[[publications]]
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発表論文

並びの順序は、年内は著者のアルファベット順です。下線は業務参加者、下線＋ボールドは、業務主任者です．

2013

  1. Misawa, K., RF: A method for filtering short reads with tandem repeats for genome mapping. Genomics 102: 35–37, 2013.

2012

  1. Akihiro Fujimoto, Yasushi Totoki, Tetsuo Abe, Keith A Boroevich, Fumie Hosoda, Ha Hai Nguyen, Masayuki Aoki, Naoya Hosono, Michiaki Kubo, Fuyuki Miya, Yasuhito Arai, Hiroyuki Takahashi, Takuya Shirakihara, Masao Nagasaki, Tetsuo Shibuya, Kaoru Nakano, Kumiko Watanabe-Makino, Hiroko Tanaka, Hiromi Nakamura, Jun Kusuda, Hidenori Ojima, Kazuaki Shimada, Takuji Okusaka, Masaki Ueno, Yoshinobu Shigekawa, Yoshiiku Kawakami, Koji Arihiro, Hideki Ohdan, Kunihito Gotoh, Osamu Ishikawa, Shun-ichi Ariizumi, Masakazu Yamamoto, Terumasa Yamada, Kazuaki Chayama, Tomoo Kosuge, Hiroki Yamaue, Naoyuki Kamatani, Satoru Miyano, Hitoshi Nakagama, Yusuke Nakamura, Tatsuhiko Tsunoda, Tatsuhiro Shibata & Hidewaki Nakagawa. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nature Genetics 44:760-764, 2012.
  2. Misawa, K. Estimating human point mutation rates from codon substitution rates. Point Mutation, 31-42, 2012.
  3. Misawa, K., & Tajima, F., New weighting methods for phylogenetic tree reconstruction using multiple loci. Journal of Molecular Evolution, 75: 1-10, 2012.

2011

  1. Fujita, A., Sato, J.R., Demasi, M.A.A., Yamaguchi, R., Shimamura, T., Ferreira, C.E., Sogayar, M.C., Miyano, S. Inferring contagion in regulatory networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(2), 570-576, 2011.
  2. Kato, S., Misawa, K., Takahashi, F., Sakayama, H., Sano, S., Kosuge, K., Kasai, F., Watanabe, M., Tanaka, J. and Nozaki, H. Aquatic plant speciation affected by diversifying selection of organelle DNA regions. J. Phycol. 47(5), 999-1008, 2011.
  3. Misawa, K. A codon substitution model that incorporates the effect of the GC contents, the gene density and the density of CpG islands of human chromosomes. BMC Genomics 12:397, 2011.
  4. Misawa, K., Kamatani, N. ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing. Source Code for Biology and Medicine 6:10, 2011.
  5. Misawa, K., Kikuno, R.F. Relationship between amino acid composition and gene expression in the mouse genome. BMC Research Notes 4:20, 2011.
  6. Ohue, M., Matsuzaki, Y., Akiyama, Y.: Docking-calculation-based method for predicting protein-RNA interactions. Genome Informatics 2011, 25(1):25-39, 2011.
  7. Shimamura, T., Imoto, S., Shimada, Y., Hosono, Y., Niida, A., Nagasaki, M., Yamaguchi R., Takahashi T, Miyano, S. A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition. PLoS ONE 6:e20804, 2011.
  8. Tamada, Y., Imoto, S., Araki, H., Nagasaki, M., Print, C., Charnock-Jones, D.S., and Miyano, S. Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers, IEEE/ACM Transactions on Computational Biology and Bioinformatics 8:683-697, 2011.
  9. Tamada, Y., Imoto, S., and Miyano, S. Parallel algorithm for learning optimal Bayesian network structure, Journal of Machine Learning Research 12:2437−2459, 2011.
  10. Tamada, Y., Shimamura, T., Yamaguchi, R., Imoto, S., Nagasaki, M., and Miyano, S., SiGN: Large-scale gene network estimation environment for high performance computing, Genome Informatics, 25:40-52, 2011.
  11. Tamada, Y., Yamaguchi, R., Imoto, S., Hirose, O., Yoshida, R., Nagasaki, M., and Miyano, S. SiGN-SSM: open source parallel software for estimating gene networks with state space models, Bioinformatics, 27: 1172-1173, 2011.

2010

  1. Fujimoto, A., Nakagawa, H., Hosono, N., Nakano, K., Abe, T., Boroevich, K. A., Nagasaki, M., Yamaguchi, R., Shibuya, T., Kubo, M., Miyano, S., Nakamura, Y. and Tsunoda, T. Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nature Genetics 42:931–936. 2010.
  2. Fujita, A., Nagasaki, M., Imoto, S., A. Saito, E. Ikeda, Shimamura, T., Yamaguchi, R., H. Suzuki, Y. Hayashizaki, Miyano, S. Comparison of gene expression profiles produced by CAGE, illumina microarray and Real Time RT-PCR, Genome Informatics, 24, 56-68, 2010.
  3. Higashigaki, T., Kojima, K., Yamaguchi, R., Inoue, M., Imoto, S., Miyano, S. Identifying hidden confounders in gene networks by Bayesian networks, Proc. 10th IEEE Bioinformatics and Bioengineering, 168-173, 2010.
  4. Kojima, K., Imoto, S., Nagasaki, M., Miyano, S. Gene regulatory network clustering for graph layout based on microarray gene expression data, Genome Informatics, 24, 84-95, 2010.
  5. Kojima, K., Perrier, E., Imoto, S. and Miyano, S. Optimal search on clustered structural constraint for learning Bayesian network structure. Journal of Machine Learning Research, 11, 285-310, 2010.
  6. Misawa, K., Kamatani, N. ParaHaplo 2.0: a program package for haplotype-estimation and haplotype-based whole-genome association study using parallel computing. Source Code Biol Med. 5:5. 2010.
  7. Misawa K, Kikuno RF. Genewaltz —A New Method for Reducing False Positives of Gene Finding. BioData Mining 3:6. 2010.
  8. Niida, A., Imoto, S., Yamaguchi, R., Nagasaki, M., Fujita, A., Shimamura, T., Miyano, S. Model-free unsupervised gene set screening based on information enrichment in expression profiles, Bioinformatics, 26, 3090-3097, 2010.
  9. Shimamura, T., Imoto, S., Nagasaki, M., Yamauchi, M., Yamaguchi, R., Fujita, A., Tamada, Y., Gotoh, N., and Miyano, S. Collocation-based sparse estimation for inferring continuous-time dynamic gene networks, Genome Informatics, 24, 164-178, 2010.
  10. Shimamura, T., Imoto, S., Yamaguchi, R., Nagasaki, M., Miyano, S. Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinformatics, 26(8), 1064-1072, 2010.
  11. Yamaguchi, R., Imoto, S. and Miyano, S. Network-based predictions and simulations by biological state space models: search for drug mode of action, Journal of Computer Science and Technology, 25(1), 131-153, 2010.
  12. Yoshida R., Saito M. M., Nagao H., Higuchi T. Bayesian experts in exploring reaction kinetics of transcription circuits. Bioinformatics. 26:i589-95. 2010.

