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【論 文】
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(1) Hasegawa, M., Cao, Y., Adachi, J. and Yano T. (1992): Rodent polyphyly? Nature, 355, 595-595.
(2) Adachi, J., Cao, Y. and Hasegawa, M. (1993): Tempo and mode of
mitochondrial DNA evolution in vertebrates at the amino acid sequence level:
rapid evolution in warm-blooded vertebrates, J. Mol. Evol.,
36, 270-281.
(3) Cao, Y., Adachi, J., Janke, A., Paabo, S. and Hasegawa, M. (1994): Phylogenetic
relationships among eutherian orders estimated from
inferred sequences of mitochondrial proteins, J. Mol. Evol.,
39, 519-527.
(4) Cao, Y., Adachi, J., Yano, T. and Hasegawa, M. (1994): Phylogenetic place of guinea pigs: no support of the
rodent polyphyly hypothesis from maximum likelihood
analyses of multiple protein sequences, Mol. Biol. Evol.,
11, 593-604.
(5) Cao, Y., Adachi, J. and Hasegawa, M. (1994): Eutherian
phylogeny as inferred from mitochondrial DNA sequence data, Jpn. J. Genet., 69, 455-472.
(6)
Shirakura T., Hashimoto, T., Nakamura, Y., Kamaishi, T., Cao, Y., Adachi, J., Hasegawa, M.,
Yamamoto, A. and Goto, N. (1994): Phylogenetic place of a mitochondria-lacking protozoan, Entamoeba histolytica,
inferred from amino acid sequences of elongation factor 2. Jpn. J. Genet., 69, 119-135.
(7) Cao, Y., Okada, N. and Hasegawa, M. (1997): Phylogenetic
position of guinea-pigs revisited, Mol. Biol. Evol.,
14, 461-464.
(8) Ishida, K., Cao, Y., Hasegawa, M., Okada, N. and Hara, Y. (1997): The
origin of chlorarachniophyte plastids inferred from
EF-Tu amino acid sequence phylogeny, J. Mol. Evol., 45, 682-687.
(9) Cao, Y., Adachi, J. and Hasegawa, M. (1998): Comment on the quartet
puzzling method for finding maximum-likelihood tree topologies. Mol. Biol.
Evol., 15, 87-89.
(10) Cao, Y., Janke, A., Waddell, P. J., Westerman, M., Takenaka, O.,
Murata, S., Okada, N., Paabo, S. and Hasegawa, M.
(1998): Conflict among individual mitochondrial proteins in resolving the
phylogeny of eutherian orders, J. Mol. Evol., 47, 307-322.
(11) Cao, Y., Waddell P. J., Okada N. and Hasegawa M. (1998): The complete
mitochondrial DNA sequence of the shark Mustelus manazo: Resolving vertebrate phylogeny with mitochondrial
genome sequences when all known methods fail completely, Mol. Biol. Evol., 15, 1637-1646.
(12) Zardoya, R., Cao, Y., Hasegawa, M. and Meyer,
A. (1998): Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial
and nuclear data, Mol. Biol. Evol., 15, 506-517.
(13) Hasegawa, M., Cao, Y. and Yang, Z. (1998): Preponderance of slightly
deleterious polymorphism in mitochondrial DNA: Nonsynonymous/synonymous
rate ratio is much higher within species than between species, Mol. Biol. Evol., 15, 1499-1505.
(14) Shimodaira, H. and Cao, Y. (1998): A graphical
technique for model selection diagnosis, Research Memorandum Inst Statist Math., 680, 1-24.
(15) 曹纓、長谷川政美 (1998): 最尤系統樹の探索法. 統計数理, 46, 401-409.
(16) 長谷川政美、曹纓 (1998): 哺乳動物の歴史. 高畑尚之（編）「生命体システムの由来と未来」,
総合研究大学院大学, 94-105
(17) Cao, Y., Kim, K. S., Ha, J. H. and Hasegawa, M. (1999): Model dependence of
the phylogenetic inference: Relationship among
carnivores, perissodactyls and cetartiodactyls
as inferred from mitochondrial genome sequences, Genes Genet. Syst., 74, 211-217.
(18) Waddell, P., Cao, Y., Hauf, J. and Hasegawa,
M. (1999): Using novel phylogenetic methods to
evaluate mammalian mtDNA, including amino
acid-invariant sites-LogDet plus site stripping, to
detect internal conflicts in the data, with special reference to the
positions of hedgehog, armadillo, and elephant, System. Biol., 48, 31-53.
(19) Waddell, P., Cao, Y., Hasegawa, M. and Mindell,
D.P. (1999): Assessing the Cretaceous superordinal
divergence times within birds and placental mammals by using whole
mitochondrial protein sequences and an extended statistical framework,
System. Biol., 48, 119-137.
(20) Tohyama, Y., Kasama-Yoshida,
H., Sakuma, M., Kobayashi, Y., Cao, Y., Hasegawa, M., Kojima, H., Tamai, Y., Tanokura, M. and Kurihara, T. (1999): Gene structure and amino acid
sequence of Latimeria chalumnae
(coelacanth) myelin DM20: Phylogenetic relation of
the fish, Neurochemica Reserch, 24, 867-873.
(21) 長谷川政美、曹纓 (1999): 大陸の移動と哺乳類の進化, 科学, 69,
440-448.
