1. Hayashida, H., Kuma, K., and Miyata, T. (1986) Similarity of mas and rhodopsin gene products. Nature 323, 116.

2. Miyata, T., Hayashida, H., Kuma, K., and Yasunaga, T. (1987) Male-driven molecular evolution demonstrated by different rates of silent substitutions between autosome- and sex chromosome-linked genes. Proc. Japan Acad., 63, 327-331.

3. Kuma, K., and Miyata, T. (1987) Limited divergence of X-linked gene: further supporting evidence for male-driven molecular evcolution. Proc. Japan Acad. 63, 332-335.

4. Miyata, T., Hayashida, H., Kuma, K., Mitsuyasu, K., and Yasunaga, T. (1987) Male-driven molecular evolution: a model and nucleotide sequence analysis. Cold Spring Harb. Symp. Quant. Biol. 52, 863-867.

5. Ohtsubo, M., Kai, R., Furuno, N., Sekiguchi, T., Sekiguchi, M., Hayashida, H., Kuma, K., Miyata, T., Fukushige, S., Murotsu, T., Matsubara, K. and Nishimoto, T. (1987) Isolation and characterization of the active cDNA of the human cell cycle gene (RCC1) involved in the regulation of onset of chromosome condensation. Genes Dev. 1, 585-593.

6. Tokunaga, F., Miyata, T., Nakamura, T., Morita, T., Kuma, K., Miyata, T., and Iwanaga, S. (1987) Lipopolysaccharide-sensitive serine-protease zymogen (factor C) of horseshoe crab hemocytes. Identification and alignment of proteolytic fragments produced during the activation show that it is a novel type of serine protease. Eur. J. Biochem. 167, 405-416.

7. Hayashida, H., Kuma, K., and Miyata, T. (1987) Immunoglobin-like sequemces in the extracellular domains of proto-oncogene fms and platelet-derived growth factor receptor. Proc. Japan Acad. 64, 113-118.

8. Kuma, K., Hayashida, H., and Miyata, T. (1988) Recent gene conversion between genes encoding human red and green visual pigments. Jpn. J. Genet. 63, 367-371.

9. Sakaguchi, T., Toyoda, T., Gotoh, B., Inocencio, N.M., Kuma, K., Miyata, T., and Nagai, Y. (1989) Newcastle disease virus evolution. I. Multiple lineages defined by sequence variability of the hemagglutinin-neuraminidase gene. Virology 169, 260-272.

10. Toyoda, T., Sakaguchi, T., Hirota, H., Gotoh, B., Kuma, K., Miyata, T., and Nagai, Y. (1989) Newcastle disease virus evolution. II. Lack of gene recombination in generating virulent and avirulent strains. Virology 169, 273-282.

11. Iwabe, N., Kuma, K., and Miyata, T. (1989) Sequence similarity of bacteriophage SPO2 DNA polymerase with E. coli DNA polymerase I. Nucleic Acids Res. 17, 8866.

12. Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S., and Miyata, T. (1989) Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA 86, 9355-9359.

13. Iwabe, N., Kuma, K., Saitou, N., Tsuda, M., and Miyata, T. (1989) Evolution of rhodopsin supergene family: Independent divergence of visual pigments in vertebrates and insects and possibly in mollusks. Proc. Japan Acad., 65, 195-198.

14. Kuma, K., Iwabe, N., Kawanishi, Y., and Miyata, T. (1990) RNA-binding protein-related sequence in a malaria antigen, clustered-asparagine-rich protein. FEBS Lett. 260, 67-69.

15. Miyata, T., Kuma, K., Iwabe, N., Hayashida, H., and Yasunaga,T. (1990) Different rates of evolution of autosome-, X chromosome- and Y chromosome-linked genes: hypothesis of male-driven molecular evolution. In: Population Biology of Genes and Molecules (ed. Takahata, T. and Crow, J. F.) pp341-357, Baifukan, Tokyo.

16. Iwabe, N., Kuma, K., Kishino, H., Hasegawa, M., and Miyata, T. (1990) Compartmentalized isozyme genes and the origin of introns. J. Mol. Evol. 31, 205-210.

17. Iwabe, N., Kuma, K., Kishino, H., Hasegawa, M., and Miyata, T. (1991) Evolution of RNA polymerases and branching patterns of the three major groups of Archaebacteria. J. Mol. Evol. 32, 70-78.

18. Miyata, T., Iwabe, N., Kuma, K., Kawanishi, Y., Mukohata, Y., Ihara, K., and Hasegawa, M. (1991) Phylogenetic position of archaebacteria and branching patterns among three archaebacterial groups and eukaryotes. In New aspects of the genetics of molecular evolution, 1991, eds. Kimura, K., and Takahata, N., pp. 279-290.