2009

  1. Asano, K., Matsushita, T., Umeno, J., Hosono, N., Takahashi, A., Kawaguchi, T., Matsumoto, T., Matsui, T., Kakuta, Y., Kinouchi, Y., Shimosegawa, T., Hosokawa, M., Arimura, Y., Shinomura, Y., Kiyohara, Y., Tsunoda, T., Kamatani, N., Iida, M., Nakamura, Y. and Kubo, M. A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population. Nature Genetics. 41: 1325-1329, 2009.
  2. Araki, H.*, Tamada, Y.*, Imoto, S.*, Dunmore, B., Sanders, D., Humphrey, S., Nagasaki, M., Doi, A., Nakanishi, Y., Yasuda, K., Tomiyasu, Y., Tashiro, K., Print, C., Charnock-Jones, D.S, Kuhara, S., and Miyano, S.. Analysis of PPARα-dependent and PPARα-independent transcript regulation following fenofibrate treatment of human endothelial cells, Angiogenesis, 12(3), 221-229, 2009. (* These authors equally contributed to this work.)
  3. Betcheva ET, Mushiroda T, Takahashi A, Kubo M, Karachanak SK, Zaharieva IT, Vazharova RV, Dimova II, Milanova VK, Tolev T, Kirov G, Owen MJ, O'Donovan MC, Kamatani N, Nakamura Y, Toncheva DI. Case-control association study of 59 candidate genes reveals the DRD2 SNP rs6277 (C957T) as the only susceptibility factor for schizophrenia in the Bulgarian population. J Hum Genet. 54(2):98-107. 2009
  4. Cui, R., Kamatani, Y., Takahashi, A., Usami, M., Hosono, N., Kawaguchi, T., Tsunoda, T., N.Kamatani, Kubo, M., Nakamura, Y., Matsuda, K. Functional variants in ADH1B and ALDH2 coupled with alcohol and smoking synergistically enhance esophageal cancer risk. Gastroenterology. 137: 1768-1775, 2009.
  5. Fujita, A., Patriota, A.G., Sato, J.R., Miyano, S. The impact of measurement error in the identification of regulatory networks. BMC Bioinformatics. 10:412, 2009.
  6. Fujita, A., Sato, J.R., da Silva, F.H.L., Galvao, M.C., Sogayar, M.C., Miyano, S. Quality control and reproducibility in DNA microarray experiments. Genome Informatics. 23:21-31, 2009.
  7. Fujita, A., Sato, J.R., Demasi, M.A.A., Sogayar, M.C., Ferreira, C.E., Miyano, S. Comparing Pearson, Spearman and Hoeffding's D measure for gene expression association analysis. Journal of Bioinformatics and Computational Biology. 7(4):663-684, 2009.
  8. Fujimoto, A., Nishida, A., Kimura, R., Miyagawa, T., Yuliwulandari, R., Batubara, L., Mustofa, M.S., Samakkarn, U., Settheetham-Ishida, W., Ishida, T., Morishita, Y., Tsunoda, T., Tokunaga, K., and Ohashi, J. FGFR2 is associated with hair thickness in Asian populations. Journal of Human Genetics. 54: 461-465, 2009.
  9. Hosono, N., Kato, M., Kiyotani, K., Mushiroda, T., Takata, S., Sato, H., Amitani, H., Tsuchiya, Y., Yamazaki, K., Tsunoda, T., Zembutsu, H., Nakamura, Y., and Kubo, M. CYP2D6 genotyping for functional gene dosage analysis by allele copy number detection. Clinical Chemistry. 55: 1546-1554, 2009.
  10. Hotta K, Nakamura M, Nakamura T, Matsuo T, Nakata Y, Kamohara S, Miyatake N, Kotani K, Komatsu R, Itoh N, Mineo I, Wada J, Masuzaki H, Yoneda M, Nakajima A, Funahashi T, Miyazaki S, Tokunaga K, Kawamoto M, Ueno T, Hamaguchi K, Tanaka K, Yamada K, Hanafusa T, Oikawa S, Yoshimatsu H, Nakao K, Sakata T, Matsuzawa Y, Kamatani N, Nakamura Y. Association between obesity and polymorphisms in SEC16B, TMEM18, GNPDA2, BDNF, FAIM2 and MC4R in a Japanese population. J Hum Genet. 2009
  11. Hotta K, Nakamura T, Takasaki J, Takahashi H, Takahashi A, Nakata Y, Kamohara S, Kotani K, Komatsu R, Itoh N, Mineo I, Wada J, Masuzaki H, Yoneda M, Nakajima A, Funahashi T, Miyazaki S, Tokunaga K, Hamaguchi K, Tanaka K, Yamada K, Hanafusa T, Oikawa S, Yoshimatsu H, Nakao K, Sakata T, Matsuzawa Y, Kamatani N, Nakamura Y. Screening of 336 single-nucleotide polymorphisms in 85 obesity-related genes revealed McKusick-Kaufman syndrome gene variants are associated with metabolic syndrome. J Hum Genet. 54(4):230-5. 2009
  12. Inazu, D., Sato, T., Miura, S., Ohta, Y., Nakamura, K., Fujimoto, H., Larsen, C. F., and Higuchi, T. Accurate ocean tide modeling in southeast Alaska and large tidal dissipation around Glacier Bay. J. Oceanography. 65(3):335-347. 2009
  13. Inazu, D., Higuchi, T., and Nakamura, K. Optimization of boundary condition and physical parameter in an ocean tide model using an evolutionary algorithm. Theoretical and Applied Mechanics Japan, Vol. 58, 58th Japan National Congress for Theoretical Applied Mechanics (accepted) 2009
  14. Kamatani Y, Wattanapokayakit S, Ochi H, Kawaguchi T, Takahashi A, Hosono N, Kubo M, Tsunoda T, Kamatani N, Kumada H, Puseenam A, Sura T, Daigo Y, Chayama K, Chantratita W, Nakamura Y, Matsuda K. A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians. Nat Genet. 41(5):591-5. 2009
  15. Kato, M., Kawaguchi, T., Ishikawa, S., Umeda, T., Nakamichi, R., Shapero, M.H., Jones, K.W., Nakamura, Y., Aburatani, H., and Tsunoda, T. Population-genetic nature of copy number variations in the human genome. Human Molecular Genetics, doi:10.1093/hmg/ddp541 (published online on December 5, 2009).
