda, C. Zhao, A. Fujiyama and K. Agata (2015). A Colony Multiplex Quantitative PCR-Based 3S3DBC Method and Variations of It for Screening DNA Libraries. PLoS One 10(2): e0116997.
2014
  1. Yoshida, K., T. Makino, K. Yamaguchi, S. Shigenobu, M. Hasebe, M. Kawata, M. Kume, S. Mori, C. L. Peichel, A. Toyoda, A. Fujiyama and J. Kitano (2014). Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species. PLoS Genet 10(3): e1004223.
  2. Takehana, Y., M. Matsuda, T. Myosho, M. L. Suster, K. Kawakami, I. T. Shin, Y. Kohara, Y. Kuroki, A. Toyoda, A. Fujiyama, S. Hamaguchi, M. Sakaizumi and K. Naruse (2014). Co-option of Sox3 as the male-determining factor on the Y chromosome in the fish Oryzias dancena. Nat Commun 5: 4157.
  3. Swann, J. B., A. Weyn, D. Nagakubo, C. C. Bleul, A. Toyoda, C. Happe, N. Netuschil, I. Hess, A. Haas-Assenbaum, Y. Taniguchi, M. Schorpp and T. Boehm (2014). Conversion of the thymus into a bipotent lymphoid organ by replacement of FOXN1 with its paralog, FOXN4. Cell Rep 8(4): 1184-1197.
  4. Spivakov, M., T. O. Auer, R. Peravali, I. Dunham, D. Dolle, A. Fujiyama, A. Toyoda, T. Aizu, Y. Minakuchi, F. Loosli, K. Naruse, E. Birney and J. Wittbrodt (2014). Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish. G3 (Bethesda) 4(3): 433-445.
  5. Shimono, K., K. Fujishima, T. Nomura, M. Ohashi, T. Usui, M. Kengaku, A. Toyoda and T. Uemura (2014). An evolutionarily conserved protein CHORD regulates scaling of dendritic arbors with body size. Sci Rep 4: 4415.
  6. Sakurai, M., H. Ueda, T. Yano, S. Okada, H. Terajima, T. Mitsuyama, A. Toyoda, A. Fujiyama, H. Kawabata and T. Suzuki (2014). A biochemical landscape of A-to-I RNA editing in the human brain transcriptome. Genome Res 24(3): 522-534.
  7. Mori, H., F. Maruyama, H. Kato, A. Toyoda, A. Dozono, Y. Ohtsubo, Y. Nagata, A. Fujiyama, M. Tsuda and K. Kurokawa (2014). Design and experimental application of a novel non-degenerate universal primer set that amplifies prokaryotic 16S rRNA genes with a low possibility to amplify eukaryotic rRNA genes. DNA Res 21(2): 217-227.
  8. Mori, H., F. Maruyama, H. Kato, A. Toyoda, A. Dozono, Y. Ohtsubo, Y. Nagata, A. Fujiyama, M. Tsuda and K. Kurokawa (2014). Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes. DNA Res 21(2): 217-227.
  9. Kosaka, T., H. Toh, A. Fujiyama, Y. Sakaki, K. Watanabe, X. Y. Meng, S. Hanada and A. Toyoda (2014). Physiological and genetic basis for self-aggregation of a thermophilic hydrogenotrophic methanogen, Methanothermobacter strain CaT2. Environ Microbiol Rep 6(3): 268-277.
  10. Kosaka, T., H. Toh, A. Fujiyama, Y. Sakaki, K. Watanabe, X. Y. Meng, S. Hanada and A. Toyoda (2014). Physiological and genetic basis for self-aggregation of a thermophilic hydrogenotrophic methanogen, Methanothermobacter strain CaT2. Environ Microbiol Rep 6(3): 268-277.
  11. Kobayashi, M., H. Nagasaki, V. Garcia, D. Just, C. Bres, J. P. Mauxion, M. C. Le Paslier, D. Brunel, K. Suda, Y. Minakuchi, A. Toyoda, A. Fujiyama, H. Toyoshima, T. Suzuki, K. Igarashi, C. Rothan, E. Kaminuma, Y. Nakamura, K. Yano and K. Aoki (2014). Genome-wide analysis of intraspecific DNA polymorphism in ‘Micro-Tom’, a model cultivar of tomato (Solanum lycopersicum). Plant Cell Physiol 55(2): 445-454.
