Publication List

Note: This is Rui Yamaguchi's publication list including Japanese fonts.

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  1. Hayashi S, Yamaguchi R, Mizuno S, Komura M, Miyano S, Miyano S, Nakagawa H, Imoto S. ALPHLARD: a Bayesian method for analyzing HLA genes from whole genome sequence data. BMC Genomics. (in press).
  2. Ito S, Yadome M, Nishiki T, Ishiduki S, Inoue H, Yamaguchi R, Miyano S. Virtual Grid Engine: Accelerating thousands of omics sample analyses using large-scale supercomputers. Proc. IEEE Bioinformatics and Biomedicine 2018 (BIBM2018). (in press).
  3. Muraoka D, Seo N, Hayashi T, Tahara Y, Fuujii K, Tawara I, Miyahara Y, Okamori K, Yagita H, Imoto S, Yamaguchi R, Komura M, Miyano S, Goto M, Sawada S, Asai A, Ikeda H, Akiyoshi K, Harada N, Shiku H. Antigen Delivery Tumor-Associated Macrophages Overcomes Tumor Immune Resistance. Journal of Clinical Investigation. (in press).
  4. Yokoyama K, Shimizu E, Yokoyama N, Nakamura S, Kasajima R, Ogawa M, Takei T, Ito M, Kobayashi A, Yamaguchi R, Imoto S, Miyano S, Tojo A*. Cell lineage level-targeted sequencing to identify acute myeloid leukemia with myelodysplasia related changes, Blood Advances. (in press).
  5. Nakamura S, Yokoyama K, Yusa N, Ogawa M, Takei T, Kobayashi A, Ito M, Shimizu E, Kasajima R, Wada Y, Yamaguchi R, Imoto S, Nagamura-Inoue T, Miyano S, Tojo A. Circulating tumor DNA dynamically predicts response and/or relapse in patients with hematological malignancies. Int J Hematol. doi: 10.1007/s12185-018-2487-2, (2018).
  6. Takei T, Yokoyama K, Shimizu E, Konuma T, Takahashi S, Yamaguchi R, Imoto S, Miyano S, Tojo A. Azacitidine effectively reduces TP53-mutant leukemic cell burden in secondary acute myeloid leukemia after cord blood transplantation. Leuk Lymphoma. 12:1-2, doi: 10.1080/10428194.2018.1443335, (2018).
  7. Inoue D, Fujino T, Sheridan P, Zhang YZ, Nagase R, Horikawa S, Li Z, Matsui H, Kanai A, Saika M, Yamaguchi R, Kozuka-Hata H, Kawabata KC, Yokoyama A, Goyama S, Inaba T, Imoto S, Miyano S, Xu M, Yang FC, Oyama M, Kitamura T. A novel ASXL1-OGT axis plays roles in H3K4 methylation and tumor suppression in myeloid malignancies. Leukemia. 32:1327-1337, doi: 10.1038/s41375-018-0083-3, (2018).
  8. VanderWeele DJ, Finney R, Katayama K, Gillard M, Paner G, Imoto S, Yamaguchi R, Wheeler D, Lack J, Cam M, Pontier A, Nguyen YTM, Maejima K, Sasaki-Oku A, Nakano K, Tanaka H, Vander Griend D, Kubo M, Ratain MJ, Miyano S, Nakagawa H. Genomic Heterogeneity Within Individual Prostate Cancer Foci Impacts Predictive Biomarkers of Targeted Therapy. Eur Urol Focus. pii: S2405-4569(18)30007-5, doi: 10.1016/j.euf.2018.01.006, (2018).
  9. Kiyotani K, Mai TH, Yamaguchi R, Yew PY, Kulis M, Orgel K, Imoto S, Miyano S, Burks AW, Nakamura Y. Characterization of the B-cell receptor repertoires in peanut allergic subjects undergoing oral immunotherapy, Journal of Human Genetics. 63(2):239-248, doi: 10.1038/s10038-017-0364-0, (2018).
  10. Kobayashi M, Yokoyama K, Shimizu E, Yusa N, Ito M, Yamaguchi R, Imoto S, Miyano S, Tojo A. Phenotype-based gene analysis allowed successful diagnosis of X-linked neutropenia associated with a novel WASp mutation. Ann Hematol. 97(2):367-369, doi: 10.1007/s00277-017-3134-3, (2018).
