LIST OF PUBLICATIONS

Akinori Sarai

BioInfo Bank.

1.       J. Sinclair and A. Sarai "Variations in Photosynthetic Electron-Transport Pathways in Chlorella Vulgaris." Biochem. Soc. Trans. 6, 904-905 (1978).

2.       J. Sinclair, A. Sarai , T. Arnason and S. Garland "Recent Studies on Photosystem II with the Modulated Oxygen Electrodes" In Photosynthetic Oxygen Evolution (ed., H. Metzner) pp. 294-320 (1978) Academic Press, London.

3.       J. Sinclair, A. Sarai and S. Garland "A Backflow of Electrons around Photosystem II in Chlorella Cells" Biochim. Biophys. Acta 546, 256-269 (1979).

4.       A. Sarai "Energy-Gap and Temperature Dependence of Electron and Excitation Transfer in Biological Systems" Chem. Phys. Lett. 63, 360-366 (1979).

5.       S. Kawamura, F. Tokunaga, T. Yoshizawa, A. Sarai and T. Kakitani "Orientational Changes of the Transition Dipole Moment of Retinal Chromophore on the Disk Membrane due to the Conversion of Rhodopsin to Bathorhodopsin and to Isorhodopsin" Vision Res. 19, 879-884 (1979).

6.       A. Sarai "Possible Role of Protein in Photosynthetic Electron Transfer" Biochim. Biophys. Acta 589, 71-83 (1980).

7.       A. Sarai and S. Yomosa "Temperature Dependence of Photosynthetic Excitation Transfer - Activationless Transfer -" Photochem. Photobiol. 31, 579-583 (1980).

8.       A. Sarai, T. Kakitani, Y. Shichida, F. Tokunaga and T. Yoshizawa "Simulation Analysis of Photoconversion Process of Squid Rhodopsin at Liquid Helium Temperature" Photochem. Photobiol. 32, 199-206 (1980).

9.       A. Sarai and S. Yomosa "Effect of Environment on the Temperature Dependence of Electron and Energy Transfer in Photosynthesis" In Photosynthesis (ed., G. Akoyunoglou) Vol. I, pp. 173-182 (1981) Balaban Inter-national Science Service.

10.  A. Sarai and T. Kakitani "Radiationless Transition of Molecules with Large Nuclear Rearrangement" Chem. Phys. Lett. 77, 427-432 (1981).

11.  A. Sarai, T. Kakitani and H. Kakitani "Proton Transfer in the Primary Process of Vision" Photochem. Photobiol. 33, 875-881 (1981).

12.  A. Sarai "Conformation-Coupled Proton Migration in Tetraphenylporphine" Chem. Phys. Lett. 83, 50-54 (1981).

13.  C.C. Schenck, W.W. Parson, D. Holten, M.W. Windsor and A. Sarai "Temperature Dependence of Electron Transfer between Bacteriopheophytin and Ubiquinone in Protonated and Deuterated Reaction Centers of Rhodopseudomonas sphaeroides" Biophys. J. 36, 479-489 (1981).

14.  A. Sarai "Dynamics of Proton Migration in Free Base Porphines" J. Chem. Phys. 76, 5554-5563 (1982).

15.  T. Kakitani, A. Sarai and H. Kakitani "Theoretical Study of Photoisomerization in Visual Pigments I. Formulation" J. Phys. Soc. Jpn. 51, 3302-3308 (1982)

16.  T. Kakitani, A. Sarai and H. Kakitani "Theoretical Study of Photoisomerization in Visual Pigments II. Numerical Calculation" J. Phys. Soc. Jpn. 51, 3309-3317 (1982).

17.  A. Sarai "Efficiency of Electron Transport Process" J. Theor. Biol. 99, 341-355 (1982).

18.  A. Sarai and D. DeVault "Temperature Dependence of High-Potential Cytochrome Photooxidation in C. vinosum" In Advances in Photosynthesis Research (ed., C. Sybesma) Vol. I, pp.653-656 (1983) Martinus Nijhoff/Dr W.Junk Publishers.

19.  A. Sarai and M. Saito "Theoretical Studies on the Interaction of Proteins with Base Pairs. I. Ab Initio Calculation for the Effect of H-Bonding Interaction of Proteins on the Stability of Adenine-Uracil Pair" Int. J. Quant. Chem. 25, 527-533 (1984).

20.  A. Sarai "Comment on 'IR-Spectroscopic Study of Isotope Effects on the NH/ND-Stretching Bands of meso-Tetraphenylporphine and Vibrational Hydrogen Tunneling' " J. Chem. Phys. 80, 5341-5343 (1984).

21.  A. Sarai "Stress-Induced Nonlinear Structural Transition in DNA" Phys. Letters 103A, 397-401 (1984).

22.  A. Sarai "Control of Base-Pair Stability by H-Bond Interactions with Proteins" In The Molecular Basis of Cancer Part B, pp. 37-43 (1985) Alan R. Liss, Inc., NewYork.

23.  A. Sarai and R. Jernigan "A Model of the Strain-Induced B-Z Transition" J. Biomol. Struct. Dynam. 2, 767-784 (1985).

24.  A. Sarai and M. Saito "Theoretical Studies on the Interaction of Proteins with Base Pairs. II. Effect of External H-Bond Interactions on the Stability of Guanine-Cytocine and Non-Watson-Crick Pairs" Int. J. Quant. Chem. 28, 399-409 (1985).

25.  A. Sarai "Self-Consistent Evaluation of Static Solitons, Pinning Energy and Soliton Energy in Discrete One-Dimensional Soliton Models" Phys. Letters 114A, 477-481 (1986).

26.  A. Sarai and D. DeVault "Proton Tunneling" Methods in Enzymology 127, 79-91 (1986).

27.  R.L. Jernigan, A. Sarai, K-L. Ting and R. Nussinov "Hydrophobic Interactions in the Major Groove Can Influence DNA Local Structure" J. Biomol. Struct. Dynam. 4, 41-48 (1986).

28.  R.L. Jernigan, A. Sarai, B. Shapiro and R. Nussinov "Relationship Between Curved DNA Conformations and Slow Gel Migration" J. Biomol. Struct. Dynam. 4, 561-567 (1987).

29.  A. Sarai and Y. Takeda "How Cro and Lambda Repressor Recognize Operator DNA Sequences" In Protein Structure, Folding and Design (ed., D.L. Oxtender) Vol. 2, pp. 57-64(1987) Alan R. Liss Inc., New York.