  12. Kobayashi, M., H. Nagasaki, V. Garcia, D. Just, C. Bres, J. P. Mauxion, M. C. Le Paslier, D. Brunel, K. Suda, Y. Minakuchi, A. Toyoda, A. Fujiyama, H. Toyoshima, T. Suzuki, K. Igarashi, C. Rothan, E. Kaminuma, Y. Nakamura, K. Yano and K. Aoki (2014). Genome-wide analysis of intraspecific DNA polymorphism in ‘Micro-Tom’, a model cultivar of tomato (Solanum lycopersicum). Plant Cell Physiol 55(2): 445-454.
  13. Kawai-Toyooka, H., T. Mori, T. Hamaji, M. Suzuki, B. J. Olson, T. Uemura, T. Ueda, A. Nakano, A. Toyoda, A. Fujiyama and H. Nozaki (2014). Sex-specific posttranslational regulation of the gamete fusogen GCS1 in the isogamous volvocine alga Gonium pectorale. Eukaryot Cell 13(5): 648-656.
  14. Kawai, M., T. Futagami, A. Toyoda, Y. Takaki, S. Nishi, S. Hori, W. Arai, T. Tsubouchi, Y. Morono, I. Uchiyama, T. Ito, A. Fujiyama, F. Inagaki and H. Takami (2014). High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes. Front Microbiol 5: 80.
  15. Kamada, M., S. Hase, K. Sato, A. Toyoda, A. Fujiyama and Y. Sakakibara (2014). Whole Genome Complete Resequencing of Bacillus subtilis Natto by Combining Long Reads with High-Quality Short Reads. PLoS One 9(10): e109999.
  16. Kajitani, R., K. Toshimoto, H. Noguchi, A. Toyoda, Y. Ogura, M. Okuno, M. Yabana, M. Harada, E. Nagayasu, H. Maruyama, Y. Kohara, A. Fujiyama, T. Hayashi and T. Itoh (2014). Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res.
  17. Hori, T., W. H. Shang, A. Toyoda, S. Misu, N. Monma, K. Ikeo, O. Molina, G. Vargiu, A. Fujiyama, H. Kimura, W. C. Earnshaw and T. Fukagawa (2014). Histone H4 Lys 20 monomethylation of the CENP-A nucleosome is essential for kinetochore assembly. Dev Cell 29(6): 740-749.
  18. Chisada, S., T. Kurokawa, K. Murashita, I. Ronnestad, Y. Taniguchi, A. Toyoda, Y. Sakaki, S. Takeda and Y. Yoshiura (2014). Leptin receptor-deficient (knockout) medaka, Oryzias latipes, show chronical up-regulated levels of orexigenic neuropeptides, elevated food intake and stage specific effects on growth and fat allocation. Gen Comp Endocrinol 195: 9-20.
2013
  1. Yamazaki, M., K. Mochida, T. Asano, R. Nakabayashi, M. Chiba, N. Udomson, Y. Yamazaki, D. B. Goodenowe, U. Sankawa, T. Yoshida, A. Toyoda, Y. Totoki, Y. Sakaki, E. Gongora-Castillo, C. R. Buell, T. Sakurai and K. Saito (2013). Coupling deep transcriptome analysis with untargeted metabolic profiling in Ophiorrhiza pumila to further the understanding of the biosynthesis of the anti-cancer alkaloid camptothecin and anthraquinones. Plant Cell Physiol 54(5): 686-696.
  2. Yamamoto, Y., T. Watanabe, Y. Hoki, K. Shirane, Y. Li, K. Ichiiyanagi, S. Kuramochi-Miyagawa, A. Toyoda, A. Fujiyama, M. Oginuma, H. Suzuki, T. Sado, T. Nakano and H. Sasaki (2013). Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus. Genome Res 23(2): 292-299.
