[[publications]]
差分
この文書の現在のバージョンと選択したバージョンの差分を表示します。
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publications [2010/09/03 12:43] mlabadm |
publications [2017/07/27 14:50] (現在) superregulator [Papers] |
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| ====== Papers ====== | ====== Papers ====== | ||
| - | ===== 2010 ===== | + | ===== 2017 ===== |
| - | - Chalkidis, G., Nagasaki, M., Miyano, S. High performance hybrid functional Petri net simulations of biological pathway models on CUDA. IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press. | + | - Anderson WP; Global Life Science Data Resources Working Group: Apweiler R, Bateman A, Bauer GA, Berman H, Blake JA, Blomberg N, Burley SK, Cochrane G, Di Francesco V, Donohue T, Durinx C, Game A, Green E, Gojobori T, Goodhand P, Hamosh A, Hermjakob H, Kanehisa M, Kiley R, McEntyre J, McKibbin R, Miyano S, Pauly B, Perrimon N, Ragan MA, Richards G, Teo YY, Westerfield M, Westhof E, Lasko PF. Data management: A global coalition to sustain core data. Nature. 543(7644):179. doi: 10.1038/543179a |
| - | - Do, J.H., Nagasaki, M., Miyano, S. The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis. Biosystems. 100 : 178-184, 2010. | + | - da Silva-Coelho P, Kroeze LI, Yoshida K, Koorenhof-Scheele TN, Knops R, van de Locht LT, de Graaf AO, Massop M, Sandmann S, Dugas M, Stevens-Kroef MJ, Cermak J, Shiraishi Y, Chiba K, Tanaka H, Miyano S, de Witte T, Blijlevens NMA, Muus P, Huls G, van der Reijden BA, Ogawa S, Jansen JH. Clonal evolution in myelodysplastic syndromes. Nat Commun. 8:15099, 2017. doi: 10.1038/ncomms15099. |
| - | - Fujita, A., Kojima, K., Patriota, A.G., Sato, J.R., Severino, P., Miyano, S. A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets. Bioinformatics. 26(18):2349-2351, 2010. | + | - Ding LW, Sun QY, Tan KT, Chien W, Thippeswamy AM, Eng Juh Yeoh A, Kawamata N, Nagata Y, Xiao JF, Loh XY, Lin DC, Garg M, Jiang YY, Xu L, Lim SL, Liu LZ, Madan V, Sanada M, Fernández LT, Preethi H, Lill M, Kantarjian HM, Kornblau SM, Miyano S, Liang DC, Ogawa S, Shih LY, Yang H, Koeffler HP. Mutational Landscape of Pediatric Acute Lymphoblastic Leukemia. Cancer Res. 77(2):390-400, 2017. Erratum in: Cancer Res. 77(8):2174, 2017. doi: 10.1158/0008-5472.CAN-16-1303. |
| - | - Fujita, A., Nagasaki, M., Imoto, S., Saito, A., Ikeda, E., Shimamura, T., Yamaguchi, R., Hayashizaki, Y., Miyano, S. Comparison of gene expression profiles produced by CAGE, illumina microarray and Real Time RT-PCR. Genome Informatics. In press. | + | - 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, 2017. doi: 10.1080/2162402X.2017.1306617. |
| - | - Fujita, A., Sato, J.R., Demas, 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. In press. | + | - Furuta M, Ueno M, Fujimoto A, Hayami S, Yasukawa S, Kojima F, Arihiro K, Kawakami Y, Wardell CP, Shiraishi Y, Tanaka H, Nakano K, Maejima K, Sasaki-Oku A, Tokunaga N, Boroevich KA, Abe T, Aikata H, Ohdan H, Gotoh K, Kubo M, Tsunoda T, Miyano S, Chayama K, Yamaue H, Nakagawa H. Whole genome sequencing discriminates hepatocellular carcinoma with intrahepatic metastasis from multi-centric tumors. J Hepatol. 66(2):363-373, 2017. doi: 10.1016/j.jhep.2016.09.021. |
| - | - Fujita, A., Sato, J.R., Kojima, K., Gomes, L.R., Sogayar, M.C., Miyano, S. Identification of Granger causality between gene sets. J. Bioinformatics and Computational Biology. 8(4): 679?701, 2010. | + | - Hirabayashi S, Seki M, Hasegawa D, Kato M, Hyakuna N, Shuo T, Kimura S, Yoshida K, Kataoka K, Fujii Y, Shiraishi Y, Chiba K, Tanaka H, Kiyokawa N, Miyano S, Ogawa S, Takita J, Manabe A. Constitutional abnormalities of IDH1 combined with secondary mutations predispose a patient with Maffucci syndrome to acute lymphoblastic leukemia. Pediatr Blood Cancer. 2017 May 24. doi: 10.1002/pbc.26647. [Epub ahead of print]. |
| - | - Fujita, A., Severino, P., Sato, J.R., Miyano, S. Granger causality in systems biology: modeling gene networks in time series microarray data using vector autoregressive models. Lecture Notes in Bioinformatics. 6268: 13-24, 2010. | + | - Hosono N, Makishima H, Mahfouz R, Przychodzen B, Yoshida K, Jerez A, LaFramboise T, Polprasert C, Clemente MJ, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Sanada M, Cui E, Verma AK, McDevitt MA, List AF, Saunthararajah Y, Sekeres MA, Boultwood J, Ogawa S, Maciejewski JP. Recurrent genetic defects on chromosome 5q in myeloid neoplasms. Oncotarget. 8(4):6483-6495, 2017. doi: 10.18632/oncotarget.14130. |
| - | - International Cancer Genome Consortium, Hudson, T.J. et al. International network of cancer genome projects. Nature. 464(7291):993-998, 2010. | + | - Ichimura T, Yoshida K, Okuno Y, Yujiri T, Nagai K, Nishi M, Shiraishi Y, Ueno H, Toki T, Chiba K, Tanaka H, Muramatsu H, Hara T, Kanno H, Kojima S, Miyano S, Ito E, Ogawa S, Ohga S. Diagnostic challenge of Diamond-Blackfan anemia in mothers and children by whole-exome sequencing. Int J Hematol. 105(4):515-520, 2017. doi: 10.1007/s12185-016-2151-7. |
| - | - Koh, C.H., Nagasaki, M., Saito, A., Wong, L., Miyano, S. DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinformatics. 26(14):1794-1796, 2010. | + | - 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, 2017. doi: 10.3892/or.2017.5536. |
| - | - Kojima, K., Nagasaki, M., Miyano, S. An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. BMC Bioinformatics. 11:335, 2010. | + | - Ikeda F, Yoshida K, Toki T, Uechi T, Ishida S, Nakajima Y, Sasahara Y, Okuno Y, Kanezaki R, Terui K, Kamio T, Kobayashi A, Fujita T, Sato-Otsubo A, Shiraishi Y, Tanaka H, Chiba K, Muramatsu H, Kanno H, Ohga S, Ohara A, Kojima S, Kenmochi N, Miyano S, Ogawa S, Ito E. Exome sequencing identified RPS15A as a novel causative gene for Diamond-Blackfan anemia. Haematologica. 2102(3):e93-e96, 2017. doi: 10.3324/haematol.2016.153932. |
| - | - Kojima, K., Perrier, E., Imoto, S., Miyano, S. Optimal search on clustered structural constraint for learning Bayesian network structure. J. Machine Learning Research.11: 285?310, 2010. [[http://www.jmlr.org/papers/volume11/kojima10a/kojima10a.pdf|Link]] | + | - Kato M, Ishimaru S, Seki M, Yoshida K, Shiraishi Y, Chiba K, Kakiuchi N, Sato Y, Ueno H, Tanaka H, Inukai T, Tomizawa D, Hasegawa D, Osumi T, Arakawa Y, Aoki T, Okuya M, Kaizu K, Kato K, Taneyama Y, Goto H, Taki T, Takagi M, Sanada M, Koh K, Takita J, Miyano S, Ogawa S, Ohara A, Tsuchida M, Manabe A. Long-term outcome of 6-month maintenance chemotherapy for acute lymphoblastic leukemia in children. Leukemia. 31(3):580-584, 2017. doi: 10.1038/leu.2016.274. |
| - | - 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, 2010. | + | - Kato I, Nishinaka Y, Nakamura M, Akarca AU, Niwa A, Ozawa H, Yoshida K, Mori M, Wang D, Morita M, Ueno H, Shiozawa Y, Shiraishi Y, Miyano S, Gupta R, Umeda K, Watanabe K, Koh K, Adachi S, Heike T, Saito MK, Sanada M, Ogawa S, Marafioti T, Watanabe A, Nakahata T, Enver T. Hypoxic adaptation of leukemic cells infiltrating the CNS affords a therapeutic strategy targeting VEGFA. Blood. 129(23):3126-3129, 2017. doi: 10.1182/blood-2016-06-721712. |
| - | - Li, C., Nagasaki, M., Saito, A., Miyano, S. Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. BMC Systems Biology. 4:39, 2010. | + | - Makishima H, Yoshizato T, Yoshida K, Sekeres MA, Radivoyevitch T, Suzuki H, Przychodzen B, Nagata Y, Meggendorfer M, Sanada M, Okuno Y, Hirsch C, Kuzmanovic T, Sato Y, Sato-Otsubo A, LaFramboise T, Hosono N, Shiraishi Y, Chiba K, Haferlach C, Kern W, Tanaka H, Shiozawa Y, Gómez-Seguí I, Husseinzadeh HD, Thota S, Guinta KM, Dienes B, Nakamaki T, Miyawaki S, Saunthararajah Y, Chiba S, Miyano S, Shih LY, Haferlach T, Ogawa S, Maciejewski JP. Dynamics of clonal evolution in myelodysplastic syndromes. Nature Genetics. 49(2):204-212, 2017. doi: 10.1038/ng.3742. |
| - | - Miwa, Y.*, Li, C.*, Ge, Q.W., Matsuno, H., Miyano, S., On determining delay time of transitions for Petri net based signaling pathways by introducing stochastic decision rules, In Silico Biol. 10: 0004, 2010. (*Equally contributed) [[http://www.bioinfo.de/isb/2010/10/0004/|Link]] | + | - Matsui Y, Niida A, Uchi R, Mimori K, Miyano S, Shimamura T. phyC: Clustering cancer evolutionary trees. PLoS Comput Biol. 13(5):e1005509, 2017. doi: 10.1371/journal.pcbi.1005509. |
| - | - Nagasaki, M., Saito, A., Jeong, E., Li, C., Kojima, K., Ikeda, E., Miyano, S., Cell Illustrator 4.0: A computational platform for systems biology, In Silico Biol. 10: 0002, 2010. [[http://www.bioinfo.de/isb/2010/10/0002/|Link]] | + | - 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. 16(2): 116-122, 2017. doi: 10.1109/TNB.2017.2670601. |
| - | - Niida, A., Imoto, S., Nagasaki, M., Yamaguchi, R., Miyano, S. novel meta-analysis approach of cancer transcriptomes reveals prevailing transcriptional networks in cancer cells. Genome Informatics. 22:121-131, 2010. | + | - Muramatsu H, Okuno Y, Yoshida K, Shiraishi Y, Doisaki S, Narita A, Sakaguchi H, Kawashima N, Wang X, Xu Y, Chiba K, Tanaka H, Hama A, Sanada M, Takahashi Y, Kanno H, Yamaguchi H, Ohga S, Manabe A, Harigae H, Kunishima S, Ishii E, Kobayashi M, Koike K, Watanabe K, Ito E, Takata M, Yabe M, Ogawa S, Miyano S, Kojima S. Clinical utility of next-generation sequencing for inherited bone marrow failure syndromes. Genet Med. doi: 10.1038/gim.2016.197. 2017 Jan 19. [Epub ahead of print]. |
| - | - 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. | + | - Nagata H, Kozaki KI, Muramatsu T, Hiramoto H, Tanimoto K, Fujiwara N, Imoto S, Ichikawa D, Otsuji E, Miyano S, Kawano T, Inazawa J. Genome-wide screening of DNA methylation associated with lymph node metastasis in esophageal squamous cell carcinoma. Oncotarget. 8(23):37740-37750, 2017. doi: 10.18632/oncotarget.17147. |
| - | - Sato, H, Nakada, H., Yamaguchi, R., Imoto, S., Miyano, S., Kami, M. When should we intervene to control the 2009 influenza A(H1N1) pandemic? Euro Surveill. 7:15(1), pii: 19455, 2010. | + | - Nguyen TB, Sakata-Yanagimoto M, Asabe Y, Matsubara D, Kano J, Yoshida K, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Izutsu K, Nakamura N, Takeuchi K, Miyoshi H, Ohshima K, Minowa T, Ogawa S, Noguchi M, Chiba S. Identification of cell-type-specific mutations in nodal T-cell lymphomas. Blood Cancer J. 7(1):e516, 2017. doi: 10.1038/bcj.2016.122. |
