Publications

2025

Enviromental genomics

1. Kawamura, K., Sekida, S., Nishitsuji, K., Satoh, N.
   The property of larval cells of the scleractinian coral, Acropora tenuis, deduced from in vitro cultured cells
   Development, Growth & Differentiation, 1–17. (2025) LINK PUBMED
2. Yoshioka, Y., Kanai, M., Tsuhako, T., Satoh, N., Nagata, T.
   Complete mitochondrial genomes of Palauastrea ramosa Yabe & Sugiyama, 1941 and Stylocoeniella guentheri (Bassett-Smith, 1890) reveal their molecular phylogenetic position
   Galaxea, 27:7-12 (2025) https://doi.org/10.3755/galaxea.G27-4

2024

Developmental and Evolutionary

1. Takahashi, H., Hisata, K., Iguchi, R., Kikuchi, S., Ogasawara, M., Satoh, N.
   scRNA-seq analysis of cells comprising the amphioxus notochord
   Developmental Biology 508:24–37 (2024)  PUBMED
2. Makabe, K.W., Jensen, H.I., Fodor, A.C.A., Hsu, J., Jeffery, W.R., Satoh, N., and Swalla, B.J.
   Cymric, a Maternal and Zygotic HTK-16-Like SHARK Family Tyrosine Kinase Gene, Is Disrupted in Molgula occulta, a Tailless Ascidian
   The Biological Bulletin, 245:1-8 (2024) PUBMED

Enviromental Genomics

3. Nishitsuji, K., Nagahama, S., Narisoko, H., Shimada, K., Okada, N., Shimizu, Y., Satoh, N.
   Possible monitoring of mesophotic scleractinian corals using an underwater mini-ROV to sample coral eDNA
   R. Soc. Open Sci. 11: 221586. PUBMED
4. Açıkbaş, A.H.O., Narisoko, H., Huerlimann, R., Nishitsuji, K., Satoh, N., Reimer, J.D., Ravasi, T.
   Fish and coral assemblages of a highly isolated oceanic island: The first eDNA survey of the Ogasawara Islands
   Environmental DNA. 2024;6:e509 https://doi.org/10.1002/edn3.509
5. Shikina, S., Yoshioka, Y., Chiu, Y.L., Uchida, T., Chen, E., Cheng, Y.C., Lin, T.C., Chu, Y.L., Kanda, M., Kawamitsu, M., Fujie, M., Takeuchi, T., Zayasu, Y., Satoh, N., Shinzato, C.
   Genome and tissue-specific transcriptomes of the large-polyp coral, Fimbriaphyllia (Euphyllia) ancora: a recipe for a coral polyp.
   Commun Biol. 7(1):899. doi: 10.1038/s42003-024-06544-4. (2024) PUBMED
6. Yoshioka, Y., Yamashita, H., Uchida, T., Shinzato, C., Kawamitsu, M., Fourreau, C.J.L., Castelló, G.M., Fiedler, B.K., van den Eeckhout, T.M., Borghi, S., Reimer, J.D., Shoguchi, E.
   Azooxanthellate Palythoa (Cnidaria: Anthozoa) Genomes Reveal Toxin-related Gene Clusters and Loss of Neuronal Genes in Hexacorals
   Genome Biol Evol, 16(9):evae197. doi: 10.1093/gbe/evae197.(2024) PUBMED
7. Kawamura, K. and Satoh, N.
   Embryonic development of the gastrodermis in the coral Acropora tenuis
   Zoological Science, 41(6) https://doi.org/10.2108/zs240032
8. Yoshioka, Y., Nagata, F., Nonaka, M., Satoh, N.
   Molecular phylogenetic position of the family Fungiidae (Cnidaria: Anthozoa) based on complete mitochondrial genome sequences
   Galaxea, 26:43-7. (2024) https://doi.org/10.3755/galaxea.G26N-7
9. Satoh, N., Sinniger, F., Narisoko, H., Nagahama, S., Okada, N., Shimizu, Y., Yoshioka, Y., Hisata, K., Harii, S.
   Using underwater mini-ROV for coral eDNA survey: a case study in Okinawan mesophotic ecosystems.
   Coral Reefs. LINK (2024)

Functional genomics

10. Shoguchi, E., Kawachi, M., Shinzato, C. & Beedessee, G.
    Functional analyses of bacterial genomes found in Symbiodiniaceae genome assemblies.
    Environmental Microbiology Reports, 16(2), e13238. Available from: https://doi.org/10.1111/1758-2229.13238 PUBMED

Genome Collaborative Research

11. Kudo, K., Nishimura, T., Izumikawa, M., Kozone, I., Hashimoto, J., Fujie, M., Suenaga, H., Ikeda, H., Satoh, N., Shin-ya, K.
    Capability of a large bacterial artificial chromosome clone harboring multiple biosynthetic gene clusters for the production of diverse compounds.
    J Antibiot (2024). https://doi.org/10.1038/s41429-024-00711-9 PUBMED

2023

Developmental and Evolutionary Genomics

1. Tominaga, H., Nishitsuji, K., Satoh, N.
   A single-cell RNA-seq analysis of early larval cell-types of the starfish, Patiria pectinifera : Insights into evolution of the chordate body plan
   Developmental Biology, 496:52-62. PUBMED
2. Li, K., Nakashima, K., Hisata, K., Satoh, N.
   Expression and possible functions of a horizontally transferred glycosyl hydrolase gene, GH6‐1, in Ciona embryogenesis
   EvoDevo, 14:11 (2023) PUBMED
3. Arimoto, A., Nishitsuji, K., Hisata, K., Satoh, N., Tagawa, K.
   Transcriptomic evidence for Brachyury expression in the caudal tip region of adult Ptychodera flava (Hemichordata)
   DGD, 65: 370-480 (2023)PUBMED LINK
4. Noda, T., Satoh, N., Gittenberger, E., Asami, T.
   Left-right reversals recurrently evolved regardless of diaphanous-related formin gene duplication or loss in snails
   Journal of Molecular Evolution, 91:721-729 (2023)PUBMED LINK

Environmental Genomics

5. Nishitsuji, K., Nagata, T., Narisoko, H., Kanai, M., Hisata, K., Shinzato, C., Satoh, N.
   An environmental DNA metabarcoding survey reveals generic-level occurrence of scleractinian corals at reef slopes of Okinawa Island.
   Proceedings B, 290:20230026 PUBMED
6. Hillberg, A., Smith, M., Lausen, B., Suwansa-ard, S., Johnston, R., Mitu, S., MacDonald, L., Zhao, M., Motti, C., Wang, T., Elizur, A., Nakashima, K., Satoh, N., Cummins, S.
   Crown-of-thorns starfish spines secrete defence proteins
   PeerJ 11:e15689 (2023) LINK
7. Davies, S.W., Gamache, M.H., Howe-Kerr, L.I., Kriefall, N.G., Baker, A.C., Banaszak, A.T., Bay, L.K., Bellantuono, A.J., Bhattacharya, D., Chan, C.X., Claar, D.C., Coffroth, M.A., Cunning, R., Davy, S.K., del Campo, J., Díaz-Almeyda, E.M., Frommlet, J.C., Fuess, L.E., González-Pech, R.A., Goulet, T.L., Hoadley, K.D., Howells, E.J., Hume, B.C.C., Kemp, D.W., Kenkel, C.D., Kitchen, S.A., LaJeunesse, T.C., Lin, S., McIlroy, S.E., McMinds, R., Nitschke, M.R., Oakley, C.A., Peixoto, R.S., Prada, C., Putnam, H.M., Quigley, K., Reich, H.G., Reimer, J.D., Rodriguez-Lanetty, M., Rosales, S.M., Saad, O.S., Sampayo, E.M., Santos, S.R., Shoguchi, E., Smith, E.G., Stat, M., Stephens, T.G., Strader, M.E., Suggett, D.J., Swain, T.D., Tran, C., Traylor-Knowles, N., Voolstra, C.R., Warner, M.E., Weis, V.M., Wright, R.M., Xiang, T., Yamashita, H., Ziegler, M., Correa, A.M.S., Parkinson, J.E.
   Building consensus around the assessment and interpretation of Symbiodiniaceae diversity.
   PeerJ 11:e15023 (2023)LINK PUBMED 
8. Kawamura, K., Shioguchi, E., Nishitsuji, K., Sekida, S., Narisoko, H., Zhao, H., Shu, H., Fu, P., Yamashita., H., Fujiwara, S., Satoh, N.
   In vitro Phagocytosis of Different Dinoflagellate Species by Coral Cells
   Zoological Science, 40:444-454.LINK PUBMED 

Functional Genomics

9. Smith, M.K., Rotgans, B.A., Lang, T., Johnston, R., Wang, T., Suwansa-Ard, S., Bose, U., Satoh, N., Egertova, M., Hall, M.R., Bryne, M., Elphick, M.R., Motti, C.A., Cummins, S.F.
   Structure and proteomic analysis of the crown-of-thorns starfish (Acanthaster sp.) radial nerve cord.
   Sci Rep. 13(1):3349. doi: 10.1038/s41598-023-30425-1.PUBMED 

2022

Developmental and Evolutionary Genomics

1. Khalturin, K., Shunatova, N., Shchenkov, S., Sasakura, Y., Kawamitsu, M., Satoh, N.
   Polyzoa is back: The effect of complete gene sets on the placement of Ectoprocta and Entoprocta
   Science Advances, 8(26):eabo4400. (2022)  PUBMED
2. Satoh, N., Hisata, K., Foster, S., Morita, S., Nishitsuji, K., Oulhen, N., Tominaga, H., Wessel, G.
   A single-cell RNA-seq analysis of Brachyury-expressing cell clusters suggests a morphogenesis-associated signal center of oral ectoderm in sea urchin embryos
   Developmental Biology, 483: 128-142 (2022) PUBMED
3. Humphreys, T., Weiser, K., Arimoto, A., Sasaki, A., Uenishi, G., Fujimoto, B., Kawashima, T., Taparra, K., Molnar, J., Satoh, N., Marikawa, Y., Tagawa, K.
   Ancestral stem cell reprogramming genes active in hemichordate regeneration
   Frontiers in Ecology and Evolution, 10: 769433 (2022) LINK
4. Kashimoto, R., Tanimoto, M., Miura, S., Satoh, N., Laudet, V., Khalturin, K.
   Transcriptomes of giant sea anemones from Okinawa as a tool for understanding their phylogeny and symbiotic relationships with anemonefish
   Zoological Science, 39(4) (2022)  LINK PUBMED

Environmental Genomics

5. Yasuda, N., Inoue, J., Hall, M.R., Nair, M.R., Adjeroud, M., Miguel D. Fortes, M.D., Nishida, M., Tuivavalagi, N., Ravago-Gotanco, R., Forsman, Z.H., Soliman, T., Koyanagi, R., Hisata, K., Motti, C.A., Satoh, N.
   Two Hidden mtDNA-Clades of Crown-of-Thorns Starfish in the Pacific Ocean
   Frontiers Marine Science, 9: 831240, doi: 10.3389/fmars.2022.831240 (2022)  LINK 
6. Shimakawa, G., Shoguchi, E., Burlacot, A., Ifuku, K., Che, Y., Kumazawa, M., Tanaka, K., Nakanishi, S.
   Coral symbionts evolved a functional polycistronic flavodiiron gene.
   Photosynth Res. 151(1):113-124. doi: 10.1007/s11120-021-00867-7. (2022)  PUBMED
7. Tsuchiya, K., Zayasu, Y., Nakajima, Y., Arakaki, N., Suzuki, G., Satoh, N., Shinzato, C.
   Genomic analysis of a reef-building coral, Acropora digitifera, reveals complex population structure and a migration network in the Nansei Islands, Japan
   Molecular Ecology, 31, 5270– 5284. (2022)  PUBMED
8. Kitchen, S.,A., Jiang, D., Harii, S., Satoh, N., Weis, V.M., and Shinzato, C.
   Coral larvae suppress the heat stress response during the onset of symbiosis thereby decreasing their odds of survival
   Molecular Ecology, 31:5813-5830. (2022) PUBMED
9. Kiyono, S., Miyashita, S., Yamaguchi, K., Saito, I., Saito, Y., Manta, S., Ishikawa, M., Narita, M., Watanabe, T., Ito, R., Taguchi, M., Furukawa, R., Ikeuchi, A., Matsuo, K., Kurita, G., Kumagai, T., Shirakashi, S., Ogawa, K., Sakamoto, K., Koyanagi, R., Satoh, N., Sasaki, M., Maezawa, T., Ichikawa-Seki, M., Kobayashi. K.
   Sex-inducing effects toward planarians widely present among parasitic flatworms
   iScience, 26:105776 (2022)   LINK PUBMED

Functional Genomics

10. Takeuchi, T., Suzuki, Y., Watabe, S., Nagai, K., Tetsuji Masaoka, T., Fujie, M., Kawamitsu, M., Satoh, N., Myers, E.W.
    A high-quality, haplotype-phased genome reconstruction reveals unexpected 3 haplotype diversity in a pearl oyster
    DNA Research, 29:dsac035. (2022)  PUBMED
11. Isomoto, A., Shoguchi, E., Hisata, K., Inoue, J., Inaba, K., Satoh, N., Ogawa, T., Hiroki Shibata, H.
    Active Expression of Genes for Protein Modification Enzymes in Habu Venom Glands
    toxins, 14, 300. (2022) PUBMED LINK
12. Nishitsuji, K., Nishitsuji, Y., Yonashiro, Y., Satoh, N.
    Development of DNA markers that distinguish male and female haploid germlings of the brown alga, Cladosiphon okamuranus
    Phycological Research, 70: 160-166. LINK
13. Shimizu, K., Takeuchi, T., Negishi, L., Kurumizaka, H., Kuriyama, I., Endo, K., Suzuki, M.
    Evolution of Epidermal Growth Factor (EGF)-like and Zona Pellucida Domains Containing Shell Matrix Proteins in Mollusks.
    Mol Biol Evol. 39(7):msac148. doi: 10.1093/molbev/msac148. (2022) PUBMED LINK 
14. Adi, T.K., Fujie, M., Satoh, N., Ueki, T.
    The acidic amino acid-rich C-terminal domain of VanabinX enhances reductase activity, attaining 1.3- to 1.7-fold vanadium reduction
    Biochemistry and Biophysics Reports, 32, 101349 (2022)  LINK PUBMED
15. Boutet, I., Alves Monteiro, H. J., Baudry, L., Takeuchi, T., Bonnivard, E., Billoud, B., Farhat, S., Gonzales-Araya, R., Salaun, B., Andersen, A. C., Toullec, J.-Y., Lallier, F. H., Flot, J.-F., Guiglielmoni, N., Guo, X., Li, C., Allam, B., Pales-Espinosa, E., Hemmer-Hansen, J., Moreau, P., Marbouty, M., Koszul, R., Tanguy, A.
    Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic resource for aquaculture
    Evolutionary Applications, 00, 1– 19. LINK 

