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システム解析学分野

研究業績

【論文業績(2015年以降)】

  1. Zhang YZ, Akdemir A, Tremmel G, Imoto S, Miyano S, Shibuya T, Yamaguchi R. Nanopore base-calling from a perspective of instance segmentation. BMC Bioinformatics. (in press)
  2. Ito S, Yadome M, Nishiki T, Ishiduki S, Inoue H, Yamaguchi R, Miyano S. Virtual Grid Engine: A simulated grid engine environment for large-scale supercomputers. BMC Bioinformatics. (in press)
  3. Kasajima R, Yamaguchi R, Shimizu E, Tamada Y, Niida A, Tremmel G, Kishida T, Aoki I, Imoto S, Miyano S, Uemura H, Miyagi Y. Variant analysis of prostate cancer in the Japanese and a new attempt to predict related biological pathways. Oncology Reports. (in press)
  4. Yoshino T, Katayama K, Yamaguchi R, Imoto S, Miyano S, Mima H, Watanabe K. Classification of patients with cold sensation by a review of systems database: A single-centre observational study. Complement Ther Med. 2019;45:7-13. Epub 2019/07/25. doi: 10.1016/j.ctim.2019.05.011. PMID: 31331585.
  5. Yamaguchi K, Shimizu E, Yamaguchi R, Imoto S, Komura M, Hatakeyama S, Noguchi R, Takane K, Ikenoue T, Gohda Y, Yano H, Miyano S, Furukawa Y. Development of an MSI-positive colon tumor with aberrant DNA methylation in a PPAP patient. J Hum Genet. 2019;64(8):729-40. Epub 2019/05/16. doi: 10.1038/s10038-019-0611-7. PMID: 31089268.
  6. 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. 2019;5(3):416-24. Epub 2018/02/06. doi: 10.1016/j.euf.2018.01.006. PMID: 29398457.
  7. Tsuda Y, Hirata M, Katayama K, Motoi T, Matsubara D, Oda Y, Fujita M, Kobayashi H, Kawano H, Nishida Y, Sakai T, Okuma T, Goto T, Ogura K, Kawai A, Ae K, Anazawa U, Suehara Y, Iwata S, Miyano S, Imoto S, Shibata T, Nakagawa H, Yamaguchi R, Tanaka S, Matsuda K. Massively parallel sequencing of tenosynovial giant cell tumors reveals novel CSF1 fusion transcripts and novel somatic CBL mutations. Int J Cancer. 2019;145(12):3276-84. Epub 2019/05/21. doi: 10.1002/ijc.32421. PMID: 31107544.
  8. Takeda R, Yokoyama K, Ogawa M, Kawamata T, Fukuyama T, Kondoh K, Takei T, Nakamura S, Ito M, Yusa N, Shimizu E, Ohno N, Uchimaru K, Yamaguchi R, Imoto S, Miyano S, Tojo A. The first case of elderly TCF3-HLF-positive B-cell acute lymphoblastic leukemia. Leuk Lymphoma. 2019;60(11):2821-4. Epub 2019/05/07. doi: 10.1080/10428194.2019.1602267. PMID: 31058556.
  9. Takeda R, Yokoyama K, Kobayashi S, Kawamata T, Nakamura S, Fukuyama T, Ito M, Yusa N, Shimizu E, Ohno N, Yamaguchi R, Imoto S, Miyano S, Uchimaru K, Tojo A. An Unusually Short Latent Period of Therapy-Related Myeloid Neoplasm Harboring a Rare MLL-EP300 Rearrangement: Case Report and Literature Review. Case Rep Hematol. 2019;2019:4532434. Epub 2019/10/31. doi: 10.1155/2019/4532434. PMID: 31662917.
  10. Nakamura S, Yokoyama K, Shimizu E, Yusa N, Kondoh K, Ogawa M, Takei T, Kobayashi A, Ito M, Isobe M, Konuma T, Kato S, Kasajima R, Wada Y, Nagamura-Inoue T, Yamaguchi R, Takahashi S, Imoto S, Miyano S, Tojo A. Prognostic impact of circulating tumor DNA status post-allogeneic hematopoietic stem cell transplantation in AML and MDS. Blood. 2019;133(25):2682-95. Epub 2019/04/03. doi: 10.1182/blood-2018-10-880690. PMID: 30936070.