  11. Zhang Y-Z, Imoto S, Miyano S, Yamaguchi R. Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning. Proceedings of International Workshop on Deep Learning in Bioinformatics, Biomedicine, and Healthcare Informatics (DLB2H 2017). 1227-1232, doi: 10.1109/BIBM.2017.8217832, (2017).
  12. Miyamoto T, Tanikawa C, Yodsurang V, Zhang YZ, Imoto S, Yamaguchi R, Miyano S, Nakagawa H, Matsuda K. Identification of a p53-repressed gene module in breast cancer cells. Oncotarget. 8(34):55821-55836. doi: 10.18632/oncotarget.19608, (2017).
  13. Sato R, Shibata T, Tanaka Y, Kato C, Yamaguchi K, Furukawa Y, Shimizu E, Yamaguchi R, Imoto S, Miyano S, Miyake K. Requirement of glycosylation machinery in Toll-like receptor responses revealed by CRISPR/Cas9 screening. Int Immunol. doi: 10.1093/intimm/dxx044, (2017).
  14. Tsuda Y, Tanikawa C, Miyamoto T, Hirata M, Yodsurang V, Zhang Y-Z, Imoto S, Yamaguchi R, Miyano S, Takayanagi H, Kawano H, Nakagawa H, Tanaka S, Matsuda K. Identification of a p53 target, CD137L, that mediates growth suppression and immune response of osteosarcoma cells. Sci Rep 7, 10739, (2017).
  15. Tanikawa C, Zhang Y-Z, Yamamoto R, Tsuda Y, Tanaka M, Funauchi Y, Mori J, Imoto S, Yamaguchi R, Nakamura Y, Miyano S, Nakagawa H, Matsuda K. The Transcriptional Landscape of p53 Signalling Pathway, EBioMedicine. 20:109-119. doi: 10.1016/j.ebiom.2017.05.017, (2017).
  16. Ikeda Y, Kiyotani K, Yew PY, Sato S, Imai Y, Yamaguchi R, Miyano S, Fujiwara K, Hasegawa K, Nakamura Y. Clinical significance of T cell clonality and expression levels of immune-related genes in endometrial cancer. Oncol Rep. 37(5):2603-2610, doi: 10.3892/or.2017.5536, (2017).
  17. Onuki R, Yamaguchi R, Shibuya T, Kanehisa M, Goto S. Revealing phenotype-associated functional differences by genome-wide scan of ancient haplotype blocks, PLoS ONE. 12:e0176530. doi: 10.1371/journal.pone.0176530, (2017).
  18. Moriyama T, Shiraishi Y, Chiba K, Yamaguchi R, Imoto S, Miyano S. OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads, IEEE Transactions on NanoBioscience. 16(2):116-122, doi: 10.1109/TNB.2017.2670601, (2017).
  19. Fujii K, Miyahara Y, Harada N, Muraoka D, Komura M, Yamaguchi R, Yagita H, Nakamura J, Sugino S, Okumura S, Imoto S, Miyano S, Shiku H. Identification of an immunogenic neo-epitope encoded by mouse sarcoma using CXCR3 ligand mRNAs as sensors. OncoImmunology, 6(5):e1306617. doi: 10.1080/2162402X.2017.1306617, (2017).
  20. Zhang Y-Z, Yamaguchi R, Imoto S, Miyano S. Sequence-specific bias correction for RNA-seq data using recurrent neural networks. BMC Genomics 18:1044, doi: 10.1186/s12864-016-3262-5, (2017).
  21. Yoshino T, Katayama K, Horiba Y, Munakata K, Yamaguchi R, Imoto S, Miyano S, Mima H, Watanabe K. Predicting Japanese Kampo Formulas by Analyzing Database of Medical Records: A Preliminary Observational Study, BMC Medical Informatics and Decision Making. 16(1):118, (2016).
  22. Sugimachi K, Yamaguchi R, Eguchi H, Ueda M, Niida A, Sakimura S, Hirata H, Uchi R, Shinden Y, Iguchi T, Morita K, Yamamoto K, Miyano S, Mori M, Maehara Y, Mimori K. 8q24 Polymorphisms and Diabetes Mellitus Regulate Apolipoprotein A-IV in Colorectal Carcinogenesis. Ann Surg Oncol. 23(Suppl 4):546-551, (2016).
  23. Yamaguchi K, Nagayama S, Shimizu E, Komura M, Yamaguchi R, Shibuya T, Arai M, Hatakeyama S, Ikenoue T, Ueno M, Miyano S, Imoto S, Furukawa Y. Reduced expression of APC-1B but not APC-1A by the deletion of promoter 1B is responsible for familial adenomatous polyposis. Scientific Reports. 6: 26011, (2016).