Sequencing Collaboration

16. Yamamoto, K., Yoneda, Y., Makino, A., Tanaka, Y., Meng, X.Y, Hashimoto, Y., Shin-ya, K., Satoh, N., Fujie, M., Toyama, T., Mori, K., Ike, M., Morikawa, M., Kamagata, Y., and Tamaki H.
    Draft genome sequence of Bryobacteraceae strain F-183
    Microbiology Resource Announcements, 11(1):e0045321. doi: 10.1128/mra.00453-21. (2022)  PUBMED
17. Yamamoto, K., Yoneda, Y., Makino, A., Tanaka, Y., Meng, X.Y, Hashimoto, Y., Shin-ya, K., Satoh, N., Fujie, M., Toyama, T., Mori, K., Ike, M., Morikawa, M., Kamagata, Y., and Tamaki H.
    Complete Genome Sequence of Luteitalea sp. Strain TBR-22.
    Microbiol Resour Announc. 11(2):e0045521. doi: 10.1128/mra.00455-21. (2022) PUBMED
18. Choirunnisa, A. R., Arima, K., Abe, Y., Kagaya, N., Kudo, K., Suenaga, H., Hashimoto, J., Fujie, M., Satoh, N., Shin-ya, K., Matsuda, K., Wakimoto, T.
    New azodyrecins identified by a genome mining-directed reactivity-based screening
    Beilstein J. Org. Chem. 18, 1017–1025. https://doi.org/10.3762/bjoc.18.102  LINK PUBMED

2021

Environmental Genomics

1. Shinzato, C., Takeuchi, T., Yoshioka, Y., Tada, I., Kanda, M., Broussard, C., Iguchi, A., Kusakabe, M., Marin, F., Satoh, N., Inoue, M.
   Whole-genome sequencing highlights conservative genomic strategies of a stress-tolerant, long-lived scleractinian coral, Porites australiensis Vaughan, 1918.
   GBE, 1;13(12):evab270. doi: 10.1093/gbe/evab270.  PUBMED
2. Kawamura, K., Sekida, S., Nishitsuji, K., Shoguchi, E., Hisata, K., Fujiwara, S., Satoh, N.
   In vitro symbiosis of reef-building coral cells with photosynthetic dinoflagellates
   frontiers in Marine Science, doi:10.3389/fmars.2021.706308 (2021) LINK
3. Shinzato, C., Khalturin, K., Inoue, J., Zayasu, Y., Kanda, M., Kawamitsu, M., Yoshioka, Y., Yamashita, H., Suzuki, G., Satoh, N.
   Eighteen coral genomes reveal the evolutionary origin of Acropora strategies to accommodate environmental changes
   Molecular Biology and Evolution, 38: 16-30. (2021)  LINK PUBMED
4. Satoh, N., Kinjo, K., Kohei Shintaku, K., Kezuka, D., Ishimori, H., Yokokura, A., Hagiwara, K., Hisata, K., Kawamitsu, M., Koizumi, K., Shinzato, C., Zayasu, Y.
   Color morphs of the coral, Acropora tenuis, show different responses to environmental stress and different expression profiles of fluorescent-protein genes
   G3: Genes|Genomes|Genetics, 11(2), jkab018 (2021)  LINK PUBMED
5. Shinzato, C., Narisoko, H., Nishitsuji, N., Nagata, T., Satoh, N., Inoue, J.
   Novel mitochondrial DNA markers for Scleractinian corals and generic-level environmental DNA metabarcoding.
   Front. Mar. Sci. 8:758207. (2021) doi: 10.3389/fmars.2021.758207 LINK 
6. Kawamura, K., Nishitsuji, K., Shoguchi, E., Fujiwara, S., Satoh, N.
   Establishing sustainable cell lines of a coral, Acropora tenuis
   Marine Biotechnology, doi: 10.1007/s10126-021-10031-w PUBMED
7. Mason, B., Cooke, I., Moya, A., Augustin, R., Lin, M., Satoh, N., Bosch, T., Bourne, D., Hayward, D., Andrade, N., Forêt, S., Ying, H., Ball, E., Miller, D.J.
   AmAMP1 from Acropora millepora and damicornin define a family of coral-specific antimicrobial peptides related to the Shk toxins of sea anemones
   Developmental and Comparative Immunology, 114: 103866. (2021) PUBMED
8. Zayasu, Y., Takeuchi, T., Nagata, T., Kanai, M., Fujie, M., Kawamitsu, M. Chinen, W. Shinzato, C., Satoh, N.
   Genome-wide SNP genotyping reveals hidden population structure of an acroporid species at a subtropical coral island: Implications for coral restoration.
   Aquatic Conservation: Marine and Freshwater Ecosystems, 1–11. (2021) LINK 
9. Sassa, M., Takagi, T., Kinjo, A., Yoshioka, Y., Zayasu, Y., Shinzato, C., Kanda, S., Murakami-Sugihara, N., Shirai, K., Inoue, K.
   Divalent metal transporter-related protein restricts animals to marine habitats
   Communication Biology 4, 463 (2021)  LINK PUBMED

Developmental and Evolutionary Genomics

10. Satoh, N., Tominaga, H., Kiyomoto, M., Hisata, K., Inoue, J., Nishitsuji, K.
    A Preliminary Single-Cell RNA-Seq Analysis of Embryonic Cells That Express Brachyury in the Amphioxus, Branchiostoma japonicum
    Front. Cell Dev. Biol., doi:10.3389/fcell.2021.696875 LINK 
11. Kashimoto, R., Hisata, K., Shinzato, C., Satoh, N., Shoguchi, E.
    Expansion and diversification of fluorescent protein genes in fifteen Acropora species during evolution of acroporid corals
    Genes, 12:397 PUBMED
12. Satou, Y., Sato, A., Yasuo, H., Mihirogi, Y., Bishop, J., Fujie, M., Kawamitsu, M., Hisata, K., Satoh, N.
    Chromosomal inversion polymorphisms in two sympatric ascidian lineages
    Genome Bioogy and Evolution, evab068 PUBMED

Functional Genomics

13. Takeuchi, T., Fujie, M., Koyanagi, R., Plasseraud, L., Ziegler-Devin, I., Brosse, N., Broussard, C., Satoh, N., Marin, F.
    The ‘Shellome’ of the Crocus Clam Tridacna crocea Emphasizes Essential Components of Mollusk Shell Biomineralization
    Front. Genet., doi:10.3389/fgene.2021.674539 (2021) LINK 
14. Maeda, T., Takahashi, S., Yoshida, T., Shimamura, S., Takaki, Y., Nagai, Y., Toyoda, A., Suzuki, Y., Arimoto, A., Ishii, H., Satoh, N., Nishiyama, T., Hasebe, M., Maruyama, T., Minagawa, J., Obokata, J., Shigenobu, S.
    Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus
    eLife, 10:e60176. doi: 10.7554/eLife.60176.PUBMED
15. Patwary, Z.P., Paul, N.A., Nishitsuji, K., Campbell, A.H., Shoguchi, E., Zhao, M., Cummins, S.F.
    Application of omics research in seaweeds with a focus on red seaweeds
    Brief Funct Genomics, elab023. doi: 10.1093/bfgp/elab023. PUBMED 
16. Okubo, S., Ena, E., Okuda, A., Kozone, I., Hashimoto, J., Nishitsuji, Y., Fujie, M., Satoh, N., Ikeda, H., Shin-Ya, K.
    Identification of functional cytochrome P450 and ferredoxin from Streptomyces sp. EAS-AB2608 by transcriptional analysis and their heterologous expression.
    Appl Microbiol Biotechnol, 105(10):4177-4187. doi: 10.1007/s00253-021-11304-z. PUBMED
17. Yoneda, Y., Yamamoto, K., Makino, A., Tanaka, Y., Meng, X.Y., Hashimoto, J., Shin-ya, K., Satoh, N., Fujie, M., Toyama, T., Mori, K., Ike, M., Morikawa, M., Kamagata, Y., Tamaki, H.
    Novel Plant-Associated Acidobacteria Promotes Growth of Common Floating Aquatic Plants, Duckweeds.
    Microorganisms. 9(6):1133. https://doi.org/10.3390/microorganisms9061133  LINK PUBMED
18. Kawato, S., Nishitsuji, K., Arimoto, A., Hisata, K., Kawamitsu, M., Nozaki, R., Kondo, H., Shinzato, C., Ohira, T., Satoh, N., Shoguchi, E., Hirono, I.
    Genome and transcriptome assemblies of the kuruma shrimp, Marsupenaeus japonicus
    G3, 5;11(11):jkab268 (2021)   PUBMED
19. Shoguchi, E.
    Gene clusters for biosynthesis of mycosporine-like amino acids in dinoflagellate nuclear genomes: Possible recent horizontal gene transfer between species of Symbiodiniaceae (Dinophyceae)
    Journal of Phycology.  LINK PUBMED
20. Maeda, K., Shinzato, C., Koyanagi, R., Kunishima, T., Kobayashi, H., Satoh, N., Palla, H.P.
    Two new species of Rhinogobius (Gobiiformes: Oxudercidae) from Palawan, Philippines, with their phylogenetic placement
    Zootaxa, 5068(1), 81–98. LINK

Sequencing collaboration

2020

(a) Developmental and Evolutionary Genomics

1. Hozumi, A., Matsunobu, S., Mita, K., Treen, N., Sugihara, T., Horie, T., Sakuma, T., Yamamoto, T., Shiraishi, A., Hamada, M., Satoh, N., Sakurai, K., Satake, Honoo, Sasakura, Y.
   GABA-induced GnRH release triggers chordate metamorphosis
   Current Biology, 30:1555-1561 (2020)PUBMED
2. Onuma, T.A., Hayashi, M., Gyoja, F., Kishi, K., Wang, K., Nishida, H.
   A chordate species lacking Nodal utilizes calcium oscillation and Bmp for left-right patterning.
   Proc Natl Acad Sci U S A., 117(8):4188-4198 (2020) PUBMED
3. Ilsley, G.R., Suyama, R., Noda, T., Satoh, N., Luscombe, N.M.
   Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq
   Scientific Reports, 10:4961 (2020)PUBMED
4. Simakov, O., Marlétaz, F., Yue, J.X., O'Connell, B., Jenkins, J., Brandt, A., Calef, R., Tung, C.H., Huang, T.K., Schmutz, J., Satoh, N., Yu, J.K., Putnam, N.H., Green, R.E., Rokhsar, D.S.
   Deeply conserved syntheny resolves early events in vertebrate evolution
   Nature Ecology & Evolution, 4(6): 820–830 (2020)PUBMED
5. Yasuoka, Y.
   Morphogenetic mechanisms forming the notochord rod: The turgor pressure‐sheath strength model.
   Develop Growth Differ. 62(6):379-390. DOI: 10.1111/dgd.12665 PUBMED LINK 
6. Li, K.L., Nakashima, K., Inoue, J., Satoh, N.
   Phylogenetic analyses of Glycosyl Hydrolase Family 6 genes in tunicates: Possible horizontal transfer
   Genes 11, 937, doi:10.3390/genes11080937 PUBMED
7. Hamada, M., Satoh, N., Khalturin, K.
   A Reference Genome from the symbiotic hydrozoan, Hydra viridissima
   G3: Genes|Genomes|Genetics, 10(11):3883-3895. (2020) PUBMED
8. Nesterenko, M.A., Starunov, V.V., Shchenkov, S.V., Maslova, A.R., Denisova, S.A., Granovich, A.I., Dobrovolskij, A.A., Khalturin, K.
   Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae)
   Parasites & Vectors volume 13, Article number: 559 (2020) PUBMED
9. Zhao, R., Takeuchi, T., Koyanagi, R., Villar-Briones, A., Yamada, L., Sawada, H., Ishikawa, A., Iwanaga, S., Nagai, K., Che, Y., Satoh, N., Endo, K.
   Phylogenetic comparisons reveal mosaic histories of larval and adult shell matrix protein deployment in pteriomorph bivalves.
   Sci Rep 10, 22140 (2020). LINK 

(b) Environmental Genomics

10. Shoguchi, E., Yoshioka, Y., Shinzato, C., Arimoto, A., Bhattacharya, D., Satoh, N.
    Correlation between organelle genetic variation and RNA editing in dinoflagellates associated with the coral Acropora digitifera
    Genome Biology and Evolution, 12:203-209 (2020)LINK PUBMED
11. Inoue, J., Hisata, K., Yasuda, N., Satoh, N.
    An investigation into the genetic history of Japanese populations of three starfish, Acanthaster planci, Linckia laevigata, and Asterias amurensis, based on complete mitochondrial DNA sequences
    G3: Genes|Genomes|Genetics, 10: 2519-2528 (2020)PUBMED
12. Takagi, T., Yoshioka, Y., Zayasu, Y., Satoh, N., Shinzato, C.
    Transcriptome analyses of immune system behaviors in primary polyp of coral Acropora digitifera exposed to the bacterial pathogen Vibrio coralliilyticus under thermal loading
    Marine Biotechnology, 22:748-759. (2020)PUBMED LINK 
13. Selmoni, O., Lecellier, G., Ainley, L., Collin, A., Doucet, R., Dubousquet, V., Feremaito, H., Waia, E.I., Kininmonth, S.J., Magalon, H., Malimali, S., Maugateau, A., Meibom, A., Mosese, S., Rene-Trouillefou, M., Satoh, N., van Oppen, M.J.H., Xozame, A., Yekawene, M., Joost, S., Berteaux-Lecellier, V.
    Using modern conservation tools for innovative management of coral reefs: the MANACO Consortium Journal: Frontiers in Marine Science, section Marine Conservation and Sustainability
    Frontiers in Marine Science, 7:609 LINK 
14. Shoguchi, E., Beedessee, G., Hisata, K., Tada, I., Narisoko, H., Satoh, N., Kawachi, M., Shinzato, C.
    A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis
    Genome Biology and Evolution, 13:evaa235. PUBMED
15. Yoshioka, Y., Yamashita, H., Suzuku, G., Zayasu, Y., Tada I., Kanda, M., Satoh, N., Shoguchi, E., Shinzato, C.
    Whole-genome transcriptome analyses of native symbionts reveal host coral genomic novelties for establishing coral-algae symbioses.
    Genome Biology and Evolution, 13:evaa240. PUBMED