  11. Muraoka D, Seo N, Hayashi T, Tahara Y, Fujii K, Tawara I, Miyahara Y, Okamori K, Yagita H, Imoto S, Yamaguchi R, Komura M, Miyano S, Goto M, Sawada SI, Asai A, Ikeda H, Akiyoshi K, Harada N, Shiku H. Antigen delivery targeted to tumor-associated macrophages overcomes tumor immune resistance. J Clin Invest. 2019;129(3):1278-94. Epub 2019/01/11. doi: 10.1172/JCI97642. PMID: 30628894.
  12. Moriyama T, Imoto S, Hayashi S, Shiraishi Y, Miyano S, Yamaguchi R. A Bayesian model integration for mutation calling through data partitioning. Bioinformatics. 2019;35(21):4247-54. Epub 2019/03/30. doi: 10.1093/bioinformatics/btz233. PMID: 30924874.
  13. Moriyama T, Imoto S, Miyano S, Yamaguchi R. Accurate and flexible Bayesian mutation call from multi-regional tumor samples. Lecture Notes in Computer Science. 2019; 11826:47-61.
  14. Maeda-Minami A, Yoshino T, Katayama K, Horiba Y, Hikiami H, Shimada Y, Namiki T, Tahara E, Minamizawa K, Muramatsu S, Yamaguchi R, Imoto S, Miyano S, Mima H, Mimura M, Nakamura T, Watanabe K. Prediction of deficiency-excess pattern in Japanese Kampo medicine: Multi-centre data collection. Complement Ther Med. 2019;45:228-33. Epub 2019/07/25. doi: 10.1016/j.ctim.2019.07.003. PMID: 31331566.
  15. Konishi H, Komura D, Katoh H, Atsumi S, Koda H, Yamamoto A, Seto Y, Fukayama M, Yamaguchi R, Imoto S, Ishikawa S. Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning. BMC Bioinformatics. 2019;20(1):267. Epub 2019/05/30. doi: 10.1186/s12859-019-2853-y. PMID: 31138102.
  16. Hosono Y, Masuishi T, Mitani S, Yamaguchi R, Kato S, Yoshino T, Ebi H. Evaluation of ALK Fusion Newly Identified in Colon Cancer by a Comprehensive Genomic Analysis. JCO Precision Oncology. 2019; 2019(3):1-5. doi: 10.1200/po.19.00268.
  17. Hayashi S, Moriyama T, Yamaguchi R, Mizuno S, Komura M, Miyano S, Nakagawa H, Imoto S. ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data. J Comput Biol. 2019;26(9):923-37. Epub 2019/04/04. doi: 10.1089/cmb.2018.0224. PMID: 30942618.
  18. Hasegawa T, Yamaguchi R, Niida A, Miyano S, Imoto S. Ensemble Smoothers for Inference of Hidden States and Parameters in Combinatorial Regulatory Model. Journal of the Franklin Institute. 2019. doi: https://doi.org/10.1016/j.jfranklin.2019.10.015.
  19. 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 Adv. 2018;2(19):2513-21. Epub 2018/10/05. doi: 10.1182/bloodadvances.2017010744. PMID: 30282643.
  20. 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. 2018;59(11):2755-6. Epub 2018/04/13. doi: 10.1080/10428194.2018.1443335. PMID: 29648492.
  21. Ogawa M, Yokoyama K, Hirano M, Jimbo K, Ochi K, Kawamata T, Ohno N, Shimizu E, Yokoyama N, Yamaguchi R, Imoto S, Uchimaru K, Takahashi N, Miyano S, Imai Y, Tojo A. Different clonal dynamics of chronic myeloid leukaemia between bone marrow and the central nervous system. Br J Haematol. 2018;183(5):842-5. Epub 2017/12/22. doi: 10.1111/bjh.15065. PMID: 29265350.
