ORTHOSCOPE: an automatic web tool for phylogenetically inferring bilaterian orthogroups with user-selected taxa.
Inoue J, Satoh N.
Molecular Biology and Evolution. in press. 2018年 [査読有り]
Deuterostome genomics: Lineage-specific protein expansions that enabled chordate muscle evolution.
Inoue J, Satoh N.
Molecular Biology and Evolution. 35(4) 914-924 2018年 [査読有り]
A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement.
Kim OTP, Nguyen PT, Shoguchi E, Hisata K, Vo TTB, Inoue J, Shinzato C, Le BTN, Nishitsuji K, Kanda M, et al.
BMC Genomics 19 733 2018年 [査読有り]
The chordate ancestor possessed a single copy of the Brachyury gene for notochord acquisition.
Inoue J, Yasuoka Y, Takahashi H, Satoh N.
Zoological Letters. 3 4 2017年 [査読有り]
Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling.
Inoue J, Sato Y, Sinclair R, Tsukamoto K, Nishida M.
Proceedings of the National Academy of Sciences of the United States of America 112(48) 14918-14923 2015年 [査読有り]
Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families.
Miya M., Friedman M, Satoh TP., Takeshima H., Sado T., Iwasaki W., Yamanoue Y., Nakatani M., Mabuchi K., Inoue JG., Poulsen JY., Fukunaga T., Sato Y., Nishida M.
Plos One 8(9) e73535 2013年 [査読有り]
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny.
dos Reis M., Inoue J., Hasegawa M., Asher R.J., Donoghue P.C.J. Yang Z.
Proceedings of the Royal Soceity B. 279 3491-3500 2012年 [査読有り]
Best practices for justifying fossil calibrations.
Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi).
Saitoh, K., Sado, T., Doosey, M.H., Bart, Jr., H.L., Inoue, J.G., Nishida, M., Mayden, R.L., Miya, M.
Zoological Journal of the Linnean Society, Zoological Journal of the Linnean Society 161 633-662 2011年 [査読有り]
Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea)
Aschliman N.C., Nishida M., Miya M., Inoue J.G., Rosana K.M., Naylor G.J.P.
Molecular Phylogenetics and Evolution 63 28-42 2011年 [査読有り]
The impact of the representation of fossil calibration on Bayesian estimation of species divergence times.
Inoue, J., Donoghue, P.C.J., Yang, Z.
Systematic Biology 59 74-89 2010年 [査読有り]
Inter- specific and subspecific genetic divergences of freshwater eels, genus Anguilla including a recently described species, A. luzonensis, based on whole mitochondrial genome sequences.
Minegishi, Y., Aoyama, J., Inoue, J.G., Azanza, R.V., Tsukamoto, K.
Coastal Marine Science 33 64-77 2010年 [査読有り]
Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective.
Inoue, J.G., Miya, M., Lam, K., Tay B.H., Danks, J.A., Bell, J., Walker, T.I., Venkatesh, B.
Molecular Biology and Evolution 27 2576-2586 2010年 [査読有り]
Deep-ocean origin of the freshwater eels.
Inoue, J.G., Miya, M., Miller, M.J., Sado, T., Hanel, R., Hatooka, K., Aoyama, J., Minegishi, M., Nishida, M., Tsukamoto, K.
Biology Letters 6 363-366 2010年 [査読有り]
The historical biogeography of the freshwater knifefishes using mitogenomic approaches: A Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha)
Inoue, J.G., Kumazawa, Y., Miya, M., Nishida, M.
Molecular Phylogenetics and Evolution 51 486-499 2009年 [査読有り]
Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates.
Setiamarga, D.H., Miya, M., Inoue, J.G., Ishiguro, N.B., Mabuchi, K., Nishida, M.
Biology Letters 23 812-816 2009年 [査読有り]
Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts
Kawahara, R., Miya, M. Mabuchi, K., Lavoue, S., Inoue, J.G., Satoh, T. P., Kawaguchi, A., Nishida. M.
Molecular Phylogenetics and Evolution 46 224-236 2008年 [査読有り]
Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences.