(c) Functional Genomics

16. Takeuchi, T., Masaoka, T., Aoki, H., Koyanagi, R., Fujie, M., Satoh, N.
    Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs
    Evolutionary Applications, 13: 838–854 (2020)LINK PUBMED
17. Choi, J.W., Graf, L., Peters, A.F., Cock, J.M., Nishitsuji, K., Arimoto, A., Shoguchi, E., Nagasato, C., Choi, C.G., Yoon, H.S.
    Organelle inheritance and genome architecture variation in isogamous brown algae.
    Sci Rep. 10:2048. doi: 10.1038/s41598-020-58817-7 PUBMED
18. Ishikawa, A., Shimizu, K., Isowa, Y., Takeuchi, T., Zhao, R., Kito, K., Fujie, M., Satoh, N., Endo, K.
    Functional shell matrix proteins tentatively identified by asymmetric snail shell morphology.
    Scientific Reports, 10:9768.PUBMED LINK 
19. Nishitsuji, K., Arimoto, A., Yonashiro, Y., Hisata, K., Fujie, M., Kawamitsu, M., Shoguchi, E., Satoh, N.
    Comparative genomics of four strains of the edible brown alga, Cladosiphon okamuranus
    BMC Genomics, 21: 422 (2020)PUBMED LINK 
20. Hashimoto, T., Kozone, I., Hashimoto, J., Suenaga, H., Fujie, M., Satoh, N., Ikeda, H., Shin-Ya, K.
    Identification, Cloning and Heterologous Expression of Biosynthetic Gene Cluster for Desertomycin
    J Antibiot , 73(9):650-654 (2020). PUBMED
21. Beedessee, G., Kubota, T., Arimoto, A., Nishitsuji, K., Waller, R.F., Hisata, K., Yamasaki, S., Satoh, N., Kobayashi, J., Shoguchi, E.
    Integrated omics unveil the secondary metabolic landscape of a basal dinoflagellate
    BMC Biology, 18, Article number: 139 (2020)LINK PUBMED
22. Nogawa, T., Terai, A., Amagai, K., Hashimoto, J., Futamura, Y., Okano, A., Fujie, M., Satoh, N., Ikeda, H., Shin-Ya, K., Osada, H., Takahashi, S.
    Heterologous Expression of the Biosynthetic Gene Cluster for Verticilactam and Identification of Analogues.
    J Nat Prod. doi: 10.1021/acs.jnatprod.0c00755. PUBMED

(d) Other Fields

23. Gelineau, Y., Saget, M., Brault, V., Anamparéla, B., Aboulker, C., Martinet, J., Maeda, K., Feutry P.
    Biology of jungle perch, Kuhlia rupestris, identification of threats and knowledge gaps to improve local and global management
    Cybium 44: 45–55 (2020)LINK

2019

(a) Developmental and Evolutionary Genomics

1. Khalturin, K., Shinzato, C., Khalturina, M., Hamada, M., Fujie, M., Koyanagi, R., Kanda, M., Goto, H., Anton-Erxleben, F., Toyokawa, M., Toshino, S., Satoh, N.
   Medusozoan genomes inform the evolution of the jellyfish body plan
   Nature Ecology & Evolution, 3(5):811-822 (2019)PUBMED LINK PDF
   
2. Satoh, N.
   A deep dive into sea-squirt development
   Nature 571, 333-334 (2019)PUBMED LINK
3. Arimoto, A., Hikosaka-Katayama, T., Hikosaka, A., Tagawa, K., Inoue, T., Ueki, T., Yoshida, M., Kanda, M., Shoguchi, E., Hisata, K., Satoh, N.
   A draft genome assembly of the acoel flatworm Praesagittifera naikaiensis.
   GigaScience, 8(4) (2019) PUBMED 
4. Lu, T.M., Kanda, M., Furuya, H., Satoh, N.
   Dicyemid mesozoans: a unique parasitic lifestyle and a reduced genome
   Genome Biology and Evolution, 11:2232–2243 (2019) PUBMED 
5. Inoue, J., Satoh, N.
   ORTHOSCOPE: an automatic web tool for phylogenetically inferring bilaterian orthogroups with user-selected taxa
   Molecular Biology and Evolution, 36: 621-631 (2019) PUBMED 
6. Inoue, J., Nakashima, K., Satoh, N.
   ORTHOSCOPE Analysis Reveals the Presence of the Cellulose Synthase Gene in All Tunicate Genomes but not in Other Animal Genomes
   Genes, 10: 294 (2019)PUBMED LINK
7. Noda, T., Satoh, N., Asami, T.
   Heterochirality results from reduction of maternal diaph expression in a terrestrial pulmonate snail
   Zoological Letters, 2019 5:2 (2019).PUBMED LINK
8. Marlétaz, F., Peijnenburg, K.T.C.A., Goto, T., Satoh, N., Rokhsar, D.S.
   A new spiralian phylogeny places the enigmatic arrow worms among gnathiferans
   Current Biology, 29, 1–7. (2019)PUBMED LINK
9. Philippe, H., Poustka, A.J., Chiodin, M., Hoff, K.J., Dessimoz, C., Tomiczek, B., Schiffer, P.H., Muller, S., Domman, D., Horn, M., Kuhl, H., Timmermann, B., Satoh, N., Hikosaka-Katayama, T., Nakano, H., Rowe, M.L., Elphick, M.R., Thomas-Chollier, M., Hankeln, T., Mertes, F., Wallberg, A., Rast, J.P., Copley, R.R., Martinez, P., Telford M.J.
   Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria
   Current Biology, 29: 1818-1826 (2019)PUBMED LINK
10. Ueki, T., Arimoto, A., Tagawa, K., Satoh, N.
    Xenacoelomorph-Specific Hox Peptides: Insights into the Phylogeny of Acoels, Nemertodermatids, and Xenoturbellids
    Zoological Science, 36: 395-401. (2019) LINK
11. Ishikawa, A., Kabeya, N., Ikeya, K., Kakioka, R., Cech, J.N., Osada, N., Leal, M.C., Inoue, J., Kume, M., Toyoda, A., Tezuka, A., Nagano, A.J., Yamasaki, Y.Y,. Suzuki, Y., Kokita, T., Takahashi, H., Lucek, K., Marques, D., Takehana, Y., Naruse, K., Mori, S., Monroig, O., Ladd, N., Schubert, C., Matthews, B., Peichel, C.L., Seehausen, O., Yoshizaki, G., Kitano, J.
    A key metabolic gene for recurrent freshwater colonization and radiation in fishes
    Science, 364: 886-889 (2019)PUBMED LINK
12. Shiraishi, A., Okuda, T., Miyasaka, N., Osugi, T., Okuno, Y., Inoue, J., & Satake, H.
    Repertoires of G protein-coupled receptors for Ciona-specific neuropeptides.
    PNAS, 116: 7847–7856. doi:10.1073/pnas.1816640116 (2019)PUBMED LINK
13. Yasuoka, Y., Tando, Y., Kubokawa, K., Taira, M.
    Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus
    Zoological Letters, 5: 27 (2019)PUBMED LINK
14. Lu, T.M., Furuya, H., Satoh, N.
    Gene expression profiles of dicyemid life-cycle stages may explain how dispersing larvae locate new hosts.
    Zoological Letters, 5: 32 (2019) LINK
15. Maiorova, M.A., Satoh, N., Khalturin, K., Odintsova, N.A.
    Transcriptomic profiling of the mussel Mytilus trossulus with a special emphasis on integrin-like genes during development
    Invertebrate Reproduction & Development, 63: 231-240 (2019) LINK
16. Satou, Y., Nakmura, R., Deli, Y., Yoshida, R., Hamada, M., Fujie, M., Hisata, K., Takeda, H., Satoh, N.
    A nearly-complete genome of Ciona intestinalis type A (C. robusta) reveals the contribution of inversion to chromosomal evolution in the genus Ciona.
    Genome Biology and Evolution, 1;11:3144-3157 (2020)PUBMED LINK

(b) Environmental Genomics

17. Zayasu, Y., Suzuki, G.
    Comparisons of population density and genetic diversity in artificial and wild populations of an arborescent coral, Acropora yongei: implications for the efficacy of "artificial spawning hotspots"
    Restoration Ecology, https://doi.org/10.1111/rec.12857 LINK
18. Mao, Y., Satoh, N.
    A likely ancient genome duplication in the speciose reef-building coral genus, Acropora
    iScience, 13: 20-32 (2019)PUBMED LINK
19. Miyake, T., Aihara, N., Maeda, K., Shinzato, C., Koyanagi, R., Kobayashi, H., Yamahira, K.
    Bloodmeal host identification with inferences to feeding habits of a fish-fed mosquito, Aedes baisasi
    Scientific Reports, 9: 4002 (2019)PUBMED LINK
20. Hanahara, N., Higashiji, T., Shinzato, C., Koyanagi, R., Maeda, K.
    First record of Larsonella pumilus (Teleostei: Gobiidae) from Japan, with phylogenetic placement of the genus Larsonella
    Zootaxa 4695: 367-377 (2019)LINK

(c) Functional Genomics

21. Beedessee, G., Hisata, K., Roy, M.C., Van Dolah, F.M., Satoh, N., Shoguchi, E.
    Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates
    Scientific Reports, 9: 1204 (2019)PUBMED LINK
22. Ueki, T., Fujie, M., Romaidi, Satoh, N.
    Symbiotic bacteria associated with Ascidian vanadium accumulation identified by 16S rRNA amplicon Sequencing
    Marine Genomics, 43: 33-42 (2019)PUBMED LINK
23. Arimoto, A., Nishitsuji, K., Arakaki, N., Hisata, K., Shinzato, C., Satoh, N., Shoguchi, E.
    A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants.
    DNA Research, 26: 183–192 (2019) PUBMED 
24. Nishitsuji, K., Arimoto, A., Higa, Y., Mekaru, M., Kawamitsu, M., Satoh, N., Shoguchi, E.
    Draft genome of the brown alga, Nemacystus decipiens, Onna-1 strain: Fusion of genes involved in the sulfated fucan biosynthesis pathway
    Scientific Reports, 9: 4607 (2019) PUBMED 
25. Arimoto, A., Nishitsuji, K., Narisoko, H., Shoguchi, E., Satoh, N.
    Differential gene expression in fronds and stolons of the siphonous macroalga, Caulerpa lentillifera
    Dev. Growth Diff, doi:10.1111/dgd.12634 (2019)PUBMED LINK
26. Ogawa, T., Oda-Ueda, N., Hisata, K., Nakamura, H., Chijiwa, T., Hattori, S., Isomoto, A., Yugeta, H., Yamasaki, S., Fukumaki, Y., Ohno, M., Satoh, N., Shibata, S.
    Extensive alternative mRNA splicing underlying highly divergent venom proteins of the habu snake Protobothrops flavoviridis
    Toxins, 11,581 (2019)LINK PUBMED 

(d) Other Fields

27. Nakashima, K., Kikuchi, S.
    Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota. (in Japanese)
    実験医学37, 69-72 (2019)
28. Arimoto, A.
    Exploring the mysteries of morphogenesis of sea grapes: insights from the sea grape genome. (in Japanese)
    academist journal (2019) LINK

2018

(a) Developmental and Evolutionary Genomics

1. Luo, Y.J., Kanda, M., Koyanagi, R., Hisata, K., Akiyama, T., Sakamoto, H., Sakamoto, T., Satoh, N.
   Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads.
   Nature Ecology & Evolution 2, 141–151 (2018), doi:10.1038/s41559-017-0389-y.LINK PUBMED
2. Inoue, J., Satoh, N.
   Deuterostome Genomics: Lineage-specific Protein Expansions that Enabled Chordate Muscle Evolution
   Molecular Biology and Evolution. 35(4):914-924. (2018)LINK PUBMED
3. Nakano, H., Miyazawa, H., Maeno, A., Shiroishi, T., Kakui, K., Koyanagi, R., Kanda, M., Satoh, N., Omori, A., Kohtsuka, H.
   Correction to: A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella.
   BMC Evolutionary Biology. 18:83. doi:10.1186/s12862-018-1190-5. (2018)LINK PUBMED
4. Gerdol, M., Luo, Y.J., Satoh, N., Pallavicini, A.
   Genetic and molecular basis of the immune system in the brachiopod Lingula anatina
   Developmental and Comparative Immunology. 82: 7-30. (2018)LINK PUBMED
5. Tominaga, H., Satoh, N., Ueno, N., Takahashi, H.
   Enhancer activities of amphioxus Brachyury genes in embryos of the ascidian, Ciona intestinalis.
   genesis. 56(8):e23240. (2018)LINK PUBMED
6. Horie, T., Horie, R., Chen, K., Cao, C., Nakagawa, M., Kusakabe, T.G., Satoh, N., Sasakura, Y., Levine, M.
   Regulatory cocktail for dopaminergic neurons in a proto-vertebrate identified by whole embryo single cell transcriptomics
   Genes and Development, 32(19-20):1297-1302. doi: 10.1101/gad.317669.118. (2018)LINK PUBMED
7. Irie, N., Satoh, N., Kuratani, S.
   The phylum Vertebrata: a case for zoological recognition
   Zoological Letters, 2018 4:32. (2018)LINK PUBMED
8. Nakashima, K.
   A comparative approach to decipher intestinal animal-microbe associations.
   Microbial Cell. 5: 522-524. (2018) PUBMED

