Publication List

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
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 (Eds. Gresser et al.),  Academic Press, London, pp.1-30

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, (Eds. Ohta and Aoki)
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
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
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 gene from 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 (Eds. Imahori and Sakiyama)
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, H., 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.
Similarity among the Drosophila (6-4) photolyase, a human photolyase homolog,
and the DNA photolyase-blue-light photoreceptor family.
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.,
Urade, 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)
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. 45, 535-548  (1997).

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, pp25-46 (1998).

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

56. Horimoto, K., Suyama, M., Toh, H., Mori, K., Otsuka, J.
A method for 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 and phylogenetic analysis
of highly conserved archaeal gene.
System. Appl. Microbiol. 21, 478-486 (1998).

58. Satoh, K, Toh, H.
Tertiary Structure Database Searching with Peripheral 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 novo 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
Biochemistry 38, 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. 181, 6591-6599 (1999).

64. Tsutsui, Y., Morishita, T., Iwasaki, H., Toh, H., Shinagawa, H.
A recombination repair gene of Schizosaccharomyces 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., Ohnishi, 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 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, 725-738 (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 b-lactamase fold. (Minireview)
FEBS Lett. 503, 1-6 (2001).

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

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

78. Horimoto, K, Toh, H.
Statistical estimation of cluster 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 Gaussian 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).

81. Toh, H., Horimoto, K.
System for automatically inferring a genetic network from expression profiles
J. Biol. Phys. 28, 449-464 (2002).

82. Daiyasu, H., Hiroike, T., Koga, Y., Toh, H.
An analysis of membrane stereochemistry with homology modeling of sn-glycerol-1-phosphate dehydrogenase.
Protein Engineering 15, 987-995 (2002).

83. Brudler, R.  Hitomi, K. Daiyasu, H., Toh, H.,  Kucho, K., Ishiura, M., Kanehisa, M.,  Roberts, V.A., Todo, T., Tainer, J.A., Getzoff, E. G.
Identification of a New Cryptochrome Class: Structure, Function, and Evolution.
Molecular Cell 11, 59-67 (2003).

84. Suzuki T, Yamasaki K, Fujita S, Oda K, Iseki M, Yoshida K, Watanabe M, Daiyasu H, Toh H, Asamizu E, Tabata S, Miura K, Fukuzawa H, Nakamura S, Takahashi T.
Archaeal-type rhodopsins in Chlamydomonas: model structure and intracellular localization.
Biochem Biophys Res Com. 301, 711-717 (2003).

85. Aburatani, S., Kuhara, S., Toh, H., Horimoto, K.
Deduction of a regulatory network from gene expression data by the application of graphical Gaussian modeling.
Signal Processing 83, 777-788 (2003).

86. Ichihara, H., Daiyasu, H, Toh, H.
How does a topological inversion change the evolutionary constraints on membrane proteins?
Protein Eng Des Sel. 17, 235-244(2004).

87. Daiyasu, H., Ishikawa, T., Kuma, K., Iwai, S., Todo, T., Toh, H.
Identification of cryptochrome DASH from vertebrates.
Genes to Cells 9, 479-495 (2004).

88. Stamdley, D., Toh, H., Nakamura, H.
Detecting Local Structural Similarity in Proteins by Maximizing the Number of Equivalent Residues
PROTEINS: Structure, Function, and Bioinformatics 57, 381-391 (2004)

89. Toh, H., Osaka, K., Takei, T.
Molecular phylogenetic analysis of pulmonary surfactant protein C and the relatives.
J. Jpn. Med. Soc. Biol. Interface 35, 24-31 (2004).

90. Aburatani S, Goto K, Saito S, Fumoto M, Imaizumi A, Sugaya N, Murakami H, Sato M, Toh H, Horimoto K.
ASIAN: a web site for network inference.
Bioinformatics 20, 2853-2856 (2004).

91. Nemoto, W., Toh, H.
Prediction of interfaces for oligomerizations of G-protein coupled receptors
PROTEINS 58, 644-660 (2005)

92. Katoh, K., Kuma, K. Toh, H., Miyata, T.
MAFFT version 5: improvement in accuracy of multiple sequence alignment.
Nucleic Acids Res. 33, 511-518 (2005)

93. Aburatani, S., Goto, K., Saito, S., Toh, H., Horimoto, K.
ASIAN: a web server for inferring a regulatory network framework from gene expression profiles.
Nucleic Acids Res. 33, W659-W664. (2005)

94. Sato, T., Yamanishi, Y., Kanehisa, M., Toh, H.
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships.
Bioinformatics 21, 3482-3489 (2005).

