Publication List

2010

1.Suwa, M., and Ono, Y. “A bioinformatics strategy to produce a cyclically developing project structure",
Synthesiology, 3, 1-12, (2010). <

2009

2.Tanaka, K., Uda, Y., Ono, Y., Nakagawa, T., Suwa, M., Yamaoka, R. and Touhara, K. "Highly selective tuning of a silkworm olfactory receptor to a key mulberry leaf volatile.",
Curr. Biol. ;19, 881-890, (2009).

3.Gromiha MM, Yabuki Y, Suresh MX, Thangakani AM, Suwa M, Fukui K. "TMFunction: database for functional residues in membrane proteins.",
Nucleic Acids Res. 37(Database issue):D201-204, (2009).

4. Makiko Suwa, Yukiteru Ono "Computational Overview of GPCR Gene Universe to Support Reverse Chemical Genomics Study"
Methods in MOLECULAR BIOLOGY, 577:47-54, (2009).

2008

5. The International Silkworm Genome Consortium (Suwa, M and Ono, Y. are member of this consortium as authors.)"The genome of a lepidopteran model insect, the silkworm Bombyx mori Insect Biochemistry and Molecular Biology"
Insect Biochemistry and Molecular Biology, 1036-1045,(2008).

6. Genome Information Integration Project and H-Invitational 2 group, Yamasaki, C et al. (Suwa, M. is one of the authors) “The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.”
Nucleic Acids Res. 36 (Database issue): D793-D799, (2008).

7. Yu-Yen Ou., Gromiha.M. M., Shu-Am Chen, Suwa, M. "TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. "
Computational Biology and Chemistry. 32., 227-231, (2008).

2007

8. Gromiha, M. M., Yabuki, Y., Kundu, S., Suharnan, S. and Suwa, M.，”TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences.”，
Nucleic Acids Research，35，.D314-D316, (2007).

9. Mukai, Y.,　 Hitrokawa, T, Tomii, K, Asai, K, Akiyama, Y, Suwa, M.， “Identification of glycosyltransferases focusing on Golgi transmembrane region”，
Trends in Glycoscience and Glycotechnology，19, .41-47, (2007).

10. Gromiha M. M, Suwa M. “Current developments on beta-barrel membrane proteins: sequence and structure analysis, discrimination and prediction.“,
Curr. Protein Pept. Sci. 8:580-599.(2007).

11. Gromiha, M., M., Yabuki,Y. and Suwa, M. “TMB finding pipeline: novel approach for detecting beta-barrel membrane proteins in genomic sequences”,
J Chem. Inf. Model, 47, 2456-2461, (2007).

2006

12. Muramatsu, T & Suwa, M. "Statistical analysis and prediction of residues effective for GPCR-G protein copling selectivity"
Protein Engeneering, Design & Selection vol. 19 no. 6 oo.277-283, 2006

13. Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O "Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns."
　Bioinformatics. 2006 Feb 24;

14. Gromiha M. M, Suwa. M.,"Discrimination of outer membrane proteins using machine learning algorithms."
Proteins. 2006 Feb 21;

15. Oka, Y., Katada, S., Omura, M., Suwa, M., Yoshihara, Y. and Touhara, K., Odorant Receptor Map in the Mouse Olfactory Bulb: In Vivo Sensitivity and Specificity of Receptor-Defined Glomeruli,
Neuron, 857-869, (2006)

16. Gromiha M. M., Suwa, M.，Influence of amino acid properties for discriminating outer membrane proteins at better accuracy，
Biochemica et Biophysica Acta-Proteins and Proteomics，1764, .1493-1(2006).

2005

17. Terashima, Y., Onai, N., Enomoto, M., Poonpiriya, V., Hamada, T., Motomura, K., Suwa, M., Ezaki, T., Haga, T., Kanagasaki, S. And Matsushima, K. “Pivotal function for cyteplasmic protein FROUNT in CCR2-mediated monocyte chemotaxis.” Nature immunology, 6, 827-835,（2005).