30.  A. Sarai , J. Mazur, R. Nussinov and R.L. Jernigan "Sequence Dependence of DNA Conformations: Means and Fluctuations" In Structure and Expression (eds. W.K. Olson, et al.) Vol. 3: DNA Bending and Curvature, pp. 213-223 (1987) Alan R. Liss Inc., New York.

31.  R. Nussinov, A. Sarai, D. Wang and R.L. Jernigan "Sequence Context of Homooligomer Tracts in Eukaryotic Genomes: Some DNA Conformational Implications" In Structure and Expression (eds. W.K. Olson, et al.) Vol. 3: DNA Bending and Curvature, pp. 129-138 (1987) Alan R. Liss Inc., New York.

32.  J. Mazur, A. Sarai and R.L. Jernigan "Interaction Range in B-Form DNA Double Helix" Proc. IMACS pp. 1-9 (1988).

33.  R.L. Jernigan, A. Sarai, D.G. Covell and J. Mazur "Exhaustive Enumeration and Evaluation of Feasible Conformations for Double Helix DNA and Folded Proteins" Proc. Int. Conf. Supercomputing 3, 197-200 (1988).

34.  A. Sarai, J. Mazur, R. Nussinov and R.L. Jernigan "Origin of DNA Helical Structures and Its Sequence Dependence" Bichemistry 27, 8498-8502 (1988).

35.  R. Nussinov, A. Sarai, G. Smythers, and R.L. Jernigan "Sequence Context of Oligomer Tracts in Eukaryotic DNA: Biological and Conformational Implications" J. Biomol. Struct. Dynam. 6, 543-562 (1988).

36.  Y. Takeda, A. Sarai and V.M. Rivera "Analysis of The Sequence-Specific Interactions between Cro Repressor and Operator DNA by Systematic Base Substitution Experiments" Proc. Natl. Acad. Sci. USA. 86, 439-443 (1989).

37.  J. Mazur, A. Sarai and R.L. Jernigan "Sequence Dependence of B-A DNA Conformational Transition" Biopolymers 28, 1223-1233 (1989).

38.  Sarai "Molecular Recognition and Information Gain" J. Theor. Biol. 140, 137-144 (1989).

39.  R. Nussinov, A. Sarai, G. Smythers, and R.L. Jernigan "Distinct Patterns in Homooligomer Tract Sequence Context in Prokaryotic and Eukaryotic DNA" Biochim. Biophys. Acta. 1008, 329-338 (1989).

40.  R. Nussinov, A. Sarai, G. Smythers, and R.L. Jernigan "Strong Patterns in Homooligomer Tracts Occur in Non-coding and Potential Regulatory Sites in Eukaryotic Genomes" J. Biomol. Struct. Dynam. 7, 707-722 (1989).

41.  A. Sarai and Y. Takeda "Lambda Repressor Recognizes the Approximately 2-fold Symmetric Half-Operator Sequences Asymmetrically" Proc. Natl. Acad. Sci. USA. 86, 6513-6517 (1989).

42.  A. Sarai, J. Mazur, R. Nussinov and R.L. Jernigan "Sequence Dependence of Conformational Flexibility of DNA" Biochemistry 28, 7842-7849 (1989).

43.  S. Goodman, C.-C. Yang, H. Nash, A. Sarai , and R.L. Jernigan "Bending of DNA by IHF Protein" In DNA Protein Complexes and Proteins (eds., R.H. Sarma and M.H. Sarma) pp. 51-62 (1990) Academic Press, New York.

44.  A.K. Konopka and A. Sarai "Somatic Cell Illegitimate Recombination via Tetraplex DNA Intermediate" In Human Genome Initiative and DNA Recombination (eds., R.H. Sarma and M.H. Sarma) pp. 243-251 (1990) Academic Press, New York.

45.  C. Kanei-Ishii, A. Sarai, T. Sawazaki, H. Nakagoshi, D.-M. He, K. Ogata, Y. Nishimura, and S. Ishii "The Tryptophan Cluster: A Hypothetical Structure of the DNA-binding Domain of the myb Protooncogene Product" J. Biol. Chem. 265, 19990-19995 (1990).

46.  Raghunathan, K.-L. Ting, R. L. Jernigan and A. Sarai "Effect of Hydration Energy on the Sequence-Dependent Conformation Variation of DNA" J. Biomol. Struct. Dynam. 8, 187-198 (1990).

47.  K.I. Nakayama, A. Sarai, and H. Nakauchi "Single Amino Acid Substitutions Determine Mouse CD8 Allotypes: Epitope Mapping of Mouse CD8" Immunogenetics 33, 206-209 (1991).

48.  C. Kanei-Ishii, E.M. Macmillan, T. Nomura, A. Sarai, R.G. Ramsay, S. Aimoto, S. Ishii, and T.J. Gonda "Transactivation and Transformation by Myb are Negatively Regulated by a Leucine Zipper Structure" Proc. Natl. Acad. Sci. USA 89, 3088-3092 (1992).

49.  K. Ogata, H. Hojo, S. Aimoto, T. Nakai, H. Nakamura, A. Sarai, S. Ishii, and Y. Nishimura "Solution Structure of a DNA-Binding Unit of Myb: A Helix-Turn-Helix-Related Motif with Conserved Tryptophans Forming a Hydrophobic Core" Proc. Natl. Acad. Sci. USA 89, 6428-6432 (1992).

50.  Y. Nishimura, K. Ogata, H. Hojo, S. Aimoto, T. Nakai, H. Nakamura, A. Sarai , and S. Ishii "Three-dimentional Structure of the DNA-Binding Domain of a Proto-oncogene Product, Myb" In Molecular Structure and Life (eds., Y. Kyogoku and Y. Nishimura) pp. 103-113 (1992) Japan Sci. Soc. Press, Tokyo / CRC Press, Boca Raton.

51.  T. Yamamori, and A. Sarai "Coevolution of Cytokine Receptor Families in the Immune and Nervous Systems" Neurosci. Res. 15, 151-161 (1992).

52.  R. Wadhwa, S.C. Kaul, Y. Komatsu, Y. Ikawa, A. Sarai, and Y. Sugimoto "Identification and differential expression of Yeast SEC23-related gene (Msec23) in Mouse Tissues" FEBS Lett. 315, 193-196 (1993).

53.  M. Sakimata, M. Takabe, A. Sarai, J. Yamamoto, A. Kariyone, H. Nakauchi, K. Egawa, and M. Takiguchi "Different Effect of Substitutions at Residues 224 and 228 of MHC class I on the Recognition of CD8" J. Immunol. 150, 4416-4426 (1993).