| - | - 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. | + | - Park H, Niida A, Imoto S, Miyano S. Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level. J Comput Biol. 24(2):138-152, 2017. doi: 10.1089/cmb.2016.0140. |
| - | - Shimamura, T., Imoto, S., Nagasaki, M., Yamauchi, M., Yamaguchi, R., Fujita, A., Tamada, Y., Gotoh, N., Miyano, S. Collocation-based sparse estimation for constructing dynamic gene networks. Genome Informatics. In press. | + | - Park H, Shiraishi Y, Imoto S, Miyano S. A novel adaptive penalized logistic regression for uncovering biomarker associated with anti-cancer drug sensitivity. IEEE/ACM Trans Comput Biol Bioinform. DOI: 10.1109/TCBB.2016.2561937. [Epub ahead of print] PubMed PMID: 27164605. |
| - | - Tamada, Y., Imoto, S., Araki, H., Nagasaki, M., Print, C., Charnock-Jones, D.S., Miyano, S. Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers. IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press. | + | - Seki M, Kimura S, Isobe T, Yoshida K, Ueno H, Nakajima-Takagi Y, Wang C, Lin L, Kon A, Suzuki H, Shiozawa Y, Kataoka K, Fujii Y, Shiraishi Y, Chiba K, Tanaka H, Shimamura T, Masuda K, Kawamoto H, Ohki K, Kato M, Arakawa Y, Koh K, Hanada R, Moritake H, Akiyama M, Kobayashi R, Deguchi T, Hashii Y, Imamura T, Sato A, Kiyokawa N, Oka A, Hayashi Y, Takagi M, Manabe A, Ohara A, Horibe K, Sanada M, Iwama A, Mano H, Miyano S, Ogawa S, Takita J. Recurrent SPI1 (PU.1) fusions in high-risk pediatric T cell acute lymphoblastic leukemia. Nature Genetics. 2017 Jul 3. doi: 10.1038/ng.3900. [Epub ahead of print] |
| - | - Yamaguchi, R., Imoto, S., Miyano, S. Network-based predictions and simulations by biological state space models: Search for drug mode of action. J. Computer Science and Technology. 25(1): 13-153, 2010. | + | - Sekinaka Y, Mitsuiki N, Imai K, Yabe M, Yabe H, Mitsui-Sekinaka K, Honma K, Takagi M, Arai A, Yoshida K, Okuno Y, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Muramatsu H, Kojima S, Hira A, Takata M, Ohara O, Ogawa S, Morio T, Nonoyama S. Common variable immunodeficiency caused by FANC mutations. J Clin Immunol. 37(5):434-444, 2017. doi: 10.1007/s10875-017-0396-4. |
| - | - Yuji, K., Matsumura, T., Miyano, S., Tsuchiya, R., Kami, M. Human papillomavirus vaccine coverage. Lancet. 376(9738):329-330, 2010. | + | - Sun QY, Ding LW, Tan KT, Chien W, Mayakonda A, Lin DC, Loh XY, Xiao JF, Meggendorfer M, Alpermann T, Garg M, Lim SL, Madan V, Hattori N, Nagata Y, Miyano S, Yeoh AE, Hou HA, Jiang YY, Takao S, Liu LZ, Tan SZ, Lill M, Hayashi M, Kinoshita A, Kantarjian HM, Kornblau SM, Ogawa S, Haferlach T, Yang H, Koeffler HP. Ordering of mutations in acute myeloid leukemia with partial tandem duplication of MLL (MLL-PTD). Leukemia. 31(1):1-10, 2017. doi: 10.1038/leu.2016.160. |
| + | - Takagi M, Ogata S, Ueno H, Yoshida K, Yeh T, Hoshino A, Piao J, Yamashita M, Nanya M, Okano T, Kajiwara M, Kanegane H, Muramatsu H, Okuno Y, Shiraishi Y, Chiba K, Tanaka H, Bando Y, Kato M, Hayashi Y, Miyano S, Imai K, Ogawa S, Kojima S, Morio T. Haploinsufficiency of TNFAIP3 (A20) by germline mutation is involved in autoimmune lymphoproliferative syndrome. J Allergy Clin Immunol. 139(6):1914-1922, 2017. doi: 10.1016/j.jaci.2016.09.038. | ||
| + | - 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. 20:109-119, 2017. doi: 10.1016/j.ebiom.2017.05.017. | ||
| + | - Togasaki E, Takeda J, Yoshida K, Shiozawa Y, Takeuchi M, Oshima M, Saraya A, Iwama A, Yokote K, Sakaida E, Hirase C, Takeshita A, Imai K, Okumura H, Morishita Y, Usui N, Takahashi N, Fujisawa S, Shiraishi Y, Chiba K, Tanaka H, Kiyoi H, Ohnishi K, Ohtake S, Asou N, Kobayashi Y, Miyazaki Y, Miyano S, Ogawa S, Matsumura I, Nakaseko C, Naoe T. Frequent somatic mutations in epigenetic regulators in newly diagnosed chronic myeloid leukemia. Blood Cancer J. 7(4):e559, 2017. doi: 10.1038/bcj.2017.36. | ||
| + | - Tominaga K, Shimamura T, Kimura N, Murayama T, Matsubara D, Kanauchi H, Niida A, Shimizu S, Nishioka K, Tsuji EI, Yano M, Sugano S, Shimono Y, Ishii H, Saya H, Mori M, Akashi K, Tada KI, Ogawa T, Tojo A, Miyano S, Gotoh N. Addiction to the IGF2-ID1-IGF2 circuit for maintenance of the breast cancer stem-like cells. Oncogene. 36(9):1276-1286, 2017. doi: 10.1038/onc.2016.293. | ||
| + | - Uchi R, Takahashi Y, Niida A, Shimamura T, Hirata H, Sugimachi K, Sawada G, Iwaya T, Kurashige J, Shinden Y, Iguchi T, Eguchi H, Chiba K, Shiraishi Y, Nagae G, Yoshida K, Nagata Y, Haeno H, Yamamoto H, Ishii H, Doki Y, Iinuma H, Sasaki S, Nagayama S, Yamada K, Yachida S, Kato M, Shibata T, Oki E, Saeki H, Shirabe K, Oda Y, Maehara Y, Komune S, Mori M, Suzuki Y, Yamamoto K, Aburatani H, Ogawa S, Miyano S, Mimori K. Correction: Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution. PLoS Genet. 13(5):e1006798, 2017. doi: 10.1371/journal.pgen.1006798. | ||
| + | - Yamato G, Shiba N, Yoshida K, Shiraishi Y, Hara Y, Ohki K, Okubo J, Okuno H, Chiba K, Tanaka H, Kinoshita A, Moritake H, Kiyokawa N, Tomizawa D, Park MJ, Sotomatsu M, Taga T, Adachi S, Tawa A, Horibe K, Arakawa H, Miyano S, Ogawa S, Hayashi Y. ASXL2 mutations are frequently found in pediatric AML patients with t(8;21)/ RUNX1-RUNX1T1 and associated with a better prognosis. Genes Chromosomes Cancer. 56(5):382-393, 2017. doi: 10.1002/gcc.22443. | ||
| + | - Yoshizato T, Nannya Y, Atsuta Y, Shiozawa Y, Iijima-Yamashita Y, Yoshida K, Shiraishi Y, Suzuki H, Nagata Y, Sato Y, Kakiuchi N, Matsuo K, Onizuka M, Kataoka K, Chiba K, Tanaka H, Ueno H, Nakagawa MM, Przychodzen B, Haferlach C, Kern W, Aoki K, Itonaga H, Kanda Y, Sekeres MA, Maciejewski JP, Haferlach T, Miyazaki Y, Horibe K, Sanada M, Miyano S, Makishima H, Ogawa S. Genetic abnormalities in myelodysplasia and secondary acute myeloid leukemia: impact on outcome of stem cell transplantation. Blood. 129(17):2347-2358, 2017. doi: 10.1182/blood-2016-12-754796. | ||
| + | - Zhang YZ, Yamaguchi R, Imoto S, Miyano S. Sequence-specific bias correction for RNA-seq data using recurrent neural networks. BMC Genomics. 18(Suppl 1):1044, 2017. doi: 10.1186/s12864-016-3262-5. | ||
| + | - Arashiki N, Takakuwa Y, Mohandas N, Hale J, Yoshida K, Ogura H, Utsugisawa T, Ohga S, Miyano S, Ogawa S, Kojima S, Kanno H. ATP11C is a major flippase in human erythrocytes and its defect causes congenital hemolytic anemia. Haematologica. 101(5):559-565, 2016. doi: 10.3324/haematol.2016.142273. May; Epub 2016 Mar 4. PubMed PMID: 26944472; PubMed Central PMCID: PMC5004368. | ||
| + | - Ayada E, Hasegawa T, Niida A, Miyano S, Imoto S. Binary contingency table method for analysing gene mutation in cancer genome. International Journal of Bioinformatics Research and Applications. 12(3): 211-226, 2016. DOI: 10.1007/978-3-319-19048-8_2. | ||
| + | - 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. 22(6):1275-1285, 2016. doi: 10.1097/MIB.0000000000000752. | ||
| + | - Fujimoto A, Furuta M, Totoki Y, Tsunoda T, Kato M, Shiraishi Y, Tanaka H, Taniguchi H, Kawakami Y, Ueno M, Gotoh K, Ariizumi S, Wardell CP, Hayami S, Nakamura T, Aikata H, Arihiro K, Boroevich KA, Abe T, Nakano K, Maejima K, Sasaki-Oku A, Ohsawa A, Shibuya T, Nakamura H, Hama N, Hosoda F, Arai Y, Ohashi S, Urushidate T, Nagae G, Yamamoto S, Ueda H, Tatsuno K, Ojima H, Hiraoka N, Okusaka T, Kubo M, Marubashi S, Yamada T, Hirano S, Yamamoto M, Ohdan H, Shimada K, Ishikawa O, Yamaue H, Chayama K, Miyano S, Aburatani H, Shibata T, Nakagawa H. Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nature Genetics. 48(5):500-509, 2016. doi: 10.1038/ng.3547. Erratum: Nature Genetics. 48(6):700. doi: 10.1038/ng0616-700a. | ||
| + | - 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. | ||
| + | - Hoshino A, Okada S, Yoshida K, Nishida N, Okuno Y, Ueno H, Yamashita M, Okano T, Tsumura M, Nishimura S, Sakata S, Kobayashi M, Nakamura H, Kamizono J, Mitsui-Sekinaka K, Ichimura T, Ohga S, Nakazawa Y, Takagi M, Imai K, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S, Kojima S, Nonoyama S, Morio T, Kanegane H. Abnormal hematopoiesis and autoimmunity in human subjects with germline IKZF1 mutations. J Allergy Clin Immunol. pii: S0091-6749(16) 31273-31278, 2016. doi: 10.1016/j.jaci.2016.09.029. | ||
| + | - Imashuku S, Muramatsu H, Sugihara T, Okuno Y, Wang X, Yoshida K, Kato A, Kato K, Tatsumi Y, Hattori A, Kita S, Oe K, Sueyoshi A, Usui T, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S, Kojima S, Kanno H. PIEZO1 gene mutation in a Japanese family with hereditary high phosphatidylcholine hemolytic anemia and hemochromatosis-induced diabetes mellitus. Int J Hematol. 104(1):125-129, 2016. doi: 10.1007/s12185-016-1970-x. | ||
| + | - Kataoka K, Shiraishi Y, Takeda Y, Sakata S, Matsumoto M, Nagano S, Maeda T, Nagata Y, Kitanaka A, Mizuno S, Tanaka H, Chiba K, Ito S, Watatani Y, Kakiuchi N, Suzuki H, Yoshizato T, Yoshida K, Sanada M, Itonaga H, Imaizumi Y, Totoki Y, Munakata W, Nakamura H, Hama N, Shide K, Kubuki Y, Hidaka T, Kameda T, Masuda K, Minato N, Kashiwase K, Izutsu K, Takaori-Kondo A, Miyazaki Y, Takahashi S, Shibata T, Kawamoto H, Akatsuka Y, Shimoda K, Takeuchi K, Seya T, Miyano S, Ogawa S. Aberrant PD-L1 expression through 3'-UTR disruption in multiple cancers. Nature. 534(7607):402-406, 2016. doi: 10.1038/nature18294. | ||
| + | - Kato M, Seki M, Yoshida K, Sato Y, Oyama R, Arakawa Y, Kishimoto H, Taki T, Akiyama M, Shiraishi Y, Chiba K, Tanaka H, Mitsuiki N, Kajiwara M, Mizutani S, Sanada M, Miyano S, Ogawa S, Koh K, Takita J. Genomic analysis of clonal origin of Langerhans cell histiocytosis following acute lymphoblastic leukaemia. Br J Haematol. 175(1):169-172, 2016. doi: 10.1111/bjh.13841. | ||
| + | - 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. doi: 10.1093/biostatistics/kxv037. | ||
| + | - Ki Kim S, Ueda Y, Hatano E, Kakiuchi N, Takeda H, Goto T, Shimizu T, Yoshida K, Ikura Y, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Uemoto S, Chiba T, Ogawa S, Marusawa H. TERT promoter mutations and chromosome 8p loss are characteristic of nonalcoholic fatty liver disease-related hepatocellular carcinoma. Int J Cancer. 139(11):2512-2518, 2016. doi: 10.1002/ijc.30379. | ||