19. Kuma, K., Iwabe, N., and Miyata, T. (1991) The immunoglobulin family. Curr. Opin. Struct. Biol. 1, 384-393.

20. Miyata, T., Iwabe, N., Kuma, K., Kawanishi, Y., Hasegawa, M., Kishino, H., Mukohata, Y., Ihara, K., and Osawa, S. (1991) Evolution of archaebacteria: phylogenetic relationships among archaebacteria, eubacteria, and eukaryotes. In Evolution of life, eds. Osawa, S., and Honjo, T., pp.337-351. Spring-Verlag, Tokyo.

21. Kuma, K., Iwabe, N., and Miyata, T. (1991) Motifs of immunoglobulin-like domains: neurotrophic factor receptors trk and trkB are members of the immunoglobulin family. Proc. Japan Acad. 67, 188-192.

22. Hayashida, H., Kuma, K., and Miyata, T. (1992) Inter-chromosomal gene conversion as a possible mechanism for explaining divergence patterns of ZFY-related genes. J. Mol. Evol. 35, 181-183.

23. Kuma, K., Miyata, T., and Takeichi, M. (1992) Proto-oncogene ret has cadherin-like repeats in the extracellular region. Proc. Japan Acad. 68, 106-108.

24. Ogawara, H., Kuma, K., and Miyata, T. (1993) Gene transfer of a part of a beta-lactamase gene? Microbiol. Immunol. 37, 399-403.

25. Tokunaga, F., Muta, T., Iwanaga, S., Ichinose, A., Davie, E.W., Kuma, K., and Miyata, T. (1993) Limulus hemocyte transglutaminase. cDNA cloning, amino acid sequence, and tissue localization. J. Biol. Chem. 268, 262-268.

26. Kuma, K., Iwabe, N., and Miyata, T. (1993) Motifs of cadherin- and fibronectin type III-related sequences and evolution of the receptor-type-protein tyrosine kinases: sequence similarity between proto-oncogene ret and cadherin family. Mol. Biol. Evol. 10, 539-551.

27. Seki, N., Muta, T., Oda, T., Iwaki, D., Kuma, K., Miyata, T., and Iwanaga, S. (1994) Horseshoe crab (1,3)-beta-D-glucan-sensitive coagulation factor G. A serine protease zymogen heterodimer with similarities to beta-glucan-binding proteins. J. Biol. Chem. 269, 1370-1374.

28. Ohashi, K., Mizuno, K., Kuma, K., Miyata, T., and Nakamura, T. (1994) Cloning of the cDNA for a novel receptor tyrosine kinase, Sky, predominantly expressed in brain. Oncogene 9, 699-705.

29. Mizuno, K., Okano, I., Ohashi, K., Nunoue, K., Kuma, K., Miyata, T., and Nakamura, T. (1994) Identification of a human cDNA encoding a novel protein kinase with two repeats of the LIM/double zinc finger motif. Oncogene 9, 1605-1612.

30. Nikoh, N., Hayase, N., Iwabe, N., Kuma, K., and Miyata, T. (1994) Phylogenetic relationship of the kingdoms Animalia, Plantae, and Fungi, inferred from 23 different protein species. Mol. Biol. Evol. 11, 762-768.

31. Miyata, T., Kuma, K., Iwabe, N., and Nikoh, N. (1994) A possible link between molecular evolution and tissue evolution demonstrated by tissue specific genes. Jpn. J. Genet. 69, 473-480.

32. Kuma, K., and Miyata, T. (1994) Mammalian phylogeny inferred from multiple protein data. Jpn. J. Genet. 69, 555-566.

33. Kuma, K., Iwabe, N., and Miyata, T. (1995) Functional constraints against variations on molecules from the tissue level: slowly evolving brain-specific genes demonstrated by protein kinase and immunoglobulin supergene families. Mol. Biol. Evol. 12, 123-130. (PMID: 7877487)

34. Yokoyama, N., Hayashi, N., Seki, T., Pante, N., Ohba, T., Nishii, K., Kuma, K., Hayashida, T., Miyata, T., Aebi, U., and Nishimoto, N. (1995) A giant nucleopore protein that binds Ran/TC4. Nature 376, 184-188.

35. Kuma, K., Nikoh, N., Iwabe, N., and Miyata, T. (1995) Phylogenetic position of Dictyostelium inferred from multiple protein data sets. J. Mol. Evol. 41, 238-246.

36. Iwabe, N., Kuma, K., Nikoh, N., and Miyata, T. (1995) Molecular clock for dating of divergence between animal phyla. Jpn. J. Genet. 70, 687-692.

37. Toshima, J., Ohashi, K., Okano, I., Nunoue, K., Kishioka, M., Kuma, K., Miyata, T., Hirai, M., Baba, T., and Mizuno, K. (1995) Identification and characterization of a novel protein kinase, TESK1, specifically expressed in testicular germ cells. J. Biol. Chem. 270, 31331-31337.