  3. Takahashi, Y., Y. Fukuda, J. Yoshimura, A. Toyoda, K. Kurppa, H. Moritoyo, V. V. Belzil, P. A. Dion, K. Higasa, K. Doi, H. Ishiura, J. Mitsui, H. Date, B. Ahsan, T. Matsukawa, Y. Ichikawa, T. Moritoyo, M. Ikoma, T. Hashimoto, F. Kimura, S. Murayama, O. Onodera, M. Nishizawa, M. Yoshida, N. Atsuta, G. Sobue, JaCals, J. A. Fifita, K. L. Williams, I. P. Blair, G. A. Nicholson, P. Gonzalez-Perez, R. H. Brown, Jr., M. Nomoto, K. Elenius, G. A. Rouleau, A. Fujiyama, S. Morishita, J. Goto and S. Tsuji (2013). ERBB4 mutations that disrupt the neuregulin-ErbB4 pathway cause amyotrophic lateral sclerosis type 19. Am J Hum Genet 93(5): 900-905.
  4. Takada, T., T. Ebata, H. Noguchi, T. M. Keane, D. J. Adams, T. Narita, I. T. Shin, H. Fujisawa, A. Toyoda, K. Abe, Y. Obata, Y. Sakaki, K. Moriwaki, A. Fujiyama, Y. Kohara and T. Shiroishi (2013). The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains. Genome Res 23(8): 1329-1338.
  5. Shoguchi, E., C. Shinzato, T. Kawashima, F. Gyoja, S. Mungpakdee, R. Koyanagi, T. Takeuchi, K. Hisata, M. Tanaka, M. Fujiwara, M. Hamada, A. Seidi, M. Fujie, T. Usami, H. Goto, S. Yamasaki, N. Arakaki, Y. Suzuki, S. Sugano, A. Toyoda, Y. Kuroki, A. Fujiyama, M. Medina, M. A. Coffroth, D. Bhattacharya and N. Satoh (2013). Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure. Curr Biol 23(15): 1399-1408.
  6. Shiomi, D., A. Toyoda, T. Aizu, F. Ejima, A. Fujiyama, T. Shini, Y. Kohara and H. Niki (2013). Mutations in cell elongation genes mreB, mrdA and mrdB suppress the shape defect of RodZ-deficient cells. Mol Microbiol 87(5): 1029-1044.
  7. Shang, W. H., T. Hori, N. M. Martins, A. Toyoda, S. Misu, N. Monma, I. Hiratani, K. Maeshima, K. Ikeo, A. Fujiyama, H. Kimura, W. C. Earnshaw and T. Fukagawa (2013). Chromosome engineering allows the efficient isolation of vertebrate neocentromeres. Dev Cell 24(6): 635-648.
  8. Nikaido, M., H. Suzuki, A. Toyoda, A. Fujiyama, K. Hagino-Yamagishi, T. D. Kocher, K. Carleton and N. Okada (2013). Lineage-specific expansion of vomeronasal type 2 receptor-like (OlfC) genes in cichlids may contribute to diversification of amino acid detection systems. Genome Biol Evol 5(4): 711-722.
  9. Nikaido, M., H. Noguchi, H. Nishihara, A. Toyoda, Y. Suzuki, R. Kajitani, H. Suzuki, M. Okuno, M. Aibara, B. P. Ngatunga, S. I. Mzighani, H. W. Kalombo, K. W. Masengi, J. Tuda, S. Nogami, R. Maeda, M. Iwata, Y. Abe, K. Fujimura, M. Okabe, T. Amano, A. Maeno, T. Shiroishi, T. Itoh, S. Sugano, Y. Kohara, A. Fujiyama and N. Okada (2013). Coelacanth genomes reveal signatures for evolutionary transition from water to land. Genome Res 23(10): 1740-1748.
  10. Mori, H., F. Maruyama, H. Kato, A. Toyoda, A. Dozono, Y. Ohtsubo, Y. Nagata, A. Fujiyama, M. Tsuda and K. Kurokawa (2013). Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes. DNA Res.
  11. Miyake, K., C. Yang, Y. Minakuchi, K. Ohori, M. Soutome, T. Hirasawa, Y. Kazuki, N. Adachi, S. Suzuki, M. Itoh, Y. I. Goto, T. Andoh, H. Kurosawa, M. Oshimura, M. Sasaki, A. Toyoda and T. Kubota (2013). Comparison of Genomic and Epigenomic Expression in Monozygotic Twins Discordant for Rett Syndrome. PLoS One 8(6): e66729.