  16. Kiyotani, K., Mushiroda, T., Imamura, C.K., Hosono, N., Tsunoda, T., Kubo, M., Tanigawara, Y., Flockhart, D.A., Desta, Z., Skaar, T.C., Aki, F., Hirata, K., Takatsuka, Y., Okazaki, M., Ohsumi, S., Yamakawa, T., Sasa, M., Nakamura, Y., and Zembutsu, H. Significant Effect of Polymorphisms in CYP2D6 and ABCC2 on Clinical Outcomes of Adjuvant Tamoxifen Therapy for Breast Cancer Patients. Journal of Clinical Oncology, in press (2009).
  17. Kojima, K., Yamaguchi, R., Imoto, S., Yamauchi, M., Nagasaki, M., Yoshida, R., Shimamura, T., Ueno, K., Higuchi, T., Gotoh N. and Miyano, S. (2009) A state space representation of VAR models with sparse learning for dynamic gene networks. Genome Informatics, 22, 56-68.
  18. Makarasara W, Kumasaka N, Assawamakin A, Takahashi A, Intarapanich A, Ngamphiw C, Kulawonganunchai S, Ruangrit U, Fucharoen S, Kamatani N, Tongsima S. pHCR: a parallel haplotype configuration reduction algorithm for haplotype interaction analysis. J Hum Genet. 54(11):634-41. 2009
  19. Maruyama S, Matsuzaki M, Misawa K, Nozaki H. Cyanobacterial contribution to the genomes of the plastid-lacking protists. BMC Evol Biol 9:197. 2009.
  20. Matsuzaki, Y., Matsuzaki, Y., Toshiyuki, S. and Akiyama, Y., In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis. Journal of Bioinformatics and Computational Biology 7(1):991–1012, 2009.
  21. Misawa K, Kamatani N. ParaHaplo: A program package for haplotype-based whole-genome association study using parallel computing. Source Code Biol Med. 4:7. 2009
  22. Misawa K, Kikuno RF. Evaluation of the effect of CpG hypermutability on human codon substitution. Gene 431:18-22. 2009
  23. Miyano, S., Yamaguchi, R., Tamada, Y., Nagasaki, M., and Imoto, S. Gene Networks Viewed through Two Models, Proceedings of the 1st International Conference on Bioinformatics and Computational Biology (BICoB 2009), LNBI 4652, 54-66, 2009.
  24. Nakamura, K., Hirose, N., Choi, B.H., Higuchi, T. Particle filtering in data assimilation and its application to boundary condition of tsunami simulation model. Data Assimilation for Atmospheric, Oceanic and Hydrologic Applications:353-366, S.K. Park and L. Xu (ed.), Springer, 2009.
  25. Nakamura, K., Yoshida, R., Nagasaki, M., Miyano, S., Higuchi, T. Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing. Pacific Symposium on Biocomputing. 14: 227-238, 2009.
  26. Nakamura N, Ito K, Takahashi M, Hongo S, Hashimoto K, Kawamoto M, Taniguchi A, Kamatani N, Gemma N. Clinical verification of a combination technology of a loop-mediated isothermal amplification method and an electrochemical DNA chip for personalized medicine. Clin Biochem. 42(10-11):1158-61. 2009
  27. Nakano, S. and Higuchi, T. Estimation of a long-term variation of a magnetic-storm index using the merging particle filter. IEICE Transactions on Information and Systems. E92-D(7): 1382-1387. 2009.
  28. Ng CC, Yew PY, Puah SM, Krishnan G, Yap LF, Teo SH, Lim PV, Govindaraju S, Ratnavelu K, Sam CK, Takahashi A, Kubo M, Kamatani N, Nakamura Y, Mushiroda T. A genome-wide association study identifies ITGA9 conferring risk of nasopharyngeal carcinoma. J Hum Genet. 54(7):392-7. 2009
  29. Nozaki H, Maruyama S, Matsuzaki M, Nakada T, Kato S, Misawa K. Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes. Mol Phylogenet Evol 53:872-880. 2009.
  30. Nuinoon M, Makarasara W, Mushiroda T, Setianingsih I, Wahidiyat PA, Sripichai O, Kumasaka N, Takahashi A, Svasti S, Munkongdee T, Mahasirimongkol S, Peerapittayamongkol C, Viprakasit V, Kamatani N, Winichagoon P, Kubo M, Nakamura Y, Fucharoen S. A genome-wide association identified the common genetic variants influence disease severity in beta(0)-thalassemia/hemoglobin E. Hum Genet. 2009
  31. Ozaki, K., Sato, H., Inoue, K., Tsunoda, T., Sakata, Y., Mizuno, H., Lin, T., Miyamoto, Y., Aoki, A., Onouchi, Y., Sheu, S., Ikegawa, S., Odashiro, K., Nobuyoshi, M., Juo, S.H., Hori, M., Nakamura, Y., and Tanaka, T. SNPs in BRAP associated with risk of myocardial infarction in Asian populations. Nature Genetics. 41: 329-333, 2009.
  32. Shimamura, T., Imoto, S., Yamaguchi, R., Fujita, A., Nagasaki, M. and Miyano, S. Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Systems Biology. 3:41, 2009.
  33. Tamada, Y., Araki, H., Imoto, S., Nagasaki, M., Doi, A., Nakanishi, Y., Tomiyasu, Y., Yasuda, K., Dunmore, B., Sanders, D., Humphreys, S., Print, C., Charnock-Jones, D.S., Tashiro, K., Kuhara, S., Miyano, S. Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks. Pacific Symposium on Biocomputing. 14: 25–263, 2009.
  34. Tsukada H, Ochi H, Maekawa T, Abe H, Fujimoto Y, Tsuge M, Takahashi H, Kumada H, Kamatani N, Nakamura Y, Chayama K. A polymorphism in MAPKAPK3 affects response to interferon therapy for chronic hepatitis C. Gastroenterology. 136(5):1796-805.e6. 2009
  35. Zembutsu, H., Suzuki, Y., Sasaki, A., Tsunoda, T., Hasegawa, T., Hirata, K., and Nakamura, Y. Predicting Response to Docetaxel Neoadjuvant Chemotherapy for Advanced Breast Cancers through Genome-Wide Gene Expression Profiling. International Journal of Oncology. 34: 361-370, 2009.