95. Katoh, K., Kuma, K., Miyata, T., Toh, H.
Improvement in the accuracy of multiple sequence alignment program MAFFT
Genome Informatics 16, 22-33 (2005)

96. Standley,D.M., Toh,H., Nakamura,H.
GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures.
BMC Bioinformatics 6, 221 (2005)

97. Matsuda, S., Vert,J.-P., Saigo, H., Ueda, N., Toh, H., Akutsu, T.
A novel representation of protein sequences for predictionof subcellular localization using support vector machines.
Protein Sci. 14, 2804-2813 (2005).

98. Daiyasu, H., Kuma, K., Yokoi, T., Morii, H., Koga, Y., Toh, H.
A study on archaeal enzymes involved in polar lipids synthesis by an approach linking the information about amino acid sequences, genomic  contexts and lipid composition
Archaea 1, 399-410 (2005)

99. Aburatani, S., Saito, S., Toh, H., Horimoto, K.
A graphical chain model for inferring regulatory system networks from  gene expression profiles.
Statistical Methodology 3, 17-28 (2006).

100. Ichihara, H., Kuma, K., Toh, H.
Positive selection in the ComC-ComD system of streptococcal species.
J. Bacteriol. 188, 6429-6434 (2006)..

101. Kojima, K., Kuma, K., Toh, H., Fujiwara, H.
Identification of rDNA-specific non-LTR retrotransposons in Cnidaria.
Mol. Biol. Evol. 23, 1984-1993 (2006)

102. Sato, T., Yamanishi, Y., Horimoto, K., Kanehisa, M., Toh, H.
Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions.
Bioinformatics 22, 2488-2492 (2006)

103. Nemoto, W., Toh, H.
Membrane interactive a-helices in GPCRs as a  novel drug target (review)
Curr. Protein Pept Sci. 7, 561-575 (2006).

104. Katoh, K., Toh, H.
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences.
Bioinformatics 23, 372-374 (2007).

105. Standley, D.M., Toh, H., Nakamura, H.
ASH structural alignment package: Sensitivity and selectivity in domain classification.
BMC Bioinformatics 8, 116 (2007).

106.  Sato, T., Yamanishi, Y., Horimoto, K., Kanehisa, M., Toh, H.
Inference of Protein-Protein Interaction by Using Co-evolutionary Information.
Algebraic Biology - 2nd International Conference, Algebraic Biology 2007  Proceedings - (Eds. Anai, H., Horimoto, K., Kursita T.), Springer, Berlin, pp322- 333 (2007).

107. Ichihara, H., Kuma, K., Urade, Y., Toh, H.
Evoltionary analysis of lipocalin-type prostaglandin D2 synthase.
In: prostaglandin D2 synthase -  A Multitude of Biological Functions (Ed. Ragolia, L.),
Research Signpost, Kerala, pp. 29– 46 (2007). 

108. Moriuchi H, Koda N, Okuda-Ashitaka E, Daiyasu H, Ogasawara K, Toh H, Ito S, Woodward DF, Watanabe K.
Molecular Characterization of a Novel Type of Prostamide/Prostaglandin F Synthase, Belonging to the Thioredoxin-like Superfamily.
J. Biol. Chem. 283, 792-801 (2008).

109. Daiyasu, H., Watanabe, K., Toh, H.
Recruitment of thioredoxin-like domains into prostaglandin synthases. (Minireview)
Biochem, Biophys. Res. Commun. 369, 281-286 (2008).

110. Standley, D.M., Toh, H., Nakamura, H.
Functional annotation by sequence-weighted structure alignments: Statistical analysis and case studies from the Protein 3000 structural genomics project in Japan.
PROTEINS 72, 1333-1351 (2008).

111. Katoh, K.,  Toh, H.
Recent developments in the MAFFT multiple sequence alignment program.  (Review)
Brief. Bioinform. 9, 286-298 (2008)

112. Katoh, K., Toh, H.
Four-way Consistency: an objective function for multiple structural alignment of ncRNAs with an iterative refinement method.
BMC Bioinformatics 9, 212 (2008).