54.  H. Torigoe, H. Shindo and A. Sarai "Thermodynamics of Tetraplex (T2G4)n and (T4G4)n" Nucleic Acids Symp. Ser. 29, 189-190 (1993).

55.  K. Yoshida, Y. Fujita, and A. Sarai "Missense Mutations in the Bacillus subtilis gnt Repressor that Diminish the Ability of Operator Binding" J. Mol. Biol. 231, 167-174 (1993).

56.  A. Sarai, H. Uedaira, H. Morii, T. Yasukawa, K. Ogata, Y. Nishimura, and S. Ishii "Thermal Stability of the DNA-Binding Domain of Myb Onco-protein" Biochemistry 32, 7759-7764 (1993).

57.  H. Shindo, H. Torigoe, and A. Sarai "Thermodynamic and Kinetic Studies of DNA Triplex Formation of and Oligohomopyrimidine and a Matched Duplex by Filter Binding Assay" Biochemistry 32, 8963-8969 (1993).

58.  A. Sarai, S. Sugiura, H. Torigoe, and H. Shindo "Thermodynamic and Kinetic Analyses of DNA Triplex Formation: Application of Filter-Binding Assay" J. Biomol. Struct. Dynam. 11, 245-252 (1993).

59.  J. Tanikawa, T. Yasukawa, M. Enari, K. Ogata, Y. Nishimura, S. Ishii, and A. Sarai "Recognition of Specific DNA Sequences by the c-myb Proto-oncogene Product: Role of Three Repeat Units in the DNA-binding Domain" Proc. Natl. Acad. Sci. USA 90, 9320-9324 (1993).

60.  T. Nomura, N. Sasaki, A. Sarai, T. Sudo, C. Kanei-Ishii, R.G. Ramsay, D. Favier, T.J. Gonda, and S. Ishii "Negative Autoregulation of c-Myb Activity by Homodimer Formation through the Leucine Zipper" J. Biol. Chem. 268, 21914-21923 (1993).

61.  X. Tang, Y.F. Wang, Y. Nakata, H.-O. Li, A. Fujita, H. Gao, A. Sarai and K. Yokoyama "A Mathematically Designed STS Primer without Any Mismatches for Direct Sequencing of Cosmid DNA Clones" Jpn. J. Human Genet. 38, 383-392 (1993).

62.  Y.F. Wang, X. Tang, Z. Wang, K. Yokoyama and A. Sarai "Prediction of Mutational Effect in the Protein-DNA Recognition with the Aid of Computer Graphics" Bioimages 2, 15-20 (1994).

63.  H. Torigoe, H. Shindo and A. Sarai "Multi-stranded DNA" RIKEN Review 6, 35-36 (1994).

64.  D.-X. Hou, Y. Wang, H. Yamashita, S. Okamoto, K. Yokoyama, E. Soeda and A. Sarai "Evolutionary Conservation of Chymotrypsinogen Gene: Genomic Analysis and Protein Modeling" Jpn. J. Human Genet. 39, 235-242 (1994).

65.  T. Yamamori and A. Sarai "Evolution of the IL-6/Class IB Cytokine Receptor Family in the Immune and Nervous Systems" J. Physiology 88, 165-171 (1994).

66.  X. Tang, Y.F. Wang, H.-O. Li, O. Sakatsume, A. Sarai and K. Yokoyama "DNA Fingerprinting Involving Fluorescence-Labeled Termini of Any Enzymatically Generated Fragments of DNA" Jpn. J. Human Genet. 39, 379-391 (1994).

67.  Y.F. Wang and A. Sarai "A Simple Method for Assessing Mutational Effect on the Specificity of Protein-DNA Interaction - Application to Amino-Acid Substitutions" Protein Eng. 7, 1083-1087 (1994).

68.  K. Ogata, S. Morikawa, H. Nakamura, A. Sekikawa, T. Inoue, H. Kanai, A. Sarai, S. Ishii and Y. Nishimura "Solution Structure of a Specific DNA Complex of the Myb DNA-Binding Domain with Cooperative Recognition Helices" Cell 79, 639-648 (1994).

69.  H. Torigoe, M Kamiya, H. Shindo and A. Sarai "Structural polymorphism and thermal stability of telomere DNAs (T2G4)n and (T4G4)n" Nucleic Acids Symp. Ser. 34, 199-200 (1995).

70.  T. Takahashi, H. Nakagoshi, A. Sarai, N. Nomura, T. Yamamoto and S. Ishii "Human A-myb Gene Encodes a Transcriptional Activator Containing the Negative Regulatory Domains" FEBS Lett. 358, 89-96 (1995).

71.  N. Shimba, H. Torigoe, H. Takahashi, K. Masuda, I. Shimada, Y. Arata and A. Sarai "Comparative Thermodynamic Analyses of the Fv, Fab* and Fab Fragments of Anti-Dansyl Mouse Monoclomal Antibody" FEBS Lett. 360, 247-250 (1995).

72.  K. Ogata, S. Morikawa, H. Nakamura, H. Hojo, S. Yoshimura, R. Zhang, S. Aimoto, Y. Ametani, Z. Hirata, A. Sarai, S. Ishii and Y. Nishimura "High-Resolution Structure of c-Myb DNA-Binding Domain in Solution: Comparison with DNA-Complexed Structure" Nature Struct. Biol. 2, 309-319 (1995).

73.  H. Torigoe, T. Nakayama, M. Imazato, I. Shimada, Y. Arata and A. Sarai "The Affinity Maturation of Anti-4-Hydroxy-3-Nitrophenylacetyl Mouse Monoclonal Antibody: A Calorimetric Study of the Antigen-Antibody Interaction" J. Biol. Chem. 270, 22218-22222 (1995).

74.  T. Kanno, T. Inoue, Y.-F. Wang, A. Sarai and S. Yamaguchi "Identification of the Location of Antigenic Sites of Swine Vesicular Disease Virus with Neutralization-Resistant Mutants" J. Gen. Virol. 76, 3099-3106 (1995).

75.  S. Morikawa, K. Ogata, A. Sekikawa, A. Sarai, S. Ishii, Y. Nishimura and H. Nakamura "Determination of the Nuclear Magnetic Resonance Solution Structure of a Specific DNA Complex of the Myb DNA-Binding Domain" J. Biomol. NMR. 6, 294-305 (1995).

