1. Toh, H., Hayashida, H., Miyata, T.
Sequence homology between retroviral reverse transcriptase and putative polymerase of hepatitis B virus and cauliflower mosaic virus.
Nature 305, 827-829 (1983).

2. Kikuno, R., Toh, H., Hayashida, H., Miyata, T.
Sequence similarity between putative gene products of geminiviral DNAs.
Nature 308, 562 (1984).

3. Toh, H., Kikuno, R., Hayashida, H., Miyata, T., Kugimiya, W., Inouye, S., Yuki, S., Saigo, K.
Close structural resemblance between putative polymerase of a Drosophila transposable genetic element 17.6 and pol gene product of Moloney murine leukaemia virus.
EMBO J. 4, 1267-1272 (1985).

4. Miyata, T., Toh, H., Saigo, K.
Reverse transcriptase-containing DNA viruses and plasmids lack integrase.
Proc. Japan Acad. 61, 464-466 (1985).

5. Toh, H., Hayashida, H., Kikuno, R., Yasunaga, T., Miyata, T.
Sequence similarity between EGF receptor and a1-acid glycoprotein.
Nature 314, 199 (1985).

6. Toh, H., Ono, M., Saigo, K., and Miyata, T.
Retroviral protease-like sequence in the yeast transposon Ty1.
Nature 315, 691-692 (1985).

7. Toh, H., Miyata, T.
Is the AIDS virus recombinant ?
Nature 316, 21-22 (1985).

8. Toh, H., Ono, M., Miyata, T.
Retroviral gag and DNA endonuclease coding sequence in IgE-binding factor gene.
Nature 318, 388-389 (1985).

9. Hayashida, H., Toh, H., Kikuno, R., Miyata, T.
Evolution of influenza virus genes.
Mol. Biol. Evol. 2, 289-303 (1985).

10. Ono, M., Toh, H., Miyata, T., Awaya, Y.
Nucleotide sequence of the Syrian hamster intracisternal A-particle gene: Close evolutionary relationship of type A particle gene to type B and D oncovirus genes.
J. Virol. 55, 387-394 (1985).

11. Miyata, T., Hayashida, H., Kikuno, R., Toh, H., Kawade, Y.
Evolution of Interferon Genes.
In: Interferon 6, Gresser et al. eds., Academic Press, London, pp.1-30 (1985).

12. Miyata, T., Toh, H., Hayashida, H., Kikuno, R., Inokuchi, Y., Saigo, K.
Sequence homology among reverse transcriptase-containing viruses and transposable genetic element: functional and evolutionary implications.
In: Populaton Genetics and Molecular Evolution, Ohta, T. and Aoki, K. eds., Japan Sci. Soc. Press, Tokyo/ Springer-Verlag, Berlin, pp. 313-331 (1985).

13. Toh, H.
T7 and E. coli share homology for replication-related gene products.
FEBS Lett. 194, 245-248 (1986).

14. Toh, H., Imamura, A., Kanda, K.
Role of Mg2+ in the ribozyme system.
FEBS Lett. 219, 279-282 (1987).

15. Toh, H. Imamura, A., and Kanda, K.
Whether Zn2+ for polymerase system was selected inevitably or by historical accident.
J. Theor. Biol. 136, 79-85 (1989).

16. Toh, H.
Prostaglandin endoperoxide synthase contains an EGF-like domain.
FEBS Lett. 258, 317-319 (1989).

17. Toh, H., Minami, M., Shimizu, T.
Molecular evolution and zinc ion binding motif of leukotriene A4 hydrolase.
Biochem. Biophys. Res. Commun. 171, 216-221 (1990).

18. Yoshimoto, T., Yamamoto, Y., Arakawa, T., Suzuki, H., Yamamoto, S., Yokoyama, C., Tanabe, T., Toh, H.
Molecular cloning and expression of human arachidonate 12-lipoxygenase.
Biochem. Biophys. Res. Commun. 172, 1230-1235 (1990).