(b) Environmental Genomics

9. Hamada, M., Schröder, K., Bathia, J., Kürn, U., Fraune, S., Khalturina, M., Khalturin, K., Shinzato, C., Satoh, N., Bosch, T.C.G
   Metabolic co-dependence drives the evolutionary ancient Hydra-Chlorella symbiosis
   eLife. 31;7. pii: e35122. doi: https://doi.org/10.1101/234757 (2018)LINK PUBMED
10. Shoguchi, E., Beedessee, G., Tada, I., Hisata, K., Kawashima, T., Takeuchi, T., Arakaki, N., Fujie, M., Koyanagi, R., Roy, M.C., Kawachi, M., Hidaka, M., Satoh, N., Shinzato, C.
    Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes
    BMC Genomics. 19:458. doi:10.1186/s12864-018-4857-9. (2018)LINK PUBMED
11. Zayasu, Y., Satoh, N., Shinzato, C.
    Genetic diversity of farmed and wild populations of the reef building coral, Acropora tenuis. 
    Restoration Ecology. 26(6):1195-1202. doi: 10.1111/rec.12687 (2018) LINK 
12. Shinzato, C., Zayasu, Y., Kanda, M., Kawamitsu, M., Satoh, N., Yamashita, H., Go Suzuki, G.
    Using seawater to document coral-zoothanthella diversity: A new approach to coral reef monitoring using environmental DNA
    Front. Mar. Sci. 5:28. doi: 10.3389/fmars.2018.00028 (2018) LINK 
13. Guzman, C., Han, X., Shoguchi, E., Nic Chormaic, S.
    Fluorescence from a single Symbiodinium cell.
    Methods Appl Fluoresc. 8(1): 8397. doi: 10.1088/2050-6120/aaba89. (2018)PUBMED
14. Guzman, C., Shinzato, C., Lu, T.M., Conaco, C.
    Transcriptome analysis of the reef-building octocoral, Heliopora coerulea
    Scientific Reports 8:8397. DOI:10.1038/s41598-018-26718-5 (2018)LINK PUBMED
15. Mohamed, A., Cumbo, V., Harii, S., Shinzato, C., Chan, C.X., Ragan, M., Satoh, N., Ball, E., Miller, D.
    Deciphering the nature of the coral-Chromera association.
    The ISME Journal. 12(3): 776-790 (2018) PUBMED
16. Higa, Y., Shinzato, C., Zayasu, Y., Nagata, T., Nakamura, R., Yokokura, A., Shanado, S., Ohmori M.
    Flexible development of techniques for coral reef restoration using asexual reproduction in the Coral Reef Preservation and Rehabilitation Project by Okinawa Prefectural Government, Japan (in Japanese)
    Journal of the Japanese Coral Reef Society, 20: 21-37 (2018) LINK
17. Mao, Y.F., Economo, E.P., Satoh, N.
    The roles of introgression and climate change in the rise to dominance of Acropora corals.
    Current Biology. 28(21):3373-3382.e5. doi: 10.1016/j.cub.2018.08.061. (2018)LINK PUBMED
18. Maeda, K., Saeki, T.
    Revision of species in Sicyopterus (Gobiidae: Sicydiinae) described by de Beaufort (1912), with a first record of Sicyopterus longifilis from Japan
    Species Diversity 23: 253–262 (2018) LINK 
19. Nakajima, Y., Shinzato, C., Khalturina, M., Nakamura, M., Watanabe, H.K., Nakagawa, S., Satoh, N., Mitarai, S.
    Isolation and characterization of novel polymorphic microsatellite loci for the deep-sea hydrothermal vent limpet, Lepetodrilus nux, and the vent-associated squat lobster, Shinkaia crosnieri
    Mar Biodiv 48: 677-684. (2018) LINK
20. Maeda, K., Saeki, T., Shinzato, C., Koyanagi, R., Satoh, N.
    Review of Schismatogobius (Gobiidae) from Japan, with the description of a new species
    Ichthyol Res 65: 56-77. (2018) LINK

(c) Functional Genomics

21. Shibata H., Chijiwa T., Oda-Ueda N., Nakamura H., Yamaguchi K., Hattori S., Matsubara K., Matsuda Y., Yamashita A., Isomoto A., Mori K., Tashiro K., Kuhara S., Yamasaki S., Fujie M., Goto H., Koyanagi R., Takeuchi T., Fukumaki Y., Ohno M., Shoguchi E., Hisata K., Satoh N., Ogawa T.
    The habu genome reveals accelerated evolution of venom protein genes.
    Sci Rep. 26;8(1):11300. doi: 10.1038/s41598-018-28749-4. (2018) PUBMED
22. Nakashima, K., Kimura, S., Ogawa, Y., Watanabe, S., Soma, S., Kaneko, T., Yamada, L., Sawada, H., Tung, CH., Lu, T.M., Yu, J.K., Villar-Briones, A., Kikuchi, S., Satoh, N.
    Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota.
    Nat Commun. 9(1):3402. doi: 10.1038/s41467-018-05884-0. (2018)LINK PUBMED
23. Matsuura, A., Yoshimura, K., Kintsu, H., Atsumi, T., Tsuchihashi, Y., Takeuchi, T., Satoh, N., Negishi, L., Sakuda, S., Asakura, T., Imura, Y., Yoshimura, E.
    Structural and functional analyses of calcium ion response factors in the mantle of Pinctada fucata.
    Journal of Structural Biology. 204(2):240-249. (2018)LINK PUBMED
24. Kawahara, T., Izumikawa, M., Kozone, I., Hashimoto, J., Kagaya, N.,Koiwai, H., Komatsu, M., Fujie, M., Sato, N., Ikeda, H., Shin-ya, K.
    Neothioviridamide, a Polythioamide Compound Produced by Heterologous Expression of a Streptomyces sp. Cryptic RiPP Biosynthetic Gene Cluster
    J. Nat. Prod. 81(2):264-269. (2018) PUBMED
25. Iwasaka, H., Koyanagi, R., Satoh, R., Nagano, A., Watanabe, K., Hisata, K., Satoh, N., Aki, T.
    A Possible Trifunctional β-Carotene Synthase Gene Identified in the Draft Genome of Aurantiochytrium sp. Strain KH105.
    Genes. 9(4): 200 (2018)LINK PUBMED
26. Tsutsumi, H., Katsuyama, Y., Izumikawa, M., Takagi, M., Fujie, M., Satoh, N., Shin-ya, K., Ohnishi, Y.
    Unprecedented Cyclization Catalyzed by a Cytochrome P450 in Benzastatin Biosynthesis
    JACS 140(21):6631-6639. (2018) PUBMED
27. Takeuchi, T., , Plasseraud, L., Ziegler-Devin, I., Brosse, N., Shinzato, C., Satoh, N., Marin, F.
    Biochemical characterization of the skeletal matrix of the massive coral, Porites australiensis - The saccharide moieties and their localization
    Journal of Structural Biology. S1047-8477(18)30135-7. (2018)LINK PUBMED
28. Zhao, R., Takeuchi, T., Luo, Y.J., Ishikawa, A., Kobayashi, T., Koyanagi, R., Villar-Briones, A., Yamada, L., Sawada, H., Iwanaga, S., Nagai, K., Satoh, N., Endo, K.
    Dual gene repertoires for larval and adult shells reveal molecules essential for molluscan shell formation.
    Molecular Biology and Evolution. msy172. https://doi.org/10.1093/molbev/msy172 (2018)LINK PUBMED
29. Kubota, K., Kintsu, H., Matsuura, A., Tsuchihashi, Y., Takeuchi, T., Satoh, N., Suzuki, M.
    Functional analyses of MMPs for aragonite crystal formation in the ligament of Pinctada fucata.
    Frontiers in Marine Science, 5:373. doi: 10.3389/fmars.2018.00373 (2018) LINK
30. Kim, O.T.P., Nguyen, P.T., Shoguchi, E., Hisata, K., Vo, T.T.B., Inoue, J., Shinzato, C., Le, B.T.N, Nishitsuji, K., Kanda, M., Nguyen, V.H., Nong, H.V., Satoh, N.
    A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement.
    BMC Genomics, 19(1):733. doi: 10.1186/s12864-018-5079-x. (2018) PUBMED
31. Marin, F., Chmiel, A., Takeuchi, T., Bundeleva, I., Durlet, C., Samankassou, E., Medakovic, D.
    Skeletal Organic Matrices in Molluscs: Origin, Evolution, Diagenesis.
    In. Biomineralization. Switzerland: Springer Nature. p. 325-332. (2018) LINK 

2017

1. Hall, M.R., Kocot, K.M., Baughman, K.W., Fernandez-Valverde, S.L., Gauthier, M.E.A., Hatleberg, W.L., Krishnan, A., McDougall, C., Motti, C.A., Shoguchi, E., Wang, T., Xiang, X., Zhao, M., Bose, U., Shinzato, C., Hisata, K., Fujie, M., Kanda, M., Cummins, S.F., Satoh, N., Degnan, S.M., Degnan. B.M.
   The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest.
   Nature, 5;544(7649):231-234.LINK PUBMED

(a) Developmental and Evolutionary Genomics

2. Simion, P., Philippe, H., Baurain, D., Jager, M., Richter, D.J., Franco, A.D., Roure, B., Satoh, N., Quéinnec, E., Ereskovsky, A., Lapébie, P., Corre, E., Delsuc, F., King, N., Wörheide, G., Manuel, M.
   A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals.
   Current Biology. 27(7):958-967. doi: 10.1016/j.cub.2017.02.031. (2017)LINK PUBMED
3. Michiue, T., Yamamoto, T., Yasuoka, Y., Goto, T., Ikeda, T., Nagurab, K., Nakayama, T., Taira, M., Kinoshita T.
   High variability of expression profiles of homeologous genes for Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus laevis
   Developmental Biology. 426(2):270-290 (2017)LINK PUBMED
4. Inoue, J., Yasuoka, Y., Takahashi, H., & Satoh, N.
   The chordate ancestor possessed a single copy of the Brachyury gene for notochord acquisition.
   Zoological Letters. 23;3:4. doi: 10.1186/s40851-017-0064-9. (2017)LINK PUBMED
5. Charney, R.M., Forouzmand, E., Cho, J.S., Cheung, J., Paraiso, K.D., Yasuoka, Y., Takahashi, S., Taira, M., Blitz, I.L., Xie, X., Cho, K.W.Y.
   Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program.
   Developmental Cell 40(6):595-607.e4. (2017)LINK PUBMED
6. Lu, T.M., Kanda, M.,Satoh, N., Furuya, H.
   The phylogenetic position of dicyemid mesozoans offers insights into spiralian evolution.
   Zoological Letters 3:6 DOI 10.1186/s40851-017-0068-5 (2017)LINK PUBMED
7. Shimizu, K., Luo, Y.J., Satoh, N., Endo, K.
   Possible co-option of engrailed during brachiopod and mollusc shell development.
   Biology Letters 13: 20170254. (2017)LINK PUBMED
8. Gyoja, F.
   Basic Helix-Loop-Helix Transcription Factors in Evolution: Roles in Development of Mesoderm and Neural Tissues.
   genesis. 55, e23051. (2017) PUBMED
9. Sekigami, Y., Kobayashi, T., Omi, A., Nishitsuji, K., Ikuta, T., Fujiyama, A., Satoh, N., Saiga, H.
   Hox gene cluster of the ascidian, Halocynthia roretzi, reveals several ancient steps of cluster disintegration during ascidian evolution.
   Zoological Letters 3:17. (2017)LINK PUBMED
10. Nakano, H., Miyazawa, H., Maeno, A., Shiroishi, T., Kakui, K., Koyanagi, R., Kanda, M., Satoh, N., Omori, A., Kohtsuka, H.
    A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella
    BMC Evolutionary Biology. 17(1):245.PUBMED

(b) Environmental Genomics

11. Ohno Y, Iguchi A, Shinzato C, Inoue M, Suzuki A, Sakai K, Nakamura T.
    An aposymbiotic primary coral polyp counteracts acidification by active pH regulation.
    Scientific Report 7: 40324. (2017)LINK PUBMED
12. Ponnudurai, R., Kleiner, M., Sayavedra, L., Petersen, J.M., Moche, M., Otto, A., Becher, D., Takeuchi, T., Satoh, N., Dubilier, N., Schweder, T., Markert, S.
    Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis.
    ISME J. 11,463-477. doi: 10.1038/ismej.2016.124. (2017)LINK PUBMED
13. Campbell, M.A., Nielsen, J.G., Sado, T., Shinzato, C., Kanda, M., Satoh, T.P., Miya, M.
    Evolutionary affinities of the unfathomable Parabrotulidae: Molecular data indicate placement of Parabrotula within the family Bythitidae, Ophidiiformes.
    Mol Phylogenet Evol. 109:337-342. (2017)LINK PUBMED
14. Roberts, R.E., Motti, C.A., Baughman, K.B., Satoh, N., Hall, M. R., Cummins, S.
    Identification of putative olfactory G-protein coupled receptors in Crown-of-Thorns starfish, Acanthaster planci.
    BMC Genomics. 18(1):400. (2017) PUBMED
15. Ikeuchi E., Ohno Y., Iguchi A., Nakamura T.
    Non-bleached colonies of massive Porites may attract fishes for selective grazing during mass bleaching events.
    PeerJ. 5:e3470. (2017) PUBMED
16. Matsuyama, T., Yasuike, M., Fujiwara, A., Nakamura, Y., Takano, T., Takeuchi, T., Satoh, N., Adachi, Y., Tsuchihashi, Y., Aoki, H., Odawara, K., Iwanaga, S., Kurita, J., Kamaishi T., Nakayasu, C.
    A Spirochaete is suggested as the causative agent of Akoya oyster disease by metagenomic analysis.
    PLoS ONE 12(8): e0182280. https://doi.org/10.1371/journal.pone.0182280 (2017)LINK PUBMED
17. Nakajima, Y., Wepfer, P.H., Suzuki, S., Zayasu, Y., Shinzato, C., Satoh, N., Mitarai, S.
    Microsatellite markers for multiple Pocillopora genetic lineages offer new insights about coral populations.
    Scientific Reports 2017; 7: 6729.LINK PUBMED
18. Anbutsu, H., Moriyama, M., Nikoh, N., Hosokawa, T., Futahashi, R., Tanahashi, M.,
    Menga, X.Y., Kuriwada, T., Mori, N., Oshima, K., Hattori, M., Fujie, M., Satoh, N., Maeda, T., Shigenobu, S., Koga, R., Fukatsu, T.
    Small genome symbiont underlies cuticle hardness in beetles.
    PNAS 114: E8382–E8391. (2017) PUBMED
19. Takeuchi, T.
    Molluscan Genomics: Implications for Biology and Aquaculture.
    Curr Mol Bio Rep (2017). LINK
20. Higa, H., Shinzato, C., Zayasu, Y., Nagata, T., Kubo, H.
    Restoration efforts for coral reefs by fishery cooperatives ~A case in Onna Village, Okinawa~
    Journal of the Japanese Coral Reef Society 19:119–128 (2017) [in Japanese]

(d) Other Fields

21. Maeda, K., Tsuhako, Y., Tachihara, K.
    Early Development of Mudskippers.
    In Fishes Out of Water: Biology and Ecology of Mudskippers. (pp. 69–88). CRC Press, Taylor & Francis Group (2017) LINK
22. Tran, H.D., Iida, M., Maeda, K.
    Downstream migration of newly-hatched ayu (Plecoglossus altivelis) in the Tien Yen River of northern Vietnam.
    Environmental Biology of Fishes 100: 1329–1341. (2017) LINK
23. Kunishima, T., Maeda, K., Tachihara, K.
    Newly discovered habitat of a threatened goby, Acanthogobius insularis (Perciformes: Gobiidae), in southern part of Okinawa-jima Island, Japan.
    Biogeography 19: 69-74 (2017)