  12. Matsui, H., F. Sato, S. Sato, M. Koike, Y. Taruno, S. Saiki, M. Funayama, H. Ito, Y. Taniguchi, N. Uemura, A. Toyoda, Y. Sakaki, S. Takeda, Y. Uchiyama, N. Hattori and R. Takahashi (2013). ATP13A2 deficiency induces a decrease in cathepsin D activity, fingerprint-like inclusion body formation, and selective degeneration of dopaminergic neurons. FEBS Lett 587(9): 1316-1325.
  13. Kosaka, T., H. Toh and A. Toyoda (2013). Complete Genome Sequence of a Thermophilic Hydrogenotrophic Methanogen, Methanothermobacter sp. Strain CaT2. Genome Announc 1(4).
  14. Kobayashi, S., Y. Totoki, M. Soma, K. Matsumoto, Y. Fujihara, A. Toyoda, Y. Sakaki, M. Okabe and F. Ishino (2013). Identification of an imprinted gene cluster in the X-inactivation center. PLoS One 8(8): e71222.
  15. Kobayashi, M. N., H.; Garcia, V.; Just, D.; Bres, C.; Mauxion, JP.; Paslier, MC. Le; Brunel, D.; Suda, K.; Minakuchi, Y.; Toyoda, A.; Fujiyama, A.; Toyoshima, H.; Suzuki, T.; Igarashi, K.; Rothan, C.; Kaminuma, E.; Nakamura, Y.; Yano, K.; Aoki, K. (2013). Genome-wide analysis of intraspecific DNA polymorphism in ‘Micro-Tom’, a model cultivar of tomato (Solanum lycopersicum). Plant and Cell Physiology: pct181.
  16. Ishikawa, T., T. Okada, T. Ishikawa-Fujiwara, T. Todo, Y. Kamei, S. Shigenobu, M. Tanaka, T. L. Saito, J. Yoshimura, S. Morishita, A. Toyoda, Y. Sakaki, Y. Taniguchi, S. Takeda and K. Mori (2013). ATF6alpha/beta-mediated adjustment of ER chaperone levels is essential for development of the notochord in medaka fish. Mol Biol Cell 24(9): 1387-1395.
  17. Horikawa, D. D., J. Cumbers, I. Sakakibara, D. Rogoff, S. Leuko, R. Harnoto, K. Arakawa, T. Katayama, T. Kunieda, A. Toyoda, A. Fujiyama and L. J. Rothschild (2013). Analysis of DNA repair and protection in the Tardigrade Ramazzottius varieornatus and Hypsibius dujardini after exposure to UVC radiation. PLoS One 8(6): e64793.
  18. Hamaji, T., D. R. Smith, H. Noguchi, A. Toyoda, M. Suzuki, H. Kawai-Toyooka, A. Fujiyama, I. Nishii, T. Marriage, B. J. Olson and H. Nozaki (2013). Mitochondrial and plastid genomes of the colonial green alga Gonium pectorale give insights into the origins of organelle DNA architecture within the volvocales. PLoS One 8(2): e57177.
  19. Fu, Y., A. Kawabe, M. Etcheverry, T. Ito, A. Toyoda, A. Fujiyama, V. Colot, Y. Tarutani and T. Kakutani (2013). Mobilization of a plant transposon by expression of the transposon-encoded anti-silencing factor. EMBO J 32(17): 2407-2417.
  20. Chisada, S. I., T. Kurokawa, K. Murashita, I. Ronnestad, Y. Taniguchi, A. Toyoda, Y. Sakaki, S. Takeda and Y. Yoshiura (2013). Leptin receptor-deficient (knockout) medaka, Oryzias latipes, show chronical up-regulated levels of orexigenic neuropeptides, elevated food intake and stage specific effects on growth and fat allocation. Gen Comp Endocrinol.