  24. Moriyama T, Shiraishi Y, Chiba K, Yamaguchi R, Imoto S, Miyano S. OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads. Lecture Notes in Bioinformatics. 9683: 40-51, (2016).
  25. Chapman CG, Yamaguchi R, Tamura K, Weidner J, Imoto S, Kwon J, Marino SR, Miyano S, Nakamura Y, Kiyotani K. Characterization of T Cell Receptor Repertoire in Inflamed Tissues of Crohn's Disease through Deep Sequencing. Inflammatory Bowel Diseases. 22(6): 1275-1285, (2016).
  26. Muramatsu T, Kozaki K, Imoto S, Yamaguchi R, Tsuda H, Kawano T, Fujiwara N, Morishita M, Miyano S, Inazawa J. The hypusine cascade promotes cancer progression and metastasis through the regulation of RhoA in squamous cell carcinoma. Oncogene. 35(40): 5304-5316, (2016).
  27. Tamura K, Hazama S, Yamaguchi R, Imoto S, Takenouchi H, Inoue Y, Kanekiyo S, Shindo Y, Miyano S, Nakamura Y, Kiyotani K. Characterization of T cell repertoire in tumor tissues and blood in advanced colorectal cancers through deep T cell receptor sequencing. Oncology Letters. 11(6): 3643-3649, (2016).
  28. Yoshino T, Katayama K, Horiba Y, Munakata K, Yamaguchi R, Imoto S, Miyano S, Mima H, Kenji Watanabe K, Mimura M. The Difference between the Two Representative Kampo Formulas for Treating Dysmenorrhea: An Observational Study. Evid Based Complement Alternat Med, 2016:3159617, (2016).
  29. Kayano M, Matsui H, Yamaguchi R, Imoto S, Miyano S. Gene set differential analysis of time course expression profiles via sparse estimation in functional logistic model with application to time-dependent biomarker detection. Biostatistics. 17(2):235-248, (2016).
  30. Hasegawa T, Niida A, Mori T, Shimamura T, Yamaguchi R, Miyano S, Akutsu T, Imoto S, A Likelihood-free Filtering Method via Approximate Bayesian Computation in Evaluating Biological Simulation Models. Computational Statistics & Data Analysis. 94:63-74, (2016).
  31. Nakata A, Yoshida R, Yamaguchi R, Yamauchi M, Tamada Y, Fujita A, Shimamura T, Imoto S, Higuchi T, Nomura M, Kimura T, Nokihara H, Higashiyama M, Kondoh K, Nishihara H, Tojo A, Yano S, Miyano S, Gotoh N, Elevated β-catenin pathway as a novel target for patients with resistance to EGF receptor targeting drugs. Scientific Reports. 5:13076, (2015).
  32. Yew PY, Alachkar H, Yamaguchi R, Kiyotani K, Fang H, Yap KL, Liu HT, Wickrema A, Artz A, van Besien K, Imoto S, Miyano S, Bishop MR, Stock W, Nakamura Y, Quantitative characterization of T-cell repertoire in allogeneic hematopoietic stem cell transplant recipients. Bone Marrow Transplantation. 50(9): 1227-1234, (2015).
  33. Iwakawa R, Kohno T, Totoki Y, Shibata T, Tsuchihara K, Mimaki S, Tsuta K, Narita Y, Nishikawa R, Noguchi M, Harris CC, Robles AI, Yamaguchi R, Imoto S,Miyano S, Totsuka H, Yoshida T, Yokota J, Expression and Clinical Significance of Genes Frequently Mutated in Small Cell Lung Cancers Defined by Whole Exome/RNA Sequencing, Carcinogenesis, 36(6): 612-621 (2015).
  34. Chikahara Y, Niida A, Yamaguchi R, Imoto S, Miyano S, Integrative Clustering of Cancer Genome Data using Infinite Relational Models, in proceedings of the International Conference on Bioinformatics and Computational Biology (BICoB 2015 is a refereed conference), (in press).
  35. Ikenoue T, Yamaguchi K, Koumura M, Imoto S, Yamaguchi R, Shimizu E, Kasuya S, Shibuya T, Hatakeyama S, Miyano S, Furukawa Y. Attenuated familial adenomatous polyposis with desmoids caused by an APC mutation. Human Genome Variation, 2: 15011. doi:10.1038/hgv.2015.11 (2015).
