Ying CAO
Assistant Professor, Graph Modeling Group, Department of Statistical Modeling; Molecular Evolution Research Group, Prediction and Knowledge Discovery Research Center





Doctor of Science, Tokyo Institute of Technology, 1998, Title of Doctoral Thesis: Molecular Phylogeny and Evolution of Vertebrates.


2003- Assistant Professor, The Institute of Statistical Mathematics

2003- Assistant Professor, Department of Biosystems Science, The Graduate University for Advanced Studies [SOKENDAI]
2005- Assistant Professor, Department of Statistical Modeling;-Prediction and Knowledge Discovery Research Center, The Institute of Statistical Mathematics

Honors &

Inoue research award, Inoue Foundation for Science, 2001


Molecular Phylogeny, Statistical Genetics


Model Misspecification in Molecular Phylogenetic Inference, Methods for Searching the Maximum Likelihood Tree, Statistical Analysis of Molecular Phylogeny and Estimating Molecular Timescales of Evolution

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.
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.
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.
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.
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.
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.
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.
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
ieds. Y. Cao and Y. Zhongj, 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