18. Katada, S, Hirokawa, T., Oka, Y., Suwa, M and Touhara, K. "Structural Basis for a Broad But Selective Ligand Spectrum of a Mouse Olfactory Receptor: Mapping the Odorant-Binding Site", J. Neurosci., 25, 1806-1815, (2005).

19. Nakao, M., Barrero, R.A., Mukai, Y., Motono, C., Suwa, M., Nakai, K. "Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.", Nucleic Acids Res., 33, 2355-63 (2005).

20. Yabuki, Y., Muramatsu, T., Hirokawa, T., Mukai, H. and Suwa, M., “GRIFFIN: a system for predicting GPCR-G-protein coupling selectivity using support vector machines and a hidden Marcov model”, Nucleic acid Research, 33. W 148-W153 (2005)..

21. Gromiha, M. M, Ahmad, S., and Suwa, M. ”TMBETA-NET: discrimination and prediction of membrane spanning ß-strands in outer membrane proteins” Nucleic Acids Res., 33, W164 - W167 (2005).

22. Gromiha, M. M. and Suwa, M. “A Simple Statistical Method for Discriminating Outer Membrane Proteins with Better Accuracy.” Bioinformatics, 21, 961-968 (2005).

23. Ono, Y., Fujibuchi, W and Suwa M., “Automatic gene collection system for Genome-Scale overview of G-Protein coupled receptors in Eukaryotes” Gene, 364, 63-73, (2005).

24. Gromiha, M. M. and Suwa, M. "Structural Analysis of Residues Involving Cation- Interactions in Different Folding Types of Membrane Proteins", Int. J. Biol. Macromol. 35, 55-62 (2005).

25. Gromiha, M. M., Ahmad, S and Suwa, M. “Application of residue distribution along the sequence for discriminating outer memebrane proteins. “ Computational Biology and Chemistry. 29, 135-142 (2005).

26. M. Michael Gromiha and M. Suwa"A Simple Statistical Method for Discriminating Outer Membrane Proteins with Better Accuracy". Bioinformatics, 21,961-968, (2005).

2004

27. Yabuki, Y., Mukai. Y., Swindells, M.B.and Suwa, M.: GENIUS II: A database system for assigning coding regions in complete genomes to protein three-dimensional structures,
Bioinformatics. 20, 596-598, (2004).

28. Gromiha, M. M., Ahmad, S. and Suwa, M: Neural Network Based Prediction of Transmembrane b-strand Segments in outer membrane proteins. Journal of Computational Chemistry.
J. Compt. Chem. 25, 762-767 (2004)

29. Gromiha, M. M, C. Santhosh and Suwa, M., Influence of cation-pai interactions in protein-DNA complexes,
Polymer, 45, 633-639 (2004)

30.Gromiha MM, Saraboji K, Ahmad S, Ponnuswamy MN, Suwa M., Role of non-covalent interactions for determining the folding rate of two-state proteins.
Biophys Chem., 15, 263-272, (2004)

31. Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda JI, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Md M, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, R Gopinath G, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.
: Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones., PLoS Biol. 20 (2004)

2003

32. M.Michael Gromiha and Makiko Suwa (2003). Variation of Amino Acid Properties in All-beta Globular and Outer Membrane Protein Structures.
Int. J. Biol. Macromol. 32, 93-98.

33. Makiko Suwa, Toshiyuki Sato, Ikuo Okouchi, Toshitaka Kumagai, Motonori Arita, Kiyoshi Asai and Yutaka Akiyama Shinichi Matsumoto, Shuichi Tsutsumi, Hiroyuki Aburatani
“SEVENS: A database of seven transmembrane helix receptors comprehensively detected from human genome.” Nucl. Acids Res. 31, 1 (2003) Online summary paper
( http://www3.oup.co.uk/nar/database/summary/373).

34. Mizuno, M., Gotoh, S. and Suwa, M., “Human Full-length Pre-mRNA Sequence Dataset for Computational Gene Prediction and Alternative Splicing Analysis “,
Genome Informatics Series，14，pp.412-413,(2003).

35. Nagasaki,, H., Suwa,, M. and Gotoh,, O., “An Algorithm for Classification of Alternative Splicing and Transcriptional Initiation and Its Genome-Wide Application”,
Genome Informatics Series，14，pp.424-425,(2003).