  36. Hasegawa T, Mori T, Yamaguchi R, Shimamura T, Miyano S, Imoto S, Akutsu T. Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. BMC Systems Biology, 9(1): 14. doi:10.1186/s12918-015-0154-2 (2015).
  37. Yamaguchi K, Komura M, Yamaguchi R, Imoto S, Shimizu E, Kasuya S, Shibuya T, Hatakeyama S, Takahashi N, Ikenoue T, Hata K, Tsurita G, Shinozaki M, Suzuki Y, Sugano S, Miyano S, Furukawa Y. Detection of APC mosaicism by next-generation sequencing in an FAP patient. Journal of Human Genetics, doi:10.1038/jhg.2015.14 (2015).
  38. Fang H, Yamaguchi R, Liu X, Daigo Y, Yew PY, Tanikawa C, Matsuda K, Imoto S, Miyano S, Nakamura Y, Quantitative T cell repertoire analysis by deep cDNA sequencing of T cell receptor α and β chains using next-generation sequencing (NGS). OncoImmunology, 3(12), e968467. doi:10.4161/21624011.2014.968467 (2014).
  39. Hasegawa T, Yamaguchi R, Nagasaki M, Miyano S, Imoto S. Inference of gene regulatory networks incorporating multi-source biological knowledge via a state space model with L1 regularization. PLoS ONE, 9(8): e105942. doi:10.1371/journal.pone.0105942 (2014).
  40. Hasegawa T, Mori T, Yamaguchi R, Imoto S, Miyano S, Akutsu T. An efficient data assimilation schema for restoration and extention of gene regulatory networks using time-course observation data. Journal of Computational Biology, 21(11): 785-798. doi:10.1089/cmb.2014.0171 (2014).
  41. Hasegawa T, Nagasaki M, Yamaguchi R, Imoto S, Miyano S. An efficient method of exploring simulation models by assimilating literature and biological observational data. BioSystems, 121, 54-66 (2014).
  42. Tokunaga H, Munakata K, Katayama K, Yamaguchi R, Imoto S, Miyano S, Watanabe K. Clinical Data Mining Related to the Japanese Kampo Concept "Hie" (Oversensitivity to Coldness) in Men and Pre- and Postmenopausal Women. Evidence-Based Complementary and Alternative Medicine, 2014:832824. doi:10.1155/2014/832824 (2014).
  43. Nishiura H, Ejima K, Mizumoto K, Nakaoka S, Inaba H, Imoto S, Yamaguchi R, Saito MM. Cost-effective length and timing of school closure during an influenza pandemic depend on the severity. Theor Biol Med Model 11(1):5. doi:10.1186/1742-4682-11-5 (2014).
  44. Yamaguchi K, Yamaguchi R, Takahashi N, Ikenoue T, Fujii T, Shinozaki M, Tsurita G, Hata K, Niida A, Imoto S, Miyano S, Nakamura Y, Furukawa Y. Overexpression of Cohesion Establishment Factor DSCC1 through E2F in Colorectal Cancer. PLoS ONE 9(1):e85750. doi:10.1371/journal.pone.0085750 (2014).
  45. Yoshino T, Katayama K, Munakata K, Horiba Y, Yamaguchi R, Imoto S, Miyano S, Watanabe K. Statistical Analysis of Hie (Cold Sensation) and Hiesho (Cold Disorder) in Kampo Clinic. Evidence-Based Complementary and Alternative Medicine 2013:398458. doi:10.1155/2013/398458 (2013).
  46. Katayama K, Yoshino T, Munakata K, Yamaguchi R, Imoto S, Miyano S, Watanabe K. Prescription of Kampo Drugs in the Japanese Health Care Insurance Program. Evidence-Based Complementary and Alternative Medicine 2013:576973. doi:10.1155/2013/576973 (2013).
  47. Saito MM, Imoto S, Yamaguchi R, Sato H, Nakada H, Kami M, Miyano S, Higuchi T. Extension and verification of the SEIR model on the 2009 influenza A (H1N1) pandemic in Japan. Math Biosci 246(1):47-54 doi:10.1016/j.mbs.2013.08.009 (2013).
  48. Yoshimaru T, Komatsu M, Matsuo T, Chen Y-A, Murakami Y, Mizuguchi K, Mizohata E, Inoue T, Akiyama M, Yamaguchi R, Imoto S, Miyano S, Miyoshi Y, Sasa M, Nakamura Y, Katagiri T. Targeting BIG3-PHB interaction to overcome tamoxifen resistance in breast cancer cells. Nat. Commun. 4:2443 doi:10.1038/ncomms3443 (2013).