  21. Araki, R., A. Hasumi, O. I. Nishizawa, K. Sasaki, A. Kuwahara, Y. Sawada, Y. Totoki, A. Toyoda, Y. Sakaki, Y. Li, K. Saito, T. Ogawa and M. Y. Hirai (2013). Novel bioresources for studies of Brassica oleracea: identification of a kale MYB transcription factor responsible for glucosinolate production. Plant Biotechnol J 11(8): 1017-1027.
2012
  1. Yamaguchi, A., S. Tanaka, S. Yamaguchi, H. Kuwahara, C. Takamura, S. Imajoh-Ohmi, D. D. Horikawa, A. Toyoda, T. Katayama, K. Arakawa, A. Fujiyama, T. Kubo and T. Kunieda (2012). Two novel heat-soluble protein families abundantly expressed in an anhydrobiotic tardigrade. PLoS One 7(8): e44209.
  2. Tsukahara, S., A. Kawabe, A. Kobayashi, T. Ito, T. Aizu, T. Shin-i, A. Toyoda, A. Fujiyama, Y. Tarutani and T. Kakutani (2012). Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata. Genes Dev 26(7): 705-713.
  3. Takami, H., H. Noguchi, Y. Takaki, I. Uchiyama, A. Toyoda, S. Nishi, G. J. Chee, W. Arai, T. Nunoura, T. Itoh, M. Hattori and K. Takai (2012). A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem. PLoS One 7(1): e30559.
  4. Ohnishi, Y., Y. Totoki, A. Toyoda, T. Watanabe, Y. Yamamoto, K. Tokunaga, Y. Sakaki, H. Sasaki and H. Hohjoh (2012). Active role of small non-coding RNAs derived from SINE/B1 retrotransposon during early mouse development. Mol Biol Rep 39(2): 903-909.
  5. Nakamura, S., I. Watakabe, T. Nishimura, A. Toyoda, Y. Taniguchi and M. Tanaka (2012). Analysis of medaka sox9 orthologue reveals a conserved role in germ cell maintenance. PLoS One 7(1): e29982.
  6. Nakamura, S., I. Watakabe, T. Nishimura, J. Y. Picard, A. Toyoda, Y. Taniguchi, N. di Clemente and M. Tanaka (2012). Hyperproliferation of mitotically active germ cells due to defective anti-Mullerian hormone signaling mediates sex reversal in medaka. Development 139(13): 2283-2287.
  7. Murtagh, V. J., D. O’Meally, N. Sankovic, M. L. Delbridge, Y. Kuroki, J. L. Boore, A. Toyoda, K. S. Jordan, A. J. Pask, M. B. Renfree, A. Fujiyama, J. A. Graves and P. D. Waters (2012). Evolutionary history of novel genes on the tammar wallaby Y chromosome: Implications for sex chromosome evolution. Genome Res 22(3): 498-507.
  8. Moriyama, Y., T. Kawanishi, R. Nakamura, T. Tsukahara, K. Sumiyama, M. L. Suster, K. Kawakami, A. Toyoda, A. Fujiyama, Y. Yasuoka, Y. Nagao, E. Sawatari, A. Shimizu, Y. Wakamatsu, M. Hibi, M. Taira, M. Okabe, K. Naruse, H. Hashimoto, A. Shimada and H. Takeda (2012). The medaka zic1/zic4 mutant provides molecular insights into teleost caudal fin evolution. Curr Biol 22(7): 601-607.
  9. Morita, S., R. U. Takahashi, R. Yamashita, A. Toyoda, T. Horii, M. Kimura, A. Fujiyama, K. Nakai, S. Tajima, R. Matoba, T. Ochiya and I. Hatada (2012). Genome-Wide Analysis of DNA Methylation and Expression of MicroRNAs in Breast Cancer Cells. Int J Mol Sci 13(7): 8259-8272.
  10. Morita, A., K. Nakahira, T. Hasegawa, K. Uchida, Y. Taniguchi, S. Takeda, A. Toyoda, Y. Sakaki, A. Shimada, H. Takeda and I. Yanagihara (2012). Establishment and characterization of Roberts syndrome and SC phocomelia model medaka (Oryzias latipes). Dev Growth Differ 54(5): 588-604.