  22. 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. 2018;108(4):402-10. Epub 2018/07/01. doi: 10.1007/s12185-018-2487-2. PMID: 29959746.
  23. 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. 2018;97(2):367-9. Epub 2017/09/29. doi: 10.1007/s00277-017-3134-3. PMID: 28956125.
  24. 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. J Hum Genet. 2018;63(2):239-48. Epub 2017/12/02. doi: 10.1038/s10038-017-0364-0. PMID: 29192240.
  25. Ito S, Yadome M, Nishiki T, Ishiduki S, Inoue H, Yamaguchi R, Miyano S, editors. Virtual Grid Engine: Accelerating thousands of omics sample analyses using large-scale supercomputers. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM); 2018 3-6 Dec. 2018.
  26. 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. 2018;32(6):1327-37. Epub 2018/03/21. doi: 10.1038/s41375-018-0083-3. PMID: 29556021.
  27. Hayashi S, Yamaguchi R, Mizuno S, Komura M, Miyano S, Nakagawa H, Imoto S. ALPHLARD: a Bayesian method for analyzing HLA genes from whole genome sequence data. BMC Genomics. 2018;19(1):790. Epub 2018/11/06. doi: 10.1186/s12864-018-5169-9. PMID: 30384854.
  28. Zhang YZ, Yamaguchi R, Imoto S, Miyano S. Sequence-specific bias correction for RNA-seq data using recurrent neural networks. BMC Genomics. 2017;18(Suppl 1):1044. Epub 2017/02/16. doi: 10.1186/s12864-016-3262-5. PMID: 28198674.
  29. Zhang YZ, Imoto S, Miyano S, Yamaguchi R, editors. Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM); 2017 13-16 Nov. 2017.
  30. Tsuda Y, Tanikawa C, Miyamoto T, Hirata M, Yodsurang V, Zhang YZ, 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. 2017;7(1):10739. Epub 2017/09/08. doi: 10.1038/s41598-017-11208-x. PMID: 28878391.
  31. Tanikawa C, Zhang YZ, 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. 2017;20:109-19. Epub 2017/06/01. doi: 10.1016/j.ebiom.2017.05.017. PMID: 28558959.
  32. Takano Y, Masuda T, Iinuma H, Yamaguchi R, Sato K, Tobo T, Hirata H, Kuroda Y, Nambara S, Hayashi N, Iguchi T, Ito S, Eguchi H, Ochiya T, Yanaga K, Miyano S, Mimori K. Circulating exosomal microRNA-203 is associated with metastasis possibly via inducing tumor-associated macrophages in colorectal cancer. Oncotarget. 2017;8(45):78598-613. Epub 2017/11/08. doi: 10.18632/oncotarget.20009. PMID: 29108252.
  33. 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 TLR responses revealed by CRISPR/Cas9 screening. Int Immunol. 2017;29(8):347-55. Epub 2017/10/11. doi: 10.1093/intimm/dxx044. PMID: 28992181.
  34. 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. 2017;12(4):e0176530. Epub 2017/04/27. doi: 10.1371/journal.pone.0176530. PMID: 28445522.
  35. Moriyama T, Shiraishi Y, Chiba K, Yamaguchi R, Imoto S, Miyano S. OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads. IEEE Trans Nanobioscience. 2017;16(2):116-22. Epub 2017/03/10. doi: 10.1109/TNB.2017.2670601. PMID: 28278479.
  36. 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. 2017;8(34):55821-36. Epub 2017/09/17. doi: 10.18632/oncotarget.19608. PMID: 28915555.
  37. Jimbo K, Yokoyama K, Ogawa M, Hirano M, Ochi K, Kobayashi M, Yusa N, Shimizu E, Kawamata T, Yasui H, Ohno N, Yamaguchi R, Imoto S, Furukawa Y, Miyano S, Imai Y, Tojo A. [Autologous peripheral blood stem cell transplantation for double-refractory myeloma with K-RAS and N-RAS mutations]. Rinsho Ketsueki. 2017;58(12):2380-5. Epub 2018/01/16. doi: 10.11406/rinketsu.58.2380. PMID: 29332870.