  49. Saito MM, Imoto S, Yamaguchi R, Tsubokura M, Kami Masahiro, Nakada H, Sato H, Miyano S, Higuchi T. Enhancement of Collective Immunity in Tokyo Metropolitan Area by Selective Vaccination against an Emerging Influenza Pandemic. PLoS ONE 8(9): e72866EP. doi:10.1371/journal.pone.0072866 (2013).
  50. Kayano M, Imoto S, Yamaguchi R, Miyano S. Multi-omics approach for estimating metabolic networks using low-order partial correlations, Journal of Computational Biology 20(8):571-582. doi:10.1089/cmb.2013.0043 (2013).
  51. Ishikawa T, Shimizu T, Ueki A, Yamaguchi S, Onishi N, Sugihara E, Kuninaka S, Miyamoto T, Morioka H, Nakayama R, Kobayashi E, Toyama Y, Mabuchi Y, Matsuzaki Y, Yamaguchi R, Miyano S, Saya H. Twist2 functions as a tumor suppressor in murine osteosarcoma cells, Cancer Science 104(7):880-888. doi:10.1111/cas.12163 (2013).
  52. Yamaguchi R, Imoto S, Kami M, Watanabe K, Miyano S, Yuji K. Does Twitter Trigger Bursts in Signature Collections?, PLoS ONE 8(3): e58252. doi:10.1371/journal.pone.0058252 (2013).
  53. Komatsu M, Yoshimaru T, Matsuo T, Kiyotani K, Miyoshi Y, Tanahashi T, Rokutan K, Yamaguchi R, Saito A, Imoto S, Miyano S, Nakamura Y, Sasa M, Shimada M, Katagiri T. Molecular features of triple negative breast cancer cells by genome-wide gene expression profiling analysis. Int. J. Oncol. 42(2):478-506 (2013).
  54. Ogami K, Yamaguchi R, Imoto S, Tamada Y, Araki H, Print C, Miyano S. Computational gene network analysis reveals TNF-induced angiogenesis, BMC Systems Biology, 6 Suppl 2:S12 (2012). (Selected as a full paper of Special Issue of GIW2012. Competition rate is 10/120).
  55. Takatsuno Y, Mimori K, Yamamoto K, Sato T, Niida A, Inoue H, Imoto S, Kawano S, Yamaguchi R, Toh H, Iinuma H, Ishimaru S, Ishii H, Suzuki S, Tokudome S, Watanabe M, Tanaka J, Kudo S, Mochizuki H, Kusunoki M, Yamada K, Shimada Y, Moriya Y, Miyano S, ugihara K, Mori M. The rs6983267 SNP is associated with MYC transcription efficiency, which promotes progression and worsens prognosis of colorectal cancer, Annals of Surgical Oncology, 20(4): 1395-1402. (Pub: 2013 Apr, Epub 2012 Sep 14)
  56. Katayama K, Yamaguchi R, Imoto S, Matsuura K, Watanabe K, Miyano S. Analysis of questionnaire for Traditional Medical and develop decision support system. Proc. International Workshop on Biomedical and Health Informatics, 762-763 (2012).
  57. Yuji K, Imoto S, Yamaguchi R, Matsumura T, Murashige N, Kodama Y, Miyano S, Imai K, Kami M. Forecasting Japan's physician shortage in 2035 as the first full-fledged aged society, PLoS ONE, 7(11):e50410. doi:10.1371/journal.pone.0050410, (2012).
  58. Yamauchi M*, Yamaguchi R*, Nakata A*, Kohno T*, Nagasaki M, Shimamura T, Imoto S, Saito A, Ueno K, Hatanaka Y, Yoshida R, Higuchi T, Nomura M, Beer DG, Yokota J, Miyano S, Gotoh N. Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma, PLoS ONE 7(9): e43923. doi:10.1371/journal.pone.0043923, (2012). (*These authors equally contributed to this work).
  59. Yamamoto M, Yamaguchi R, Munakata K, Takashima K, Nishiyama M, Hioki K, Ohnishi Y, Nagasaki M, Imoto S, Miyano S, Ishige A, Watanabe K. A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development, BMC Genomics, 13:335, (2012).