| + | - Kitamura K, Okuno Y, Yoshida K, Sanada M, Shiraishi Y, Muramatsu H, Kobayashi R, Furukawa K, Miyano S, Kojima S, Ogawa S, Kunishima S. Functional characterization of a novel GFI1B mutation causing congenital macrothrombocytopenia. J Thromb Haemost. 14(7):1462-1469, 2016. doi: 10.1111/jth.13350. | ||
| + | - Koso H, Yi H, Sheridan P, Miyano S, Ino Y, Todo T, Watanabe S. Identification of RNA-Binding Protein LARP4B as a Tumor Suppressor in Glioma. Cancer Res. 76(8):2254-2264, 2016. doi: 10.1158/0008-5472.CAN-15-2308. 2016 Apr 15; Epub 2016 Mar 1. PubMed PMID: 26933087. | ||
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| + | - Madan V, Shyamsunder P, Han L, Mayakonda A, Nagata Y, Sundaresan J, Kanojia D, Yoshida K, Ganesan S, Hattori N, Fulton N, Tan KT, Alpermann T, Kuo MC, Rostami S, Matthews J, Sanada M, Liu LZ, Shiraishi Y, Miyano S, Chendamarai E, Hou HA, Malnassy G, Ma T, Garg M, Ding LW, Sun QY, Chien W, Ikezoe T, Lill M, Biondi A, Larson RA, Powell BL, Lübbert M, Chng WJ, Tien HF, Heuser M, Ganser A, Koren-Michowitz M, Kornblau SM, Kantarjian HM, Nowak D, Hofmann WK, Yang H, Stock W, Ghavamzadeh A, Alimoghaddam K, Haferlach T, Ogawa S, Shih LY, Mathews V, Koeffler HP. Comprehensive mutational analysis of primary and relapse acute promyelocytic leukemia. Leukemia. 30(12):2430, 2016. doi: 10.1038/leu.2016.237. | ||
| + | - Madan V, Shyamsunder P, Han L, Mayakonda A, Nagata Y, Sundaresan J, Kanojia D, Yoshida K, Ganesan S, Hattori N, Fulton N, Tan KT, Alpermann T, Kuo MC, Rostami S, Matthews J, Sanada M, Liu LZ, Shiraishi Y, Miyano S, Chendamarai E, Hou HA, Malnassy G, Ma T, Garg M, Ding LW, Sun QY, Chien W, Ikezoe T, Lill M, Biondi A, Larson RA, Powell BL, Lübbert M, Chng WJ, Tien HF, Heuser M, Ganser A, Koren-Michowitz M, Kornblau SM, Kantarjian HM, Nowak D, Hofmann WK, Yang H, Stock W, Ghavamzadeh A, Alimoghaddam K, Haferlach T, Ogawa S, Shih LY, Mathews V, Koeffler HP. Comprehensive mutational analysis of primary and relapse acute promyelocytic leukemia. Leukemia. 30(8):1672-1681, 2016. doi: 10.1038/leu.2016.69. | ||
| + | - Mao Y, Tamura T, Yuki Y, Abe D, Tamada Y, Imoto S, Tanaka H, Homma H, Tagawa K, Miyano S, Okazawa H. The hnRNP-Htt axis regulates necrotic cell death induced by transcriptional repression through impaired RNA splicing. Cell Death Dis. 7:e2207, 2016. doi: 10.1038/cddis.2016.101. | ||
| + | - Matsui Y, Mizuta M, Ito S, Miyano S, Shimamura T. D3M: detection of differential distributions of methylation levels. Bioinformatics. 32(15):2248-2255, 2016. doi: 10.1093/bioinformatics/btw138. | ||
| + | - Mitani K, Nagata Y, Sasaki K, Yoshida K, Chiba K, Tanaka H, Shiraishi Y, Miyano S, Makishima H, Nakamura Y, Nakamura Y, Ichikawa M, Ogawa S. Somatic mosaicism in chronic myeloid leukemia in remission. Blood. 128(24):2863-2866, 2016. | ||
| + | - Mori T, Nagata Y, Makishima H, Sanada M, Shiozawa Y, Kon A, Yoshizato T, Sato-Otsubo A, Kataoka K, Shiraishi Y, Chiba K, Tanaka H, Ishiyama K, Miyawaki S, Mori H, Nakamaki T, Kihara R, Kiyoi H, Koeffler HP, Shih LY, Miyano S, Naoe T, Haferlach C, Kern W, Haferlach T, Ogawa S, Yoshida K. Somatic PHF6 mutations in 1760 cases with various myeloid neoplasms. Leukemia. 30(11):2270-2273, 2016. doi: 10.1038/leu.2016.212. | ||
| + | - 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. 35(40):5304-5316, 2016. doi: 10.1038/onc.2016.71. | ||
| + | - Nagata Y, Kontani K, Enami T, Kataoka K, Ishii R, Totoki Y, Kataoka TR, Hirata M, Aoki K, Nakano K, Kitanaka A, Sakata-Yanagimoto M, Egami S, Shiraishi Y, Chiba K, Tanaka H, Shiozawa Y, Yoshizato T, Suzuki H, Kon A, Yoshida K, Sato Y, Sato-Otsubo A, Sanada M, Munakata W, Nakamura H, Hama N, Miyano S, Nureki O, Shibata T, Haga H, Shimoda K, Katada T, Chiba S, Watanabe T, Ogawa S. Variegated RHOA mutations in adult T-cell leukemia/lymphoma. Blood. 127(5):596-604, 2016. doi: 10.1182/blood-2015-06-644948. | ||
| + | - Sakurai M, Kasahara H, Yoshida K, Yoshimi A, Kunimoto H, Watanabe N, Shiraishi Y, Chiba K, Tanaka H, Harada Y, Harada H, Kawakita T, Kurokawa M, Miyano S, Takahashi S, Ogawa S, Okamoto S, Nakajima H. Genetic basis of myeloid transformation in familial platelet disorder/acute myeloid leukemia patients with haploinsufficient RUNX1 allele. Blood Cancer J. 6:e392, 2016. doi: 10.1038/bcj.2015.81. | ||
| + | - Sawada G, Niida A, Uchi R, Hirata H, Shimamura T, Suzuki Y, Shiraishi Y, Chiba K, Imoto S, Takahashi Y, Iwaya T, Sudo T, Hayashi T, Takai H, Kawasaki Y, Matsukawa T, Eguchi H, Sugimachi K, Tanaka F, Suzuki H, Yamamoto K, Ishii H, Shimizu M, Yamazaki H, Yamazaki M, Tachimori Y, Kajiyama Y, Natsugoe S, Fujita H, Mafune K, Tanaka Y, Kelsell DP, Scott CA, Tsuji S, Yachida S, Shibata T, Sugano S, Doki Y, Akiyama T, Aburatani H, Ogawa S, Miyano S, Mori M, Mimori K. Genomic Landscape of Esophageal Squamous Cell Carcinoma in a Japanese Population. Gastroenterology. 150(5):1171-1182, 2016. doi: 10.1053/j.gastro.2016.01.035. | ||
| + | - Shiba N, Yoshida K, Shiraishi Y, Okuno Y, Yamato G, Hara Y, Nagata Y, Chiba K, Tanaka H, Terui K, Kato M, Park MJ, Ohki K, Shimada A, Takita J, Tomizawa D, Kudo K, Arakawa H, Adachi S, Taga T, Tawa A, Ito E, Horibe K, Sanada M, Miyano S, Ogawa S, Hayashi Y. Whole-exome sequencing reveals the spectrum of gene mutations and the clonal evolution patterns in paediatric acute myeloid leukaemia. Br J Haematol. 175(3):476-489, 2016. doi: 10.1111/bjh.14247. | ||
| + | - 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. 2016 Aug; Epub 2016 Jul 7. PubMed PMID: 27387680. | ||
| + | - Tsujita Y, Mitsui-Sekinaka K, Imai K, Yeh TW, Mitsuiki N, Asano T, Ohnishi H, Kato Z, Sekinaka Y, Zaha K, Kato T, Okano T, Takashima T, Kobayashi K, Kimura M, Kunitsu T, Maruo Y, Kanegane H, Takagi M, Yoshida K, Okuno Y, Muramatsu H, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Kojima S, Ogawa S, Ohara O, Okada S, Kobayashi M, Morio T, Nonoyama S. Phosphatase and tensin homolog (PTEN) mutation can cause activated phosphatidylinositol 3-kinase δ syndrome-like immunodeficiency. J Allergy Clin Immunol. 138(6):1672-1680.e10, 2016. doi: 10.1016/j.jaci.2016.03.055. | ||
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| + | - Ueda M, Iguchi T, Masuda T, Nakahara Y, Hirata H, Uchi R, Niida A, Momose K, Sakimura S, Chiba K, Eguchi H, Ito S, Sugimachi K, Yamasaki M, Suzuki Y, Miyano S, Doki Y, Mori M, Mimori K. Somatic mutations in plasma cell-free DNA are diagnostic markers for esophageal squamous cell carcinoma recurrence. Oncotarget. 7(38):62280-62291, 2016. doi: 10.18632/oncotarget.11409. | ||
| + | - 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. 6:26011. doi: 10.1038/srep26011. | ||
| + | - 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. 16:118, 2016. doi: 10.1186/s12911-016-0361-9. | ||
| + | - 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. 2016:3159617, 2016. doi: 10.1155/2016/3159617. | ||
| + | - Chiba K, Shiraishi Y, Nagata Y, Yoshida K, Imoto S, Ogawa S, Miyano S. Genomon ITDetector: A tool for somatic internal tandem duplication detection from cancer genome sequencing data. Bioinformatics. 31(1), 116-118, 2015. | ||
| + | - Fang H, Yamaguchi R, Liu X, DaigoY, 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, 2015. | ||
| + | - Fujimoto A, Furuta M, Shiraishi Y, Gotoh K, Kawakami Y, Arihiro K, Nakamura T, Ueno M, Ariizumi SI, Hai Nguyen H, Shigemizu D, Abe T, Boroevich KA, Nakano K, Sasaki A, Kitada R, Maejima K, Yamamoto Y, Tanaka H, Shibuya T, Shibata T, Ojima H, Shimada K, Hayami S, Shigekawa Y, Aikata H, Ohdan H, Marubashi S, Yamada T, Kubo M, Hirano S, Ishikawa O, Yamamoto M, Yamaue H, Chayama K, Miyano S, Tsunoda T, Nakagawa H. Whole-genome mutational landscape of liver cancers displaying biliary phenotype reveals hepatitis impact and molecular diversity. Nat Commun. 6:6120, 2015. | ||
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| + | - 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. 9:14, 2015. doi: 10.1186/s12918-015-0154-2. | ||
| + | - Hira A, Yoshida K, Sato K, Okuno Y, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Shimamoto A, Tahara H, Ito E, Kojima S, Kurumizaka H, Ogawa S, Takata M, Yabe H, Yabe M. Mutations in the gene encoding the E2 conjugating enzyme UBE2T cause Fanconi anemia. Am J Hum Genet. 96(6):1001-1007, 2015. doi: 10.1016/j.ajhg.2015.04.022. | ||
| + | - Hoshino A, Nomura K, Hamashima T, Isobe T, Seki M, Hiwatari M, Yoshida K, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S, Takita J, Kanegane H. Aggressive transformation of anaplastic large cell lymphoma with increased number of ALK-translocated chromosomes. Int J Hematol. 101(2):198-202, 2015. doi: 10.1007/s12185-014-1701-0. | ||
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| + | - 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. 2:15011, 2015. doi: 10.1038/hgv.2015.11. | ||
| + | - Ito H, Shiwaku H, Yoshida C, Homma H, Luo H, Chen X, Fujita K, Musante L, Fischer U, Frints SGM, Romano C, Ikeuchi Y, Shimamura T, Imoto S, Miyano S, Muramatsu S, Kawauchi T, Hoshino M, Sudol M, Arumughan A, Wanker EE, Rich T, Schwartz C, Matsuzaki F, Bonni A, Kalscheuer VM, Okazawa H. In utero gene therapy rescues microcephaly caused by Pqbp1-hypofunction in neural stem progenitor cells. Mol Psychiatry. 20(4):459-471, 2015. doi: 10.1038/mp.2014.69. | ||
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| + | - Kataoka K, Nagata Y, Kitanaka A, Shiraishi Y, Shimamura T, Yasunaga J, Totoki Y, Chiba K, Sato-Otsubo A, Nagae G, Ishii R, Muto S, Kotani S, Watatani Y, Takeda J, Sanada M, Tanaka H, Suzuki H, Sato Y, Shiozawa Y, Yoshizato T, Yoshida K, Makishima H, Iwanaga M, Ma G, Nosaka K, Hishizawa M, Itonaga H, Imaizumi Y, Munakata W, Ogasawara H, Sato T, Sasai K, Muramoto K, Penova M, Kawaguchi T, Nakamura H, Hama N, Shide K, Kubuki Y, Hidaka T, Kameda T, Nakamaki T, Ishiyama K, Miyawaki S, Yoon SS, Tobinai K, Miyazaki Y, Takaori-Kondo A, Matsuda F, Takeuchi K, Nureki O, Aburatani H, Watanabe T, Shibata T, Matsuoka M, Miyano S, Shimoda K, Ogawa S. Integrated molecular analysis of adult T cell leukemia/lymphoma. Nature Genetics. 47(11):1304-1315, 2015. doi: 10.1038/ng.3415. | ||