  11. Kim, R. N., D. S. Kim, S. H. Choi, B. H. Yoon, A. Kang, S. H. Nam, D. W. Kim, J. J. Kim, J. H. Ha, A. Toyoda, A. Fujiyama, A. Kim, M. Y. Kim, K. H. Park, K. S. Lee and H. S. Park (2012). Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing. DNA Res 19(3): 275-287.
  12. Kagoshima, H., K. Kito, T. Aizu, T. Shin-i, H. Kanda, S. Kobayashi, A. Toyoda, A. Fujiyama, Y. Kohara, P. Convey and H. Niki (2012). Multi-decadal survival of an Antarctic nematode, Plectus murrayi, in a -20 degrees C stored moss sample. Cryo Letters 33(4): 280-288.
  13. Izutsu, M., J. Zhou, Y. Sugiyama, O. Nishimura, T. Aizu, A. Toyoda, A. Fujiyama, K. Agata and N. Fuse (2012). Genome features of Dark-fly, a Drosophila line reared long-term in a dark environment. PLoS One 7(3): e33288.
  14. Huang, X., N. Kurata, X. Wei, Z. X. Wang, A. Wang, Q. Zhao, Y. Zhao, K. Liu, H. Lu, W. Li, Y. Guo, Y. Lu, C. Zhou, D. Fan, Q. Weng, C. Zhu, T. Huang, L. Zhang, Y. Wang, L. Feng, H. Furuumi, T. Kubo, T. Miyabayashi, X. Yuan, Q. Xu, G. Dong, Q. Zhan, C. Li, A. Fujiyama, A. Toyoda, T. Lu, Q. Feng, Q. Qian, J. Li and B. Han (2012). A map of rice genome variation reveals the origin of cultivated rice. Nature 490(7421): 497-501.
  15. Hirakawa, H. T., S.; Sakai, H.; Nakayama, S.; Fujishiro, T.; Kishida, Y.; Kohara, M.; Watanabe, A.; Yamada, M.; Aizu, T.; Toyoda, A.; Fujiyama, A.; Tabata, S.; Fukui, K.; Sato, S. (2012). Upgraded genomic information of Jatropha curcas L. Plant Biotechnology 29(2): 123-130.
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2011
  1. Watanabe, T., S. Tomizawa, K. Mitsuya, Y. Totoki, Y. Yamamoto, S. Kuramochi-Miyagawa, N. Iida, Y. Hoki, P. J. Murphy, A. Toyoda, K. Gotoh, H. Hiura, T. Arima, A. Fujiyama, T. Sado, T. Shibata, T. Nakano, H. Lin, K. Ichiyanagi, P. D. Soloway and H. Sasaki (2011). Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus. Science 332(6031): 848-852.
  2. Watanabe, T., S. Chuma, Y. Yamamoto, S. Kuramochi-Miyagawa, Y. Totoki, A. Toyoda, Y. Hoki, A. Fujiyama, T. Shibata, T. Sado, T. Noce, T. Nakano, N. Nakatsuji, H. Lin and H. Sasaki (2011). MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline. Dev Cell 20(3): 364-375.
  3. Takahashi, S., A. Toyoda, Y. Sekiyama, H. Takagi, T. Nogawa, M. Uramoto, R. Suzuki, H. Koshino, T. Kumano, S. Panthee, T. Dairi, J. Ishikawa, H. Ikeda, Y. Sakaki and H. Osada (2011). Reveromycin A biosynthesis uses RevG and RevJ for stereospecific spiroacetal formation. Nat Chem Biol 7(7): 461-468.
  4. Sato, S., H. Hirakawa, S. Isobe, E. Fukai, A. Watanabe, M. Kato, K. Kawashima, C. Minami, A. Muraki, N. Nakazaki, C. Takahashi, S. Nakayama, Y. Kishida, M. Kohara, M. Yamada, H. Tsuruoka, S. Sasamoto, S. Tabata, T. Aizu, A. Toyoda, T. Shin-i, Y. Minakuchi, Y. Kohara, A. Fujiyama, S. Tsuchimoto, S. Kajiyama, E. Makigano, N. Ohmido, N. Shibagaki, J. A. Cartagena, N. Wada, T. Kohinata, A. Atefeh, S. Yuasa, S. Matsunaga and K. Fukui (2011). Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Res 18(1): 65-76.
