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Ying
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Selected
Papers
(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) 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.
(16) 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.
(17) 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.
(18) 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.
(19) 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.
(20) 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.
(21) 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.
(22) 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.
(23) 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.
(24) 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.
(25) 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.
(26) 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.
(27) 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.
(28) 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.
(29) 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.
(30) 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.
(31) 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.
(32) 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.
(33) 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.
(34) 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.
(35) 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.
Selected Publications
Hasegawa, Masami et al. (2005): Our
Ancestor: A Saga, Gene Tells（eds.
Y. Cao and Y. Zhong）, Shanghai Scientific and
Technological Education Publishing House
Membership of Academic
Societies
International Society
for Molecular Biology and Evolution, Genetics Society of Japan, Society of
Evolution Studies, Japan, Molecular Biology Society of Japan, The Society of Biosophia Studies
Professional
Services
2002-2005: Systematics
Biology, Editorial Board Member