19. Minami, M., Ohnishi, N., Mutoh, H., Izumi, T., Bito, H., Wada, H., Seyama, Y., Toh, H., Shimizu, T.
Leukotriene A4 hydrolase is a zinc-containing aminopeptidase.
Biochem. Biophys. Res. Commun. 173, 620-626 (1990).

20. Toh, H.
N-terminal halves of gramicidine S synthetase 1, and tyrocidine synthetase 1 as novel members of firefly luciferase family.
Protein Seq. Data Anal. 3, 517-521 (1990).

21. Honda, Z., Nakamura, M., Miki, I., Minami, M., Watanabe, T., Seyama Y., Okado, H., Toh, H., Ito, K., Miyamoto, T., Shimizu, T.
Cloning by functional expression of platelet-activating factor receptor from guinea-pig lung.
Nature 349, 342-346 (1991).

22. Nagata, A., Suzuki, Y., Igarashi, M., Eguchi, N., Toh, H., Urade, Y., Hayaishi, O.
Human brain PGD synthase has been evolutinarily differentiated from lipophilic-ligand carrier proteins.
Proc. Natl. Acad. Sci. USA 88, 4020-4024 (1991).

23. Iwasaki, H., Ishino, Y., Toh, H., Nakata, A., Shinagawa, H.
Escherichia coli DNA polymerase II is homologous to a-like DNA polymerases.
Mol. Gen. Genet. 226, 24-33 (1991).

24. Toh, H.
Sequence analysis of firefly luciferase family reveals a conservative sequence motif.
Protein Seq. Data Anal. 4, 111-117 (1991).

25. Abe, T., Fujino, T., Fukuyama, R., Minoshima, S., Shimizu, N., Toh, H., Suzuki, H., Yamamoto, T.
Human long-chain acyl-CoA synthetase: structure and chromosomal location.
J. Biochem. 111, 123-128 (1992).

26. Igarashi, M., Nagata, A., Toh, H., Urade, Y., Hayaishi, O.
Structural organization of the gene for prostaglandin D synthase in the rat brain.
Proc. Natl. Acad. Sci. USA 89, 5376-5380 (1992).

27. Kawamura, T., Shigesada, K., Toh, H., Okumura, S., Yanagisawa, S., Izui, K.
Molecular evolution of phosphoenolpyruvate carboxylase for C4 photosynthesis in maize: Comparison of its cDNA sequence with a newly isolated cDNA encoding an isozyme involved in the anaplerotic function.
J. Biochem. 112, 147-154 (1992).

28. Toh, H., Urade, Y., Tanabe, T.
Molecular evolution of enzymes involved in the arachidonic acid cascade.
Mediators of Inflammation 1, 223-233 (1992).

29. Toh, H., Yokoyama, C., Tanabe, T., Yoshimoto, T., Yamamoto, S.
Molecular evolution of cyclooxygenase and lipoxygenase.
Prostaglandins 44, 291-315 (1992).

30. Uemori, T., Ishino, Y., Toh, H., Asada, K., Kato, I.
Organization and nucleotide sequence of the DNA polymerase generom the archaeon Pyrococcus furiosus.
Nucleic Acids Res. 21, 259-265 (1993).

31. Miyata, A., Yoshida, T., Yamaguchi, K., Yokoyama, C., Tanabe, T., Toh, H., Mitsunaga, T., Izumi, Y.
Molecular cloning and expression of the gene for serine hydroxymethyltransferase from an obligate methyltroph Hyphomicrobium methylovorum GM2.
Eur, J. Biochem. 212, 745-750 (1993).

32. Toh, H.
Homology search and prediction of biological function of protein from amino acid sequences.
In: Methods in Protein Sequence Analysis, In: Imahori, K. and Sakiyama, F. eds., Plenum Press, New York, pp. 233-240 (1993).

33. Toh, H., Kondo, H., Tanabe, T.
Molecular evolution of biotin-dependent carboxylases.
Eur. J. Biochem. 215, 687-696 (1993).

34. Toh, H., Kawamura, T., Izui, K.
Molecular evolution of phosphoenolpyruvate carboxylase.
Plant, Cell and Environment 17, 31-43 (1994).