76.  K. Ogata, C. Kanei-Ishii, M. Sasaki, H. Hatanaka, A. Nagadoi, M. Enari, H. Nakamura, Y. Nishimura, S. Ishii and A. Sarai "The Cavity in the Hydrophobic Core of c-Myb DNA-Binding Domain is Reserved for DNA Recognition and trans-Activation" Nature Struct. Biol. 3, 178-187 (1996).

77.  Q.-L. Deng, S. Ishii and A. Sarai "Binding-Site Analysis of c-Myb: Screening of Potential Binding Sites by the Mutational Matrix Derived from Systematic Binding Affinity Measurements" Nucleic Acids Res. 24, 766-774 (1996).

78.  M. Kamiya, H. Torigoe, H. Shindo and A. Sarai "Temperature Dependence and Sequence Specificity of DNA Triplex Formation: An Analysis using Isothermal Titration Calorimetry" J. Am. Chem. Soc. 118, 4532-4538 (1996).

79.  J. Mazur, R.L. Jernigan and A. Sarai "Constructing Optimal Backbone Segments for Joining Fixed DNA Base Pairs" Biophys. J. 71, 1493-1506 (1996).

80.  A. Sarai, R.L. Jernigan and J. Mazur "Interdependence of Conformational Variables in Double Helical DNA" Biophys. J. 71, 1507-1517 (1996).

81.  H. Kurumizaka, S. Ikawa, H. Aihara, T. Kashima, L.R. Bazemore, K. Kawasaki, A. Sarai, C.M. Radding and T. Shibata "Point Mutations in a C-Terminal Domain of RecA Protein That Cause Defective Double-Stranded DNA-Binding for Homologous Pairing with Single-Stranded DNA" J. Biol. Chem. 271, 33515-33524 (1996).

82.  K. Sayano, T. Shirakawa, Y. Kubota and A. Sarai "Protein Sequence Homology Search Based on the Correlation Matrix Method: A Vectorization Algorithm" RIKEN Review 14, 11-12 (1996).

83.  C. Kanei-Ishii, T. Nomura, K. Ogata, A. Sarai, T. Yasukawa, S. Tashiro, T. Takahashi, Y. Tanaka and S. Ishii, "Structure and function of the proteins encoded by the myb gene family" in Current Topics in Microbiology and Immunology 211 "Molecular Aspects of Myeloid Stem Cell Development", ed. by L. Wolff, A.S. Perkins, Springer-Verlag Berlin Heidelberg, 89-98 (1996).

84.  M. Oda, K. Furukawa, K. Ogata, A. Sarai, S. Ishii, Y. Nishimura and H. Nakamura "Investigation of the Pyrimidine Preference by the c-Myb DNA-Binding Domain at the Initial Base of the Consensus Sequence" J. Biol. Chem. 272, 17966-17971 (1997).

85.  T. Nakama, J. An, A.C.H. Scott, Y. Kubota and A. Sarai "Visualization of Functional Sites on Protein Structures by Virtual Reality Modeling Language" Bioimages 5, 59-64 (1997).

86.  Z. Lin, Y. Wang, A. Sarai and H. Yasue "Swine Catalase Deduced from cDNA and Localization of Catalase Gene on Swine Chromosome 2p16 -> p15" Biochem. Gen. 35, 297-302 (1997).

87.  M. Oda, K. Furukawa, K. Ogata, A. Sarai, S. Ishii, Y. Nishimura and H. Nakamura "Identification of Indispensable Residues for Specific DNA-Binding in the Imperfect Tandem Repeats of c-Myb R2R3" Protein Eng. 10, 1407-1414 (1997).

88.  J. An, T. Nakama, Y. Kubota and A. Sarai "3DinSight: An Integrated Relational Database and Search Tool for Structure, Function and Property of Biomolecules" Bioinformatics 14, 188-195 (1998).

89.  M. Oda, K. Furukawa, K. Ogata, A. Sarai, and H. Nakamura "Thermodynamics of Specific and Non-specific DNA Binding by the c-Myb DNA-Binding Domain" J. Mol. Biol. 276, 571-590 (1998).

90.  H. Uedaira, H. Morii, K. Ogata, S. Ishii and A. Sarai "Multi-state Thermal Transitions of Proteins -- DNA-Binding Domain of the c-Myb Oncoprotein" Pure Appl. Chem. 70, 671-676 (1998).

91.  D. Hao, M. Ohme-Takagi and A. Sarai "Specific interactions between EREBP and GCC box in plant" J. Biol. Chem. 273, 26857-26861 (1998).

92.  H. Kono, M. Saito and A. Sarai "Stability analysis for the cavity filling mutations of Myb DNA-binding domain by molecular dynamics simulations" RIKEN Review 19, 128-129 (1998).

93.  F. Pichierri, M. Aida, M. Gromiha and A. Sarai "Free-energy calculations of base-amino acid interactions in DNA-protein recognition" RIKEN Review 19, 130-131 (1998).

94.  K. Sayano, K. Misumada, T. Shirakawa, Y. Kubota and A. Sarai "Protein Sequence Homology Search Based on the Correlation Matrix Method " RIKEN Review 19, 132-133 (1998).

95.  A. Kittaka, T. Kuze, H. Tanaka, T. Miyasaka, K. Hirose, T. Yoshida, A. Sarai, T. Yasukawa, S. Ishii "Oligonucleotides containing a 6-substituted pyrimidine base: a design for Myb inhibitors." Nucleosides Nucleotides 18, 1501-1502 (1999).

96.  F. Pichierri and A. Sarai "Properties of phosphorothioate DNA backbones. An ab initio study of prototype model linkages derived from dimethyl-phosphate anion" J. Mol. Struct. (Theochem) 460, 103-116 (1999).

97.  M. Gromiha, H. Kono, J. An, M. Oobatake,H. Uedaira and A. Sarai "ProTherm: Thermodynamic Database for Proteins and Mutants" Nucleic Acids Res. 27, 286-288 (1999).

98.  M. Oda, K. Furukawa, K. Ogata, A. Sarai, and H. Nakamura "Thermodynamic analysis of protein induced folding upon DNA Binding " in Old and New Views of Protein Folding, eds. K. Kuwajima and M Arai, pp. 297-306 (1999) Elsevier, Amsterdam.

99.  H. Kono and A. Sarai "Structure-based prediction of DNA target sites by regulatory proteins" Proteins 35, 114-131 (1999).

100.           F. Pichierri, M. Aida, M. Gromiha and A. Sarai "Free energy maps of base-amino acid interaction for protein-DNA recognition" J. Am. Chem. Soc. 121, 6152-6157 (1999).