| + | - Kawashima-Goto S, Imamura T, Seki M, Kato M, Yoshida K, Sugimoto A, Kaneda D, Fujiki A, Miyachi M, Nakatani T, Osone S, Ishida H, Taki T, Takita J, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S, Hosoi H. Identification of a homozygous JAK3 V674A mutation caused by acquired uniparental disomy in a relapsed early T-cell precursor ALL patient. Int J Hematol. 101(4):411-416, 2015. doi: 10.1007/s12185-014-1711-y. | ||
| + | - Kurtovic-Kozaric A, Przychodzen B, Singh J, Konarska MM, Clemente MJ, Otrock ZK, Nakashima M, Hsi ED, Yoshida K, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S, Boultwood J, Makishima H, Maciejewski JP, Padgett RA. PRPF8 defects cause missplicing in myeloid malignancies. Leukemia. 29(1):126-136, 2015. doi: 10.1038/leu.2014.144. | ||
| + | - Madan V, Kanojia D, Li J, Okamoto R, Sato-Otsubo A, Kohlmann A, Sanada M, Grossmann V, Sundaresan J, Shiraishi Y, Miyano S, Thol F, Ganser A, Yang H, Haferlach T, Ogawa S, Koeffler HP. Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome. Nat Commun. 6:6042, 2015. doi: 10.1038/ncomms7042. | ||
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| + | - Molenaar RJ, Thota S, Nagata Y, Patel B, Clemente M, Przychodzen B, Hirsh C, Viny AD, Hosano N, Bleeker FE, Meggendorfer M, Alpermann T, Shiraishi Y, Chiba K, Tanaka H, van Noorden CJ, Radivoyevitch T, Carraway HE, Makishima H, Miyano S, Sekeres MA, Ogawa S, Haferlach T, Maciejewski JP. Clinical and biological implications of ancestral and non-ancestral IDH1 and IDH2 mutations in myeloid neoplasms. Leukemia. 29(11):2134-4212, 2015. doi: 10.1038/leu.2015.91. | ||
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| + | - Okuno Y, Hoshino A, Muramatsu H, Kawashima N, Wang X, Yoshida K, Wada T, Gunji M, Toma T, Kato T, Shiraishi Y, Iwata A, Hori T, Kitoh T, Chiba K, Tanaka H, Sanada M, Takahashi Y, Nonoyama S, Ito M, Miyano S, Ogawa S, Kojima S, Kanegane H. Late-Onset Combined Immunodeficiency with a Novel IL2RG Mutation and Probable Revertant Somatic Mosaicism. J Clin Immunol. 35(7):610-614, 2015. doi: 10.1007/s10875-015-0202-0. | ||
| + | - Ono A, Fujimoto A, Yamamoto Y, Akamatsu S, Hiraga N, Imamura M, Kawaoka T, Tsuge M, Abe H, Hayes CN, Miki D, Furuta M, Tsunoda T, Miyano S, Kubo M, Aikata H, Ochi H, Kawakami YI, Arihiro K, Ohdan H, Nakagawa H, Chayama K. Circulating Tumor DNA Analysis for Liver Cancers and Its Usefulness as a Liquid Biopsy. Cell Mol Gastroenterol Hepatol. 1(5):516-534, 2015. doi: 10.1016/j.jcmgh.2015.06.009. | ||
| + | - Park H, Niida, A, Miyano S, Imoto S. Sparse overlapping group lasso for integrative multi-omics analysis. J Comput Biol. 22(2): 73-84, 2015. | ||
| + | - Park H, Imoto S, Miyano S. Recursive Random Lasso (RRLasso) for Identifying Anti-Cancer Drug Targets. PLoS One. 10(11):e0141869, 2015. doi: 10.1371/journal.pone.0141869. | ||
| + | - Polprasert C, Schulze I, Sekeres MA, Makishima H, Przychodzen B, Hosono N, Singh J, Padgett RA, Gu X, Phillips JG, Clemente M, Parker Y, Lindner D, Dienes B, Jankowsky E, Saunthararajah Y, Du Y, Oakley K, Nguyen N, Mukherjee S, Pabst C, Godley LA, Churpek JE, Pollyea DA, Krug U, Berdel WE, Klein HU, Dugas M, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Yoshida K, Ogawa S, Müller-Tidow C, Maciejewski JP. Inherited and Somatic Defects in DDX41 in Myeloid Neoplasms. Cancer Cell. 27(5):658-670, 2015. doi: 10.1016/j.ccell.2015.03.017. | ||
| + | - Saini H, Raicar G, Sharma A, Lal S, Dehzangi A, Lyons J, Paliwal KK, Imoto S, Miyano S. Probabilistic expression of spatially varied amino acid dimers into general form of Chou׳s pseudo amino acid composition for protein fold recognition. J Theor Biol. 380:291-298, 2015. doi: 10.1016/j.jtbi.2015.05.030. | ||
| + | - Sakaguchi H, Muramatsu H, Okuno Y, Makishima H, Xu Y, Furukawa-Hibi Y, Wang X, Narita A, Yoshida K, Shiraishi Y, Doisaki S, Yoshida N, Hama A, Takahashi Y, Yamada K, Miyano S, Ogawa S, Maciejewski JP, Kojima S. Aberrant DNA Methylation Is Associated with a Poor Outcome in Juvenile Myelomonocytic Leukemia. PLoS One. 10(12):e0145394, 2015. doi: 10.1371/journal.pone.0145394. | ||
| + | - Sawada G, Niida A, Hirata H, Komatsu H, Uchi R, Shimamura T, Takahashi Y, Kurashige J, Matsumura T, Ueo H, Takano Y, Ueda M, Sakimura S, Shinden Y, Eguchi H, Sudo T, Sugimachi K, Yamasaki M, Tanaka F, Tachimori Y, Kajiyama Y, Natsugoe S, Fujita H, Tanaka Y, Calin G, Miyano S, Doki Y, Mori M, Mimori K. An Integrative Analysis to Identify Driver Genes in Esophageal Squamous Cell Carcinoma. PLoS One. 10(10):e0139808, 2015. doi: 10.1371/journal.pone.0139808. | ||
| + | - Seki M, Nishimura R, Yoshida K, Shimamura T, Shiraishi Y, Sato Y, Kato M, Chiba K, Tanaka H, Hoshino N, Nagae G, Shiozawa Y, Okuno Y, Hosoi H, Tanaka Y, Okita H, Miyachi M, Souzaki R, Taguchi T, Koh K, Hanada R, Kato K, Nomura Y, Akiyama M, Oka A, Igarashi T, Miyano S, Aburatani H, Hayashi Y, Ogawa S, Takita J. Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma. Nat Commun. 6:7557, 2015. doi: 10.1038/ncomms8557. | ||
| + | - Shiota M, Yang X, Kubokawa M, Morishima T, Tanaka K, Mikami M, Yoshida K, Kikuchi M, Izawa K, Nishikomori R, Okuno Y, Wang X, Sakaguchi H, Muramatsu H, Kojima S, Miyano S, Ogawa S, Takagi M, Hata D, Kanegane H. Somatic mosaicism for a NRAS mutation associates with disparate clinical features in RAS-associated leukoproliferative disease: a report of two cases. J Clin Immunol. 35(5):454-458, 2015. doi: 10.1007/s10875-015-0163-3. | ||
| + | - Shiraishi Y, Tremmel G, Miyano S, Stephens M. A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures. PLoS Genet. 11(12):e1005657 2015 doi: 10.1371/journal.pgen.1005657. | ||
| + | - Suzuki H, Aoki K, Chiba K, Sato Y, Shiozawa Y, Shiraishi Y, Shimamura T, Niida A, Motomura K, Ohka F, Yamamoto T, Tanahashi K, Ranjit M, Wakabayashi T, Yoshizato T, Kataoka K, Yoshida K, Nagata Y, Sato-Otsubo A, Tanaka H, Sanada M, Kondo Y, Nakamura H, Mizoguchi M, Abe T, Muragaki Y, Watanabe R, Ito I, Miyano S, Natsume A, Ogawa S. Mutational landscape and clonal architecture in grade II and III gliomas. Nature Genetics. 47(5):458-468, 2015. doi: 10.1038/ng.3273. | ||
| + | - Tagawa K, Homma H., Saito A, Fujita K, Chen X, Imoto S, Oka T, Ito H, Motoki K, Yoshida C, Hatsuta H, Murayama S, Iwatsubo T, Miyano S, Okazawa H. Comprehensive phosphoproteome analysis unravels the core signaling network that initiates the earliest synapse pathology in preclinical Alzheimer’s disease brain. Hum Mol Genet. 24(2), 540-558, 2015. | ||
| + | - Takahashi Y, Sheridan P, Niida A, Sawada G, Uchi R, Mizuno H, Kurashige J, Sugimachi K, Sasaki S, Shimada Y, Hase K, Kusunoki M, Kudo S, Watanabe M, Yamada K, Sugihara K, Yamamoto H, Suzuki A, Doki Y, Miyano S, Mori M, Mimori K. The AURKA/TPX2 axis drives colon tumorigenesis cooperatively with MYC. Ann Oncol. 26(5):935-942, 2015. doi: 10.1093/annonc/mdv034. | ||
| + | - Wang R, Yoshida K, Toki T, Sawada T, Uechi T, Okuno Y, Sato-Otsubo A, Kudo K, Kamimaki I, Kanezaki R, Shiraishi Y, Chiba K, Tanaka H, Terui K, Sato T, Iribe Y, Ohga S, Kuramitsu M, Hamaguchi I, Ohara A, Hara J, Goi K, Matsubara K, Koike K, Ishiguro A, Okamoto Y, Watanabe K, Kanno H, Kojima S, Miyano S, Kenmochi N, Ogawa S, Ito E. Loss of function mutations in RPL27 and RPS27 identified by whole-exome sequencing in Diamond-Blackfan anaemia. Br J Haematol. 168(6):854-864, 2015. doi: 10.1111/bjh.13229. | ||
| + | - Wang X, Muramatsu H, Okuno Y, Sakaguchi H, Yoshida K, Kawashima N, Xu Y, Shiraishi Y, Chiba K, Tanaka H, Saito S, Nakazawa Y, Masunari T, Hirose T, Elmahdi S, Narita A, Doisaki S, Ismael O, Makishima H, Hama A, Miyano S, Takahashi Y, Ogawa S, Kojima S. GATA2 and secondary mutations in familial myelodysplastic syndromes and pediatric myeloid malignancies. Haematologica. 100(10):e398-401, 2015. doi: 10.3324/haematol.2015.127092. | ||
| + | - Yamaguchi H, Sakaguchi H, Yoshida K, Yabe M, Yabe H, Okuno Y, Muramatsu H, Takahashi Y, Yui S, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Inokuchi K, Ito E, Ogawa S, Kojima S. Clinical and genetic features of dyskeratosis congenita, cryptic dyskeratosis congenita, and Hoyeraal-Hreidarsson syndrome in Japan. Int J Hematol. 102(5):544-552, 2015. doi: 10.1007/s12185-015-1861-6. | ||
| + | - 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 germline mosaicism by next-generation sequencing in an FAP patient. J Hum Genet. 60(5):227-231, 2015. doi: 10.1038/jhg.2015.14. | ||
| + | - Yang X, Hoshino A, Taga T, Kunitsu T, Ikeda Y, Yasumi T, Yoshida K, Wada T, Miyake K, Kubota T, Okuno Y, Muramatsu H, Adachi Y, Miyano S, Ogawa S, Kojima S, Kanegane H. A female patient with incomplete hemophagocytic lymphohistiocytosis caused by a heterozygous XIAP mutation associated with non-random X-chromosome inactivation skewed towards the wild-type XIAP allele. J Clin Immunol. 35(3):244-248, 2015. doi: 10.1007/s10875-015-0144-6. | ||
| + | - Yasuda T, Miyano S. Yasuda T, Miyano S. Inferring the global structure of chromosomes from structural variations. BMC Genomics. 16 Suppl 2:S13, 2015. doi: 10.1186/1471-2164-16-S2-S13. Erratum: BMC Genomics. 16:276, 2015. doi: 10.1186/s12864-015-1338-2. | ||
| + | - 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. 50(9):1227-1234, 2015. doi: 10.1038/bmt.2015.133. | ||
| + | - Yoshizato T, Dumitriu B, Hosokawa K, Makishima H, Yoshida K, Townsley D, Sato-Otsubo A, Sato Y, Liu D, Suzuki H, Wu CO, Shiraishi Y, Clemente MJ, Kataoka K, Shiozawa Y, Okuno Y, Chiba K, Tanaka H, Nagata Y, Katagiri T, Kon A, Sanada M, Scheinberg P, Miyano S, Maciejewski JP, Nakao S, Young NS, Ogawa S. Somatic Mutations and Clonal Hematopoiesis in Aplastic Anemia. N Engl J Med. 373(1):35-47, 2015. doi: 10.1056/NEJMoa1414799. | ||
| + | ===== 2014 ===== | ||
| + | - Arima C, Kajino T, Tamada Y, Imoto S, Shimada Y, Nakatochi M, Suzuki M, Isomura H, Yatabe Y, Yamaguchi T, Yanagisawa K, Miyano S, Takahashi T. Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features. Carcinogenesis. 35(10): 2224-2231, 2014. | ||
| + | - Barclay SS, Tamura T, Ito H, Fujita K, Tagawa K, Shimamura T, Katsuta A, Shiwaku H, Sone M, Imoto S, Miyano S, Okazawa H. Systems biology analysis of Drosophila in vivo screen data elucidates core networks for DNA damage repair in SCA1. Hum Mol Genet. 23(5):1345-1364, 2014. | ||