35. Yoshida, T., Yamaguchi, K., Hagishita, T., Mitsunaga, T., Miyata, A., Tanabe, T., Toh, H., Ohshiro, T., Shimao, M., Izumi, Y.
Cloning and expression of the gene for hydroxypyruvate reductase (D-glycerate dehydrogenase) from an obligate methylotroph Hyphomicrobium methyovorum GM2.
Eur. J. Biochem. 223, 727-732 (1994).

36. Sone, N., Toh, H.
Membrane-bound Bacillus cytochrome c and their phylogenetic position among bacterial Class I cytochromes c.
FEMS Microbiol. Lett. 122, 203-210 (1994).

37. Todo, T., Ryo, H., Takemori,., Toh, H., Nomura, T., Kondo, S.
High-level expression of the photorepair gene in Drosophila ovary and evolutionary implications.
Mutation Res. DNA Repair 315, 213-228 (1994).

38. Urade, Y., Tanaka, T., Eguchi, N., Kikuchi, M., Kimura, H., Toh, H., Hayashi, H.
Structural and functional significance of cysteine residues of glutathione-independent prostaglandin D synthase.
J. Biol. Chem. 270 1422-1428 (1995).

39. Toh, H., Ichikawa, A., Narumiya, S.
Molecular evolution of receptors for eicosanoids.
FEBS Lett. 361, 17-21 (1995).

40. Nakamura, T., Yoshioka, I., Takahashi, M., Toh, H., Izui, K.
Cloning and sequence analysis of the gene for phosphoenol-pyruvate carboxylase from an extreme thermophile, Thermus sp.
J. Biochem. 118, 319-324 (1995).

41. Ohmiya, Y., Ohba, N., Toh, H., Tsuji, F. I.
Cloning, expression and sequence analysis of cDNA for the luciferases from the Japanese fireflies, Pyrocoelia miyako and Hotaria parvula.
Photochemistry and Photobiology 62, 309-313 (1995).

42. Tsuji, F. I., Ohmiya, Y., Fagan, T. F., Toh, H., Inouye, S.
Molecular evolution of the Ca2+-binding photoproteins of the hydrozoa.
Photochemistry and Photobiology 52, 657-661 (1995).

43. Todo, T., Ryo, H., Yamamoto, K., Toh, H., Inui, T., Ayaki, H., Nomura, T., Ikenaga, M.
Science 272, 109-112 (1996).

44. Fruh, Th., Saika, H., Svensson, L., Pitterna, Th., Sakaki, J., Okada, T., Urade, Y., Oda, K., Fujitani, Y., Takimoto, M., Yamamura, T., Inui, T., Makatani, M., Takai, M., Umemura, I., Teno, N., Toh, H., Hayakawa, K., Murata, T.
IRL2500: A potent ETB selective endothelin anatagonist.
Bioorganic & Medical Chemistry Lett. 6, 2323-2328 (1996).

45. Toh, H., Kubodera, H., Nakajima, N., Sekiya, T., Eguchi, N., Tanaka, T., Udade, Y., Hayaishi, O.
Glutathione-independent prostaglandin D synthase as a lead molecule for designing new functional proteins.
Protein Engineering 9, 1067-1082 (1996).

46. Todo, T., Kim, S.-T., Hitomi, K., Otoshi, E., Inui, T., Morioka, H., Kobayashi, H., Ohtsuka, E., Toh, H., Ikenaga, M.
Flavin adenine dinucleotide as a chromophore of the Xenopus (6-4) photolyase.
Nucleic Acids Res. 25, 764-768 (1997).

47.Yoshinobu, K., Kondo, T., Takai, M., Katagiri, C., Toh, H., Abe, S., Takamune, K.
Primary structures of sperm-specific basic nuclear proteins and gene expression in Japanese newt, Cynops pyrrhogaster.
Mol. Reproduction and Development 46, 243-251 (1997).

48.Kanai, S., Toh, H., Ryo, H., Todo, T.
Molecular evolution of the photolyase - blue-light photoreceptor family.
J. Mol. Evol. (1997) 45, 535-548.

49.Toh, H.
Introduction of a distance cut-off approximation into structural alignment by the double dynamic programming algorithm.
CABIOS 13, 387-396 (1997).