101.           T. H. Tahirov, H. Morii, H. Uedaira, A. Sarai and K. Ogata "Crystallization and preliminary X-ray analysis of wild type and V103L mutant of Myb R2 DNA-binding domain" Acta Cryst. D. 55, 1345-1347 (1999).

102.           H. Kurumizaka, S. Ikawa, A. Sarai, and T. Shibata "The Mutant RecA Proteins, RecAR243Q and RecAK245N, Exhibit Defective DNA Binding in Homologous Pairing" Arch. Biochem. Biophys. 365, 83-91 (1999).

103.           M. Gromiha, M. Oobatake, H. Kono, H. Uedaira and A. Sarai "Role of Structural and Sequence Information for Predicting Protein Stability: Comparison between Buried and Partially Buried Mutations" Protein Eng. 12, 549-555 (1999).

104.           J. Higo, H, Kono, N. Nakajima, H. Shirai, H. Nakamura and A. Sarai "Molecular dynamics study on mobility and dipole ordering of solvent around binding proteins: effects of periodic-box size and protein charge" Chem. Phys. Lett. 306, 395-401 (1999).

105.           M. Oda, K. Furukawa, A. Sarai and H. Nakamura "Kinetic analysis of DNA Binding by the c-Myb DNA-Binding Domain Analyzed Using Surface Plasmon Resonance" FEBS Lett. 454, 288-292 (1999).

106.           M. Gromiha, M. Oobatake, H. Kono, H. Uedaira and A. Sarai "Relationship between amino acid properties and protein stability: buried mutation" J. Protein Chem. 18, 565-578 (1999).

107.           H. Morii, H. Uedaira, K. Ogata, S. Ishii and A. Sarai "Shape and Energetics of a Cavity in c-Myb Probed by Natural and Non-natural Amino-Acid Mutations" J. Mol. Biol. 292, 909-920 (1999).

108.           M. Oda, K. Furukawa, A. Sarai and H. Nakamura "Construction of Artificial Tandem Protein of the c-Myb DNA-Binding Domain and Analysis of Its DNA Binding Specificity" Biochem. Biophys. Res. Commun. 262, 94-97 (1999).

109.           H. Torigoe, R. Shimizume, A. Sarai and H. Shindo "Triplex formation of chemically modified homopyrimidine oligonucleotides: thermodynamic and kinetic studies" Biochemistry 38, 14653-14659 (1999).

110.           M. Gromiha, M. Oobatake and A. Sarai "Important amino acid properties to enhance the thermostability from methophilic to thermophilic proteins" Biophys. Chem. 82, 51-67 (1999).

111.           A. Kittaka, T. Kuze, M. Amano, H. Tanaka, T. Miyasaka, K. Hirose, T. Yoshida, A. Sarai, T. Yasukawa, S. Ishii "Introduction of 6-formylcytidine into a Myb binding sequence." Nucleosides Nucleotides 18, 2769-83 (1999).

112.           H. Kono, M. Saito and A. Sarai "Stability Analysis for the Cavity-Filling Mutations of the Myb DNA-Binding Domain Utilizing Free-Energy Calculations" Proteins 38, 197-209 (2000).

113.           M. Gromiha, H. Kono, J. An, M. Oobatake, H. Uedaira, P. Prabakaran and A. Sarai "ProTherm, Version 2.0: Thermodynamic Database for Proteins and Mutants" Nucleic Acids Res. 28, 283-285 (2000).

114.           M. Saito, H. Kono, H. Morii, H. Uedaira, T.H. Takhirov, K. Ogata, A. Sarai " Cavity-filling mutations enhance protein stability by lowering the free energy of native state" J. Phys. Chem. 104, 3705-3711 (2000).

115.           J. Higo, H. Kono, H. Nakamura and A. Sarai "Solvent density and long-range dipole field around a DNA-binding protein studied by molecular dynamics" Proteins 40, 193-206 (2000).

116.           K. Sayano, H. Kono, M. Gromiha and A. Sarai "Multicanonical Monte Carlo Calculation of Free-Energy Map for Base-Amino Acid Interaction" J. Compt. Chem. 21, 954-962 (2000).

117.           F. Pichierri and A. Sarai "Elastic properties of the poly-L-glycine alpha-helix from periodic SCF-LMO calculations" Chem. Phys. Lett. 322, 536-542 (2000).

118.           M. Gromiha, M. Oobatake, H. Kono, H. Uedaira, and A. Sarai "Importance of Surrounding Residues for Protein Stability of Partially Buried Mutations" J. Biomol. Struct. Dyn., 18, 281-295 (2000).

119.           H. Mizuno, Y. Tanaka, K. Nakai and A. Sarai "ORI-GENE: A Tool for Functional Classification of Genes Based on the Evolutionary Tree" Bioinformatics, 17, 167-173 (2001).

120.           J.V. Ponomarenko, D.P. Furman, A.S. Frolov, N.L. Podkolodny, G.V. Orlova, M.P. Ponomarenko, N.A. Kolchanov and A. Sarai "ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another" Nucleic Acids Res. 29, 284-287 (2001).

121.           J.V. Ponomarenko, T.I. Merkulova, G.V. Vasiliev, Z.B. Levashova, G.V. Orlova, S.V. Lavryushev, O.A. Fokin, M.P. Ponomarenko, A.S. Frolov, and A. Sarai "rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations" Nucleic Acids Res. 29, 312-316 (2001).

122.           Y. Kaku, A. Sarai and Y. Murakami "Genetic reclassification of porcine porcine enteroviruses" J. Gen. Virol. 82, 417-424 (2001).

123.           P. Prabakaran, J. An, M. Gromiha, S. Selvaraj, H. Uedaira, H. Kono and A. Sarai "Thermodynamic Database for Protein-Nucleic Acid Interactions (ProNIT)" Bioinformatics 17, 1027-1034 (2001).

124.           M.W. Lassalle, H. Yamada, H. Morii, K. Ogata, A. Sarai and K. Akasaka "Filling a cavity dramatically increases pressure stability of the c-Myb R2 subdomain" Proteins 45, 96-101 (2001).

125.           Song J, Ugai H, Ogawa K, Wang Y, Sarai A, Obata Y, Kanazawa I, Sun K, Itakura K, and Yokoyama KK "Two consecutive zinc fingers in Sp1 and in MAZ are essential for interactions with cis-elements. " J. Biol. Chem. 276, 30429-30434 (2001).

126.           J. An, H. Wako and A. Sarai "Analysis of Structural motifs of Proteins in Terms of Sets of Codes Representing Local Structures" Mol. Biol. 35, 905-910 (2001).