2016

(a) Developmental and Evolutionary Genomics

1. Satoh, N.
   Chordate Origins and Evolution
   Elsevier/Academic Press, 206 pages (2016) LINK
   
2. Yasuoka, Y., Shinzato, C., Satoh, N.
   The mesoderm-forming gene brachyury regulates ectoderm-endoderm demarcation in the coral Acropora digitifera
   Current Biology pii: S0960-9822(16)30923-X. doi: 10.1016/j.cub.2016.08.011. (2016)LINK PUBMED
3. Satoh, N.
   Two decades of ascidian developmental biology: A personal research story.
   Curr. Topics Dev. Biol. 117:289-300 (2016)LINK PUBMED
4. Satoh, N.
   "Evolutionary Origin of Notochord" in "Chordomas.
   Ed, Pamir, M.N. Thieme Publishers. New York. (2016)
5. Takeuchi, T., Yamada, L., Shinzato, C., Sawada, H., Satoh, N.
   Stepwise evolution of coral biomineralization revealed with genome-wide proteomics and transcriptomics
   PLOS ONE 11(6): e0156424. DOI:10.1371/journal.pone.0156424 (2016)LINK PUBMED
6. Marin F, Bundeleva I, Takeuchi T, Immel F, Medakovic D
   Organic matrices in metazoan calcium carbonate skeletons: Composition, functions, evolution
   Journal of Structural Biology doi:10.1016/j.jsb.2016.04.006 (2016)LINK PUBMED
7. Kodama H, Miyata Y, Kuwajima M, Izuchi R, Kobayashi A, Gyoja F, Onuma TA, Kumano G, Nishida H.
   Redundant mechanisms are involved in suppression of default cell fates during embryonic mesenchyme and notochord induction in ascidians.
   Developmental Biology 416: 162-172. doi: 10.1016/j.ydbio.2016.05.033.(2016)LINK PUBMED
8. Suzuki, M., Mori, T., Satoh, N.
   The Ciona intestinalis cleavage clock is independent of DNA methylation.
   Genomics pii: S0888-7543(16)30091-X. doi: 10.1016/j.ygeno.2016.10.001. (2016)PUBMED
9. Session, A.M., Uno, Y., Kwon, T., Chapman, J.A., Toyoda, A., Takahashi, S., Fukui, A., Hikosaka, A., Suzuki, A., Kondo, M., van Heeringen, S.J., Quigley, I., Heinz, S., Ogino, H., Ochi, H., Hellsten, U., Lyons, J.B., Simakov, O., Putnam, N., Stites, J., Kuroki, Y., Tanaka, T., Michiue, T., Watanabe, M., Bogdanovic, O., Lister, R., Georgiou, G., Paranjpe, S.S., van Kruijsbergen, I., Shu, S., Carlson, J., Kinoshita, T., Ohta, Y., Mawaribuchi, S., Jenkins, J., Grimwood, J., Schmutz, J., Mitros, T., Mozaffari, S.V., Suzuki, Y., Haramoto, Y., Yamamoto, T.S., Takagi, C., Heald, R., Miller, K., Haudenschild, C., Kitzman, J., Nakayama, T., Izutsu, Y., Robert, J., Fortriede, J., Burns, K., Lotay, V., Karimi, K., Yasuoka, Y., Dichmann, D.S., Flajnik, M.F., Houston, D.W., Shendure, J., DuPasquier, L., Vize, P.D., Zorn, A.M., Ito, M., Marcotte, E.M., Wallingford, J.B., Ito, Y., Asashima,M., Ueno, N., Matsuda, Y., Veenstra, G.J.C., Fujiyama, A., Harland, R.M., Taira, M., Rokhsar, D.S.
   Genome evolution in the allotetraploid frog Xenopus laevis
   Nature 538, 336–343.LINK PUBMED
10. Watanabe, M., Yasuoka, Y., Mawaribuchi, S., Kuretani, A., Ito, M., Kondo, M., Ochi, H., Ogino, H., Fukui, A., Taira, M., Kinoshita, T.
    Conservatism and variability of gene expression profiles among homeologous transcription factors in Xenopus laevis.
    Dev Biol. pii: S0012-1606(16)30053-7. doi: 10.1016/j.ydbio.2016.09.017.PUBMED

(b) Environmental Genomics

11. Zayasu, Y., Shinzato, C.
    Hope for coral reef rehabilitation: massive synchronous spawning by outplanted corals in Okinawa, Japan.
    Coral Reefs, 35(4), 1295. DOI 10.1007/s00338-016-1463-7 (2016) LINK 
12. Zayasu, Y., Nakajima, Y., Sakai, K., Suzuki, G., Satoh, N., Shinzato, C.
    Unexpectedly complex gradation of coral population structure in the Nansei Islands, Japan.
    Ecology and Evolution. on line. 10.1002/ece3.2296 (2016).LINK PUBMED
13. Hosokawa, T., Ishii, Y., Nikoh, N., Fujie, M., Satoh, N., Fukatsu, T.
    Obligate bacterial mutualists evolving from environmental bacteria in natural insect populations.
    Nature Microbiology, 1:15011 (2016)LINK PUBMED
14. Detree, C., Chabenat, A., Lallier, F.H., Satoh, N., Shoguchi, E., Tanguy, A., Mary, J.
    Multiple I-Type Lysozymes in the Hydrothermal Vent Mussel Bathymodiolus azoricus and Their Role in Symbiotic Plasticity.
    PLoS One 11(2):e0148988. doi: 10.1371/journal.pone.0148988. (2016) PUBMED
15. Nakajima, Y., Zayasu, Y., Shinzato, C., Satoh, N., Mitarai. S.
    Genetic differentiation and connectivity of morphological types of the broadcast-spawning coral Galaxea fascicularis in the Nansei Islands, Japan
    Ecology and Evolution, 6:1457-1469 (2016)LINK PUBMED
16. Mohamed AR, Cumbo V, Harii S, Shinzato C, Chan CX, Ragan MA, Bourne DG, Willis BL, Ball EE, Satoh N, Miller DJ.
    The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome.
    Mol Ecol. doi: 10.1111/mec.13659. (2016)LINK PUBMED
17. Nakajima Y, Shinzato C, Khalturina M, Nakamura M, Watanabe H, Satoh N, Mitarai S.
    The mitochondrial genome sequence of a deep-sea, hydrothermal vent limpet, Lepetodrilus nux, presents a novel vetigastropod gene arrangement.
    Mar Genomics. pii: S1874-7787(16)30030-7. doi: 10.1016/j.margen.2016.04.005. (2016)LINK PUBMED
18. Bhattacharya, D., Agrawal, S., Aranda, M., Baumgarten, S., Belcaid, M., Drake, J.L., Erwin, D., Foret, S., Gates, R.D., Gruber, D.F., Kamel, B., Lesser, M.P., Levy, O., Liew, Y.J., MacManes, M., Mass, T., Medina, M., Mehr, S., Meyer, E., Price, D.C., Putnam, H.M., Qiu, H., Shinzato, C., Shoguchi, E., Stokes, A.J., Tambutté, S., Tchernov, D., Voolstra, C.R., Wagner, N., Walker, C.W., Weber, A.P.M., Weis, V., Zelzion, E., Zoccola, D., Falkowski, P.G.
    Comparative genomics explains the evolutionary success of reef-forming corals.
    eLife 2016;5:e13288, DOI: http://dx.doi.org/10.7554/eLife.13288 (2016)LINK PUBMED
19. Arrigoni, R., Benzoni, F., Huang, D., Fukami, H., Chen, C.A., Berumen, M.L., Hoogenboom, M., Thomson, D.P., Hoeksema, B.W., Budd, A.F., Zayasu, Y., Terraneo, T. I., Kitano, Y.F., Baird, A.H.
    When forms meet genes: revision of the scleractinian genera Micromussa and Homophyllia (Lobophylliidae) with a description of two new species and one new genus.
    Contributions to Zoology, 85 (4): 387-422. (2016) LINK 
20. Omori, M., Higa, Y., Shinzato, C., Zayasu, Y., Nagata, T., Nakamura, R., Yokokura, A., Janadou, S.
    Development of active restoration methodologies for coral reefs using asexual reproduction in Okinawa, Japan.
    Proceeding of the 13th International Coral Reef Symposium: 369–387 (2016)

(c) Functional Genomics

21. Nishitsuji, K., Arimoto, A., Iwai, K., Sudo, Y., Hisata, K., Fujie, M., Arakaki, N., Kushiro, T., Konishi, T., Shinzato, C., Satoh, N., Shoguchi, E.
    A draft genome of the brown alga, Cladosiphon okamuranus, S-strain: a platform for future studies of 'mozuku' biology.
    DNA research pii: dsw039 (2016)LINK PUBMED
22. Takeuchi, T., Koyanagi, R., Gyoja, F., Kanda, M., Hisata, K., Fujie, M., Goto, H., Yamasaki, S., Nagai, K., Morino, Y., Miyamoto, H., Endo, K., Endo, H., Nagasawa, H., Kinoshita., S., Asakawa, S., Watabe, S., Satoh, N., Kawashima, T.
    Bivalve-specific gene expansion in the pearl oyster genome: Implications of adaptation to a sessile lifestyle
    Zoological Letters, 2:3 (2016)LINK PUBMED

(d) Other Fields

23. Katsuyama Y, Sone K, Satou R, Izumikawa M, Takagi M, Fujie M, Satoh N, Shin-Ya K, Ohnishi Y.
    Involvement of the Baeyer-Villiger Monooxygenase IfnQ in the Biosynthesis of Isofuranonaphthoquinone Scaffold of JBIR-76 and -77.
    Chembiochem. 2;17(11):1021-8. doi: 10.1002/cbic.201600095. (2016) PUBMED
24. Du D, Katsuyama Y, Onaka H, Fujie M, Satoh N, Shin-Ya K, Ohnishi Y.
    Production of a Novel Amide-Containing Polyene by Activating a Cryptic Biosynthetic Gene Cluster in Streptomyces sp. MSC090213JE08.
    Chembiochem. 3;17(15):1464-71. doi: 10.1002/cbic.201600167. (2016) PUBMED
25. Iida, M., Kondo, M., Tabouret, H., Maeda, K., Pécheyran, C., Hagiwara, A., Keith, P., Tachihara, K.
    Specific gravity and migratory patterns of amphidromous gobioid fish from Okinawa Island, Japan Journal of Experimental Marine Biology and Ecology, 486: 160–169. (2016) LINK
26. 前田健（KenMaeda）
    両側回遊とは？バリエーションから考える（What is amphidromy? A discussion of various migration patterns）
    海洋と生物（Aquabiology）38 (4): 350-355 (2016) LINK

2015

(a) Developmental and Evolutionary Genomics

1. Simakov, O., Kawashima, T., Marlétaz, F., Jenkins, J., Koyanagi, R., Mitros, T., Hisata, K., Bredeson, J., Shoguchi, E., Gyoja, F., Yue, J.X., Chen, Y.C., Robert M. Freeman, R.M., Sasaki, A.,Hikosaka-Katayama, T., Sato, A., Fujie, M., Baughman, K.W., Levine, J., Paul Gonzalez, P., Cameron, C., Fritzenwanker, J.H., Pani, A.M., Goto, H., Kanda, M., Arakaki, N., Yamasaki, S., Qu, J., Cree, A., Ding, Y., Dinh, H.H., Dugan, S., Holder, M., Jhangiani, S.N., Kovar, C.L., Lee, S.L., Lewis, L.R., Morton, D., Nazareth, L.V., Okwuonu, G., Santibanez, J., Chen, R., Richards, S., Muzny, D.M., Gillis, A., Peshkin, L., Wu, M., Humphreys, T., Su, Y.H., Putnam, N.H., Schmutz, J., Fujiyama, A., Yu, J.K., Tagawa, K., Worley, K.C., Gibbs, R.A., Kirschner, M.W., Christopher J. Lowe, C.J., Satoh, N., Rokhsar, D.S., Gerhart, J.
   Hemichordate genomes and deuterostome origins
   Nature 527(7579):459-65. (2015)PUBMED LINK
2. Luo, Y.J., Takeuchi, T., Koyanagi, R., Yamada, L., Kanda, M., Khalturina, M., Fujie, M., Yamasaki, S., Endo, K., Satoh, N.
   The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization.
   Nature Communications, 18;6:8301. doi: 10.1038/ncomms9301. (2015)PUBMED LINK
3. Kawai, N., Ogura, Y., Ikuta, T., Saiga, H., Hamada, M., Sakuma, T., Yamamoto, T., Satoh, N., Sasakura, Y.
   Hox10-regulated endodermal cell migration is essential for development of the ascidian intestine.
   Developmental Biology, S0012-1606(15)00169-4. doi: 10.1016/j.ydbio.2015.03.018. (2015). PUBMED 
4. Hamada, M., Goricki, S., Byerly, M.S., Satoh, N., Jeffery, W.R.
   Evolution of the chordate regeneration blastema: Differential gene expression and conserved role of notch signaling during siphon regeneration in the ascidian Ciona
   Developmental Biology 15;405(2):304-15. (2015) PUBMED 
5. Kraus, J.E.M., Fredman, D., Wang, W., E., Khalturin, K., Technau, U.
   Adoption of conserved developmental genes in development and origin of the medusa body plan.
   EvoDevo, 6:23 (2015) PUBMED 
6. Luo, Y.J., Satoh, N., Endo, K.
   Mitochondrial gene order variation in the brachiopod Lingula anatina and its implications for mitochondrial evolution in lophotrochozoans.
   Marine Genomics, pii: S1874-7787(15)30021-0. doi: 10.1016/j.margen.2015.08.005. (2015)PUBMED LINK
7. Alié, A., Hayashi, T., Sugimura, I., Manuel, M., Sugano, W., Mano, A., Satoh, N., Agata, K., Funayama, N.
   The ancestral gene repertoire of animal stem cells
   PNAS 112(51):E7093-100 doi: 10.1073/pnas.1514789112 (2015) onlineLINK PUBMED

(b) Environmental Genomics

8. Maruyama, S., Shoguchi, E., Satoh, N., Minagawa, J.
   Diversification of light harvesting complex gene family via intra- and intergenic duplications in the coral symbiotic alga Symbiodinium.
   PLoS One 10(3):e0119406. (2015) PUBMED 
9. Nakajima, Y., Shinzato, C., Satoh, N., Mitarai S.
   Novel Polymorphic Microsatellite Markers Reveal Genetic Differentiation between Two Sympatric Types of Galaxea fascicularis.
   PLoS One. 10(7):e0130176. (2015) PUBMED 
10. Shoguchi, E., Shinzato, C., Hisata, K., Satoh, N., Mungpakdee, S.
    The Large Mitochondrial Genome of Symbiodinium minutum Reveals Conserved Noncoding Sequences between Dinoflagellates and Apicomplexans..
    Genome Biol Evol. 20;7(8):2237-44. (2015) PUBMED 
11. Sato, A., Kawashima, T., Fujie, M., Hughes, S., Satoh, N., Shimeld, S.
    Molecular basis of canalization in an ascidian species complex adapted to different thermal conditions.
    Science Reports 18;5:16717 (2015) PUBMED 
12. Shinzato, C., Mungpakdee, S., Arakaki, N., Satoh, N.
    Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago
    Scientific Reports 5, Article number: 18211 (2015) doi:10.1038/srep18211LINK PUBMED 
13. Zayasu, Y., Miyazaki, K., Lien, Y.T., Okubo, N.
    Direct evidence of sexual reproduction in the zebra coral, Oulastrea crispata (Anthozoa, Scleractinia), in Japan
    Invertebrate Reproduction and Development 59: 61-65 (2015) DOI: 10.1080/07924259.2015.1006340 LINK
14. Sayavedra, L., Kleiner, M., Ponnudurai, R., Wetzel, S., Pelletier, E., Barbe, V., Satoh, N., Shoguchi, E., Fink, D., Breusing, C., Reusch, T.B., Rosenstiel, P., Schilhabel, M.B., Becher, D., Schweder, T., Markert, S., Dubilier, N, Petersen, J.M.
    Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels.
    Elife. 15;4. pii: e07966. doi: 10.7554/eLife.07966. (2015). PUBMED 