50.Kanaoka, Y., Ago, H., Inagaki, E., Nanayama, T., Miyano, M.,
Kikuno, R., Fujii, Y., Eguchi, N., Toh, H., Urade, Y., Hayaishi, O.
Cloning and crystal structure of hematopoietic prostaglandin D synthase.
CELL 90, 1085-1095 (1997).

51.Masamoto, K., Misawa, N., Kaneko, T., Kikuno, R., Toh, H.
b-Carbon hydroxylase gene from the Cyanobacterium Synechocystis sp.PCC6803.
Plant Cell Physiol. 39, 560-564 (1998).

52.Mukae, N., Enari, M., Sakahira, H., Fukuda, Y., Inazawa, J.,
Toh, H., Nagata, S.
Molecular cloning and characterization of human caspase-activated DNase.
Proc. Natl. Acad. Sci. USA 95, 9123-9128 (1998).

53.Kanai, S., Toh, H., Hayano, T., Kikuchi, M.
Molecular evolution of the domain structures of protein disulfide isomerases.
J. Mol. Evol. 47, 200-210 (1998).

54.Toh, H., Tanabe, T.
"Cyclooxygenase (prostaglandin H synthase): structure and evolutionary aspects."
In:Eicosanoids and Related Compounds in Plants and Animals.
(Eds. Rowley et al.) Portland Press, London, pp.25-46 (1998).

55.Cann, I.K.O., Komori, K., Toh, H., Kanai, S., Ishino, Y.
A heterodimeric DNA polymerase: Evidence that members of euryarcheota possess a distinct DNA polymerse.
Proc. Natl. Acad. Sci. USA 95, 14250-14255 (1998).

56.Horimoto, K., Suyama, M., Toh, H., Mori, K., Ohtsuka, J.
A method of comparing circular genomes from gene locations: application to mitochondrial genomes.
Bioinformatics 14, 789-802 (1998).

57.Cann, I.K.O., Kanai, S., Toh, H., Ishino, Y.
Adenylosuccinate synthetase gene:Molecular cloning ans phylogenetic analysis of highly conserved arachaeal gene.
System. Appl. Microbiol. 21, 478-486 (1998).

58.Satoh, K., Toh, H.
Tertiary Structure Database Searching with peropheral distributions of a distance map.
Res. Commun. Biochem. Cell Mol. Biol. 2, 289-308 (1998).

59.Kanai, S., Toh, H.
Identification of new members of the GS ADP-forming family from de nove purine biosynthesis pathway.
J. Mol. Evol. 48, 489-492 (1999).

60.Kikuno, R., Daiyasu, H., Toh, H.
"Molecular evolution of proteins involved in the arachidonic acid cascade."
In:Comprehensive Natural Products Chemistry. (Eds. Barton et al.)
Volume I Polyketides and secondary metabolites including fatty acids and their derivatives. Elsevier, Amsterdam, pp273-284 (1999).

61.Yura, K., Toh, H., Go, M.
Putative mechanism of genetic transformation as detected from genome data.
DNA Res. 6, 75-82 (1999).

62.Beuckmann, C.T., Aoyagi, M., Okazaki, I., Hiroike, T., Toh, H., Hayaishi, O., Urade, Y.
Binding of biliverdin, biliruvin, and thyroid hormones to lipocalin-type prostaglandin D synthase.
Biochemistry 22, 8006-8013 (1999).

63.Cann, I.K., Ishino, S., Hayashi, I., Komori, K., Toh, H., Morikawa, K., Ishino, Y.
Functional interactions of a homolog of proliferating cell nuclear antigen with DNA polymerases in archaea.
J. Bacteriol. 81, 6591-6599 (1999).

64.Tsutsui, Y., Morishita, T., Iwasaki, H., Toh, H., Shinagawa, H.
A recombination repair gene of Saccharomyces pombe, rhp57, is a functional homolog of the Saccharomyces cerevisiae RAD57 gene and is phylogenetically related to the human XRCC3 gene.
Genetics 154, 1451-1461 (2000).