127.           A.V. Kochetov, D.A. Grigorovich, I.I. Titov, D.G. Vorobiev, O.A. Sirnik, O.V. Vishnevsky, A. Sarai, N.A. Kolchanov "Computer system mRNA-FAST (mRNA – Function, Activity, STructure)" Mol. Biol. 35, 890-897 (2001).

128.           M. Gromiha, H. Uedaira, J. An, S. Selvaraj, P. Prabakaran and A. Sarai "ProTherm, Thermodynamic Database for Proteins and Mutants: Developments in Version 3.0" Nucleic Acids Res. 31, 301-302 (2002).

129.           T. Yoshida, T. Nishimura, M. Aida, F. Pichierri, M.M. Gromiha and A. Sarai "Evaluation of free energy landscape for base-amino acid interactions using ab initio force field and extensive sampling" Biopolymers 61, 84-95 (2002).

130.           A. Sarai, M. Gromiha, J. An, P. Prabakaran, S. Selvaraj, H. Kono, M. Oobatake and H. Uedaira "Thermodynamic Databases for Proteins and Protein-Nucleic Acid Interactions" Biopolymers 61, 121-126 (2002).

131.           M. Gromiha, M. Oobatake, H. Kono, H. Uedaira and A. Sarai “Importance of Mutant Position in Ramachandran Plot for Predicting Protein Stability of Surface Mutations” Biopolymers 64, 210-220 (2002).

132.           D. Hao, K. Yamazaki, A. Sarai and M. Ohme-Takagi "Determinants in sequence specific binding of two plant transcription factors CBF1 and NtERF2 to DRE- and GCC-motifs" Biochemistry 41, 4202-4208 (2002).

133.           S. Selvaraj, H. Kono and A. Sarai "Specificity of Protein-DNA Recognition Revealed by Structure-Based Potentials: Symmetric/Asymmetric and Cognate/Noncognate Binding" J. Mol. Biol. 322, 907-915 (2002).

134.           A. V. Kochetov, A. Sarai, D. G. Vorob'ev, N. A. Kolchanov " The Context Organization of Functional Regions in Yeast Genes with High-Level Expression" Mol. Biol. 36, 1026-1034 (2002).

135.           A. Kittaka, T. Kuze, A. Sarai, H. Takayama, H. Tanaka, T. Miyasaka, T. Miyasaka, J. Inoue, S. Ishii "Synthesis of oligonucleotides with 6-formyl-2’-O-methyluridine and thermal stability of their duplexes." Heterocycles 59, 207-215 (2003).

136.           S. Ahmad, M. Gromiha and A. Sarai "Real Value Prediction of Solvent Accessibility from Amino Acid Sequence" Proteins 50, 629-635 (2003).

137.           M. Saito and A. Sarai "Free energy calculations for the relative binding affinity between DNA and lambda repressor" Proteins 52, 129-136 (2003).

138.           M. Oobatake, H. Kono, Y-F. Wang and A. Sarai "Anatomy of specific interactions between lambda repressor and operator DNA by energy-component analysis" Proteins 53, 33-43 (2003).

139.           J. Mazur, R.L. Jernigan and A. Sarai "Conformational Effect of Stretching DNA " Mol. Biol. 37, 277-287 (2003).

140.           K. Saito, A. Sarai, M. Oda, T Azuma, and H. Kozono "Thermodynamic Analysis of the Increased Stability of MHC Class II Molecule I-Ek Complexed with an Antigenic Peptide at an Acidic pH" J. Biol. Chem. 278, 14732-14738 (2003).

141.           H. Wako, J.-H. An and A. Sarai "Environment-dependent and position-specific frequencies of amino acid occurrences in alpha-helices" Cem-Bio Info. J. 3, 58-77 (2003).

142.           N. Mizuno, K. Miki, G. Voordouw, A. Sarai, and Y. Higuchi "Three-dimensional crystal structure of dissimilatory sulfite reductase D (DsrD) protein - possible interaction with B- and Z-DNA by its winged-helix motif" Structure 11, 1133-1140 (2003).

143.           S. Ahmad, M.M. Gromiha, and A. Sarai "RVP-net: Online Prediction of Real Valued Accessible Surface Area of Proteins from Single Sequences" Bioinformatics, 19, 1849-1851 (2003).

144.           A.V. Kochetov, N. A. Kolchanov, and A. Sarai "Interrelations between the “strength” of translation start site and sequence features of yeast mRNAs" Mol. Genetics and Genomics 270, 442-447 (2003).

145.           H. Kono and A. Sarai "Structure-Specificity Relationship In Protein-DNA Recognition" in Bioinformatics of Genome Regulation and Structure, Eds. N. Kolchanov & R. Hofestaedt, pp. 155-161, Kluwer Academic, NLD (2003).

146.           K.A. Bava, M.M. Gromiha, H. Uedaira, K. Kitajima and A. Sarai "ProTherm, version 4.0: Thermodynamic Database for Proteins and Mutants" Nucleic Acids Res. 32, D120-D121 (2004).

147.           K. Saito, M. Oda, A. Sarai, T. Azuma, and H. Kozono "Contribution of a single hydrogen bond between bHis81 of MHC class II I-Ek and the bound peptide to the pH-dependent thermal stability" Microbiol. Immunol. 48, 53-57 (2004).

148.           A. Sarai, S. Selvaraj, M.M. Gromiha, and H. Kono "Structure-Specificity Relationship in DNA Sequence Recognition by Transcription Factors" Aust. Compt. Sci. Comm. 26, 233-238 (2004).

149.           A. Sarai and H. Kono "DNA-Protein Interactions: Target Predictions" in Compact Handbook of Computational Biology eds. Crabbe, Drew and A. Konopka, pp. 241-278 (2004) Marcel Dekker Inc. New York.

150.           A.V. Kochetov and A. Sarai "Translational Polymorphism as a Potential Pource of Plant Proteins Variety in Arabidopsis thaliana" Bioinformatics 20, 445-447 (2004).

151.           S. Ahmad, M.M. Gromiha, and A. Sarai "Analysis and Prediction of DNA-Binding Proteins and Their Binding Residues Based on Composition, Sequence and Structural Information" Bioinformatics, 20, 477-489 (2004).

152.           M.M. Gromiha, J.G. Siebers, S. Selvaraj, H. Kono and A. Sarai "Intermolecular and Intramolecular Readout Mechanisms in Protein-DNA Recognition" J. Mol. Biol. 337, 285-294 (2004).