| + | - Becker H, Yoshida K, Blagitko-Dorfs N, Claus R, Pantic M, Abdelkarim M, Niemöller C, Greil C, Hackanson B, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Döhner K, Schnittger S, Henneke P, Niemeyer CM, Flotho C, Pfeifer D, Ogawa S, Lübbert M. Tracing the development of acute myeloid leukemia in CBL syndrome. Blood. 123(12):1883-1886, 2014. | ||
| + | - Chiba K, Shiraishi Y, Nagata Y, Yoshida K, Imoto S, Ogawa S, Miyano S. Genomon ITDetector: A tool for somatic internal tandem duplication detection from cancer genome sequencing data. Bioinformatics. In press. | ||
| + | - Damm F, Mylonas E, Cosson A, Yoshida K, Della Valle V, Mouly E, Diop M, Scourzic L, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Kikushige Y, Davi F, Lambert J, Gautheret D, Merle-Béral H, Sutton L, Dessen P, Solary E, Akashi K, Vainchenker W, Mercher T, Droin N, Ogawa S, Nguyen-Khac F, Bernard OA. Acquired initiating mutations in early hematopoietic cells of CLL patients. Cancer Discov. 4(9):1088-1101, 2014. | ||
| + | - Fang H, Yamaguchi R, Liu X, DaigoY, 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. In press. | ||
| + | - Fujita A, Miyano S. A tutorial to identify nonlinear associations in gene expression time series data. Methods Mol Biol. 1164:87-95, 2014. | ||
| + | - Haferlach T, Nagata Y, Grossmann V, Okuno Y, Bacher U, Nagae G, Schnittger S, Sanada M, Kon A, Alpermann T, Yoshida K, Roller A, Nadarajah N, Shiraishi Y, Shiozawa Y, Chiba K, Tanaka H, Koeffler HP, Klein HU, Dugas M, Aburatani H, Kohlmann A, Miyano S, Haferlach C, Kern W, Ogawa S. Landscape of genetic lesions in 944 patients with myelodysplastic syndromes. Leukemia. 28(2):241-247, 2014. | ||
| + | - Hasegawa S, Imai K, Yoshida K, Okuno Y, Muramatsu H, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Kojima S, Ogawa S, Morio T, Mizutani S, Takagi M. Whole-exome sequence analysis of ataxia telangiectasia-like phenotype. J Neurol Sci. 340(1-2):86-90, 2014. | ||
| + | - Hasegawa T, Mori T, Yamaguchi R, Imoto S, Miyano S, Akutsu T. An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data. J Comput Biol. 21(11):785-798, 2014. | ||
| + | - 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. | ||
| + | - 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, 2014. | ||
| + | - Hoshino A, Nomura K, Hamashima T, Isobe T, Seki M, Hiwatari M, Yoshida K, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S, Takita J, Kanegane H. Aggressive transformation of anaplastic large cell lymphoma with increased number of ALK-translocated chromosomes. Int J Hematol. In press. | ||
| + | - Hosono N, Makishima H, Jerez A, Yoshida K, Przychodzen B, McMahon S, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Sanada M, Gómez-Seguí I, Verma AK, McDevitt MA, Sekeres MA, Ogawa S, Maciejewski JP. Recurrent genetic defects on chromosome 7q in myeloid neoplasms. Leukemia. 28(6):1348-1351, 2014. | ||
| + | - Ito H, Shiwaku H, Yoshida C, Homma H, Luo H, Chen X, Fujita K, Musante L, Fischer U, Frints SGM, Romano C, Ikeuchi Y, Shimamura T, Imoto S, Miyano S, Muramatsu S, Kawauchi T, Hoshino M, Sudol M, Arumughan A, Wanker EE, Rich T, Schwartz C, Matsuzaki F, Bonni A, Kalscheuer VM, Okazawa H. In utero gene therapy rescues microcephaly caused by Pqbp1-hypofunction in neural stem progenitor cells. Mol Psychiatry. In press. | ||
| + | - Katayama K, Yamaguchi R, Imoto S, Watanabe K, Miyano S. Analysis of questionnaire for traditional medicine and development of decision support system. Evid Based Complement Alternat Med. 2014:974139, 2014. | ||
| + | - Kawashima-Goto S, Imamura T, Seki M, Kato M, Yoshida K, Sugimoto A, Kaneda D, Fujiki A, Miyachi M, Nakatani T, Osone S, Ishida H, Taki T, Takita J, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S, Hosoi H. Identification of a homozygous JAK3 V674A mutation caused by acquired uniparental disomy in a relapsed early T-cell precursor ALL patient. Int J Hematol. In press. | ||
| + | - Kihara R, Nagata Y, Kiyoi H, Kato T, Yamamoto E, Suzuki K, Chen F, Asou N, Ohtake S, Miyawaki S, Miyazaki Y, Sakura T, Ozawa Y, Usui N, Kanamori H, Kiguchi T, Imai K, Uike N, Kimura F, Kitamura K, Nakaseko C, Onizuka M, Takeshita A, Ishida F, Suzushima H, Kato Y, Miwa H, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S, Naoe T. Comprehensive analysis of genetic alterations and their prognostic impacts in adult acute myeloid leukemia patients. Leukemia. 28(8):1586-1595, 2014. | ||
| + | - Kurtovic-Kozaric A, Przychodzen B, Singh J, Konarska MM, Clemente MJ, Otrock ZK, Nakashima M, Hsi ED, Yoshida K, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S, Boultwood J, Makishima H, Maciejewski JP, Padgett RA. PRPF8 defects cause missplicing in myeloid malignancies. Leukemia. In press. | ||
| + | - Li C, Nagasaki M, Ikeda E, Sekiya Y, Miyano S. CSML2SBML: a novel tool for converting quantitative biological pathway models from CSML into SBML. Biosystems. 121:22-28, 2014. | ||
| + | - Lin TL, Nagata Y, Kao HW, Sanada M, Okuno Y, Huang CF, Liang DC, Kuo MC, Lai CL, Lee EH, Shih YS, Tanaka H, Shiraishi Y, Chiba K, Lin TH, Wu JH, Miyano S, Ogawa S, Shih LY. Clonal leukemic evolution in myelodysplastic syndromes with TET2 and IDH1/2 mutations. Haematologica. 99(1):28-36, 2014. | ||
| + | - Matsunawa M, Yamamoto R, Sanada M, Sato-Otsubo A, Shiozawa Y, Yoshida K, Otsu M, Shiraishi Y, Miyano S, Isono K, Koseki H, Nakauchi H, Ogawa S. Haploinsufficiency of Sf3b1 leads to compromised stem cell function but not to myelodysplasia. Leukemia. 28(9):1844-1850, 2014. | ||
| + | - Oki T, Nishimura K, Kitaura J, Togami K, Maehara A, Izawa K, Sakaue-Sawano A, Niida A, Miyano S, Aburatani H, Kiyonari H, Miyawaki A, Kitamura T. A novel cell-cycle-indicator, mVenus-p27K(-), identifies quiescent cells and visualizes G0-G1 transition. Sci Rep. 4:4012, 2014. | ||
| + | - Park H, Niida, A, Miyano S, Imoto S. Sparse overlapping group lasso for integrative multi-omics analysis. J Comput Biol. In press. | ||
| + | - Park H, Shimamura T, Miyano S, Imoto S. Robust prediction of anti-cancer drug sensitivity and sensitivity-specific biomarker. PLoS One. 9(1): e108990, 2014. | ||
| + | - Saini H, Raicar G, Lal S, Dehzangi A, Lyons J, Paliwal KK, Imoto S, Miyano S, Sharma A. Genetic algorithm for an optimized weighted voting scheme incorporating k-separated bigram transition probabilities to improve protein fold recognition. Asia-Pacific World Congress on Computer Science and Engineering 2014. In press. | ||
| + | - Sakata-Yanagimoto M, Enami T, Yoshida K, Shiraishi Y, Ishii R, Miyake Y, Muto H, Tsuyama N, Sato-Otsubo A, Okuno Y, Sakata S, Kamada Y, Nakamoto-Matsubara R, Tran NB, Izutsu K, Sato Y, Ohta Y, Furuta J, Shimizu S, Komeno T, Sato Y, Ito T, Noguchi M, Noguchi E, Sanada M, Chiba K, Tanaka H, Suzukawa K, Nanmoku T, Hasegawa Y, Nureki O, Miyano S, Nakamura N, Takeuchi K, Ogawa S, Chiba S. Somatic RHOA mutation in angioimmunoblastic T cell lymphoma. Nat Genet. 46(2):171-175, 2014. | ||
| + | - Sato Y, Maekawa S, Ishii R, Sanada M, Morikawa T, Shiraishi Y, Yoshida K, Nagata Y, Sato-Otsubo A, Yoshizato T, Suzuki H, Shiozawa Y, Kataoka K, Kon A, Aoki K, Chiba K, Tanaka H, Kume H, Miyano S, Fukayama M, Nureki O, Homma Y, Ogawa S. Recurrent somatic mutations underlie corticotropin-independent Cushing's syndrome. Science. 344(6186):917-920, 2014. | ||
| + | - Sawada G, Takahashi Y, Niida A, Shimamura T, Kurashige J, Matsumura T, Ueo H, Uchi R, Takano Y, Ueda M, Hirata H, Sakimura S, Shinden Y, Eguchi H, Sudo T, Sugimachi K, Miyano S, Doki Y, Mori M, Mimori K. Loss of CDCP1 expression promotes invasiveness and poor prognosis in esophageal squamous cell carcinoma. Ann Surg Oncol. 21 Suppl 4:640-647, 2014. | ||
| + | - Seki M, Yoshida K, Shiraishi Y, Shimamura T, Sato Y, Nishimura R, Okuno Y, Chiba K, Tanaka H, Kato K, Kato M, Hanada R, Nomura Y, Park MJ, Ishida T, Oka A, Igarashi T, Miyano S, Hayashi Y, Ogawa S, Takita J. Biallelic DICER1 mutations in sporadic pleuropulmonary blastoma. Cancer Res. 74(10):2742-2749, 2014. | ||
| + | - Sharma A, Paliwal KK, Imoto S, Miyano S, Sharma V, Ananthanarayanan R. A feature selection method using fixed-point algorithm for DNA microarray gene expression data. International Journal of Knowledge Based and Intelligent Engineering Systems. 18(1): 55-59, 2014. | ||
| + | - Sharma A, Dehzangi A, Lyons J, Imoto S, Miyano S, Nakai K, Patil A. Evaluation of sequence features from intrinsically disordered regions for the estimation of protein function. PLoS One. 9(2):e89890, 2014. | ||
| + | - Sharma A, Paliwal KK, Imoto S, Miyano S. A feature selection method using improved regularized linear discriminant analysis. Mach Vis Appl. 25(3):775-786, 2014. | ||
| + | - Shen W, Clemente MJ, Hosono N, Yoshida K, Przychodzen B, Yoshizato T, Shiraishi Y, Miyano S, Ogawa S, Maciejewski JP, Makishima H. Deep sequencing reveals stepwise mutation acquisition in paroxysmal nocturnal hemoglobinuria. J Clin Invest. 124(10):4529-4538, 2014. | ||
| + | - Sugimachi K, Niida A, Yamamoto K, Shimamura T, Imoto S, Iinuma H, Shinden Y, Eguchi H, Sudo T, Watanabe M, Tanaka J, Kudo S, Hase K, Kusunoki M, Yamada K, Shimada Y, Sugihara K, Maehara Y, Miyano S, Mori M, Mimori K. Allelic Imbalance at an 8q24 Oncogenic SNP is involved in activating MYC in human colorectal cancer. Ann Surg Oncol. 21 Suppl 4:515-521, 2014. | ||
| + | - Tagawa K, Homma H., Saito A, Fujita K, Chen X, Imoto S, Oka T, Ito H, Motoki K, Yoshida C, Hatsuta H, Murayama S, Iwatsubo T, Miyano S, Okazawa H. Comprehensive phosphoproteome analysis unravels the core signaling network that initiates the earliest synapse pathology in preclinical Alzheimer’s disease brain. Hum Mol Genet. In press. | ||
| + | - 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. Evid Based Complement Alternat Med. 2014:832824, 2014. | ||
| + | - Totoki Y, Yoshida A, Hosoda F, Nakamura H, Hama N, Ogura K, Yoshida A, Fujiwara T, Arai Y, Toguchida J, Tsuda H, Miyano S, Kawai A, Shibata T. Unique mutation portraits and frequent COL2A1 gene alteration in chondrosarcoma. Genome Res. 24(9):1411-1420, 2014. | ||
| + | - Usuyama N, Shiraishi Y, Sato Y, Kume H, Homma Y, Ogawa S, Miyano S, Imoto S. HapMuC: somatic mutation calling using heterozygous germline variants near candidate mutations. Bioinformatics. 30(23): 3302-3309, 2014. | ||