2008

  1. Chapman, K., Takahashi, A., Meulenbelt, I., Watson, C., Rodriguez-Lopez, J., Egli, R., Tsezou, A., Malizos, K.N., Kloppenburg, M., Shi, D., Southam, L., van der Breggen, R., Donn, R., Qin, J., Doherty, M., Slagboom, P.E., Wallis, G., Kamatani, N., Jiang, Q., Gonzalez, A., Loughlin, J., Ikegawa, S. A meta-analysis of European and Asian cohorts reveals a global role of a functional SNP in the 5' UTR of GDF5 with osteoarthritis susceptibility. Hum Mol Genet. 17:1497-504, 2008.
  2. Fujimoto, A., Ohashi, J., Nishida, N., Miyagawa, T., Morishita, Y., Tsunoda, T., Kimura, R., Tokunaga, K. A replication study confirmed the EDAR gene to be a major contributor to population differentiation regarding head hair thickness in Asia. Hum Genet. 124: 179-85, 2008.
  3. Fujita, A., Gomes, L.R., Sato, J.R., Yamaguchi, R., Thomaz, C.E., Sogayar, M.C., Miyano, S. Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. BMC Systems Biology. 2: 106, 2008.
  4. Fujita, A., Sato, J.R., Garay-Malpartida, H.M., Sogayar, M.C., Ferreira, C.E., Miyano, S. Modeling nonlinear gene regulatory networks from time-series gene expression data. Journal of Bioinformatics and Computational Biology. 6:961-79, 2008.
  5. Fukuda, J., Miyazaki, S., Higuchi, T., Kato, T. Geodetic inversion for space-time distribution of fault slip with time-varying smoothing regularization. Geophysical Journal International. 173(1):25-48, 2008.
  6. Furuichi, T., Maeda, K., Chou, C.T., Liu, Y.F., Liu, T.C., Miyamoto, Y., Takahashi, A., Mori, K., Ikari, K., Kamatani, N., Kurosawa, H., Inoue, H., Tsai, S.F., Ikegawa, S. Association of the MSX2 gene polymorphisms with ankylosing spondylitis in Japanese. J Hum Genet. 53:419-24, 2008.
  7. Hatanaka, Y., Nagasaki, M., Yamaguchi, R., Obayashi, T., Numata, K., Fujita, A., Shimamura, T., Tamada, Y., Imoto, S., Kinoshita, K., Nakai, K., Miyano, S. A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human. Genome Informatics. 20:212-221, 2008.
  8. Hirose, O., Yoshida, R., Imoto, S., Yamaguchi, R., Higuchi, T., Charnock-Jones, D.S., Print, C., Miyano, S. Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics. 24(7): 932-942, 2008.
  9. Hirose, O, Yoshida, R., Yamaguchi, R., Imoto, S., Higuchi, T. and Miyano, S. Analyzing time course gene expression data with biological and technical replicates to estimate gene networks by state space models, Proc. 2nd Asia International Conference on Modelling & Simulation, 940-946, 2008.
  10. Hotta, K., Nakamura, M., Nakata, Y., Matsuo, T., Kamohara, S., Kotani, K., Komatsu, R., Itoh, N., Mineo, I., Wada, J., Masuzaki, H., Yoneda, M., Nakajima, A., Miyazaki, S., Tokunaga, K., Kawamoto, M., Funahashi, T., Hamaguchi, K., Yamada, K., Hanafusa, T., Oikawa, S., Yoshimatsu, H., Nakao, K., Sakata, T., Matsuzawa, Y., Tanaka, K., Kamatani, N., Nakamura, Y. INSIG2 gene rs7566605 polymorphism is associated with severe obesity in Japanese. J Hum Genet. 53:857-862, 2008.
  11. Hotta, K., Nakata, Y., Matsuo, T., Kamohara, S., Kotani, K., Komatsu, R., Itoh, N., Mineo, I., Wada, J., Masuzaki, H., Yoneda, M., Nakajima, A., Miyazaki, S., Tokunaga, K., Kawamoto, M., Funahashi, T., Hamaguchi, K., Yamada, K., Hanafusa, T., Oikawa, S., Yoshimatsu, H., Nakao, K., Sakata, T., Matsuzawa, Y., Tanaka, K., Kamatani, N., Nakamura, Y. Variations in the FTO gene are associated with severe obesity in the Japanese. J Hum Genet. 53:546-53, 2008.
  12. Ishigaki, T., Higuchi, T. Parameter identification of a pressure regulator with a nonlinear structure using a particle filter based on the nonlinear state space model. The Proceedings of 11th International Conference on Information Fusion. 886-891, 2008.