  60. Ishimaru S, Mimori K, Yamamoto K, Inoue H, Imoto S, Kawano S, Yamaguchi R, Sato T, Toh H, Iinuma H, Maeda T, Ishii H, Suzuki S, Tokudome S, Watanabe M, Tanaka J, Kudo S, Sugihara K, Hase K, Mochizuki H, Kusunoki M, Yamada K, Shimada Y, Moriya Y, Barnard GF, Miyano S, Mori M. Increased risk for CRC in diabetic patients with the nonrisk allele of SNPs at 8q24, Annals of Surgical Oncology, 19(9):2853-2858, (2012).
  61. Kojima K, Imoto S, Yamaguchi R, Fujita A, Yamauchi M, Gotoh N, Miyano S. Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing, BMC Genomics, 13(Suppl 1):S6, (2012) (Special Issue of APBC2012, a refereed conference; 42 out of 129 submissions were accepted as oral presentation)
  62. Kawano S, Shimamura T, Niida A, Imoto S, Yamaguchi R, Nagasaki M, Yoshida R, Print C, Miyano S. Identifying gene pathways associated with cancer characteristics via sparse statistical methods, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(4): 966-972, (2012)
  63. Okayama H, Kohno T, Ishii Y, Shimada Y, Shiraishi K, Iwakawa R, Furuta K, Tsuta K, Shibata T, Yamamoto S, Watanabe S, Sakamoto H, Kumamoto K, Takenoshita S, Gotoh N, Mizuno H, Sarai A, Kawano S, Yamaguchi R, Miyano S, Yokota J. Identification of genes up-regulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. Cancer Research, 72(1):100-111, (2012).
  64. Katayama K, Yamaguchi R, Imoto S, Matsuura K, Watanabe K, Miyano S. Transform of visual analogue scale data and their clustering, International. Journal of Knowledge Engineering and Soft Data Paradigms, 3(2): 143-151, (2011).
  65. Katayama K, Yamaguchi R, Imoto S, Matsuura K, Watanabe K, Miyano S. Clustering for Visual Analogue Scale Data in Symbolic Data Analysis. Procedia Computer Science, 6: 370-374, (2011).
  66. Onuki R, Yamada R, Yamaguchi R, Kanehisa M, Shibuya T. Population model-based inter-diplotype similarity measure for accurate diplotype clustering. Journal of Computational Biology, 19(1):55-67, (2012).
  67. Yamauchi M, Yoshino I, Yamaguchi R, Shimamura T, Nagasaki M, Imoto S, Niida A, Koizumi F, Kohno T, Yokota J, Miyano S, Gotoh N. N-cadherin expression is a potential survival mechanism of gefitinib-resistant lung cancer cells. Am J Cancer Res, 1(7): 823-833, (2011).
  68. Katayama K, Yamaguchi R, Imoto S, Tokunaga H, Imazu Y, Matuura K, K. Watanabe, Miyano S. Symbolic hierarchical clustering for visual analogue scale data, Inteligent Decision Technologies, SIST, 10: 799-805, (2011).
  69. Saito MM, Imoto S, Yamaguchi R, Miyano S, Higuchi T. Estimation of macroscopic parameter in agent-based pandemic simulation, Proc. 14th International Conference on Information Fusion, 1-6, (2011). (Fusion2011: Refereed conference)
  70. 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(6): e20804. doi:10.1371/journal.pone.0020804, (2011).
  71. Yamaguchi K, Sakai M, Kim J, Tsunesumi S, Fujii T, Ikenoue T, Yamada Y, Akiyama Y, Muto Y, Yamaguchi R, Miyano S, Nakamura Y, Furukawa Y. MRG-binding protein contributes to development of colorectal cancer. Cancer Sci, 102(8): 1486-1492, (2011).
  72. Tamada Y, Shimamura T, Yamaguchi R, Imoto S, Nagasaki M, Miyano S. SiGN: large-scale gene network estimation environment for high performance computing. Genome Informatics, 25(1): 40-52 (2011).
  73. Hasegawa T, Yamaguchi R, Nagasaki M, Imoto S, Miyano S. Comprehensive pharmacogenomic pathway screening by data assimilation. Proc. 7th International Symposium on Bioinformatics Research and Applications (ISBRA2011), Springer-Verlag, LNCS, 6674: 160-171. (ISBRA2011: Refereed conference. 37 papers were accepted out of 92 submissions).