| + | - Wang R, Yoshida K, Toki T, Sawada T, Uechi T, Okuno Y, Sato-Otsubo A, Kudo K, Kamimaki I, Kanezaki R, Shiraishi Y, Chiba K, Tanaka H, Terui K, Sato T, Iribe Y, Ohga S, Kuramitsu M, Hamaguchi I, Ohara A, Hara J, Goi K, Matsubara K, Koike K, Ishiguro A, Okamoto Y, Watanabe K, Kanno H, Kojima S, Miyano S, Kenmochi N, Ogawa S, Ito E. Loss of function mutations in RPL27 and RPS27 identified by whole-exome sequencing in Diamond-Blackfan anaemia. Br J Haematol. In press. | ||
| + | - 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, 2014. | ||
| + | - Yoshino T, Katayama K, Munakata K, Horiba Y, Yamaguchi R, Imoto S, Miyano S, Watanabe K. Kampo traditional pattern diagnosis and the clustering analysis of patients with cold sensation. J Altern Complement Med. 20(5):A47, 2014. | ||
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| + | ===== 2013 ===== | ||
| + | - Affara M, Sanders D, Araki H, Tamada Y, Dunmore B, Humphreys S, Imoto S, Savoie C, Miyano S, Kuhara S, Print C, Charnock-Jones DS. Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis. BMC Genomics. 14(1):23, 2013. | ||
| + | - Damm F, Chesnais V, Nagata Y, Yoshida K, Scourzic L, Okuno Y, Itzykson R, Sanada M, Shiraishi Y, Gelsi-Boyer V, Renneville A, Miyano S, Mori H, Shih LY, Park S, Dreyfus F, Guerci-Bresler A, Solary E, Rose C, Cheze S, Prébet T, Vey N, Legentil M, Duffourd Y, de Botton S, Preudhomme C, Birnbaum D, Bernard OA, Ogawa S, Fontenay M, Kosmider O. Blood. 122(18):3169-77, 2013. | ||
| + | - Furuta M, Kozaki K, Tanimoto K, Tanaka S, Arii S, Shimamura T, Niida A, Miyano S, Inazawa J. The tumor-suppressive miR-497-195 cluster targets multiple cell-cycle regulators in hepatocellular carcinoma. PLoS One. 8(3):e60155, 2013. | ||
| + | - Gómez-Seguí I, Makishima H, Jerez A, Yoshida K, Przychodzen B, Miyano S, Shiraishi Y, Husseinzadeh HD, Guinta K, Clemente M, Hosono N, McDevitt MA, Moliterno AR, Sekeres MA, Ogawa S, Maciejewski JP. Novel recurrent mutations in the RAS-like GTP-binding gene RIT1 in myeloid malignancies. Leukemia. 27(9):1943-1946, 2013 | ||
| + | - Hira A, Yabe H, Yoshida K, Okuno Y, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Nakamura J, Kojima S, Ogawa S, Matsuo K, Takata M, Yabe M. Variant ALDH2 is associated with accelerated progression of bone marrow failure in Japanese Fanconi anemia patients. Blood. 122(18):3206-3209, 2013. | ||
| + | - Ishikawa T, Shimizu T, Ueki A, Yamaguchi SI, 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 Sci. 104(7):880-888, 2013. | ||
| + | - 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. Evid Based Complement Alternat Med. 2013:576973, 2013. | ||
| + | - Kayano M, Imoto S, Yamaguchi R, Miyano S. Multi-omics approach for estimating metabolic networks using low-order partial correlations. J Comput Biol. 20(8):571-582, 2013. | ||
| + | - Kitamura K, Yoshida K, Shiraishi Y, Chiba K, Tanaka H, Furukawa K, Miyano S, Ogawa S, Kunishima S. Normal neutrophil myosin IIA localization in an immunofluorescence analysis can rule out MYH9 disorders. J Thromb Haemost. 11(11):2071-2073, 2013. | ||
| + | - 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. | ||
| + | - Kon A, Shih LY, Minamino M, Sanada M, Shiraishi Y, Nagata Y, Yoshida K, Okuno Y, Bando M, Nakato R, Ishikawa S, Sato-Otsubo A, Nagae G, Nishimoto A, Haferlach C, Nowak D, Sato Y, Alpermann T, Nagasaki M, Shimamura T, Tanaka H, Chiba K, Yamamoto R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Nakamaki T, Ishiyama K, Nolte F, Hofmann WK, Miyawaki S, Chiba S, Mori H, Nakauchi H, Koeffler HP, Aburatani H, Haferlach T, Shirahige K, Miyano S, Ogawa S. Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. Nat Genet. 45(10):1232-1237, 2013. | ||
| + | - Kunishima S, Okuno Y, Yoshida K, Shiraishi Y, Sanada M, Muramatsu H, Chiba K, Tanaka H, Miyazaki K, Sakai M, Ohtake M, Kobayashi R, Iguchi A, Takahashi Y, Miyano S, Saito H, Kojima S, Ogawa S. ACTN1 mutations cause congenital macrothrombocytopenia. American Journal of Human Genetics. 92(3):431-438, 2013. | ||
| + | - Makishima H, Yoshida K, Nguyen N, Przychodzen B, Sanada M, Okuno Y, Ng KP, Gudmundsson KO, Vishwakarma BA, Jerez A, Gomez-Segui I, Takahashi M, Shiraishi Y, Nagata Y, Guinta K, Mori H, Sekeres MA, Chiba K, Tanaka H, Muramatsu H, Sakaguchi H, Paquette RL, McDevitt MA, Kojima S, Saunthararajah Y, Miyano S, Shih LY, Du Y, Ogawa S, Maciejewski JP. Somatic SETBP1 mutations in myeloid malignancies. Nat Genet. 45(8):942-946, 2013. | ||
| + | - Niida A, Tremmel G, Imoto S, Miyano S. Multilayer cluster heat map visualizing biological tensor data. Lecture Notes in Bioinformatics. 8213: 116-125, 2013. | ||
| + | - Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, Li C, Miyano S. XiP: a computational environment to create, extend and share workflows. Bioinformatics. 29(1):137-139, 2013. | ||
| + | - Osawa T, Tsuchida R, Muramatsu M, Shimamura T, Wang F, Suehiro JI, Kanki Y, Wada Y, Yuasa Y, Aburatani H, Miyano S, Minami T, Kodama T, Shibuya M. Inhibition of histone demethylase JMJD1A improves anti-angiogenic therapy and reduces tumor associated macrophages. Cancer Res. 73(10):3019-3028, 2013. | ||
| + | - Saida S, Watanabe K, Sato-Otsubo A, Terui K, Yoshida K, Okuno Y, Toki T, Wang RN, Shiraishi Y, Miyano S, Kato I, Morishima T, Fujino H, Umeda K, Hiramatsu H, Adachi S, Ito E, Ogawa S, Ito M, Nakahata T, Heike T. Clonal selection in xenografted TAM recapitulates the evolutionary process of myeloid leukemia in Down syndrome. Blood. 121(21):4377-4387, 2013. | ||
| + | - Saito MM, Imoto S, Yamaguchi R, Tsubokura M, Kami M, 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):e72866. 2013. | ||
| + | - 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, 2013. | ||
| + | - Sakaguchi H, Okuno Y, Muramatsu H, Yoshida K, Shiraishi Y, Takahashi M, Kon A, Sanada M, Chiba K, Tanaka H, Makishima H, Wang X, Xu Y, Doisaki S, Hama A, Nakanishi K, Takahashi Y, Yoshida N, Maciejewski JP, Miyano S, Ogawa S, Kojima S. Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia. Nat Genet. 45(8):937-941, 2013. | ||
| + | - Sato Y, Yoshizato T, Shiraishi Y, Maekawa S, Okuno Y, Kamura T, Shimamura T, Sato-Otsubo A, Nagae G, Suzuki H, Nagata Y, Yoshida K, Kon A, Suzuki Y, Chiba K, Tanaka H, Niida A, Fujimoto A, Tsunoda T, Morikawa T, Maeda D, Kume H, Sugano S, Fukayama M, Aburatani H, Sanada M, Miyano S, Homma Y, Ogawa S. Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet. 45(8):860-867, 2013. | ||
| + | - Sharma A, Paliwal KK, Dehzangi A, Lyons J, Imoto S, Miyano S. A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition. BMC Bioinformatics. 14(1):233, 2013. | ||
| + | - Sharma A, Paliwal KK, Imoto S, Miyano S. Principal component analysis using QR decomposition. International Journal of Machine Learning and Cybernetics. 4(6): 679-683, 2013. | ||
| + | - Shiraishi Y, Sato Y, Chiba K, Okuno Y, Nagata Y, Yoshida K, Shiba N, Hayashi Y, Kume H, Homma Y, Sanada M, Ogawa S, Miyano S. An empirical Bayesian framework for somatic mutation detection from cancer. Nucleic Acids Res. 41(7): e89, 2013. | ||
| + | - 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 JI, Kudo SE, Mochizuki H, Kusunoki M, Yamada K, Shimada Y, Moriya Y, Miyano S, Sugihara K, Mori M. The rs6983267 SNP is associated with MYC transcription efficiency, which promotes progression and worsens prognosis of colorectal cancer. Ann Surg Oncol. 20(4):1395-1402, 2013. | ||
| + | - Tamura T, Sone M, Nakamura Y, Shimamura T, Imoto S, Miyano S, Okazawa H. A restricted level of PQBP1 is needed for the best longevity of Drosophila. Neurobiol Aging. 34(1):356.e11-20. 2013. doi: 10.1016/j.neurobiolaging.2012.07.015. | ||
| + | - Yamaguchi R, Imoto S, Kami M, Watanabe K, Miyano S, Yuji K. Does Twitter trigger bursts in signature collections? PLoS One. 8(3):e58252, 2013. | ||
| + | - Yokobori T, Iinuma H, Shimamura T, Imoto S, Sugimachi K, Ishii H, Iwatsuki M, Ota D, Ohkuma M, Iwaya T, Nishida N, Kogo R, Sudo T, Tanaka F, Shibata K, Toh H, Sato T, Barnard GF, Fukagawa T, Yamamoto S, Nakanishi H, Sasaki S, Miyano S, Watanabe T, Kuwano H, Mimori K, Pantel K, Mori M. Plastin3 is a novel marker for circulating tumor cells undergoing the epithelial-mesenchymal transition and is associated with colorectal cancer prognosis. Cancer Res. 73(7):2059-2069, 2013. | ||
| + | - Yoshida K, Toki T, Okuno Y, Kanezaki R, Shiraishi Y, Sato-Otsubo A, Sanada M, Park MJ, Terui K, Suzuki H, Kon A, Nagata Y, Sato Y, Wang R, Shiba N, Chiba K, Tanaka H, Hama A, Muramatsu H, Hasegawa D, Nakamura K, Kanegane H, Tsukamoto K, Adachi S, Kawakami K, Kato K, Nishimura R, Izraeli S, Hayashi Y, Miyano S, Kojima S, Ito E, Ogawa S. The landscape of somatic mutations in Down syndrome-related myeloid disorders. Nat Genet. 45:1293–1299, 2013. Erratum in: Nat Genet. 45(12):1516, 2013. | ||
| + | - Yoshimaru T, Komatsu M, Matsuo T, Chen YA, 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-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells. Nat Commun. 4:2443, 2013. | ||
| + | - 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. Evid Based Complement Alternat Med. 2013:398458 (8 pages), 2013. | ||
| + | |||
| + | ===== 2012 ===== | ||
| + | - Fujimori S, Hino K, Saito A, Miyano S, Miyamoto-Sato E. PRD: A protein-RNA interaction database. Bioinformation. 8(15):729-730, 2012. | ||
| + | - Fujimori S, Hirai N, Masuoka K, Oshikubo T, Yamashita T, Washio T, Saito A, Nagasaki M, Miyano S, Miyamoto-Sato E. IRView: a database and viewer for protein interacting regions. Bioinformatics. 28(14):1949-1950, 2012. | ||
| + | - Fujimoto A, Totoki Y, Abe T, Boroevich KA, Hosoda F, Hai Nguyen H, Aoki M, Hosono N, Kubo M, Miya F, Arai Y, Takahashi H, Shirakihara T, Nagasaki M, Shibuya T, Nakano K, Watanabe-Makino K, Tanaka H, Nakamura H, Kusuda J, Ojima H, Shimada K, Okusaka T, Ueno M, Shigekawa Y, Kawakami Y, Arihiro K, Ohdan H, Gotoh K, Ishikawa O, Ariizumi S, Yamamoto M, Yamada T, Chayama K, Kosuge T, Yamaue H, Kamatani N, Miyano S, Nakagama H, Nakamura Y, Tsunoda T, Shibata T, Nakagawa H. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nature Genetics. 44(7):760-764, 2012. | ||
| + | - Fujita A, Severino P, Kojima K, Sato JR, Patriota AG, Miyano S. Functional clustering of time series gene expression data by Granger causality. BMC Systems Biology. 6:137, 2012. | ||