36. Gromiha, M., M., Ahmad, S. and Suwa, M., “Bioinformatics Studies on Transmembrane Strand Proteins”,
Genome Informatics, Series, 14, pp. 555-556, (2003).<

37. Nagano, T., Suwa, M and Asai, K., “Correlated Mutation Analysis of C2H2 Zinc Finger Domains”,
Genome Informatics Series，14，pp.565-566, (2003).

2002

38. Yabuki, Y., Mukai, Y. and Suwa, M., “GENIUS II: A database system including complete genome ORFs that are assigned to protein three-dimensional domains”,
Genome Informatics Series, 13, pp. 517-518., (2002).

39. Suwa, M., Arita, M., Matsumoto, S., Tsutsumi, S., Aburatani, H., Asai, K. and Akiyama, Y. “SEVENS: Comperative Collection of Human Seven Transmemebrane Helix Receptors”,
Genome Informatics Series, 13, pp. 511-512, (2002).

40. Nagano, T., Suwa, M., Asai,, K., "Classification of C2H2 Zinc Finger Domains Using Support Vector Machines”, Genome Informatics Series, 13, pp. 314-315, (2002) 2001

41. Yudate, HT., Suwa, M. et al.: HUNT: launch of a full-length cDNA database from the Helix Research Institute.,
Nucleic Acids Research,29, No.1 185-188 (2001).

42. Hirokawa, T., Suwa, M. and Akiyama, Y., “Classification and Analysis of Inter-Helical Loop Segments in Membrane Proteins”,
Genome Informatics Series, 12, pp. 332 - 333, (2001).

43. Mizuno, M., Nagasaki, H. and Suwa, M. “Dataset Construction for Gene Structure Prediction and Alternative Splicing Analysis”,
Genome Informatics Series, 12, pp. 423 - 424, (2001).

44. Suwa, M., Sato, T., Okouchi, I., Arita, M., Matsumoto, S., Tsutsumi, S., Aburatani, H., Asai, K., and Akiyama, Y.,
“An Automated System for finding seven Transmembrane Helix Receptors from Human Genome”, Genome Informatics Series, 12, pp. 425-426, (2001).

2000

45. Suwa, M., Henrik,T. Yudate, Masuho，Y., and Mitaku, S., A Novel MeasureCharacterized by a Polar Energy Surface Approximation for Recognition and Classification of
Transmembrane Protein Structures., Proteins: Struct. Funct. and Gennet. 41 504-517 (2000).

46. Pearl F, Todd AE, Bray JE, Martin AC, Salamov AA, Suwa M, Swindells MB, Thornton JM, Orengo CA.
Using the CATH domain database to assign structures and functions to the genome sequences., Biochem Soc Trans. Feb;28(2):269-275. (2000)

47. Nishikawa T, Murakami K, Harada N, Ota T, Sugiyama T, Nagai K, Irie R, Matui H, Suwa M, Isogai T.
An integrated analysis and database system for full-length cDNA.: Genome Inform Ser Workshop Genome Inform., 11, 12-23,(2000).

48. Hirokawa, T., Uechi, J., Sasamoto H., Suwa, M. and Mitaku, S.: A triangle lattice model that predicts transmembrane helix configuration using a polar　jigsaw puzzle.:,
Protein Eng. 13, 771-778 (2000).

49. Suwa, M., Sato T., Okouchi, I., Mikoshiba, M., Akiyama, Y., Asai., K., Matsumoto, S., Tsutsumi, S. and Aburatani, H., “ Gene Discovery of G-protein Coupled Receptors from Human Genome”,
Genome Informatics Series, 11, 410-411, (2000).

. 50. Suwa, M., Yudate, H. T., Masuho, Y and Mitaku,, S., "Polarity Difference Score: A New Measure for Recognition and Classification of Transmembrane Protein Structures”,
Genome Informatics Series, 11, 412-413, (2000).

. 1999

51. Salamov, AA, Suwa, M., Orengo, CA., Swindells, MB.: Combining sensitive database sequence searches with multiple intermediates to detect distant homologues.,Protein Eng.;12 95-100 (1999).