  38. 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. 2017;37(5):2603-10. Epub 2017/03/31. doi: 10.3892/or.2017.5536. PMID: 28358435.
  39. 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. 2017;6(5):e1306617. Epub 2017/06/24. doi: 10.1080/2162402X.2017.1306617. PMID: 28638727.
  40. Yoshino T, Katayama K, Horiba Y, Munakata K, Yamaguchi R, Imoto S, Miyano S, Mima H, Watanabe K, Mimura M. The Difference between the Two Representative Kampo Formulas for Treating Dysmenorrhea: An Observational Study. Evid Based Complement Alternat Med. 2016;2016:3159617. Epub 2016/03/24. doi: 10.1155/2016/3159617. PMID: 27006676.
  41. 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 Med Inform Decis Mak. 2016;16:118. Epub 2016/09/14. doi: 10.1186/s12911-016-0361-9. PMID: 27619018.
  42. 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. Sci Rep. 2016;6:26011. Epub 2016/05/25. doi: 10.1038/srep26011. PMID: 27217144.
  43. Tamura K, Hazama S, Yamaguchi R, Imoto S, Takenouchi H, Inoue Y, Kanekiyo S, Shindo Y, Miyano S, Nakamura Y, Kiyotani K. Characterization of the T cell repertoire by deep T cell receptor sequencing in tissues and blood from patients with advanced colorectal cancer. Oncol Lett. 2016;11(6):3643-9. Epub 2016/06/11. doi: 10.3892/ol.2016.4465. PMID: 27284367.
  44. 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. 2016;23(Suppl 4):546-51. Epub 2016/07/09. doi: 10.1245/s10434-016-5374-1. PMID: 27387680.
  45. Muramatsu T, Kozaki KI, 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. 2016;35(40):5304-16. Epub 2016/04/05. doi: 10.1038/onc.2016.71. PMID: 27041563.
  46. Moriyama T, Shiraishi Y, Chiba K, Yamaguchi R, Imoto S, Miyano S. OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads2016. 40-51 p.
  47. 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. 2016;17(2):235-48. Epub 2015/10/01. doi: 10.1093/biostatistics/kxv037. PMID: 26420796.
  48. 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. 2016;94:63-74. doi: https://doi.org/10.1016/j.csda.2015.08.003.
  49. Chapman CG, Yamaguchi R, Tamura K, Weidner J, Imoto S, Kwon J, Fang H, Yew PY, Marino SR, Miyano S, Nakamura Y, Kiyotani K. Characterization of T-cell Receptor Repertoire in Inflamed Tissues of Patients with Crohn's Disease Through Deep Sequencing. Inflamm Bowel Dis. 2016;22(6):1275-85. Epub 2016/05/03. doi: 10.1097/MIB.0000000000000752. PMID: 27135481.
  50. 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 Transplant. 2015;50(9):1227-34. Epub 2015/06/09. doi: 10.1038/bmt.2015.133. PMID: 26052909.
  51. 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. J Hum Genet. 2015;60(5):227-31. Epub 2015/02/27. doi: 10.1038/jhg.2015.14. PMID: 25716913.
  52. 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 beta-catenin pathway as a novel target for patients with resistance to EGF receptor targeting drugs. Sci Rep. 2015;5:13076. Epub 2015/08/14. doi: 10.1038/srep13076. PMID: 26268703.
  53. 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. 2015;36(6):616-21. Epub 2015/04/12. doi: 10.1093/carcin/bgv026. PMID: 25863124.
  54. Ikenoue T, Yamaguchi K, Komura 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. Hum Genome Var. 2015;2:15011. Epub 2015/01/01. doi: 10.1038/hgv.2015.11. PMID: 27081525.
  55. 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 Syst Biol. 2015;9:14. Epub 2015/04/19. doi: 10.1186/s12918-015-0154-2. PMID: 25890175.
  56. Chikahara Y, Niida A, Yamaguchi R, Imoto S, Miyano S. Integrative clustering of cancer genome data using infinite relational models. Proceedings of the 7th International Conference on Bioinformatics and Computational Biology, BICOB 2015. 2015:11-8.
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