153.           K. Omagari, H.Yoshimura, M. Takano, D. Hao, M. Ohmori, A. Sarai, and A. Suyama "Systematic single base-pair substitution analysis of DNA binding by the cAMP receptor protein in cyanobacterium Synechocystis sp. PCC 6803" FEBS Lett. 563, 55-58 (2004).

154.           S. Ahmad, M.M. Gromiha, H. Fawareh, and A. Sarai "ASAView: Database and tool for solvent accessibility representation in proteins" BMC Bioinformatics, 5, 51 (2004).

155.           D. Cui, G. Jin, T. Gao, T.Sun, F. Tian, G.G. Estrada, H. Gao, and A. Sarai "Characterization of BRCAA1 and Its Novel Antigen Epitope Identification" Cancer Epidemiol. Biomarkers Prev. 13, 1136-1145 (2004).

156.           S. Ahmad and A. Sarai "Qgrid: Clustering tool for detecting charged and hydrophobic regions in proteins" Nucleic Acids Res. 32: W104-W107 (2004).

157.           J.-Y. Wang, S. Ahmad, M. M. Gromiha and A. Sarai "Look-up tables for Protein Solvent Accessibility Prediction and Nearest Neighbor Effect Analysis" Biopolymers 75, 209-216 (2004).

158.           S. Ahmad and A. Sarai "Moment-based Prediction of DNA-binding Proteins" J. Mol. Biol. 341, 65-71 (2004).

159.           H. Uedaira and A. Sarai "Thermal stability and function of Myb protein" in Comprehensive Handbook of Calorimetry and Thermal Analysis Ed. Michio Sorai, pp. 422-424 John Wiley & Sons, Ltd. (2004).

160.           H. Uedaira and A. Sarai "Thermodynamic database for biomolecules" in Comprehensive Handbook of Calorimetry and Thermal Analysis Ed. Michio Sorai, pp. 276-279 John Wiley & Sons, Ltd. (2004).

161.           A. Sarai, P Prabakaran and H. Uedaira "Thermodynamic database for Protein-Nucleic Acid Interactions (ProNIT)" in Comprehensive Handbook of Calorimetry and Thermal Analysis Ed. Michio Sorai, pp. 280-284 John Wiley & Sons, Ltd. (2004).

162.           K. Saito, M. Oda, A. Sarai, T. Azuma, and H. Kozono "Bound peptide-dependent thermal stability of major histocompatibility complex class II molecule I-Ek" Biochemistry 43, 10186-10191 (2004).

163.           A. Sarai, J. Siebers, S. Selvaraj, M. M. Gromiha and H. Kono "Integration of Bioinformatics and Computational Biology to Understand Protein-DNA Recognition Mechanism" J. Bioinformatics and Computational Biology 3, 169-183 (2005).

164.           A. Sarai and H. Kono "Protein-DNA Recognition Patterns and Predictions" Ann. Rev. Biophys. Biomol. Struct. 34, 379-398 (2005).

165.           S. Ahmad and A. Sarai "PSSM-based prediction of DNA binding sites in proteins" BMC Bioinformatics, 6, 33 (2005).

166.           A.V. Kochetov, A. Sarai, V.K. Shumny, N.A. Kolchanov "The role of alternative translation start sites in the generation of human protein diversity" Mol. Genetics and Genomics 273, 491-496 (2005).

167.           G. Neshich, L.C. Borro, R.H. Higa, P.R. Kuser, M.E.B. Yamagishi, E.H. Franco, J.N. Krauchenco, R. Fileto, A.A. Ribeiro, G.B.P. Bezerra, T.M. Velludo, T.S. Jimenez, N. Furukawa, H. Teshima, K. Kitajima, A. Bava, A. Sarai, R.C. Togawa and A.L. Mancini "Diamond STING: an expanded functionality for the STING suite of programs allowing the comprehensive sequence/structure/function/stability analysis with added capability for handling local files" Nucleic Acids Res. 33, W29-W35 (2005).

168.           M. M. Gromiha, J. G. Siebers, S. Selvaraj, H. Kono and A. Sarai "Role of Inter and Intramolecular Interactions in Protein-DNA Recognition" Gene 364, 108-113 (2005).

169.           M.J. Arauzo-Bravo, S. Fujii, H. Kono, S. Ahmad and A. Sarai "Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations: Toward Understanding the Indirect Readout Mechanism in Protein-DNA Recognition" J. Am. Chem. Soc. 127, 16074-16089 (2005).

170.           M.J. Arauzo-Bravo and A. Sarai "Knowledge-based prediction of DNA atomic structure from nucleic sequence" Genome Inform. 16, 12-21 (2005).

171.           M. D. Shaji Kumar, K. A. Bava, M. M. Gromiha, P. Prabakaran, K. Kitajima, H. Uedaira and A. Sarai "ProTherm and ProNIT: Thermodynamic Databases for Proteins and Protein-Nucleic Acid Interactions" Nucleic Acids Res. 34, D204-206 (2006).

172.           M.J. Arauzo-Bravo, S. Ahmad and A. Sarai "Dimensionality of amino acid space and solvent accessibility prediction with neural networks" Compt. Biol. Chem. 30, 160-168 (2006).

173.           S. Ahmad, H. Kono, M.J. Arauzo-Bravo and A. Sarai "ReadOut: Structure-based Calculation of Direct and Indirect Readout Energies and Specificities for Protein-DNA Recognition" Nucleic Acids Res. 34, W124-W127 (2006).

174.           M.J. Arauzo-Bravo, S. Fujii, H. Kono and A. Sarai "Disentangling the Role of Tetranucleotides in the Sequence-Dependence of DNA Conformation: a Molecular Dynamics Approach" in Series on Advances in Bioinformatics and Computational Biology, Vol. 3, Proc. 4th Asia-Pacific Bioinformatics Conference. Eds. T. Jiang, U.C. Yang, Y.P.P. Chen and L. Wong, pp. 227-236, Imperial College Press, (2006).

175.           Y.H. Singh, M.M. Gromiha, A. Sarai and S. Ahmad "Atom-wise Statistics and Prediction of Solvent Accessibility in Proteins" Biophys. Chem. 124, 145-154 (2006).

176.           P. Prabakaran, J.G. Siebers, S. Ahmad, M.M. Gromiha, M.G. Singarayan and A. Sarai "Classification of Protein-DNA Complexes Based on Structural Descriptors" Structure 14,1355-1367 (2006).