113. Daiyasu, H., Saino, H., Tomoto, H., Mizutani, M., Sakata, K., Toh, H.
Computational and Experimental Analyses of Furcatin Hydrolase for Substrate Specificity Studies on Disaccharide-specific Glycosidases.
J. Biochem. 144, 467-475 (2008)

114. Ebina, T., Toh, H., Kuroda, Y.
Loop-length dependent SVM prediction of domain linkers for high-throughput structural proteomics.
Biopolymers 92, 1-8 (2009)

115. Katoh, K.,  Asimenos, G.,  Toh, H.
Multiple Alignment of DNA Sequences with MAFFT  (Review)
Methods in Molecular Biology 537, 39 – 62 (2009)

 116. Wang, Y., Kurihara, Y., Sato, T,, Toh, H., Kobayashi, H., Sekiguchi, T.
Gtr1p differentially associates with Gtr2p and Ego1p
Gene 437, 32-38 (2009)

117. Shimizu, K., Toh, H.
Interactions between intrinsically disordered proteins frequently occurs in a human protein-protein interaction network.
J. Mol. Biol. 392, 1253-1265 (2009)

118. Nemoto, W., Toh, H.
GRIP: A server for predicting interfaces for GPCR oligomerization
J. Receptors and Signal Transduction  29, 312-317 (2009).

119. Yamaguchi, A., Toh, H.
Visualization of Genetic Networks: Edge Crossing Minimization of a Graph Drawing with Vertex Pairs
Res. Commun. Biochem. Cell & Mol. Biol.  14, 5 – 14 (2009).

120 Iwatsuki M, Mimori K, Sato T, Toh H, Yokobori T, Tanaka F, Ishikawa K, Baba H, Mori M.
Overexpression of SUGT1 in human colorectal cancer and its clinicopathological significance.
Int J Oncol. 36, 569-575 (2010)

121. Kawakami Y, Yamashita C, Kashiwase Y, Morinaka T, Suzuki-Yamamoto T, Yamashita H, Kimoto M, Tsuji H, Kurahashi Y, Daiyasu H, Toh H, Sugahara M, Miyano M, Yamamoto S, Takahashi Y.
Functional expression of single-chain antibody to leukotriene C(4).
Biochem. Biophys.Res. Commun. 392, 421-425 (2010).

122. Iwatsuki, M., Mimori, K., Ishii, H., Yokobori, T., Takatsuno, Y., Sato, T., Toh, H., Onoyama, I., Nakayama, K., Baba, H., Mori, M.
Loss of FBXW7, a cell cycle regulating gene, in colorectal cancer: clinical  significance.
International Journal of Cancer, 126, 1828-1837 (2010).

123.  Osawa, H., Iwatsuki, M., Mimori, K., Sato, T., Johansson, F., Toh, H., Watanabe, M., Mori, M.
FANC2D mRNA over-expression is a bona-fide  indicator of  lymph node  metastasis in human  colorectal  cancer.
Annals of Surgical Oncology 17, 2341-2348 (2010).

124.  Katoh, H., Toh, H.
Parallelization of the MAFFT multiple sequence alignment program.
Bioinformatics 26, 1899-1900 (2010).

125. Standley, D.M., Yamashita, R., Kinjo, A.R., Toh, H., Nakamura, H.
SeSAW: balancing sequence and structural information in protein functional mapping.
Bioinformatics. 26, 1258-1259 (2010).

126. Johansson, F., Toh, H.
Relative von Neumann entropy for evaluating amino acid conservation
Journal of Bioinformatics and Computational Biology 8, 809-823 (2010).

127. Sato, T., Yamanishi, Y., Kanehisa, M., Horimoto, K., Toh, H.
Improvement of the mirrortree method by extracting evolutionary information. (review)
In: Sequence and Genome Analysis (ed. Zhao, Z.) iConcept Press (in press).

128. Iizuka, Y., Okuno‡, T.,Saeki, K., Uozaki, H., Okada, S., Misaka,, T. Sato, T., Toh, H., Fukayama, M., Takeda$, N. Kita, Y., Shimizu, T., Nakamura,, M., Yokomizo, T.
Protective roles of second leukotriene B4 receptor BLT2 in murine model of inflammatory colitis.
FASEB J. 24, 4678-4690 (2010).

129. Johansson, F., Toh, H.
A comparative study of conservation and variation scores.
BMC Bioinformatics 11, 388 (2010) (highly accessed).

130. Ebina, T., Toh, H., Kuroda, Y.
DROP: An SVM domain linker predictor trained with optimal features selected by random forest.
Bioinformatics 27, 487-494 (2011).

131. Nemoto, W., Fukui, K., Toh, H.
GRIPDB – G protein coupled receptor interaction partners database.
J. Recept. Signal Transduct. Res. 31, 199-205 (2011).

132. Shibata K, Yamada H, Sato T, Dejima T, Nakamura M, Ikawa T, Hara H, Yamasaki S, Kageyama R, Iwakura Y, Kawamoto H, Toh H, Yoshikai Y.
Notch-Hes1 pathway is required for the development of IL-17-producing γδ T cells
Blood 118, 586-593 (2011).