  74. Saito MM, Imoto S, Yamaguchi R, Miyano S, Higuchi T. Parallel agent-based simulator for inuenza pandemic. Proc. DOCMAS, Springer-Verlag, LNCS, (in press.) (DOCMAS: Refereed conference)
  75. Tamada Y, Yamaguchi R, Imoto S, Hirose O, Yoshida R, Nagasaki M, Miyano S. SiGN-SSM: open source parallel software for estimating gene networks with state space models. Bioinformatics, 27(8): 1172-1173, (2011).
  76. Fujimoto A, Nakagawa H, Hosono N, Nakano K, Abe A, Boroevich KA, Nagasaki M, Yamaguchi R, Shibuya T, Kubo M, Miyano S, Nakamura Y, Tsunoda T. Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet, 42(11): 931-936, (2010).
  77. 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(24): 3090-3097, (2010).
  78. Kawano S, Shimamura T, Niida A, Imoto S, Yamaguchi R, Nagasaki M, Yoshida R, Print C, Miyano S. Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning. Proc. IEEE Bioinformatics and Biomedicine, 253-258, (2010). (BIBM2010: Refereed conference. 61 papers are accepted as regular papers from 355 submissions (acceptance rate 17.2%)).
  79. Niida A, Imoto S, Yamaguchi R, Nagasaki M, Miyano S. Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues. PLoS One, 5(6): e10910, (2010).
  80. Shimamura T, Imoto S, Nagasaki M, Yamauchi M, Yamaguchi R, Fujita A, Tamada Y, Gotoh N, Miyano S. Collocation-based sparse estimation for inferring continuous-time dynamic gene networks, Genome Informatics, 24: 164-178, (2010).
  81. Fujita A, Nagasaki M, Imoto S, Saito A, Ikeda E, Shimamura T, Yamaguchi R, Suzuki H, Hayashizaki Y, Miyano S. Comparison of gene expression pro les produced by CAGE, illumina microarray and Real Time RT-PCR, Genome Informatics, 24: 56-68, (2010).
  82. 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). (BIBE2010: Refereed conference. Selected as a full paper with oral presentation).
  83. 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).
  84. Sato H*, Nakada H*, Yamaguchi R*, Imoto S*, Miyano S, Kami M. When should we intervene to control the novel H1N1 influenza pandemic?, Eurosurveillance, 15(1): pii=19455 , (2010). (*These authors equally contributed to this work).
  85. Yamaguchi R, Imoto S, 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).
  86. Kojima K, Yamaguchi R, Imoto S, Yamauchi M, Nagasaki M, Yoshida R, Shimamura T, Ueno K, Higuchi T, Gotoh N, Miyano S. A state space representation of VAR models with sparse learning for dynamic gene networks. Genome Informatics, 22: 56-68, (2009).
  87. Niida A, Imoto S, Nagasaki M, Yamaguchi R, Miyano, S. A novel meta-analysis approach of cancer transcriptomes reveals prevailing transcriptional networks in cancer cells. Genome Informatics, 22: 121-131, (2009).
  88. Fujita A, Sato JR, Demasi MAA, Yamaguchi R, Shimamura T, Ferreira CE, Sogayar MC, Miyano, S. Inferring contagion in regulatory networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 99, doi:10.1109/TCBB.2010.40, (2010).
  89. Do JH, Yamaguchi R, Miyano S. Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model. BMC Genomics, 10: 306, (2009).
  90. Miyano S, Yamaguchi R, Tamada Y, Nagasaki M, Imoto S. Gene networks viewed through two models. Lecture Notes in Computer Science. 5462: 54-66, (2009). (Proc. First International Conference on Bioinformatics and Computational Biology (BICoB)).
  91. Shimamura T, Imoto S, Yamaguchi R, Fujita A, Miyano S. Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Systems Biology, 3: 41, (2009).
  92. Watanabe-Fukuda Y, Yamamoto M, Miura N, Fukutake M, Ishige A, Yamaguchi R, Nagasaki M, Saito A, Imoto S, Miyano S, Takeda J, Watanabe K. Orengedokuto and berberine improve indomethacin-induced small intestinal injury via adenosine. Journal of Gastroenterology, 44: 380-389, (2009).
  93. Fujita A, Gomes LR, Sato JR, Yamaguchi R, Thomaz CE, Sogayar MC, Miyano S. Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. BMC Systems Biology, 2: 106, (2008).
  94. Yoshida R, Nagasaki M, Yamaguchi R, Imoto S, Miyano S, Higuchi T. Bayesian learning of biological pathways on genomic data assimilation. Bioinformatics, 24: 2592-2601, (2008).
  95. 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).