177.           Y. Yonetani, H. Kono, S. Fujii, A. Sarai, and N. Go "DNA deformability and hydration studied by molecular dynamics simulation" Mol. Simulation 33, 103-107 (2007).

178.           Y. Kaku, Y. Murakami, A. Sarai, Y. Wang, S. Ohashi and K. Sakamoto "Antigenic properties of porcine teschovirus 1 (PTV-1) Talfan strain and molecular strategy for serotyping of PTVs" Archives of Virology 152, 929–940 (2007).

179.           S. Fujii, H. Kono, S. Takenaka, N. Go and A. Sarai "Sequence-Dependent DNA Deformability Studied using Molecular Dynamics Simulations" Nucleic Acids Res. 35, 6063-6074 (2007).

180.           A. V. Kochetov, A. Palyanov, I. I. Titov, D. Grigorovich, A. Sarai, N.A. Kolchanov "AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site" BMC Bioinformatics 8, 318 (doi:10.1186/1471-2105-8-318) (2007).

181.           M. J. Araúzo-Bravo and A. Sarai "Indirect readout in Drug-DNA Recognition: Role of DNA Sequence-dependent DNA Conformation" Nucleic Acids Res. 36, 376-386 (2008). Epub Nov. 26 (2007).

182.           K. Omagari, H. Yoshimura, T. Suzuki, M. Takano, M. Ohmori, and A. Sarai G-based prediction and experimental confirmation of SYCRP1-binding sites on Synechocystis genome" FEBS J. 275, 4786-4795 (2008).

183.           A.V. Kochetov, S. Ahmad, V.I. Ivanisenko, N.A. Kolchanovand A. Sarai "uORFs, reinitiation and alternative translation start sites in human mRNAs" FEBS Lett. 582, 1293-1297 (2008).

184.           S. Ahmad, Y. H. Singh, M. J. Araúzo-Bravo, A. Sarai "Sequence-based prediction of residue-level properties in proteins" in Machine Learning in Bioinformatics, eds, Y.-Q. Zhang and J.C. Rajapakse, Wiley (2008).

185.           S. Ahmad, O. Keskin, A. Sarai and R. Nussinov "Protein-DNA interactions: Structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins" Nucleic Acids Res. 36, 5922-5932 (2008).

186.           H. Mizuno, Y. Nakanishi, N. Ishii, A. Sarai and K. Kitada "A signature-based method for indexing cell cycle phase distribution from microarray profiles" BMC Genomics 10, 137 (2009).

187.           H. Mizuno, K. Kitada, K. Nakai, A. Sarai "PrognoScan: a new database for meta-analysis of the prognostic value of genes" BMC Medical Genomics 2, 18 (2009).

188.           M. Andrabi, K. Mizuguchi, A. Sarai and S. Ahmad "Prediction of mono- and dinucleotide-specific DNA- binding sites in proteins using neural networks" BMC Struct. Biol. 9, 30 (2009).

189.           S. Takeshima, A. Sarai, N. Saitou and Y. Aida "MHC class II DR classification based on antigen-binding groove natural selection" Biochem. Biophys. Res. Comm., 385, 137-142 (2009).

190.           S. Yamasaki, T. Terada, K. Shimizu, H. Kono, and A. Sarai "A Generalized Conformational Energy Function of DNA Derived from Molecular Dynamics Simulations" Nucleic Acids Res. 37, e135. (Epub 2009 Sep 3) (2009).

191.           M. Fernandez, S. Fujii, H. Kono and A. Sarai "Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast" Genome Inform. 23, 13-20 (2009).

192.           M. M. Gromiha and A. Sarai "Thermodynamic Database for Proteins: Features and Applications" Biological Data Mining, Methods Mol. Biol. 609, 97-112 (2010).

193.           S. Ahmad, O. Keskin, K. Mizuguchi, A. Sarai and R. Nussinov "CCR XP: Exploring clusters of conserved residues in protein structures" Nucleic Acids Res. 38 Suppl:W398-401 (2010).

194.           M. Fernandez, J. Caballero, L. Fernandez and A. Sarai "Graphical Representations of Protein Sequences for Alignment-Free Com- parative and Predictive Studies. Recognition of Protease Inhibition Pattern from H-Depleted Molecular Graph Representation of Protease Sequences" Current Bioinformatics 5, 241-252 (2010).

195.           M. Fernandez, S. Ahmad and A. Sarai "Proteochemometric recognition of stable kinase inhibition complexes using Topological Autocorrelation and Support Vector Machines" J. Chem. Inf. Model. 50, 1179-1188 (2010).

196.           S. Ahmad and A. Sarai "Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction" BMC Struct. Biol. 11, 8 (2011).

197.           M. Fernandez, J. Caballero, L. Fernandez, A. Sarai "Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM)" Mol. Divers. DOI 10.1007/s11030-010-9234-9 (2010) 15, 269-289 (2011).

198.           M. Fernandez, Y. Kumagai, D. Standley, K. Mizuguchi, A. Sarai and S. Ahmad "Prediction of dinucleotide-specific RNA-binding Sites in Proteins" BMC Bioiformatics 12(Suppl 13), S5 (2011).

199.           H. Okayama, T. Kohno, Y. Ishii, Y. Shimada, K. Shiraishi, R. Iwakawa, K. Furuta, K. Tsuta, T. Shibata, S. Yamamoto, S.-I. Watanabe, H. Sakamoto, K. Kumamoto, S. Takenoshita, N. Gotoh, H. Mizuno, A. Sarai, S. Kawano, R. Yamaguchi, S. Miyano, and J. Yokota "Identification of Genes Up-regulated in ALK-positive and EGFR/KRAS/ALK-negative Lung Adenocarcinomas" Cancer Res. 72, 100-11 (2012) Epub 2011 Nov 11..

200.           S. Yamasaki, T. Terada, H. Kono, K. Shimizu and A. Sarai "A New Method for Evaluating the Specificity of Indirect Readout in Protein-DNA Recognition" Nucleic Acids Res. 40, e129 (doi: 10.1093/nar/gks462) (2012).

201.           H. He and A. Sarai "Analysis of Relationship among Evolvability, Thermodynamics and Function of Intrinsically Disordered Proteins/Regions" Compt. Biol. Chem. 41, 51–57 (2012).

202.           R. Fujita, M. Takayama-Tsujimoto, H. Satoh, L. Gutiérrez, H. Aburatani, S. Fujii, A. Sarai, E. Bresnick, M. Yamamoto, and H. Motohashi "NF-E2 p45 Is Important for Establishing Normal Function of Platelets" Mol. and Cell. Biol., in press (2013).