  13. Jiang, Q., Shi, D., Nakajima, M., Dai, J., Wei, J., Malizos, K.N., Qin, J., Miyamoto, Y., Kamatani, N., Liu, B., Tsezou, A., Nakamura, T., Ikegawa, S. Lack of association of single nucleotide polymorphism in LRCH1 with knee osteoarthritis susceptibility. J Hum Genet. 53:42-47, 2008.
  14. Kamatani, Y., Matsuda, K., Ohishi, T., Ohtsubo, S., Yamazaki, K., Iida, A., Hosono, N., Kubo, M., Yumura, W., Nitta, K., Katagiri, T., Kawaguchi, Y., Kamatani, N., Nakamura, Y. Identification of a significant association of a single nucleotide polymorphism in TNXB with systemic lupus erythematosus in a Japanese population. J Hum Genet. 53:64-73, 2008.
  15. Kobayashi S, Ikari K, Kneko H, Kochi Y, Yamamoto K, Shimane K, Nakamura Y, Toyama Y, Mocizuki T, Tsukahara S, Kawaguchi Y, Terai C, Hara M, Tomatsu T, Yamanaka H, Horiuchi T, Tao K, Yasutomo K, Hamada D, Yasui N, Inoue H, Itakura M, Okamoto H, Kamatani N, Momohara S, Association of STAT4 with susceptibility to rheumatoid arthritis and systemic lupus erythematosus in the Japanese population Arthritis. Rheumatism 58 (7) :1940-1946. 2008
  16. Kojima, K., Fujita, A., Shimamura, T., Imoto, S., Miyano, S. Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data. Genome Informatics. 20:37-51, 2008.
  17. Nakada T, Misawa K, Nozaki H. 2008. Molecular systematics of Volvocales (Chlorophyceae, Chlorophyta) based on exhaustive 18S rRNA phylogenetic analyses. Mol Phylogenet Evol 48:281-291.
  18. Maruyama S, Misawa K, Iseki M, Watanabe M, Nozaki H. 2008. Origins of a cyanobacterial 6-phosphogluconate dehydrogenase in plastid-lacking eukaryotes. BMC Evol Biol 8:151.
  19. Matsuo R, Misawa K, Ito E. 2008. Genomic structure of nitric oxide synthase in the terrestrial slug is highly conserved. Gene 415:74-81.
  20. Misawa, K., Fujii, S., Yamazaki, T., Takahashi, A., Takasaki, J., Yanagisawa, M., Ohnishi, Y., Nakamura, Y., Kamatani, N. New correction algorithms for multiple comparisons in case-control multilocus association studies based on haplotypes and diplotype configurations. J. Hum. Genet. 53(9):789-801, 2008.
  21. Misawa, K., Kamatani, N., Kikuno, R.F. The universal trend of amino acid gain-loss is caused by CpG hypermutability. J Mol Evol. 67:334-42, 2008.
  22. Miyamoto, Y., Shi, D., Nakajima, M., Ozaki, K., Sudo, A., Kotani, A., Uchida, A., Tanaka, T., Fukui, N., Tsunoda, T., Takahashi, A., Nakamura, Y., Jiang, Q., Ikegawa, S. Common variants in DVWA on chromosome 3p24.3 are associated with susceptibility to knee osteoarthritis. Nature Genetics, 40: 994-998, 2008.
  23. Mushiroda, T., Wattanapokayakit, S., Takahashi, A., Nukiwa, T., Kudoh, S., Ogura, T., Taniguchi, H., Kubo, M., Kamatani, N., Nakamura, Y.; Pirfenidone Clinical Study Group. A genome-wide association study identifies an association of a common variant in TERT with susceptibility to idiopathic pulmonary fibrosis. J Med Genet. 45:654-6, 2008.
  24. Nose, J., Saito, A., Kamatani, N. Statistical analysis of the associations between polymorphisms within aldehyde dehydrogenase 2 (ALDH2)., and quantitative and qualitative traits extracted from a large-scale database of Japanese single-nucleotide polymorphisms (SNPs). J Hum Genet. 53:425-38, 2008.
  25. Numata, K, Imoto, S., and Miyano, S. Partial order-based Bayesian network learning algorithm for estimating gene networks, Proc. IEEE Bioinformatics and Biomedicine, 357-360, 2008.
  26. Oishi, T., Iida, A., Otsubo, S., Kamatani, Y., Usami, M., Takei, T., Uchida, K., Tsuchiya, K., Saito, S., Ohnisi, Y., Tokunaga, K., Nitta, K., Kawaguchi, Y., Kamatani, N., Kochi, Y., Shimane, K., Yamamoto, K., Nakamura, Y., Yumura, W., Matsuda, K. A functional SNP in the NKX2.5-binding site of ITPR3 promoter is associated with susceptibility to systemic lupus erythematosus in Japanese population. J Hum Genet. 53:151-62, 2008.