| + | - Hurley D, Araki H, Tamada Y, Dunmore B, Sanders D, Humphreys S, Affara M, Imoto S, Yasuda K, Tomiyasu Y, Tashiro K, Savoie C, Cho V, Smith S, Kuhara S, Miyano S, Charnock-Jones DS, Crampin EJ, Print CG. Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Res. 40(6):2377-2398, 2012. doi: 10.1093/nar/gkr902. | ||
| + | - 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 JI, Kudo SE, Sugihara KI, 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. Ann Surg Oncol. 19(9):2853-2858, 2012. | ||
| + | - 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. | ||
| + | - Katayama K, Yamaguchi R, Imoto S, Matsuura K, Watanabe K, Miyano S. Analysis of questionnaire for Traditional Medical and develop decision support system. Proc. 2012 International Workshop on Biomedical and Health Informatics. IEEE Computer Society Press. 762-763, 2012. | ||
| + | - Katayama K, Yamaguchi R, Imoto S, Matsuura K, Watanabe K, Miyano S. Symbolic hierarchical clustering for pain vector. Intelligent Decision Technologies. 16: 17-124, 2012. | ||
| + | - Katayama K, Yamaguchi R, Imoto S, Matsuura K, Watanabe K, Miyano S. Connection between traditional medicine and disease. ACM SIGHIT Record. 2 (1): 21-21. 2012. | ||
| + | - 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. | ||
| + | - Niida A, Imoto S, Shimamura T, Miyano S. Statistical model-based testing to evaluate the recurrence of genomic aberrations. Bioinformatics. 28(12):i115-i120, 2012. | ||
| + | - 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. | ||
| + | - Okayama H, Kohno T, Ishii1 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 Res. 72(1):100-111, 2012. | ||
| + | - Saito MM, Imoto S, Yamaguchi R, Miyano S, Higuchi T. Identifiability of local transmissibility parameters in agent-based pandemic simulation. Proc. 15th International Conference on Information Fusion. IEEE Computer Society Press. 2466-2471, 2012. | ||
| + | - Saito MM, Imoto S, Yamaguchi R, Miyano S, Higuchi T. Parallel agent-based simulator for influenza pandemic. Lecture Notes in Computer Science. 7068: 361-370, 2012. | ||
| + | - Sharma A, Imoto S, Miyano S. A filter based feature selection algorithm using null space of covariance matrix for DNA microarray gene expression data. Current Bioinformatics. 7 (3): 289-294, 2012. | ||
| + | - Sharma A, Imoto S, Miyano S. A between-class overlapping filter-based method for transcriptome data analysis. J Bioinformatics and Computational Biology. 10(5):1250010, 2012. | ||
| + | - Sharma A, Imoto S, Miyano S. A top-r feature selection algorithm for microarray gene expression data. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 9(3): 754-64, 2012. | ||
| + | - Sharma A, Imoto S, Miyano S, Sharma V. Null space based feature selection method for gene expression data, International Journal of Machine Learning and Cybernetics. 3(4): 269-276, 2012. | ||
| + | - Wang L, Hurley D, Watkins W, Araki1 H, Tamada Y, Muthukaruppan A, Ranjard L, Derkac E, Imoto S, Miyano S, Crampin E, Print C. Cell cycle gene networks are associated with melanoma prognosis. PLoS One. 7(4): e34247, 2012. | ||
| + | - Yamamoto M, Yamaguchi R, Muanakata 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. | ||
| + | - 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, 2012. | ||
| + | - Yasuda T, Suzuki S, Nagasaki M, Miyano S. ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs. BMC Bioinformatics. 13(1):279, 2012. | ||
| + | - 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, 2012. | ||
| + | ===== 2011 ===== | ||
| + | - Chalkidis G, Nagasaki M, Miyano S. High performance hybrid functional Petri net simulations of biological pathway models on CUDA. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8 (6): 1545-1556, 2011. | ||
| + | - Fujita A, Sato JR, Demas MAA, Yamaguchi R, Shimamura T, Ferreira CE, Sogayar, MC, Miyano S. Inferring contagion in regulatory networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8(2):570-576, 2011. | ||
| + | - Hasegawa T, Yamaguchi R, Nagasaki M, Imoto S, Miyano S. Comprehensive pharmacogenomic pathway screening by data assimilation. Lecture Notes in Bioinformatics. 6674: 160-171, 2011. | ||
| + | - Hurley D, Araki H, Tamada Y, Dunmore B, Sanders D, Humphreys S, Affara M, Imoto S, Yasuda K, Tomiyasu Y, Tashiro K, Savoie C, Cho V, Smith S, Kuhara S, Miyano S, Charnock-Jones DS, Crampin EJ, Print CG. Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Res. 2011 Dec 6. [Epub ahead of print] | ||
| + | - Imoto S, Kojima K, Perrier E, Tamada Y, Miyano S. Searching optimal Bayesian network structure on constraint search space: super-structure approach. Lecture Notes in Computer Science. 6797: 210-218, 2011. | ||
| + | - Jeong E, Nagasaki M, Ueno K, Miyano S. Ontology-based instance data validation for high-quality curated biological pathways. BMC Bioinformatics. 12(Suppl 1): S8, 2011. | ||
| + | - Jeong E, Nagasaki M, Ikeda E, Saito A, Miyano S. CSO validator: improving manual curation workflow for biological pathways. Bioinformatics. 27(17): 2471-2472, 2011. | ||
| + | - Katayama K, Yamaguchi R, Imoto S, Tokunaga H, Imazu Y, Matuura K, K. Watanabe, Miyano S. Symbolic hierarchical clustering for visual analogue scale data. Smart Innovation, Systems and Technologies. 10: 799-805, 2011. | ||
| + | - 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. | ||
| + | - Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, Tanaka F, Shibata K, Suzuki A, Komune S, Miyano S, Mori M. Long non-coding RNA HOTAIR regulates Polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 2011 Aug 23. [Epub ahead of print] | ||
| + | - Koh CH, Nagasaki M, Saito A, Li C, Wong L, Miyano S. MIRACH: Efficient model checker for quantitative biological pathway models. Bioinformatics. 27(5): 734-735, 2011. | ||
| + | - Li C, Kuroyanagi K, Nagasaki M, Miyano S, Parameter estimation of biological pathways using data assimilation and model checking, Proceedings of the 2nd International Workshop on Biological Processes & Petri Nets (BioPPN2011). CEUR-WS. 724: 53-70, 2011. [[http://ceur-ws.org/Vol-724/paper5.pdf|Link]] | ||
| + | - Li C, Nagasaki M, Miyano S. Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension. Molecular BioSystems. 7(5):1576-1592, 2011. | ||
| + | - Matsuno H, Nagasaki M, Miyano S. Hybrid Petri net based modeling for biological pathway simulation. Natural Computing 10(3): 1099-1120, 2011. | ||
| + | - Nagasaki M, Saito A, Fujita A, Tremmel G, Ueno K, Ikeda E, Jeong E, Miyano S. Systems biology model repository for macrophage pathway simulation. Bioinformatics. 27 (11): 1591-1593, 2011. | ||
| + | - Osoda T, Miyano S. 2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope. J Cheminform. 3(1): 50, 2011. | ||
| + | - Osoda T, Miyano S. Noise-tolerant active learning algorithm. Proc. The 2011 International Conference on Data Mining. 10-14, 2011. | ||
| + | - Saito MM, Imoto S, Yamaguchi R, Miyano S, Higuchi T. Parallel agent-based simulator for influenza pandemic. Lecture Notes in Computer Science. 7068: 361-370, 2011. | ||
| + | - Saito MM, Imoto S, Yamaguchi R, Miyano S, Higuchi T. Estimation of macroscopic parameter in agent-based pandemic simulation. Proc. 13th International Conference on Information Fusion. 1-6, 2011. | ||
| + | - Sharma A, Imoto S, Miyano S. A top-r feature selection algorithm for microarray gene expression data. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2011 Nov 11. [Epub ahead of print] | ||
| + | - Sharma A, Koh CH, Imoto S, Miyano S. Strategy of finding optimal number of features on gene expression data. Electronic Letters. 47(8): 480-482, 2011. | ||
| + | - 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, 2011. | ||
| + | - Shiraishi U, Okada-Hatakeyama M, Miyano S. A rank-based statistical test for measuring synergistic effects between two gene sets. Bioinformatics. 27 (17): 2399-2405, 2011. | ||
| + | - Suzuki S, Yasuda T, Shiraishi Y, Miyano S, Nagasaki M. ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. BMC Bioinformatics. 12:S7, 2011. | ||
| + | - Tamada Y, Imoto S, Miyano S. Parallel algorithm for learning optimal Bayesian network structure. J Machine Learning Research. 12: 2437-2459, 2011. [[http://www.jmlr.org/papers/volume12/tamada11a/tamada11a.pdf|Link]] | ||
| + | - Tamada Y, Imoto S, Araki H, Nagasaki M, Print C, Charnock-Jones DS, 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(3): 683 - 697, 2011. | ||
| + | - 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: 40-52, 2011. [[http://www.jstage.jst.go.jp/article/gi/25/1/40/_pdf/-char/ja/|Link]] | ||
| + | - 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: 1172-1173, 2011. | ||
| + | - Yamaguchi K, Sakai M, Kim J, Tsunesumi SI, 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. | ||
| + | - 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. | ||
| + | - Yoshida K, Sanada M, Shiraishi Y, Nowak D, Nagata Y, Yamamoto R, Sato Y, Sato-Otsubo A, Kon A, Nagasaki M, Chalkidis G, Suzuki Y, Shiosaka M, Kawahata R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Ishiyama K, Mori H, Nolte F, Hofmann WK, Miyawaki S, Sugano S, Haferlach C, Koeffler HP, Shih LY, Haferlach T, Chiba S, Nakauchi H, Miyano S, Ogawa S. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature. 478(7367): 64-69, 2011. | ||
| + | ===== 2010 ===== | ||
| + | - Do JH, Nagasaki M, Miyano S, The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis. Biosystems. 100: 178-184, 2010. | ||
| + | - Fujimoto A, Nakagawa H, Hosono N, Nakano K, Abe G, 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. Nature Genetics. 42: 931–936, 2010. | ||
| + | - Fujita A, Kojima K, Patriota AG, Sato JR, Severino P, Miyano S. A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets. Bioinformatics. 26(18):2349-2351, 2010. | ||
| + | - Fujita A, Nagasaki M, Imoto S, Saito A, Ikeda E, Shimamura T, Yamaguchi R, Hayashizaki Y, Miyano S. Comparison of gene expression profiles produced by CAGE, illumina microarray and Real Time RT-PCR. Genome Informatics. 24: 56-68, 2010. | ||
| + | - Fujita A, Sato JR, Kojima K, Gomes LR, Sogayar MC, Miyano S. Identification of Granger causality between gene sets. J. Bioinformatics and Computational Biology. 8(4): 679–701, 2010. | ||