38. Iwabe, N., Kuma, K., and Miyata, T. (1996) Evolution of gene families and relationship with organismal evolution: rapid divergence of tissue-specific genes in the early evolution of chordates. Mol. Biol. Evol. 13, 483-493.

39. Yasojima, K., Tsujimura, A., Mizuno, T., Shigeyoshi, Y., Inazawa, J., Kikuno, R., Kuma, K., Ohkubo, K., Hosokawa, Y., Ibata, Y., Abe, T., Miyata, T., Matsubara, K., Nakajima, K., and Hashimoto-Gotoh, T. (1997) Cloning of human and mouse cDNAs encoding novel zinc finger proteins expressed in cerebellum and hippocampus. Biochem. Biophys. Res. Commun. 231, 481-487.

40. Nikoh, N., Iwabe, N., Kuma, K., Ohno, M., Sugiyama, T., Watanabe, Y., Yasui, K., Shi-cui, Z., Hori, K., Shimura, Y., and Miyata, T. (1997) An estimate of divergence time of Parazoa and Eumetazoa and that of Cephalochordata and Vertebrata by aldolase and triose phosphate isomerase clocks. J. Mol. Evol. 45, 97-106.

41. Suga, H., Kuma, K., Iwabe, N., Nikoh, N., Ono, K., Koyanagi, M., Hoshiyama, D., and Miyata, T. (1997) Intermittent divergence of the protein tyrosine kinase family during animal evolution. FEBS Lett. 412, 540-546.

42. Arakawa, H., Kuma, K., Yasuda, M., Furusawa, S., Ekino, S., and Yamagishi, H. (1998) Oligoclonal development of B cells bearing discrete Ig chains in chicken single germinal centers. J. Immunol. 160, 4232-4241.

43. Koyanagi, M., Suga, H., Hoshiyama, D., Ono, K., Iwabe, N., Kuma, K., and Miyata, T. (1998) Ancient gene duplication and domain shuffling in the animal cyclic nucleotide phosphodiesterase family. FEBS Lett. 436, 323-328. (PMID: 9801141)

44. Nakamura, M., Masuda, H., Horii, J., Kuma, K., Yokoyama, N., Ohba, T., and Nishitani, H. (1998) When overexpressed, a novel centrosomal protein, RanBPM, causes ectopic microtubule nucleation similar to gamma-tubulin. J. Cell. Biol. 143, 1041-1052.

45. Hoshiyama, D., Suga, H., Iwabe, N., Koyanagi, M., Nikoh, N., Kuma, K., Matsuda, F., Honjo, T., and Miyata, T. (1998) Sponge Pax cDNA related to Pax-2/5/8 and ancient gene duplications in the Pax family. J. Mol. Evol. 47, 640-648.

46. Matsuda, F., Ishii, K., Bourvagnet, P., Kuma, K., Hayashida, H., Miyata, T., and Honjo, T. (1998) The complete nucleotide sequence of the human immunoglobulin heavy chain variable region locus. J. Exp. Med. 188, 2151-2162.

47. Suga, H., Koyanagi, M., Hoshiyama, D., Ono, K., Iwabe, N., Kuma, K., and Miyata, T. (1999) Extensive gene duplication in the early evolution of animals before the parazoan-eumetazoan split demonstrated by G proteins and protein tyrosine kinases from sponge and hydra. J. Mol. Evol. 48, 646-653.

48. Ono, K., Suga, H., Iwabe, N., Kuma, K., and Miyata, T. (1999) Multiple protein tyrosine phosphatases in sponges and explosive gene duplication in the early evolution of animals before the parazoan-eumetazoan split. J. Mol. Evol. 48, 654-662.

49. Kitao, H., Arakawa, H., Kuma, K., Yamagishi, H., Nakamura, N., Furusawa, S., Matsuda, H., Yasuda, M., Ekino, S., and Shimizu, A. (2000) Class switch recombination of the chicken IgH chain genes: implications for the primordial switch region repeats. Int. Immunol. 12, 959-968.

50. Katoh, K., Kuma, K., Miyata, T. (2001) Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny. J. Mol. Evol. 53, 477-484.

51. Hoshiyama, D., Kuma, K., and Miyata, T. (2001) Extremely reduced evolutionary rate of TATA-box binding protein in higher vertebrates and its evolutionary implications. Gene 280, 169-173.

52. Katoh, K., Misawa, K., Kuma, K., and Miyata, T. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res. 30, 3059-3066.

53. Arakawa, H., Kuma, K., Yasuda, M., Ekino, S., Shimizu, A., and Yamagishi, H. (2002) Effect on environmental antigens on the immunoglobulin diversification and the selection of productive V-J joints in the bursa. J. Immunol. 169, 818-828.

54. Inokuchi, R., Kuma, K., Miyata, T., and Okada, M. (2002) Ammonium-assimilating enzymes in higher plants and algae: Physiological and phylogenic perspectives. Physiologia Plantarum, 116, 1-11.