(c) Functional genomics

15. Shin-ya, K., Izumikawa, M., Kozone, I., Hashimoto, J., Kagaya, N., Takagi, M., Koiwai, H., Komatsu, M., Fujie, M., Satoh, N., Ikeda, H.
    Novel thioviridamide derivative-JBIR-140-heterologous expression of the gene cluster for thioviridamide biosynthesis.
    Journal of Antibiotics, 68(8):533-6. doi: 10.1038/ja.2015.20. (2015). PUBMED 
16. Ohno, S., Katsuyama, Y., Tajima, Y., Izumikawa, M., Takagi, M., Fujie, M., Satoh, N., Shin-ya, K., Yasuo Ohnishi, Y.
    Identification and characterization of the streptazone E biosynthetic gene cluster in Streptomyces sp.
    ChemBioChem 16(16):2385-91. (2015)PUBMED 
17. Beedessee, G., Hisata, K., Roy, M.C., Satoh, N., Shoguchi, E.
    Multifunctional polyketide synthase genes identified by genomic survey of the symbiotic dinoflagellate, Symbiodinium minutum.
    BMC Genomics 16:941(2015)LINK PUBMED 
18. Ohno S, Katsuyama Y, Tajima Y, Izumikawa M, Takagi M, Fujie M, Satoh N, Shin-Ya K, Ohnishi Y.
    Identification and Characterization of the Streptazone E Biosynthetic Gene Cluster in Streptomyces sp. MSC090213JE08.
    Chembiochem. 16(16):2385-91. doi: 10.1002/cbic.201500317. (2015)LINK PUBMED 

(d) Other Fields (Fish taxonomy and ecology)

19. Maeda, K., Tran, H.D., Tan, H.H.
    Discovery of a substantial continental population of the subfamily Sicydiinae (Gobioidei: Gobiidae) from Vietnam: Taxonomic revision of the genus Stiphodon from the western South China Sea.
    Raffles Bulletin of Zoology 63: 246–258 (2015) PDF
20. Lord C., Maeda K., Keith P., Watanabe S.
    Population structure of the Asian amphidromous Sicydiinae goby, Stiphodon percnopterygionus, inferred from mitochondrial COI sequences, with comments on larval dispersal in the northwest Pacific Ocean.
    Life and Environment, 65: 63–71. (2015) LINK
21. Maeda, K., Palla, H.P.
    A new species of the genus Stiphodon from Palawan, Philippines (Gobiidae: Sicydiinae)
    Zootaxa 4018 (3): 381–395. (2015)PUBMED LINK
22. Maeda, K., Iida, M., Kondo, M.
    Diversity of larval dispersal strategies in freshwater and estuarine gobies
    Mochioka, N., Kinoshita, I., Minami, T. (eds) Early life history of fishes, Kouseisha-Kouseikaku, Tokyo. pp. 89–101(2015)
23. Keith, P., Lord, C., and Maeda, K.
    Indo-Pacific Sicydiine gobies: Biodiversity, life traits and conservation
    Publisher: Société Française d’Ichtyologie, Paris (2015) LINK
    

2014

1. Satoh N.
   Developmental Genomics of Ascidians.
   Wiley Brackwell, New York. (2014) LINK
   
2. Satoh, N., Rokhsar, D., Nishikawa, T.
   Chordate evolution and the three-phylum system.
   Proc. R. Soc. B. 281:1794 (2014) LINK

(a) Environmental Genomics

3. Shinzato, C., Yasuoka, Y., Mungpakdee, D., Arakaki, N., Fujie, M., Nakajima, Y., Satoh, N.
   Development of novel, cross-species microsatellite markers for Acropora corals using next-generation sequencing technology.
   Front. Mar. Sci., doi: 10.3389/fmars.2014.00011 (2014) LINK
4. Mungpakdee, S., Shinzato, C., Takeuchi, T., Kawashima, T., Koyanagi, R., Hisata, K., Tanaka, M., Goto, H., Fujie, M., Lin, S., Satoh, N., and Shoguchi, E.
   Massive gene transfer and extensive RNA editing of a symbiotic dinoflagellate plastid genome.
   Genome Biol Evol. 6(6):1408-22. doi: 10.1093/gbe/evu109. (2014) PUBMED
5. Shinzato C, Inoue M, Kusakabe M.
   A snapshot of a coral “holobiont”: A transcriptome assembly of the scleractinian coral, Porites, captures a wide variety of genes from both the host and symbiotic zooxanthellae.
   PLoS ONE 9(1): e85182. (2014)PUBMED LINK
6. Shinzato, C., Mungpakdee, S., Satoh, N., Shoguchi, E.
   A genomic approach to coral-dinoflagellate symbiosis: Studies of Acropora digitifera and Symbiodinium minutum. Frontier in Microbiology. doi: 10.3389/fmicb.2014.00336. (2014)PUBMED LINK
7. Tsuta H, Shinzato C, Satoh N, Hidaka M.
   Telomere Shortening in the Colonial Coral Acropora digitifera During Development.
   Zoolog Sci 31(3):129-34. (2014) PUBMED
8. Nakajima Y., Shinzato, C., Inagaki, F., Satoh, N., Khalturina, M., Mitarai, S.
   Cross-species, amplifiable microsatellite markers for neoverrucid barnacles from deep-sea hydrothermal vents developed using next-generation sequencing.
   Int. J. Mol. Sci. 2014, 15, 14364-14371; doi:10.3390/ijms150814364 (2014) LINK
9. Bosch,T.C.G., Adamska, M., Augustin, R., Domazet-Loso, T., Foret, S., Fraune, S., Funayama, N., Grasis, J., Hamada, H., Hatta, M., Hobmayer, B., Kawai, K., Klimovich, A., Manuel, M., Shinzato, C., Technau, U., Yum, S., J. Miller, D.J.
   How do environmental factors influence life cycles and development? An experimental framework for early-diverging metazoans.
   Bioessays. 36, 1185-1194 (2014) PUBMED

(b) Developmental Evolutionary Genomics

10. GIGA Community of Scientists, Bracken-Grissom H, Collins AG, Collins T, Crandall K, Distel D, Dunn C, Giribet G, Haddock S, Knowlton N, Martindale M, Medina M, Messing C, O'Brien SJ, Paulay G, Putnam N, Ravasi T, Rouse GW, Ryan JF, Schulze A, Wörheide G, Adamska M, Bailly X, Breinholt J, Browne WE, Diaz MC, Evans N, Flot JF, Fogarty N, Johnston M, Kamel B, Kawahara AY, Laberge T, Lavrov D, Michonneau F, Moroz LL, Oakley T, Osborne K, Pomponi SA, Rhodes A, Santos SR, Satoh N, Thacker RW, Van de Peer Y, Voolstra CR, Welch DM, Winston J, Zhou X.
    The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.
    J Hered 105(1):1-18. (2014) PUBMED
11. Fuchs B, Wang W, Graspeuntner S, Li Y, Insua S, Herbst EM, Dirksen P, Böhm AM, Hemmrich G, Sommer F, Domazet-Lošo T, Klostermeier UC, Anton-Erxleben F, Rosenstiel P, Bosch TC, Khalturin K.
    Regulation of polyp-to-jellyfish transition in Aurelia aurita.
    Curr Biol. 24:263-73. (2014) PUBMED
    
12. Yasuoka, Y., Suzuki, Y., Takahashi S., Someya, H., Sudou, N., Haramoto, Y., Cho, K.W., Asashima, M., Sugano, S., Taira, M.
    Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification.
    Nature communications, DOI: 10.1038/ncomms5322. (2014)PUBMED LINK
13. Iitsuka T, Mita K, Hozumi A, Hamada M, Satoh N, Sasakura Y.
    Transposon-mediated targeted and specific knockdown of maternally expressed transcripts in the ascidian Ciona intestinalis.
    Sci Rep. doi: 10.1038/srep05050. (2014) PUBMED
14. Gyoja F.
    A genome-wide survey of bHLH transcription factors in the Placozoan Trichoplax adhaerens reveals the ancient repertoire of this gene family in metazoan..
    Gene 542:29-37. (2014) PUBMED
15. Tagawa K, Arimoto A, Sasaki A, Izumi M, Humphreys T, Fujiyama A, Kagoshima H, Shin-I T, Kohara Y, Satoh N, Kawashima T.
    A cDNA resource for gene expression studies of a hemichordate, Ptychodera flava.
    Zool. Sci., 31(7):414-20. (2014) PUBMED
16. Ebchuqin E, Yokota N, Yamada L, Yasuoka Y, Akasaka M, Arakawa M, Deguchi R, Mori T, Sawada H.
    Evidence for participation of GCS1 in fertilization of the starlet sea anemone Nematostella vectensis: Implication of a common mechanism of sperm-egg fusion in plants and animals.
    Biochem Biophys Res Commun. 5;451(4):522-528. doi: 10.1016/j.bbrc.2014.08.006. (2014) PUBMED
17. Satou Y, Hirayama K, Mita K, Fujie M, Chiba S, Yoshida R, Endo T, Sasakura Y, Inaba K, Satoh N.
    Sustained heterozygosity across a self-incompatibility locus in an inbred ascidian.
    Mol Biol Evol. on line. (2014) PUBMED
18. Baughman KW, McDougall C, Cummins SF, Hall M, Degnan BM, Satoh N, Shoguchi E.
    Genomic organization of Hox and ParaHox clusters in the echinoderm, Acanthaster planci.
    Genesis. , 52(12): 952-8. (2014) PUBMED
19. Satoh N, Tagawa K, Lowe CJ, Yu JK, Kawashima T, Takahashi H, Ogasawara M, Kirschner M, Hisata K, Su YH, Gerhart J
    On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates
    genesis, 52(12): 925–934 (2014) LINK

(c) Functional genomics

20. Gusev O, Suetsugu Y, Cornette R, Kawashima T, Logacheva MD, Kondrashov AS, Penin AA, Hatanaka R, Kikuta S, Shimura S, Kanamori H, Katayose Y, Matsumoto T, Shagimardanova E, Alexeev D, Govorun V, Wisecaver J, Mikheyev A, Koyanagi R, Fujie M, Nishiyama T, Shigenobu S, Shibata TF, Golygina V, Hasebe M, Okuda T, Satoh N, Kikawada T.
    Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge.
    Nat Commun. 12;5:4784. doi: 10.1038/ncomms5784. (2014) PUBMED

(d) Other Fields (Fish taxonomy and ecology)

21. Maeda K.
    51 species in “Gobioidei (pp 1215–1339)” Okiyama M. (ed) An Atlas of Early Stage Fishes in Japan Second Edition
    Tokai University Press, Japan (2014)
22. Maeda K.
    Stiphodon niraikanaiensis, a new species of sicydiine goby from Okinawa Island (Gobiidae: Sicydiinae).
    Ichthyological Research, 61: 99-107 (2014)LINK
23. Maeda K, Tachihara K.
    Larval fish fauna of a sandy beach and an estuary on Okinawa Island, focusing on larval habitat utilization by the suborder Gobioidei.
    Fish Sci 80: 1215–1229 (2014)LINK

2013

1. Shoguchi, E., Shinzato, C., Kawashima, T., Gyoja, F., Mungpakdee, S., Koyanagi, R., Takeuchi, T., Hisata, K., Tanaka, M., Fujiwara, M., Hamada, M., Azadeh, S., Fujie, M., Usami, T., Goto, H., Yamasaki, S., Arakaki, N., Suzuki, Y., Sugano, S., Toyoda, A., Kuroki, Y., Fujiyama, A., Medina, M., Coffroth, M. A., Bhattacharya, D., and Satoh, N.
   Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure.
   Current Biology 23, 1399-1408. (2013) PUBMED
2. Husnik, F., Nikoh, N., Koga, R., Ross, L., Duncan, R. P., Fujie, M., Tanaka, M., Satoh, N., Bachtrog, D., Wilson, A. C. C., Dohlen, C. D., Fukatsu, T., and McCutcheon, J. P.
   Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis.
   Cell 153, 1567–1578. (2013) PUBMED
   
3. Shoguchi, E., Tanaka, M., Shinzato, C., Kawashima, T., Satoh, N.
   A genome-wide survey of photoreceptor and circadian genes in the coral, Acropora digitifera.
   Gene 515: 426–431. (2013) PUBMED
4. Hamada, M., Shoguchi, E., Shinzato, C., Kawashima, T., Miller, D. J., Satoh, N.
   The complex NOD-like receptor repertoire of the coral Acropora digitifera includes novel domain combinations.
   Mol Biol Evol. 30(1):167-76. (2013) PUBMED
5. Ikuta, T., Chen, Y.C., Annunziata, R., Ting, H.C., Tung, C., Koyanagi, R., Tagawa, K., Humphreys, T., Fujiyama, A., Saiga, H., Satoh, N., Yu, J. K., Arnone, M.I., Su, Y.H.
   Identification of an intact ParaHox cluster with temporal colinearity but altered spatial colinearity in the hemichordate Ptychodera flava.
   BMC Evolutionary Biology 13:129. (2013)LINK PUBMED
6. Kobayashi, K., Yamada, L., Satou, Y., Satoh, N.
   Differential gene expression in notochord and nerve cord fate segregation in the Ciona intestinalis embryo.
   Genesis 51:647–659. (2013) PUBMED
7. Matsumae ,H., Hamada, M., Fujie, M., Niimura, Y., Tanaka, H., Kawashima, T.
   A methodical microarray design enables surveying of expression of a broader range of genes in Ciona intestinalis.
   Gene 519: 82-90. (2013) PUBMED
8. Takeuchi, T., Kawashima, T., Koyanagi, R., Satoh, N.
   The genome of the Japanese pearl oyster, Pinctada fucata.
   In "Recent Advances in Pearl Research".Eds. S. Watabe, K. Maeyama, H. Nagasawa, TERRAPUB, Tokyo (2013)
9. Kawashima, T., Takeuchi, T., Koyanagi, R., Kinoshita, S., Endo, H., Endo, K.
   Initiating the Mollusk Genomics Annotation Community: Toward Creating the Complete Curated Gene-Set of the Japanese Pearl Oyster, Pinctada fucata
   Zoological Science 30: 794–796. (2013) LINK
   