(22) Cao, Y., Sorenson, M. D., Kumazawa, Y., Mindell, D. P. and Hasegawa, M. (2000): Phylogenetic position of turtles among amniotes: evidence
from mitochondrial and nuclear genes, Gene, 259, 139-148.
(23) Cao, Y., Fujiwara, M., Nikaido, M., Okada, N.
and Hasegawa, M. (2000): Interordinal relationships
and timescale of eutherian evolution as inferred
from mitochondrial genome data, Gene, 259, 149-158.
(24) Nikaido, M., Harada, M., Cao, Y., Hasegawa, M.
and Okada, N. (2000): Monophyletic origin of the order Chiroptera
and its phylogenetic position among Mammalia inferred from the complete mitochondrial DNA
sequence of a Japanese megabat; Ryukyu flying fox (Pteropus dasymallus), J.
Mol. Evol., 51, 318-328.
(25) Onuma, M., Cao, Y., Hasegawa, M. and Kusakabe, S. (2000): A close relationship of Chiroptera with Eulipotyphla
(core Insectivora) suggested by four mitochondrial
gene, Zool, 17, 1327-1332.
(26) Tohyama, Y., Ichimiya,
T., Kasama-Yoshida, H., Cao, Y., Hasegawa, M.,
Kojima, H., Tamai, Y. and Kurihara,
T. (2000): Phylogenetic relation of lungfish
indicated by the amino acid sequence of myelin DM20, Mol Brain Res, 80, 256-259.
(27) Nikaido, M., Matsuno,
F., Hamilton, H., Brownell, R. L. Jr., Cao, Y., Wang, D., Zhou, Z., Shedlock, A. M., Fordyce, R. E., Hasegawa, M. and Okada,
N. (2001): Retroposon analysis of major cetacen lineages: the monophyly
of toothed whales and the paraphyly of river
dolphins, Proc. Natl. Acad. Sci. USA, 98, 7384-7389.
(28) Nikaido, M., Kawai, K., Cao, Y., Harada, M.,
Tomita, S., Okada, N. and Hasegawa, M. (2001): Maximum likelihood analysis of
the complete mitochondrial genomes of eutherians
and a reevaluation of the phylogeny of bats and insectivores, J. Mol. Evol., 53, 508-516.
(29) Pupko, T., Huchon,
D., Cao, Y., Okada, N. and Hasegawa, M. (2002): Combining multiple data Sets
in a likelihood analysis: Which Models are the Best? Mol. Biol. Evol., 19(12), 2294-2307.
(30) 曹纓、長谷川政美 (2002): 分子系統樹推定におけるモデルのミススペシフィケーション―脊椎動物の系統進化を例として―, 統計数理, 50, 69-85.
(31) Nikaido, M.,
Cao, Y., Harada, M., Okada, N. and Hasegawa, M. (2003): Mitochondrial
phylogeny of hedgehogs and monophyly of Eulipotyphla, Mol. Phylogenet.
Evol., 28, 276-284.
(32) Murata, Y., Nikaido,
M., Sasaki, T., Cao, Y., Fukumoto, Y., Hasegawa, M.
and Okada, N. (2003): Afrotherian phylogeny as
inferred from complete mitochondrial genomes, Mol. Phylogenet.
Evol., 28, 253-260.
(33) Nikaido, M., Cao, Y., Okada, N. and Hasegawa, M. (2003): The phylogenetic relationships of insectivores with special
reference to the lesser hedgehog tenrec as inferred
from the complete sequence of their mitochondrial genome, Genes Genet. Syst., 78, 107-112.
(34) Sasaki, T., Nikaido, M.,
Hamilton, H., Goto, M., Kato, H., Kanda, N., Pastene, L., Cao, Y., Fordyce, R., Hasegawa, M. and
Okada, N. (2005): Mitochondrial
phylogenetics and evolution of mysticete
whales, System. Biol., 54(1), 77-90.
(35) Li, Z., Liu, Q., Song, M., Zheng,
Y., Nan, P., Cao, Y., Chen, G., Li, Y.and Zhong, Y. (2005): Detecting correlation between
sequence and expression divergences in a comparative analysis of human serpin genes, BioSystems,
82, 226-234.
(36) Zhang, Y., Zheng, N., Hao, P., Cao, Y. and Zhong Y.
(2005): A
molecular docking model of SARS-CoV S1 protein in
complex with its receptor, human ACE2, Computational Biology and Chemistry,
29, 254-257.
(37) Watanabe, M., Nikaido,
M., Tsuda, T.T., Kobayashi, T., Mindell,
D., Cao, Y., Okada, N. and Hasegawa, M. (2006): New candidate species most
closely related to penguins, Gene, 378, 65-73.
(38) Sasaki, T., Nikaido
M., Wada S., Yamada T.K., Cao, Y., Hasegawa, M. and Okada, N. (2006): Balaenoptera omurai is a newly discovered baleen whale that represents an
ancient evolutionary lineage, Mol. Phylogenet. Evol., 41, 40-52.
(39) Zhang, Y., Zheng, N., Nan, P., Cao, Y.,
Hasegawa, M. and Zhong, Y. (2007): Computational
simulation of interactions between SARS coronavirus
spike mutants and host species-specific receptors, Computational Biology
and Chemistry, 31, 134-137.
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