    (GIW2008: Refereed conference. The number of accepted papers is 18 out of 55 submissions. This paper was awarded as "Finalist: Best Paper Award" at the conference.)
  96. 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. Genome Informatics, 20: 212-221, (2008).
  97. Hirose O, Yoshida R, Yamaguchi R, Imoto S, Higuchi T, 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). (AMS2008: Refereed Conference)
  98. Hirose O, Yoshida R, Imoto S, Yamaguchi R, Higuchi T, Charnock-Jones DS, Print CP, Miyano S. Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics, 24: 932-942, (2008).
  99. Yamaguchi R, Saito S. Bayesian networks for probabilistic inference of complex consumer shop-around behavior. Studies in Regional Science (JSRSAI), 37: 769-785, (2007). (in Japanese)
  100. Shimamura T, Imoto S, Yamaguchi R, Miyano S. Weighted Lasso in graphical Gaussian modeling for large gene network estimation based on microarray data. Genome Informatics, 19: 142-153 (2007). (GIW2007: Refereed conference)
  101. 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). (IBSB2007: Refereed conference)
  102. Yamaguchi R, Yamamoto M, Imoto S, Nagasaki M, Yoshida R, Tsuiji K, Ishige 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). (IBSB2007: Refereed conference)
  103. Fujita A, Sato JR, Garay-Malpartida HM, Yamaguchi R, Miyano S, Sogayar MC, Ferreira CE. Modeling gene expression regulatory networks with the sparse vector autoregressive model, BMC Systems Biology, 1:39, (2007).
  104. Gupta PK, Yoshida R, Imoto S, Yamaguchi R, Miyano S. Statistical absolute evaluation of gene ontology terms with gene expression data. Proc. 3rd International Symposium on Bioinformatics Research and Applications, Lecture Note in Bioinformatics, Springer-Verlag, 4463: 146-157, (2007). (ISBRA2007: Refereed conference).
  105. 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).
  106. 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). [*: These authors equally contributed to this work.]
  107. Yamaguchi R, Higuchi T. State-space approach with the maximum likelihood principle to identify the system-generating time course gene expression data of yeast. International Journal of Data Mining and Bioinformatics, 1(1): 77-87, (2006).
  108. 小林正子, 山口類, 向井田紀子. 出生後の体重発育における日内変動，週内変動，自己回帰過程等の波動形成に関する検討:（24ヵ月まで）. 日本成長学会雑誌，12(1): 15-21, (2006).
  109. Yamaguchi R, Yamashita S, Higuchi T. Estimating gene networks with cDNA microarray data using state-space models. ICCSA 2005: International Conference Proceedings, Lecture Notes in Computer Science (Springer-Verlag), 3482: 381-388, (2005).
  110. 山口類 , 土屋映子, 樋口知之. 状態空間モデルを用いた飲食店売上の要因分解. オペレーションズ・リサーチ， 49(5): 52-60, (2004).
  111. Ohtani S, Ueno G, Yamaguchi R, Singer H, Creutzberg F, Yumoto K, Kitamura K, Mukai T. Tail dynamics during the growth phase of the November 24, 1996, substorm event: Near-Earth reconnection confined in the plasma sheet, Journal of Geophysical Research, 109(A5), A05211, doi:10.1029/2003JA010299, (2004).
  112. Yamaguchi R, Kawano H, Ohtani S, Kokubun S, Yumoto, K. Total pressure variations in the magnetotail as a function of the position and the substorm magnitude. Journal of Geophysical Research, 109(A3), A03206, doi:10.1029/2003JA010196, (2004).
  113. Ohtani S, Yamaguchi R, Kawano H, Creutzberg F, Sigwarth JB, Frank LA, Mukai T. Does the braking of the fast plasma flow trigger a substorm?: A study of the August 14, 1996, event. Geophysical Research Letters, 29(15), 1721, doi:10.1029/2001GL013785, (2002).
  114. Yamaguchi R, Kawano H, Ohtani S, Yumoto K., Mukai T, Saito Y, Hayakawa H, The Circum-pan Pacific Magnetometer Network Group. The timing relationship between bursty bulk flows and Pi2s at the geosynchronous orbit. Geophysical Research Letters, 29(6), 1092, doi:10.1029/2001GL013783, (2002).
  115. Ohtani S, Yamaguchi R , Nose M, Kawano H, Engebretson M, Yumoto K. Quiet time magnetotail dynamics and their implications for the substorm trigger. Journal of Geophysical Research, 107(A2), 1030, doi:10.1029/2001JA000116, (2002).