Setiamarga, D.H., Miya, M., Yamanoue, Y., Mabuchi, K., Satoh, T.P., Inoue, J.G., Nishida, M.
Molecular Phylogenetics and Evolution 49 598-605 2008年 [査読有り]
Genetic identification of two types of Ariosoma leptocephali.
Ma, T., Miller, M. J., Aoyama, J., Minagawa, M., Inoue, J.G., Watanabe, S., Tsukamoto, K.
Coastal Marine Science 32 48-53 2008年 [査読有り]
Genetic differentiation in the genus Uroconger in the Indo-Pacific region.
The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes.
Yamanoue, Y., Miya, M., Inoue, J.G., Matsuura, K., Nishida, M.
Gene and Genetic Systems 81 29-39 2006年 [査読有り]
The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths.
Inoue, J.G., Miya, M., Venkatesh, B., Nishida, M.
Gene and Genetic Systems 349 227-235 2005年 [査読有り]
Sundasalanx (Sundasalangidae) is a progenetic clupeiform, not a closely-related group of salangids (Osmeriformes): Mitogenomic evidence.
Ishiguro, N. B., Miya, M., Inoue J. G., Nishida, M.
Journal of Fish Biology 67 561-569 2005年 [査読有り]
Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: Implications for higher-level relationships within the Otocephala.
Lavoue, S., Miya, M., Inoue, J.G., Saitoh, K., Ishiguro, N. B., Nishida, M.
Molecular Phylogenetics and Evolution 37 165-177 2005年 [査読有り]
Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences
Minegishi, Y., Aoyama, J., Inoue, J.G., Miya, M., Nishida, M., Tsukamoto, K.
Molecular Phylogenetics and Evolution 34 134-146 2005年 [査読有り]
Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva.
Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M.
Molecular Phylogenetics and Evolution 32 274-286 2004年 [査読有り]
Ecological aspects of the downstream migration of introduced European eels in the Uono River, Japan
Miyai, T., Aoyama, J., Sasai, S., Inoue, J.G., Miller, M. J., Tsukamoto, K.
Environmental Biology of Fishes 71 105-114 2004年 [査読有り]
Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography
Saitoh, K., Miya, M., Inoue, J.G., Ishiguro, N. B., Nishida, M.
Journal of Molecular Evolution 56 464-472 2003年 [査読有り]
Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences.
Miya, M., Takeshima, H., Endo, H., Ishiguro, N. B., Inoue, J.G., Mukai, T., Satoh, T. P., Yamaguchi, M., Kawaguchi, A., Mabuchi, K., Shirai, S. M., Nishida, M.
Molecular Phylogenetics and Evolution 26 121-138 2003年 [査読有り]
Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels
Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M.
Molecular Biology and Evolution 20 1917-1924 2003年 [査読有り]
Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish."
Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M.
Molecular Phylogenetics and Evolution 26 110-120 2003年 [査読有り]
Phylogeny of the basal teleosts, with special reference to the Elopomorpha.
Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M.
Japanese Journal of Ichthyology 48 75-91 2001年 [査読有り]
Molecular approach to species identification of eggs with respect to determination of the spawning site of the Japanese eel Anguilla japonica.
Aoyama, J., Ishikawa S., Otake, T., Mochioka, N., Suzuki, Y., Watanabe, S., Shinoda, A., Inoue, J.G., et al.
Fisheries Science 67 761-763 2001年 [査読有り]
Complete mitochondrial DNA sequence of the Japanese eel Anguilla japonica.
Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M.
Fisheries Science 67 118-125 2001年 [査読有り]
Complete mitochondrial DNA sequence of the Japanese anchovy Engraulis japonicus.
Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M.
Fisheries Science 67 828-835 2001年 [査読有り]
Complete mitochondrial DNA sequence of Conger myriaster (Teleostei: Anguilliformes): novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for anguilliform families.
Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M.
Journal of Molecular Evolution 52 311-320 2001年 [査読有り]
A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences.
Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M.
Molecular Phylogenetics and Evolution 20 275-285 2001年 [査読有り]
Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus.
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