  27. Onouchi, Y., Gunji, T., Burns, J.C., Shimizu, C., Newburger, J.W., Yashiro, M., Nakamura, Y., Yanagawa, H., Wakui, K., Fukushima, Y., Kishi, F., Hamamoto, K., Terai, M., Sato, Y., Ouchi, K., Saji, T., Nariai, A., Kaburagi, Y., Yoshikawa, T., Suzuki, K., Tanaka, T., Nagai, T., Choi, H ., Fujino, A., Sekine, A., Nakamichi, R., Tsunoda, T., Kawasaki, T., Nakamura, Y., Hata, A. A functional polymorphism in ITPKC is associated with Kawasaki disease susceptibility and formation of coronary artery aneurysms. Nat Genet. 40: 35-42, 2008.
  28. Perrier, E., Imoto, S., Miyano, S. Finding optimal Bayesian network given a super-structure. J. Machine Learning Research. 9: 2251-2286, 2008.
  29. Shindo, H., Chigira, H., Tanaka, J., Kamatani, N., Inoue, M. Grouping preprocess to accurately extend application of EM algorithm to haplotype inference. J Hum Genet. 53:747-56, 2008.
  30. Suzuki, A., Yamada, R., Kochi, Y., Sawada, T., Okada, Y., Matsuda, K., Kamatani, Y., Mori, M., Shimane, K., Hirabayashi, Y., Takahashi, A., Tsunoda, T., Miyatake, A., Kubo, M., Kamatani, N., Nakamura, Y., Yamamoto, K. Functional SNPs in CD244 increase the risk of rheumatoid arthritis in a Japanese population. Nat Genet. 40:1224-9, 2008.
  31. Tominaga, D., Iguchi, F., Horimoto, K., Akiyama, Y. High-throughput automated image processing system for cell array observations. Information and Media Technologies. 3(1): 71-78, 2008.
  32. Tsukamoto, K., Yoshikawa, T., Hourai, Y., Fukui, K., Akiyama, Y. Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins. Journal of Bioinformatics and Computational Biology. 6(6):1133–1156, 2008.
  33. Unoki, H., Takahashi, A., Kawaguchi, T., Hara, K., Horikoshi, M., Andersen, G., Ng, D.P.K., Holmkvist, J., Borch-Johnsen, K., Jørgensen, T., Sandbæk, A., Lauritzen, T., Hansen, T., Nurbaya, S., Tsunoda, T., Kubo, M., Babazono, T., Hirose, H., Hayashi, M., Iwamoto, Y., Kashiwagi, A., Kaku, K., Kawamori, R., Tai, E.S., Pedersen, O., Kamatani, N., Kadowaki, T., Kikkawa, R., Nakamura, Y., Maeda, S. SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. Nature Genetics. 40: 1098-1102, 2008.
  34. Yamaguchi, R., Imoto, S., Yamauchi, M., Nagasaki, M., Yoshida, R., Shimamura, T., Hatanaka, Y., Ueno, K., Higuchi, T., Gotoh, N., Miyano, S. Predicting differences in gene regulatory systems by state space models. Genome Informatics. 21:101-113, 2008.
  35. Yamaguchi-Kabata, Y., Nakazono, K., Takahashi, A., Saito, S., Hosono, N., Kubo, M., Nakamura, Y., Kamatani, N. Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups.effects on population-based association studies. Am J Hum Genet. 83:445-56, 2008.
  36. Yamazaki, K., Takahashi, A., Takazoe, M., Kubo, M., Onouchi, Y., Fujino, A., Kamatani, N., Nakamura, Y., Hata, A. Positive association of genetic variants in the upstream region of NKX2-3 with Crohn's disease in Japanese patients. Gut. 2008 Nov 6.
  37. Yasuda, K., Miyake, K., Horikawa, Y., Hara, K., Osawa, H., Furuta, H., Hirota, Y., Mori, H., Jonsson, A., Sato, Y., Yamagata, K., Hinokio, Y., Wang, H.Y., Tanahashi, T., Nakamura, N., Oka, Y., Iwasaki, N., Iwamoto, Y., Yamada, Y., Seino, Y., Maegawa, H., Kashiwagi, A., Takeda, J., Maeda, E., Shin, H.D., Cho, Y.M., Park, K.S., Lee, H.K., Ng, M.C., Ma, R.C., So, W.Y., Chan, J.C., Lyssenko, V., Tuomi, T., Nilsson, P., Groop, L., Kamatani, N., Sekine, A., Nakamura, Y., Yamamoto, K., Yoshida, T., Tokunaga, K., Itakura, M., Makino, H., Nanjo, K., Kadowaki, T., Kasuga, M. Variants in KCNQ1 are associated with susceptibility to type 2 diabetes mellitus. Nat Genet. 2008 Aug 17.
  38. Yoshida, R., Nagasaki, M., Yamaguchi, R., Imoto, S., Miyano, S., Higuchi, T. Bayesian learning of biological pathways on genomic data assimilation. Bioinformatics. 24(22):2592-2601, 2008.
  39. 佐藤忠彦, 樋口知之, 動的個人モデルによる消費者来店行動の解析（討論付）, 日本統計学会誌, Vol.38, No.1, 1-38, 2008.
  40. 中野慎也, 上野玄太, 中村和幸, 樋口知之．Merging particle filterとその特性, 統計数理, Vol.56, 225-234, 2008.