10. Koyanagi, R., Takeuchi, T., Hisata, K., Gyoja, F., Satoh, N., Kawashima, T.
    MarinegenomicsDB: An integrated genome viewer for community-based annotation of genomes.
    Zoological Science 30: 797–800. (2013)LINK PUBMED
11. Miyamoto, H., Endo, H., Hashimoto, N., Iimura, K., Isowa, Y., Kinoshita, S., Kotaki, R., Masaoka, T., Miki, T., Nakayama, S., Nogawa, C., Notozawa, A., Ohmori, F., Sarashina, I., Suzuki, M., Takagi, R., Takahashi, J., Takeuchi, T., Yokoo, N., Satoh, N., Toyohara, H., Miyashita, T., Wada, H., Samata, T., Endo, K., Nagasawa, H., Asakawa, S., Watabe, S.
    The diversity of shell matrix proteins: genome-wide investigation of the pearl oyster Pinctada fucata.
    Zoological Science 30: 801–816. (2013)LINK PUBMED
12. Morino, Y., Okada, K., Niikura, M., Honda, M., Satoh, N., Wada, H.,
    A genome-wide survey of genes encoding transcription factors in the Japanese pearl oyster, Pinctada fucata: I. Homeobox genes.
    Zoological Science 30: 851–857. (2013)LINK PUBMED
13. Matsumoto, T., Masaoka, T., Fujiwara, Y., Nakamura, Y., Kinoshita, S., Satoh, N., Awaji, M.
    Reproduction-related genes in the pearl oyster genome.
    Zoological Science 30: 826–850. (2013)LINK PUBMED
14. Koga, H., Hashimoto, N., G. Suzuki, D., Ono, H., Yoshimura, M., Suguro, T., Yonehara, Y., Abe, T., Satoh, N., Wada, H.
    A genome-wide survey of genes encoding transcription factors in Japanese pearl oyster Pinctada fucata II. Tbx, Fox, Ets, HMG, NFκB, bZIP and C2H2 Zinc fingers.
    Zoological Science 30: 858–867. (2013)LINK PUBMED
15. Gyoja, F., Satoh, N.
    Evolutionary aspects of variability in bHLH orthologous families: insights from the pearl oyster Pinctada fucata.
    Zoological Science 30: 868–876. (2013)LINK PUBMED
16. Shoguchi, E., Tanaka, M., Takeuchi, T., Shinzato, C., Satoh, N.
    Probing a coral genome for components of the photo-protective scytonemin biosynthetic pathway and the 2-aminoethylphosphonate pathway.
    Marine Drugs, 11(2):559-70. (2013) PUBMED
17. Sota, T., Konuma, J., Fujiwara, M., Shoguchi, E.
    Genome sizes of three species in the subtribe Carabina (Coleoptera: Carabidae)
    Entomological Science 16: 122-124. (2013) LINK
18. Satoh, N.
    Ciona: a Model for Developmental Genomics
    Encyclopedia of Life Sciences on line. (2013)LINK
19. Kondo, M., Maeda, K., Hirashima, K., Tachihara, K.
    Comparative larval development of three amphidromous Rhinogobius species making reference to their habitat preferences and migration biology.
    Marine & Freshwater Research 64:249-466. (2013)LINK
20. Maeda K., Tan H.H.
    Review of Stiphodon (Gobiidae: Sicydiinae) from western Sumatra, with description of a new species.
    Raffles Bulletin of Zoology 62:749-761. (2013) LINK
21. Nishi,S., Tsubouchi, T., Takaki, Y., Koyanagi, R., Satoh, N., Maruyama, T., Hatada, Y.
    Draft genome sequence of Loktanella cinnabarina LL-001^T, isolated from deep-sea floor sediment.
    Genome Announcements, 1(6) doi: 10.1128/genomeA.00927-13. (2013) PUBMED
22. Maeda, K., Saeki, T.
    First record of a sicydiine goby, Stiphodon multisquamus (Actinopterygii: Gobioidei: Gobiidae), from Okinawa Island, Japan.
    Species Diversity 18:215–221. (2013) LINK
23. Zhang QJ, Luo YJ, Wu HR, Chen YT, Yu JK.
    Expression of germline markers in three species of amphioxus supports a preformation mechanism of germ cell development in cephalochordates.
    EvoDevo 4, 17, doi:10.1186/2041-9139-4-17 (2013).

2012

1. Takeuchi, T., Kawashima, T., Koyanagi, R., Gyoja, F., Tanaka, M., Ikuta, T., Shoguchi, E., Fujiwara, M., Shinzato, C., Hisata, K., Fujie, M., Usami, T., Nagai, k., Maeyama, K., Okamoto, K., Aoki, H., Ishikawa, T., Masaoka, T., Fujiwara, A., Endo, K., Endo, H., Nagasawa, H., Kinoshita, S., Asakawa, S., Watabe, S., and Satoh, N.
   Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology
   DNA Research 19: 117-130. (2012)PUBMED  LINK
2. Freeman R, Ikuta T, Wu M, Koyanagi R, Kawashima T, Tagawa K, Humphreys T, Fang GC, Fujiyama A, Saiga H, Lowe C, Worley K, Jenkins J, Schmutz J, Kirschner M, Rokhsar D, Satoh N, Gerhart J.
   Identical Genomic Organization of Two Hemichordate Hox Clusters.
   Current Biology 22: 2053–2058. (2012) PUBMED
3. Satoh, N., Tagawa, K., and Takahashi, H.
   How was the notochord born?
   Evolution & Development 14:56-75. (2012)PUBMED  LINK
4. Sasakura,Y., Kanda, M., Ikeda, T., Horie, T., Kawai, N., Ogura, Y., Yoshida, Y., Hozumi, A., Satoh, N., and Fujiwara, S.
   Retinoic acid-driven Hox1 is required in the epidermis for forming the otic/atrial placode during ascidian metamorphosis
   Development 139: 2156-2160. (2012)  PUBMED  LINK
5. Satou,Y., SHin-i. T., Kohara, Y., Satoh, N., and Chiba, S.
   A genomic overview of short genetic variations in a basal chordate, Ciona intestinalis
   BMC Genomics 13:208. (2012)  PUBMED  LINK
6. Shinzato, C., Shoguchi, E., Tanaka, M., and Satoh, N.
   Fluorescent Protein Candidate Genes in the Coral Acropora digitifera Genome.
   Zoolog Sci 29: 260-264. (2012) PUBMED 
   
7. DuBuc, T. Q., Ryan, J. F., Shinzato, C., Satoh, N., and Martindale, M. Q.
   Coral comparative genomics reveal expanded Hox Cluster in the Cnidarian–Bilaterian Ancestor
   Integrative and Comparative Biology. on line. (2012) LINK
8. Shinzato, C., Hamada, M., Shoguchi, E., Kawashima, T., Satoh, N..
   The Repertoire of Chemical Defense Genes in the Coral Acropora digitifera Genome.
   Zoolog Sci., 29(8):510-7. (2012) PUBMED
9. Gyoja, F., Kawashima, T. and Satoh, N.
   A genomewide survey of bHLH transcription factors in the coral Acropora digitifera identifies three novel orthologous families, pearl, amber, and peridot.
   Dev Genes Evol 222: 63-76. (2012) PUBMED
10. Taillebois, L., Maeda, K., Vigne, S., and Keith, P.
    Pelagic larval duration of three amphidromous Sicydiinae gobies (Teleostei: Gobioidei) including widespread and endemic species
    Ecology of Freshwater Ecology of Freshwater Fish 21: 552-559. (2012) LINK
    
11. Feutry, P., Tabouret, H., Maeda, K., Pécheyran, C., and Keith, P.
    Diadromous life cycle and behavioural plasticity in freshwater and estuarine Kuhliidae species (Teleostei) revealed by otolith microchemistry
    Aquatic Biology, 15: 195-204. (2012) LINK
12. Kondo, M., Maeda, K., Yamasaki, N., and Tachihara, K.
    Spawning habitat and early development of Luciogobius ryukyuensis (Gobiidae).
    Enviromental biology of Fishes 95(2): 291-300. (2012) LINK
13. Sato, A., Satoh, N. and Bishop, J. D.
    Field identification of ‘types’ A and B of the ascidian Ciona intestinalis in a region of sympatry.
    Marine Biology 159: 1611-1619. (2012) LINK
14. Morino Y, Koga H, Tachibana K, Shoguchi E, Kiyomoto M, Wada H.
    Heterochronic activation of VEGF signaling and the evolution of the skeleton in echinoderm pluteus larvae.
    Evolution and Development 14(5):428-36. (2012) PUBMED
15. Kume S, Ueki T, Matsuoka H, Hamada M, Satoh N, Michibata H.
    Differential gene regulation by V(IV) and V (V) ions in the branchial sac, intestine, and blood cells of a vanadium-rich ascidian, Ciona intestinalis.
    Biometals Oct;25(5):1037-50. (2012) PUBMED
16. Takeuchi, T., Kawashiwa, T., Koyanagi, R., Masaoka, T., Satoh, N.
    Genome-wide survey of genetic markers in the Japanese pearl oyster, Pinctada fucata.
    DNA鑑定 4: 81-85. (2012)
17. Maeda, K., Mukai, T., and Tachihara, K.
    A new species of amphidromous goby, Stiphodon alcedo, from the Ryukyu Archipelago (Gobiidae: Sicydiinae)
    Cybium 35(4): 285-298. (2012) LINK
18. Maeda, K., Yoshino, T., and Tachihara, K.
    A redescription of Stiphodon pulchellus (Herre, 1927) (Gobiidae: Sicydiinae)
    Cybium 35(4): 319-328. (2012) LINK
19. Yamasaki, N., Kondo, M., Maeda, K., and Tachihara, K.
    Reproductive biology of three amphidromous gobies, Sicyopterus japonicus, Awaous melanocephalus, and Stenogobius sp., on Okinawa Island
    Cybium 35(4): 345-359. (2012) LINK

2011

1. Shinzato, C., Shoguchi, E., Kawashima, T., Hamada, M., Hisata, K., Tanaka, M., Fujie, M., Fujiwara, M., Koyanagi, R., Ikuta, T., Fujiyama, A., Miller, D. J., and Satoh, N.
   Using the Acropora digitifera genome to understand coral responses to environmental change.
   Nature, 476(7360):320-323. (2011) PUBMED 
2. Horie, T., Shinki, R., Ogura, Y., Kusakabe, T. G., Satoh, N., and Sasakura, Y.
   Ependymal cells of chordate larvae are stem-like cells that form the adult nervous system.
   Nature 469 (7331):525-528. (2011) PUBMED
3. Ogura, Y., Sakaue-Sawano, A., Nakagawa, M., Satoh, N., Miyawaki, A., and Sasakura, Y. 2011.
   Coordination of mitosis and morphogenesis: role of a prolonged G2 phase during chordate neurulation.
   Development, 138(3):577-587. (2011) PUBMED
4. Yamada, S., Ueno, N., Satoh, N., and Takahashi, H.
   Ciona intestinalis Noto4 contains a phosphotyrosine interaction domain and is involved in the midline interaction of notochord cells.
   Intern. J. Dev. Biol., 55(1):11-18. (2011) PUBMED
5. Hamada, M., Shimozono, N., Ohta, N., Satou, Y., Horie, T., Kawada, T., Satake, H., Sasakura, Y., and Satoh, N.
   Expression of Neuropeptide- and Hormone-Encoding Genes in the Ciona intestinalis Larval Brain
   Dev. Biol., 352(2):202-214. (2011) PUBMED
6. Shoguchi, E., Fujie, M., and Hamada, M.
   No chromosomal clustering of housekeeping genes in the marine chordate Ciona intestinalis
   Marine Genomics, 4 (3):151-157. (2011) PUBMED
7. Shoguchi, E., Hamada, M., Fujie, M., and Satoh, N.
   Direct examination of chromosomal clustering of organ-specific genes in the chordate Ciona intestinalis
   Genesis, 49(8):662-72. (2011) PUBMED
8. Nakashima, K., Nishino, A., Horikawa, Y., Hirose, E., Sugiyama, J., and Satoh, N.
   The crystalline phase of cellulose changes under developmental control in a marine choradte.
   Cellular and Molecular Life Science, 68(9):1623-1631. (2011) PUBMED
9. Satoh, N.
   Tunicate embryos and cell specification (version 2.0)
   Encyclopedia of Life Sciences (2011) LINK
10. Maeda, K., Mukai, T., and Tachihara, K.
    Newly collected specimens of the sleeper Eleotris acanthopoma (Teleostei: Eleotridae) from French Polynesia indicate a wide and panmictic distribution in the West and South Pacific
    Pacific Science 65: 257–264 (2011) LINK
11. Nakashima, K., Nishino, A., Hirose, E.
    Forming a tough shell via an intracellular matrix and cellular junctions in the tail epidermis of Oikopleura dioica (Chordata: Tunicata: Appendicularia).
    Naturwissenschaften98(8): 661-669. (2011) PUBMED
    