52. Salamov AA, Suwa M, Orengo CA, Swindells MB. , Genome analysis: Assigning protein coding regions to three-dimensional structures, Protein Sci., 8, 771-777 (1999)

1997

53. Masuko M, Toyoda S, Suwa M, Mitaku S, Shimazu A, Ohtani H.
Optimal configuration of pyrene excimer induced by the excimer-forming two-probe nucleic acid hybridization method.
Nucleic Acids Symp Ser. 87, 83-84, (1997).

54.Suwa, M., Saramov, A., A., Nishikawa, T., Swindels. M., A.”GoodMotif: The System for Finding High Quality Motifs That Can Discriminate a Unique Protein Family”,
Genome Informatics Series, 8, pp342-343, (1997).

1995

55. Mitaku S, Suzuki K, Odashima S, Ikuta K, Suwa M, Kukita F, Ishikawa M, Itoh H.
Interaction stabilizing tertiary structure of bacteriorhodopsin studied by denaturation experiments.,
Proteins. ;22:350-362 (1995).

56. Suwa, M. Hirokawa, T. and Mitaku, S: A
Continuum Theory for the Prediction of Lateral and Rotational Positioning of α-Helices in Membrane Proteins: Bacteriorhodopsin.:
Proteins: Struct. Funct. and Gennet. 22. 363-377 (1995).

1994

57. Suwa, M., Hirokawa, T. and Mitaku, S., “The Prediction of Lateral and Rotational Positioning of α-Helices in Membrane Protein”
Genome Informatics Series, 5，pp-150-151. (1994).

58. Ishikawa, T., Mitaku, S., Terano, T., Hirokawa, T., Suwa, M and Chieng, S., B., “ Finding Functional Features of Proteins Using,Machine Learning Techniques”,
Genome Informatics Series , 5，pp-168-169. (1994).

59. Hirokawa, T., Chieng, S. B., Suwa, M. and Mitaku, S., “A computer system for predicting membrane protein structure”,
Genome Informatics Series, 5，pp-226-227, (1994).
<
1993

60. Suwa M, Mitaku S, Kuroda Y., Theoretical analysis of amino acid sequence of human dystrophin.
Biochem Biophys Res Commun., 191(3):782-789 (1993).

61. Suwa. M, Mitaku, S., and Saito, N., A Computer System for Predicting Membrane Protein Structure.
Computer Aided Innovation of New Material II,: 1331-1334 (1993).

1992

62. Suwa. M, Mitaku, S., and Shimazaki, K., Characterization of Transmembrane Helices by a Probe Helix Method of Molecular Energy Calculation.
Jpn. J. Appl. Phys. 31, 951-956 (1992).

1989

63. Yanagihara N, Suwa M, Mitaku S., A theoretical method for distinguishing between soluble and membrane proteins.
Biophys Chem. 34(1):69-77 (1989).

64. Mitaku S, Ikuta K, Yanagihara N, Suwa M, Kataoka R, Itoh H., Structure formation mechanism of membrane proteins
Tanpakushitsu Kakusan Koso. (1989) May;34(5):518-27. Japanese.

1988

65. Mitaku, S., Ikuta, K., Itoh, H., Kataoka, R., Naka, M., Yamada, M. and Suwa, M.

Denaturation of bacteriorhodopsin by organic solvents,:
Biophysical Chemistry, 30, 69-79 (1988).

66. Suwa, M. and Mitaku, S., “Analysis of Amino Acid Sequence of Membrane Protein with Seven Membrane Spanning Helices”,
Repts. Progr. Polymer Phys. Japan, 27, 611-612, (1988).

1987

67. Suwa, M. and Mitaku, S., “On the Special Distribution of Hydrophilic Residues of Photosynthetic Reaction Cente”
Reports Progr. in Polymer Phys., Japan, 26, 725-726, (1987).

68. Yanagihara, N., Suwa, M. and Mitaku, S., “Theoretical Method of the Discrimination of Membrane Protein from Soluble Ones Based upon Amino Acid Analysis”,
Repts. Prog. Polymer Phys. Japan, 26, 729-730, (1987)

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