65.Iwasaki, H., Han, Y.W., Okamoto, T.,Yoshikawa, M., Yamada, K., Toh, H., Daiyasu, H., Ogura, T., Shinagawa, H.
Mutational analysis of the functional motifs of RuvB, an AAA+ class helicase and motor protein for Holliday junction branch migration.
Mol. Microbiol. 36, 528-538 (2000).

66.Hitomi, K., Okamoto, K., Daiyasu, H., Miyashita, H., Iwai, S., Toh, H., Ishiura, M., Todo, T.
Bacterial cryptochrome and photolyase: characterization of two photolyase-like genes of Synechocystis sp. PCC6803.
Nucleic Acids Res. 28, 2353-2362 (2000).

67.Hiroike, T., Higo, J., Jingami, H., Toh, H.
Homology modeling of human leptin/leptin receptor complex.
Biochem. Biophys. Res. Commun.275, 154-158 (2000).

68.Kobayashi,Y., Ishikawa, T., Hirayama, J., Daiyasu, H., Kanai, S., Toh, H., Fukuda, I., Tsujimura, T., Terada, N., Kamei, Y., Yuba, S., Iwai, S., Todo, T.,
Molecular analysis of zebrafish photolyase/cryptochrome family:two types of cryptochromes present in zebrafish.
Genes Cells 5, 727-728 (2000).

69.Komori, K., Miyata, T., Daiyasu, H., Toh, H., Shinagawa, H., Ishino, Y.
Domain analysis of an archaeal RadA protein for the strand exchange activity.
J.Biol.Chem. 275, 33791-33797 (2000).

70.Daiyasu, H., Komori, K., Sakae, S., Ishino, Y., Toh, H.
Hjc resolvase is a distantly related member of the type II restriction endonuclease family.
Nucleic Acids Res. 28, 4540-4543 (2000).

71.Daiyasu, H., Toh, H.
Molecular evolution of the myeloperoxidase family.
J. Mol. Evol. 51, 433-445 (2000).

72.Kanai, S., Toh, H.
GA generates new amino acid indices through comparison between native and random sequences.
IPSJ Transaction on Mathematical Modeling and Applications 41, 23-40 (2000).

73.Komori, K., Sakae, S., Daiyasu, H., Toh, H., Morikawa, K., Shinagawa, H., Ishino, Y.
Mutational analysis of the Pyrococcus furiosus Holliday junction resolvase Hjc revealed functionally important residues for dimer formation, junction DNA binding and cleavage activities.
J. Biol. Chem. 275 40385-40391 (2000).

74. Cann, I.K., Ishino, S., Yuasa, M., Daiyasu, H., Toh, H., Ishino, Y.
Biochemical Analysis of Replication Factor C from the Hyperthermophilic Archaeon Pyrococcus furiosus.
J. Bacteriol. 183, 2614-2623 (2001).

75. Daiyasu, H., Osaka, K., Ishino, Y., Toh, H.
Expansion of the zinc-metallo hydrolase family of the beta-lactamase fold. (Minireview)
FEBS Lett. 503, 1-6 (2001).

76. Hiroike, T., Toh, H.
A local structural alignment method that accomodates with circular permutation.
CBI Journal 1, 103-114 (2001).

77. Ichihara, H., Jingami, H., Toh, H.
Three novel repetitive units of Reelin.
Mol. Brain Res. 97, 190-193 (2001).

78. Horimoto, K., Toh, H.
Statistical estimation of cluser boundaries in gene expression profile data.
Bioinformatics 17 1143-1151 (2001).

79. Toh, H., Horimoto, K.
Inference of a genetic network by a combined approach of cluster analysis and graphical modeling.
Bioinformatics 18, 287-297 (2002).

80. Ikema, Y., Hiyoshi, M., Daiyasu, H., Toh, H., Mori, M., Takamune, K.
Two Novel Genes Expressed in Xenopus Germ Line: Characteristic Features of Putative Protein Structures, Their Gene-Expression and Their Possible Roles in Gametogenesis and Embryogenesis.
Molecular Reproduction and Development 62, 421-430 (2002).