2007

  1. Cha, P.C., Mushiroda, T., Takahashi, A., Saito, S., Shimomura, H., Suzuki, T., Kamatani, N., Nakamura, Y. High-resolution SNP and haplotype maps of the human gamma-glutamyl carboxylase gene (GGCX) and association study between polymorphisms in GGCX and the warfarin maintenance dose requirement of the Japanese population. J Hum Genet. 52:856-864, 2007.
  2. Ebana, Y., Ozaki, K., Inoue, K., Sato, H., Iida, A., Lwin, H., Saito, S., Mizuno, H., Takahashi, A., Nakamura, T., Miyamoto, Y., Ikegawa, S., Odashiro, K., Nobuyoshi, M., Kamatani, N., Hori, M., Isobe, M., Nakamura, Y., Tanaka, T. A functional SNP in ITIH3 is associated with susceptibility to myocardial infarction. J Hum Genet. 52:220-229, 2007.
  3. Fujita, A., Sato, J.R., Garay-Malpartida, H.M., Yamaguchi, R., Miyano, S., Sogayar, M.C., Ferreira, C.E.　Modeling gene expression regulatory networks with the sparse vector autoregressive model. BMC Systems Biology 2007, 1:39 (doi:10.1186/1752-0509-1-39)
  4. Hirose, O., Yoshida, R., Yamaguchi, R., Imoto, S., Higuchi, T., Miyano, S. Clustering with time course gene expression profiles and the mixture of state space models. Genome Informatics. 18:258-266, 2007.
  5. Mukai, Y., Hirokawa, T., Tomii, K., Asai, K., Akiyama, Y., Suwa, M. Identification of glycosyltransferases focusing on golgi transmembrane region. Trends in Glycoscience and Glycotechnology. 19(105): 41-47, 2007.
  6. Nagano, N. Noguchi, T., Akiyama, Y. Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the ezcatdb database. Proteins: Structure, Function, and Bioinformatics. 66(1): 147-159, 2007.
  7. Nakano, S., Ueno, G., Higuchi, T. Merging particle filter for sequential data assimilation. Nonlinear Processes in Geophysics. 14:395-408, 2007.
  8. Nakamura, T., Shi, D., Tzetis, M., Rodriguez-Lopez, J., Miyamoto, Y., Tsezou, A., Gonzalez, A., Jiang, Q., Kamatani, N., Loughlin, J., Ikegawa, S. Meta-analysis of association between the ASPN D-repeat and osteoarthritis. Hum Mol Genet. 16:1676-1681, 2007.
  9. Nukada, A., Hourai, Y., Nishida, A., Akiyama, Y. High performance 3D convolution for protein docking on IBM Blue Gene. Proc. Fifth International Symposium on Parallel and Distributed Processing and Applications (ISPA07). 958-969, 2007. (Peer-reviewed paper)
  10. Numata, K., Imoto, S., Miyano, S. A structure learning algorithm for inference of gene networks from microarray gene expression data using Bayesian networks. Proc. IEEE 7th International Symposium on Bioinformatics & Bioengineering. 1280-1284, 2007. (BIBE2007: Refereed conference; Digital Object Identifier 10.1109/BIBE.2007.4375731)
  11. Saeki, M., Saito, Y., Sai, K., Maekawa, K., Kaniwa, N., Sawada, J., Kawamoto, M., Saito, A., Kamatani, N. A combinatorial haplotype of the UDP-glucuronosyltransferase 1A1 gene (#60-#IB) increases total bilirubin concentrations in Japanese volunteers. Clin Chem. 53:356-358, 2007.
  12. Sekijima, M., Doi, J., Honda, S., Noguchi, T., Shimizu, S., Akiyama, Y. Free energy landscape analysis system based on parallel molecular dynamics simulation. IPSJ Transaction on Bioinformatics. 48(No.SIG17(TBIO3)): 30-39, 2007.
  13. Sekijima, M., Doi, J., Noguchi, T., Akiyama, Y., Shimizu, S. Optimization and evaluation of parallel molecular dynamics simulation on Blue Gene/L. Proc. IASTED International Conference on Parallel and Distributed Computer and Networks (PDCN2007). 257-262, 2007. (Peer-reviewed paper)
  14. Shimamura, T., Yamaguchi, R., Imoto, S., Miyano, S. Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data. Genome Informatics. 19:142-153, 2007.
  15. Tominaga, D., Iguchi, F., Horimoto, K., Akiyama, Y. High-throughput Automated Image Processing System for Cell Array Observations. IPSJ Transaction on Bioinformatics. 48(No.SIG17(TBIO3)):1-8, 2007.
  16. Takitoh, S., Fujii, S., Mase, Y., Takasaki, J., Yamazaki, T., Ohnishi, Y., Yanagisawa, M., Nakamura, Y., Kamatani, N. Accurate automated clustering of two-dimensional data for single-nucleotide polymorphism genotyping by a combination of clustering methods: evaluation by large-scale real data. Bioinformatics. 23:408-413, 2007.
  17. Tanabe A, Yanagiya T, Iida A, Saito S, Sekine A, Takahashi A, Nakamura T, Tsunoda T, Kamohara S, Nakata Y, Kotani K, Komatsu R, Itoh N, Mineo I, Wada J, Funahashi T, Miyazaki S, Tokunaga K, Hamaguchi K, Shimada T, Tanaka K, Yamada K, Hanafusa T, Oikawa S, Yoshimatsu H, Sakata T, Matsuzawa Y, Kamatani N, Nakamura Y, Hotta K, Functional Single-Nucleotide Polymorphisms in the Secretogranin III(SCG3) Gene that Forms Secretory Granules with Appetite-Related Neuropeptides are Associated with Obesity Journal of Clinical Endocrinology and Metabolism 92 (3): 1145-1154. 2007
  18. Tominaga, D., Iguchi, F., Akiyama, Y., Horimoto, K. Development of automated image processing procedure for cell-arrays. Proc. The 11th World Multi-Conference on Systemics, Cybernetics and Informatics. 4:19-24, 2007.
  19. Tsukamoto, K., Shimizu, H., Ishida, T., Akiyama, Y., Nukina, N. Evaluation for interaction energy between glutamine and glutamine and various chemical compounds for developing the virtual screening system using quantum chemical calculations and molecular dynamics simulations. WSEAS Transactions on Computers. 6(4):636-641, 2007.
  20. Yamaguchi, R., Yamamoto, M., Imoto, S., Nagasaki, M., Yoshida, R., Tsujii, K., Ishiga, A., Asou, H., Watanabe, K., Miyano, S. Identification of activated transcription factors from microarray gene expression data of Kampo-medicine treated mice. Genome Informatics. 18:119-129, 2007.
  21. Yamaguchi, R., Yoshida, R., Imoto, S., Higuchi, T., Miyano, S. Finding module-based gene networks with state-space models? Mining high-dimensional and short time-course gene expression data. IEEE Signal Processing Magazine. 24(1):37-46, 2007.
  22. Yanagiya, T., Tanabe, A., Iida, A., Saito, S., Sekine, A., Takahashi, A., Tsunoda, T., Kamohara, S., Nakata, Y., Kotani, K., Komatsu, R., Itoh, N., Mineo, I., Wada, J., Masuzaki, H., Yoneda, M., Nakajima, A., Miyazaki, S., Tokunaga, K., Kawamoto, M., Funahashi, T., Hamaguchi, K., Tanaka, K., Yamada, K., Hanafusa, T., Oikawa, S., Yoshimatsu, H., Nakao, K., Sakata, T., Matsuzawa, Y., Kamatani, N., Nakamura, Y., Hotta, K. Association of single-nucleotide polymorphisms in MTMR9 gene with obesity. Hum Mol Genet. 16:3017-3026, 2007.