  5. Renfree, M. B., A. T. Papenfuss, J. E. Deakin, J. Lindsay, T. Heider, K. Belov, W. Rens, P. D. Waters, E. A. Pharo, G. Shaw, E. S. Wong, C. M. Lefevre, K. R. Nicholas, Y. Kuroki, M. J. Wakefield, K. R. Zenger, C. Wang, M. Ferguson-Smith, F. W. Nicholas, D. Hickford, H. Yu, K. R. Short, H. V. Siddle, S. R. Frankenberg, K. Y. Chew, B. R. Menzies, J. M. Stringer, S. Suzuki, T. A. Hore, M. L. Delbridge, H. R. Patel, A. Mohammadi, N. Y. Schneider, Y. Hu, W. O’Hara, S. Al Nadaf, C. Wu, Z. P. Feng, B. G. Cocks, J. Wang, P. Flicek, S. M. Searle, S. Fairley, K. Beal, J. Herrero, D. M. Carone, Y. Suzuki, S. Sugano, A. Toyoda, Y. Sakaki, S. Kondo, Y. Nishida, S. Tatsumoto, I. Mandiou, A. Hsu, K. A. McColl, B. Lansdell, G. Weinstock, E. Kuczek, A. McGrath, P. Wilson, A. Men, M. Hazar-Rethinam, A. Hall, J. Davis, D. Wood, S. Williams, Y. Sundaravadanam, D. M. Muzny, S. N. Jhangiani, L. R. Lewis, M. B. Morgan, G. O. Okwuonu, S. J. Ruiz, J. Santibanez, L. Nazareth, A. Cree, G. Fowler, C. L. Kovar, H. H. Dinh, V. Joshi, C. Jing, F. Lara, R. Thornton, L. Chen, J. Deng, Y. Liu, J. Y. Shen, X. Z. Song, J. Edson, C. Troon, D. Thomas, A. Stephens, L. Yapa, T. Levchenko, R. A. Gibbs, D. W. Cooper, T. P. Speed, A. Fujiyama, J. A. Graves, R. J. O’Neill, A. J. Pask, S. M. Forrest and K. C. Worley (2011). Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol 12(8): R81.
  6. Ono, R., Y. Kuroki, M. Naruse, M. Ishii, S. Iwasaki, A. Toyoda, A. Fujiyama, G. Shaw, M. B. Renfree, T. Kaneko-Ishino and F. Ishino (2011). Identification of tammar wallaby SIRH12, derived from a marsupial-specific retrotransposition event. DNA Res 18(4): 211-219.
  7. Liu, W., D. Morito, S. Takashima, Y. Mineharu, H. Kobayashi, T. Hitomi, H. Hashikata, N. Matsuura, S. Yamazaki, A. Toyoda, K. Kikuta, Y. Takagi, K. H. Harada, A. Fujiyama, R. Herzig, B. Krischek, L. Zou, J. E. Kim, M. Kitakaze, S. Miyamoto, K. Nagata, N. Hashimoto and A. Koizumi (2011). Identification of RNF213 as a susceptibility gene for moyamoya disease and its possible role in vascular development. PLoS One 6(7): e22542.
  8. Kazuki, Y., H. Hoshiya, M. Takiguchi, S. Abe, Y. Iida, M. Osaki, M. Katoh, M. Hiratsuka, Y. Shirayoshi, K. Hiramatsu, E. Ueno, N. Kajitani, T. Yoshino, K. Kazuki, C. Ishihara, S. Takehara, S. Tsuji, F. Ejima, A. Toyoda, Y. Sakaki, V. Larionov, N. Kouprina and M. Oshimura (2011). Refined human artificial chromosome vectors for gene therapy and animal transgenesis. Gene Ther 18(4): 384-393.
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  10. Chisada, S., H. Okamoto, Y. Taniguchi, Y. Kimori, A. Toyoda, Y. Sakaki, S. Takeda and Y. Yoshiura (2011). Myostatin-deficient medaka exhibit a double-muscling phenotype with hyperplasia and hypertrophy, which occur sequentially during post-hatch development. Dev Biol 359(1): 82-94.