12. Yoshida, M. A., Ishikura, Y., Moritaki, T., Shoguchi, E., Shimizu, K. K., Sese, J., Ogura, A.
    Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation.
    Gene 483 (1-2):63-71. (2011) PUBMED
13. Iguchi, A., Shinzato, C., Foret, S., and Miller, D. J.
    Identification of Fast-Evolving Genes in the Scleractinian Coral Acropora Using Comparative EST Analysis.
    PLoS One 6 (6):e20140. (2011) PUBMED
14. Ikuta, T.
    Evolution of Invertebrate Deuterostomes and Hox/ParaHox Genes.
    Genomics, Proteomics & Bioinformatics vol.9 issue3 p.77-76. (2011) PUBMED
15. Katayama, T., Wilkinson, M. D., Vos, R., Kawashima, T., Kawashima, S., Nakao, M., Yamamoto, Y., Chun, H. W., Yamaguchi, A., Kawano, S., Aerts, J., Aoki-Kinoshita, K. F., Arakawa, K., Aranda, B., Bonnal, R. J., Fernandez, J. M., Fujisawa, T., Gordon, P. M., Goto, N., Haider, S., Harris, T., Hatakeyama, T., Ho, I., Itoh, M., Kasprzyk, A., Kido, N., Kim, Y. J., Kinjo, A. R., Konishi, F., Kovarskaya, Y., von Kuster, G., Labarga, A., Limviphuvadh, V., McCarthy, L., Nakamura, Y., Nam, Y., Nishida, K., Nishimura, K., Nishizawa, T., Ogishima, S., Oinn, T., Okamoto, S., Okuda, S., Ono, K., Oshita, K., Park, K. J., Putnam, N., Senger, M., Severin, J., Shigemoto, Y., Sugawara, H., Taylor, J., Trelles, O., Yamasaki, C., Yamashita, R., Satoh, N., and Takagi, T.
    The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.
    J Biomed Semantics 2 (1):4. (2011) PUBMED
16. Shinzato, C. and Satoh, N.
    A review for the coral genome paper, "Using the Acropora digitifera genome to understand coral responses to environmental change."
    First Author's, online publication (2011) LINK
17. Onimaru, K., Shoguchi, E., Kuratani, S., and Tanaka, M. 2011.
    Development and evolution of the lateral plate mesoderm: Comparative analysis of amphioxus and lamprey with implications for the acquisition of paired fins.
    Developmental Biology, 359(1):124-136. (2011) PUBMED
18. Hirose, E., Nakashima, K., and Nishino, A.
    Is there intracellular cellulose in the appendicularian tail epidermis? A tale of the adult tail of an invertebrate chordate.
    Communicative & Integrative Biology 4 (6). (2011) LINK
19. Noda, T.
    The maternal genes Ci-p53/p73-a and Ci-p53/p73-b regulate zygotic ZicL expression and notochord differentiation in Ciona intestinalis embryos.
    Developmental Biology, 360(1):216-229. (2011)PUBMED
20. 前田健・山崎望・向井貴彦・立原一憲.
    沖縄島におけるミツボシゴマハゼとマングローブゴマハゼの形態と生息環境.
    魚類学雑誌 Japanese Journal of Ichthyology 58:127-140. (2011)
21. Maeda, K., Saeki, T., and Tachihara, K.
    New record of a freshwater terapontid fish, Mesopristes cancellatus (Teleostei: Terapontidae) from Okinawa Island in the Ryukyu Archipelago.
    Biogeography 13:45-50. (2011)
22. Miller, D. J., Ball, E. E., Foret, S., and Satoh, N.
    Coral genomics and transcriptomics – Ushering in a new era in coral biology.
    Journal of Experimental Marine Biology and Ecology 408:114-119. (2011)

2010

1. Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG, Viswanathan LD, Walenz B, Goodstein DM, Hellsten U, Kawashima T, Prochnik SE, Putnam NH, Shu S, Blumberg B, Dana CE, Gee L, Kibler DF, Law L, Lindgens D, Martinez DE, Peng J, Wigge PA, Bertulat B, Guder C, Nakamura Y, Ozbek S, Watanabe H, Khalturin K, Hemmrich G, Franke A, Augustin R, Fraune S, Hayakawa E, Hayakawa S, Hirose M, Hwang JS, Ikeo K, Nishimiya-Fujisawa C, Ogura A, Takahashi T, Steinmetz PR, Zhang X, Aufschnaiter R, Eder MK, Gorny AK, Salvenmoser W, Heimberg AM, Wheeler BM, Peterson KJ, Böttger A, Tischler P, Wolf A, Gojobori T, Remington KA, Strausberg RL, Venter JC, Technau U, Hobmayer B, Bosch TC, Holstein TW, Fujisawa T, Bode HR, David CN, Rokhsar DS, Steele RE.
   The dynamic genome of Hydra.
   Nature, 464: 592-596 (2010).PUBMED
2. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS.
   The genome of the Western clawed frog Xenopus tropicalis.
   Science, 328: 633-636 (2010).PUBMED
3. Tassy O, Dauga D, Daian F, Sobral D, Robin F, Khoueiry P, Salgado D, Fox V, Caillol D, Schiappa R, Laporte B, Rios A, Luxardi G, Kusakabe T, Joly JS, Darras S, Christiaen L, Contensin M, Auger H, Lamy C, Hudson C, Rothbächer U, Gilchrist MJ, Makabe KW, Hotta K, Fujiwara S, Satoh N, Satou Y, Lemaire P.
   The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.
   Genome Res., 20: 1459-1468 (2010).PUBMED
4. Kubo A, Suzuki N, Yuan X, Nakai K, Satoh N, Imai KS, Satou Y.
   Genomic cis-regulatory networks in the early Ciona intestinalis embryo.
   Development, 137: 1613-1623 (2010).PUBMED
5. Ikuta T, Satoh N, Saiga H.
   Limited functions of Hox genes in the larval development of the ascidian Ciona intestinalis.
   Development, 137: 1505-1513 (2010). PUBMED
6. Maeda K., Tachihara K.
   Diel and seasonal occurrence patterns of drifting fish larvae in the Teima Stream, Okinawa Island.
   Pacific Science, 64: 161-176 (2010).
7. Hozumi A, Kawai N, Yoshida R, Ogura Y, Ohta N, Satake H, Satoh N, Sasakura Y.
   Efficient transposition of a single Minos transposon copy in the genome of the ascidian Ciona intestinalis with a transgenic line expressing transposase in eggs.
   Dev Dyn., 239(4):1076-88 (2010).PUBMED
8. Sasakura Y, Suzuki M, Hozumi A, Inaba K, Satoh N.
   Maternal factor-mediated epigenetic gene silencing in the ascidian Ciona intestinalis.
   Mol Genet Genomics., 283(1):99-110 (2010).PUBMED
9. Fujikawa T, Munakata T, Kondo S, Satoh N, Wada S.
   Stress response in the ascidian Ciona intestinalis: transcriptional profiling of genes for the heat shock protein 70 chaperone system under heat stress and endoplasmic reticulum stress.
   Cell Stress Chaperones. 15(2):193-204 (2010).PUBMED
10. Minamoto T, Hanai S, Kadota K, Oishi K, Matsumae H, Fujie M, Azumi K, Satoh N, Satake M, Ishida N.
    Circadian clock in Ciona intestinalis revealed by microarray analysis and oxygen consumption.
    J Biochem. 147(2):175-84 (2010).PUBMED
11. Ohta, N., Horie, T., Satoh, N.,Sasakura, Y.
    Transposone-mediated enhancer detection reveals the location, morphology and development of the Cupular Organs, which are putative hydrodynamic sensors, in the ascidian Ciona intestinalis.
    Zool. Sci. 27:842-850 (2010).PUBMED
12. Shimozono N, Ohta N, Satoh N, Hamada M.
    Differential Regional Expression of Genes in the Developing Brain of Ciona intestinalis Embryos.
    Zoolog Sci., 27(2):103-9 (2010).PUBMED
13. Takahashi H, Hotta K, Takagi C, Ueno N, Satoh N, Shoguchi E.
    Regulation of notochord-specific expression of Ci-Bra downstream genes in Ciona intestinalis embryos.
    Zoolog Sci., 27(2):110-8 (2010).PUBMED
14. Yeats B, Matsumoto J, Mortimer SI, Shoguchi E, Satoh N, Hastings KE.
    SL RNA genes of the ascidian tunicates Ciona intestinalis and Ciona savignyi.
    Zoolog Sci., 27(2):171-80 (2010).PUBMED

2009

1. Kawashima T, Kawashima S, Tanaka C, Murai M, Yoneda M, Putnam NH, Rokhsar DS, Kanehisa M, Satoh N, Wada H.
   Domain shuffling and the evolution of vertebrates.
   Genome Res., 19:1393–1403 (2009)PUBMED
2. Chiba S, Jiang D, Satoh N, Smith WC.
   Brachyury null mutant-induced defects in juvenile ascidian endodermal organs.
   Development, 136:35-39 (2009) PUBMED
3. Nakayama-Ishimura A, Chambon JP, Horie T, Satoh N, Sasakura Y.
   Delineating metamorphic pathways in the ascidian Ciona intestinalis.
   Dev. Biol., 326:357-367 (2009)PUBMED
4. Yamada S, Hotta K, Yamamoto TS, Ueno N, Satoh N, Takahashi H.
   Interaction of notochord-derived fibrinogen-like protein with Notch regulates the patterning of the central nervous system of Ciona intestinalis embryos.
   Dev. Biol., 328:1–12 (2009)PUBMED
5. Paix A, Yamada L, Dru P, Lecordier H, Pruliere G, Chenevert J, Satoh N, Sardet C.
   Cortical anchorages and cell type segregations of maternal postplasmic/PEM RNAs in ascidians.
   Dev Biol., 336(1):96-111 (2009). PUBMED
6. Satoh N.
   An advanced filter-feeder hypothesis for urochordate evolution.
   Zoolog Sci., 26(2):97-111 (2009)PUBMED
7. Satou Y, Satoh N, Imai K.
   Gene regulatory networks in the early ascidian embryo.
   Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, 1789:268–273 (2009) PUBMED
8. Keduka E, Kaiho A, Hamada M, Watanabe-Takano H, Takano K, Ogasawara M, Satou Y, Satoh N, Endo T.
   M-Ras evolved independently of R-Ras and its neural function is conserved between mammalian and ascidian, which lacks classical Ras.
   Gene, 429:49-58 (2009)PUBMED
9. Ikuta T, Miyamoto N, Saito Y, Wada H, Satoh N, Saiga H.
   Ambulacrarian prototypical Hox and ParaHox gene complements of the indirect-developing hemichordate Balanoglossus simodensis.
   Dev Genes Evol., 219(7):383-9 (2009)PUBMED
10. Noda T, Hamada M, Hamaguchi M, Fujie M, Satoh N.
    Early zygotic expression of transcription factors and signal molecules in fully dissociated embryonic cells of Ciona intestinalis: A microarray analysis.
    Development Growth and Differentiation, 51(7):639-55 (2009)PUBMED
11. Sasakura Y, Inaba K, Satoh N, Kondo M, Akasaka K.
    Ciona intestinalis and Oxycomanthus japonicus, representatives of marine invertebrates.
    Experimental Animals, 58(5):459-69 (2009) PUBMED
12. Satoh N.
    Ciona intestinalis: An experimental model of genome-wide exploration of chordate biology (モデル生物の歴史と展望 第５回 カタユウレイボヤ-脊索動物の生命現象のゲノム科学的解明をめざすモデル動物).
    Jikken Igaku (Experimental Medicine), 27(11):1780–1783 (2009)
13. Satoh N.
    新しい眼でみた水棲無脊椎動物の系統（4） 動物の多様性：最近のトピックス―さらに進む分子系統学的解析―.
    うみうし通信, 62: 2–5 (2009)
14. Satoh N, Kawashima T, Shoguchi E.
    Decoding of amphioxus genome and evolution of chordates (ナメクジウオのゲノム解読と脊索動物の進化).
    Protein, Nucleic acid and Enzyme, 54(1):20-28 (2009) PUBMED

2008

1. Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutie'rrez EL, Dubchak I, Garcia-Ferna'ndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS.
   The amphioxus genome and the evolution of the chordate karyotype.
   Nature, 453: 1064-1071(2008) PUBMED 
2. Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, Signorovitch AY, Moreno MA, Kamm K, Grimwood J, Schmutz J, Shapiro H, Grigoriev IV, Buss LW, Schierwater B, Dellaporta SL, Rokhsar DS.
   The Trichoplax genome and the nature of placozoans.
   Nature, 454: 955-960(2008) PUBMED
3. Harada Y, Takagaki Y, Sunagawa M, Saito T, Yamada L, Taniguchi H, Shoguchi E, Sawada H.
   Mechanism of self-sterility in a hermaphroditic chordate.
   Science, 320:548-550 (2008) PUBMED
4. Christiaen L, Davidson B, Kawashima T, Powell W, Nolla H, Vranizan K, Levine M.
   The Transcription/Migration Interface in Heart Precursors of Ciona intestinalis.
   Science, 320:1349-1352 (2008) PUBMED
5. Holland LZ, Albalat R, Azumi K, Benito-Gutierrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernandez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallbook F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PW.
   The amphioxus genome illuminates vertebrate origins and cephalochordate biology.
   Genome Res., 18:1100-1111 (2008) PUBMED
6. Shoguchi E, Hamaguchi M, and Satoh N..
   Genome-wide network of regulatory genes for construction of a chordate embryo.
   Dev. Biol., 316: 498-509 (2008) PUBMED
7. Jeffery WR, Chiba T, Krajka FR, Deyts C, Satoh N, Joly JS.
   Trunk lateral cells are neural crest-like cells in the ascidian Ciona intestinalis: insights into the ancestry and evolution of the neural crest.
   Dev. Biol., 324:152-160 (2008) PUBMED
8. Satoh N.
   An aboral-dorsalization hypothesis for chordate origin.
   Genesis, 46:614-622 (2008) PUBMED
9. Aoyama M, Kawada T, Fujie M, Hotta K, Sakai T, Sekiguchi T, Oka K, Satoh N, Satake H.
   A novel biological role of tachykinins as an up-regulator of oocyte growth: identification of an evolutionary origin of tachykininergic functions in the ovary of the ascidian, Ciona intestinalis.
   Endocrinology, 149:4346-4356 (2008) PUBMED
10. Satake H, Aoyama M, Kawada T, Sekiguchi T, Sakai T, Fujie M, Satoh N.
    Neuropeptides and their receptors of the protochordate, Ciona intestinalis: the evolutionary origin of vertebrate neuropeptides.
    Acta Biol. Hung., 59 Suppl:237-239 (2008)
11. Satou Y, Mineta K, Ogasawara M, Sasakura Y, Shoguchi E, Ueno K, Yamada L, Matsumoto J, Wasserscheid J, Dewar K, Wiley GB, Macmil SL, Roe BA, Zeller RW, Hastings KE, Lemaire P, Lindquist E, Endo T, Hotta K, Inaba K.
    Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations.
    Genome Biol., 9:R152 (2008) PUBMED
12. Satou Y, Wada S, Sasakura Y, Satoh N.
    Regulatory genes in the ancestral chordate genomes.
    Dev. Gen. Evol., 218:715-21 (2008) PUBMED
13. Yu Jr-K, Wang MC, Shin T, Kohara Y, Holland LZ, Satoh N, Satou Y.
    A cDNA resource for the cephalochordate amphioxus Branchiostoma floridae.
    Dev. Gen. Evol., 218:723-727 (2008) PUBMED
14. Shinzato C, Iguchi A, Hayward DC, Technau U, Ball EE, Miller DJ.
    Sox genes in the coral Acropora millepora: divergent expression patterns reflect differences in developmental mechanisms within the Anthozoa.
    BMC Evol. Biol., 8:311 (2008) PUBMED
15. Wada S, Hamada M, Kobayashi K, Satoh N.
    Novel genes involved in canonical Wnt/beta-catenin signaling pathway in early Ciona intestinalis embryos.
    Dev Growth Differ., 50:215-227 (2008) PUBMED
16. Kawashima T, Hamada M, Shinzato C, Satoh N, Shoguchi E.
    New outlooks on evolutionary studies brought from ten years of animal genome decipherment (動物ゲノム解読の10年がもたらした新しい進化観).
    Kagaku, 78:1070-1079 (2008)