2006

  1. Furihata, S., Ito, T., Kamatani, N. Test of association between haplotypes and phenotypes in case-control studies: examination of validity of the application of an algorithm for samples from cohort or clinical trials to case-control samples using simulated and real data. Genetics. 174:1505-1516, 2006.
  2. Ikegawa S, Kawamura S, Takahashi A, Nakamura T, Kamatani N, Replication of association of the D-repeat polymorphism in asporin with osteoarthristis Arthritis research and therapy 8 (4): 4037. 2006
  3. Ishii, N., Ozaki, K., Sato, H., Mizuno, H., Saito, S., Takahashi, A., Miyamoto, Y., Ikegawa, S., Kamatani, N., Hori, M., Saito, S., Nakamura, Y., Tanaka, T. Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet. 51:1087-1099, 2006.
  4. Kamitsuji, S., Kamatani, N. Estimation of haplotype associated with several quantitative phenotypes based on maximization of area under a receiver operating characteristic (ROC) curve. J Hum Genet. 51:314-325, 2006.
  5. Kuno, S., Furihata, S., Itou, T., Saito, K., Kamatani, N. Unified method for Bayesian calculation of genetic risk. J Hum Genet. 51:387-390, 2006.
  6. Mahasirimongkol, S., Chantratita, W., Promso, S., Pasomsab, E., Jinawath, N., Jongjaroenprasert, W., Lulitanond, V., Krittayapoositpot, P., Tongsima, S., Sawanpanyalert, P., Kamatani, N., Nakamura, Y., Sura, T. Similarity of the allele frequency and linkage disequilibrium pattern of single nucleotide polymorphisms in drug-related gene loci between Thai and northern East Asian populations: implications for tagging SNP selection in Thais. J Hum Genet. 51:896-904, 2006.
  7. Mushiroda T, Ohnishi Y, Saito S, Takahashi A, Kikuchi Y, Saito S, Simomura H, Wanibuchi Y, Suzuki T, Kamatani N, Nakamura Y, Association of VKORC1 and CYP2C9 polymorphisms with warfarin dose requirements in Japanese patients Journal of Human Genetics 51 (3) :249-253. 2006
  8. Nagasaki, M., Yamaguchi, R., Yoshida, R., Imoto, S., Doi, A., Tamada, Y., Matsuno, H., Miyano, S., Higuchi, T. Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Informatics. 17(1): 46-61, 2006.
  9. Nakamura, K., Higuchi, T., Hirose, N. Sequential data assimilation : Information fusion of a numerical simulation and large scale observation data. Journal of Universal Computer Science. 12:608-626, 2006.
  10. Osawa, N., Koya, D., Araki, S., Uzu, T., Tsunoda, T., Kashiwagi, A., Nakamura, Y., Maeda, S. Combinational effect of genes for the renin-angiotensin system in conferring susceptibility to diabetic nephropathy. Journal of Human Genetics, 52, 143-151, 2006.
  11. Ozaki, K., Sato, H., Iida, A., Mizuno, H., Nakamura, T., Miyamoto, Y., Takahashi, A., Tsunoda, T., Ikegawa, S., Kamatani, N., Hori, M., Nakamura, Y., Tanaka, T. A functional SNP in PSMA6 confers risk of myocardial infarction in the Japanese population. Nat Genet. 38:921-925, 2006.
  12. Tasaki, S., Nagasaki, M., Oyama, M., Hata, H., Ueno, K., Yoshida, R., Higuchi, T., Sugano, S., Miyano, S. Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Informatics. 17(2): 226-228, 2006.
publications.txt · 最終更新: 2013/06/04 14:24 by data-analysis
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