133. Totsukawa, G., Kaneko, Y., Uchiyama, K., Toh, H., Kondo, H.
VCIP135 deubiquitinase and its binding protein, WAC, in p97 ATPase-mediated membrane fusion.
EMBO J. 30, 3581-3593 (2011)

134. Daiyasu, H. Hirokawa, T., Kamiya, N., Toh, H.
Computational Analysis of Ligand Recognition Mechanisms by Prostaglandin E2 (subtype 2) and D₂ Receptors.
Theor. Chem. Acc. 130, 1131-1143 (2011).

135. Nemoto, W. Toh, H.
Functional region prediction with a set of appropriate homologous sequences - an index for sequence selection by integrating structure and sequence information with spatial statistics.
BMC Struct. Biol. 12, 11 (2012) (highly accessed).

136. Yokobori, T., Mimori, K., Iwatsuki, M., Ishii, H., Tanaka, F., Sato, T., Toh, H., Sudo, T., Iwaya, T., Tanaka, Y., Onoyama, I., Kuwano, H., Nakayama, K.I., Mori, M.
Copy number loss of FBXW7 is related to gene expression and poor prognosis in esophageal squamous cell carcinoma.
Int J Oncol. 41, 253-259 (2012).

137. Ishimaru, S., Mimori, K., Yamamoto, K., Inoue, H., Imoto, S., Kawano, S., Yamaguchi, R., Sato, T., Toh, H., Iinuma, H., Maeda, T., Ishii, H., Suzuki, S., Tokudome, S., Watanabe, M., Tanaka, J.I., Kudo, S.E., Sugihara, K.I., Hase, K., Mochizuki, H., Kusunoki, M., Yamada K., Shimada, Y., Moriya, Y., Barnard, G.F., Miyano, S., Mori, M.
Increased Risk for CRC in Diabetic Patients with the Nonrisk Allele of SNPs at 8q24.
Ann Surg Oncol. 19, 2853-2858 (2012).

138. Daiyasu, H., Nemoto, W., Toh, H.
Evolutionary analysis of functional divergence among chemokine receptors, decoy receptors and viral receptors.
Front, Microbil. 3, 264 (2012).

139. Takatsuno, Y., Mimori, K., Yamamoto, K., Sato, T., Niida, A., Inoue, H., Imoto, S., Kawano, S., Yamaguchi, R., Toh, H., Iinuma, H., Ishimaru, S., Ishii, H., Suzuki, S., Tokudome, S., Watanabe, M., Tanaka, J.I., Kudo, S.E., Mochizuki, H., Kusunoki, M., Yamada, K., Shimada, Y., Moriya, Y., Miyano, S., Sugihara, K., Mori, M.
The rs6983267 SNP Is Associated with MYC Transcription Efficiency, Which Promotes Progression and Worsens Prognosis of Colorectal Cancer.
Ann. Surg. Oncol. 20, 1395-1402 (2012).

140. Yokobori, T., Iinuma, H., Shimamura, T., Imoto, S., Sugimachi, K., Ishii, H., Iwatsuki, M., Ota, D., Ohkuma, M., Iwaya, T., Nishida, N., Kogo, R,. Sudo, T., Tanaka, F., Shibata, K., Toh, H., Sato, T., Barnard, G.F., Fukagawa, T., Yamamoto, S., Nakanish,H., Sasaki, S., Miyano, S., Watanabe, T., Kuwano, H., Mimori, K., Pantel, K., Mori, M.
Plastin3 is a novel marker for circulating tumor cells undergoing the epithelial-mesenchymal transition and is associated with colorectal cancer prognosis.
Cancer Res. 73, 2059-2069 (2013).

141. Elahi, M., Islam, M.M., Noguchi, K., Yohda, M., Toh, H., Kuroda, Y.
Computational prediction and experimental characterization of a "size switch type repacking" during the evolution of dengue envelope protein domain III (ED3).
Biochim. Biophys. Acta 1844, 585-592 (2013)

142. Aburatani, S., Toh, H.
Estimation of Physical Transcriptional Control in Yeast Cell Cycle by Structure Equation Modeling.
In: Protein Purification and Analysis I, pp.103-121 iConcept Press (2013).

143. Aburatani, S., Toh, H.
Network Inference of AP pattern formation system in D.melanogaster by Structural Equation Modeling.
J. Physics: Conference Series, 490, pp.1-4 (2014).

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