| + | - Fujita, A, Severino P, Sato JR, Miyano S. Granger causality in systems biology: modeling gene networks in time series microarray data using vector autoregressive models. Lecture Notes in Bioinformatics. 6268: 13-24, 2010. | ||
| + | - 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. | ||
| + | - International Cancer Genome Consortium, Hudson TJ. et al. International network of cancer genome projects. Nature. 464(7291):993-998, 2010. | ||
| + | - 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 10th International Symposium on Bioinformatics & Bioengineering. 253-258, 2010. | ||
| + | - Koh CH, Nagasaki M, Saito A, Wong L, Miyano S. DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinformatics. 26(14):1794-1796, 2010. | ||
| + | - 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. | ||
| + | - Kojima K, Nagasaki M, Miyano S. An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. BMC Bioinformatics. 11: 335, 2010. | ||
| + | - Kojima K, Perrier E, Imoto S, Miyano S. Optimal search on clustered structural constraint for learning Bayesian network structure. J. Machine Learning Research. 11: 285−310, 2010. | ||
| + | - Li C, Nagasaki M, Saito A, Miyano S. Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. BMC Systems Biology. 4:39, 2010. | ||
| + | - Miwa Y, Li C, Ge Q-W, Matsuno H, Miyano S. On determining delay time of transitions for Petri net based signaling pathways by introducing stochastic decision rules. In Silico Biol. 10: 0004, 2010. | ||
| + | - Miwa Y, Murakami Y, Ge Q-W, Li C, Matsuno H, Miyano, S. Delay time determination for the timed Petri net model of a signaling pathway based on its structural information. IEICE Trans. Fundamentals of Electronics, Communications and Computer Sciences. E93-A(12), 2717-2729, 2010. | ||
| + | - Nagasaki M, Saito A, Jeong E, Li C, Kojima K, Ikeda E, Miyano S. Cell Illustrator 4.0: A computational platform for systems biology. In Silico Biol. 10: 0002, 2010. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - Sato H, Nakada H, Yamaguchi R, Imoto S, Miyano S, Kami M. When should we intervene to control the 2009 influenza A(H1N1) pandemic? Euro Surveill. 7:15(1), pii: 19455, 2010. | ||
| + | - 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. | ||
| + | - Shimamura T, Imoto S, Nagasaki M, Yamauchi M, Yamaguchi R, Fujita A, Tamada Y, Gotoh N, Miyano S. Collocation-based sparse estimation for constructing dynamic gene networks. Genome Informatics. 24: 164-178, 2010. | ||
| + | - Tasaki S, Nagasaki M, Kozuka-Hata H, Semba K, Gotoh N, Hattori S, Inoue J, Yamamoto T, Miyano S, Sugano S, Oyama M. Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling. PLoS ONE. 5(11): e13926, 2010. | ||
| + | - Yamaguchi R, Imoto S, Miyano S. Network-based predictions and simulations by biological state space models: Search for drug mode of action. J. Computer Science and Technology. 25(1): 131-153, 2010. | ||
| + | - Yuji K, Matsumura T, Miyano S, Tsuchiya R, Kami M. Human papillomavirus vaccine coverage. Lancet. 376(9738):329-330, 2010. | ||
| ===== 2009 ===== | ===== 2009 ===== | ||
| ライン 282: | ライン 525: | ||
| - Hirokawa, S., Miyano, S. A note on the regularity of fuzzy languages. Memoirs of the Faculty of Science, Kyushu University, Ser. A. 32(1):61-66, 1978. | - Hirokawa, S., Miyano, S. A note on the regularity of fuzzy languages. Memoirs of the Faculty of Science, Kyushu University, Ser. A. 32(1):61-66, 1978. | ||
| - Miyano, S. On an automaton which recognizes a family of automata. Memoirs of the Faculty of Science, Kyushu University, Ser. A. 32(1):37-51, 1978. | - Miyano, S. On an automaton which recognizes a family of automata. Memoirs of the Faculty of Science, Kyushu University, Ser. A. 32(1):37-51, 1978. | ||
| - | + | ====== Book Chapter ====== | |
| - | + | - Imoto, S., Tamada, Y., Araki, H., Miyano, S. Computational Drug Target Pathway Discovery: A Bayesian Network Approach. in H. Lu, B. Schokop, H. Zhao (Eds.), Handbook of Computational Statistics: Statistical Bioinformatics, Springer. In press. | |
| + | - Fujita, A., Sato, J.R., Demasi, M.A.A., Miyano, S., Sogayar, M.C., Ferreira, C.E. An introduction to time-varying connectivity estimation for gene regulatory networks. Frank Emmert-Streib; Matthias Dehmer. (Org.). Medical Biostatistics for complex diseases. Weinheim, Germany: Wiley VCH Verlag, p.205-230, 2010. | ||
| + | - Mitou, N., Matsuno, H., Miyano, S., Inouye, S. Essential role of Ror gene in the interaction of feedback loops in mammalian circadian clocks. In press. | ||
| + | - Saito, A., Nagasaki, M., Miyano, S. Hybrid functional Petri net with extension for dynamic pathway modeling. In press. | ||
| + | - Imoto, S., Tamada, Y., Savoie, C.J., Miyano, S., Analysis of gene networks for drug target discovery and validation. Methods in Molecular Biology. 360:33-56, 2007. (Target Discovery and Validation, Volume 1, 33-56, 2007 (a volume of "Methods in Molecular Biology" series), Walker, J. and Sioud, M. (Eds.), Humana Press, USA.). | ||
| + | - Imoto, S., Miyano, S. Bayesian network approach to estimate gene networks. A. Mittal, A. Kassim and T. Tan (Eds.), Bayesian Network Technologies: Applications and Graphical Models, Idea Group Publishers, USA. 269-299, 2007. (Refereed book chapter). | ||
| + | - Nagasaki, M., Doi, A., Matsuno, H., Miyano, S. Computational modeling of biological processes with Petri net based architecture. In "Bioinformatics Technologies" (Y.P. Chen, ed). Springer Press. 179-243, 2005. | ||
| + | - Akutsu, T., Miyano, S. Selecting informative genes for cancer classification using gene expression data. Computational and Statistical Approaches to Genomics (W. Zhang and I. Shmulevich, Eds.). Kluwer Academic Pub. 79-92, 2002. | ||
| + | - Akutsu, T., Miyano, S. Selecting informative genes for cancer classification using gene expression data. Computational and Statistical Approaches to Genomics (W. Zhang and I. Shmulevich eds.). Kluwer Academic Pub. 79-92, 2002. | ||
| + | - Miyano, S. Genome Informatics: New Frontiers of Computer Science and Biosciences. Cooperative Databases and Applications (Advances Database Research and Development Series Vol. 7). edited by Kambayashi, Y. and Yokota, K. (World Scientific), 12-21, 1997. | ||
| ライン 298: | ライン 549: | ||
| - 宮野 悟．並列アルゴリズム―理論と設計．近代科学社，1993. | - 宮野 悟．並列アルゴリズム―理論と設計．近代科学社，1993. | ||
| - 有川節夫，宮野 悟．オートマトンと計算可能性．培風館，1986. | - 有川節夫，宮野 悟．オートマトンと計算可能性．培風館，1986. | ||
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| ====== Editions ====== | ====== Editions ====== | ||
| - | - Brazma, A., Miyano, S., Akutsu, T. Proceedings of the 6th Asia-Pacific Bioinformatics Conference (APBC 2008).Imperial College Press, 2008. [[http://www.worldscibooks.com/lifesci/p544.html|]] | + | - Ferreira, C.E., Miyano, S., Stadler, P.F. (Eds.) Advances in Bioinformatics and Computational Biology, Springer, 2010. |
| - | - Knapp, E.-W., Benson, G., Holzhütter, H.-G., Kanehisa, M., Miyano, S. (Eds.) Genome Informatics. 20, 2008. [[http://www.jsbi.org/modules/journal1/index.php/GI20.html|]] | + | - DeLisi, C., Kanehisa, M., Miyano, S., Mohr, S., Wallach, I. (Eds.) Genome Informatics. 22. Imperial College Press, London, 2009. |
| - | - Miyano, S., DeLisi, C., Holzhütter, H.-G., Kanehisa, M. (Eds.) Genome Informatics. 18, 2007. [[http://www.jsbi.org/modules/journal1/index.php/GI18.html|]] | + | - Brazma, A., Miyano, S., Akutsu, T. Proceedings of the 6th Asia-Pacific Bioinformatics Conference (APBC 2008).Imperial College Press, 2008. [[http://www.worldscibooks.com/lifesci/p544.html|Link]] |
| - | - Sakakibara, Y., Smith, T.F., Kanehisa, M., Miyano, S., Takagi, T. (Eds.) Genome Informatics. 17(2), 2006. [[http://www.jsbi.org/modules/journal1/index.php/GI17_2.html|]] | + | - Knapp, E.-W., Benson, G., Holzhütter, H.-G., Kanehisa, M., Miyano, S. (Eds.) Genome Informatics. 20, 2008. [[http://www.jsbi.org/modules/journal1/index.php/GI20.html|Link]] |
| - | - DeLisi, C., Kanehisa, M., Heinrich, R., Miyano, S. (Eds.) Genome Informatics. 17(1), 2006. [[http://www.jsbi.org/modules/journal1/index.php/GI17_1.html|]] | + | - Miyano, S., DeLisi, C., Holzhütter, H.-G., Kanehisa, M. (Eds.) Genome Informatics. 18, 2007. [[http://www.jsbi.org/modules/journal1/index.php/GI18.html|Link]] |
| + | - Sakakibara, Y., Smith, T.F., Kanehisa, M., Miyano, S., Takagi, T. (Eds.) Genome Informatics. 17(2), 2006. [[http://www.jsbi.org/modules/journal1/index.php/GI17_2.html|Link]] | ||
| + | - DeLisi, C., Kanehisa, M., Heinrich, R., Miyano, S. (Eds.) Genome Informatics. 17(1), 2006. [[http://www.jsbi.org/modules/journal1/index.php/GI17_1.html|Link]] | ||
| - Miyano, S. (Ed.) Special RECOMB 2005 Issue. J. Comp. Biol. 13(2), 2006. | - Miyano, S. (Ed.) Special RECOMB 2005 Issue. J. Comp. Biol. 13(2), 2006. | ||
| - | - Heinrich, R., Mamitsuka, H., Kanehisa, M., Miyano, S., Takagi, T. (Eds.). Genome Informatics 16(2), 2005. [[http://www.jsbi.org/modules/journal1/index.php/GI16_2.html|]] | + | - Heinrich, R., Mamitsuka, H., Kanehisa, M., Miyano, S., Takagi, T. (Eds.). Genome Informatics 16(2), 2005. [[http://www.jsbi.org/modules/journal1/index.php/GI16_2.html|Lionk]] |
| - | - Heinrich, T., DeLisi, C., Kanehisa, M., Miyano, S. (Eds.). Genome Informatics 16(1), 2005. [[http://www.jsbi.org/modules/journal1/index.php/GI16_1.html|]] | + | - Heinrich, T., DeLisi, C., Kanehisa, M., Miyano, S. (Eds.). Genome Informatics 16(1), 2005. [[http://www.jsbi.org/modules/journal1/index.php/GI16_1.html|Link]] |
| - | - Miyano, S., Mesirov, J.P., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M.S. (Eds.) Proc. 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), Lecture Notes in Bioinformatics (Springer). Vol. 3500, 2005. [[http://www.springer.com/computer/foundations/book/978-3-540-25866-7| ]] | + | - Miyano, S., Mesirov, J.P., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M.S. (Eds.) Proc. 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), Lecture Notes in Bioinformatics (Springer). Vol. 3500, 2005. [[http://www.springer.com/computer/foundations/book/978-3-540-25866-7|Link]] |
| - | - Akutsu, T., Brusic, V., Miyano, S., Takagi, T., Kanehisa, M. (Eds.) Genome Informatics. 15(2), 2004. [[http://www.jsbi.org/modules/journal1/index.php/GI15_2.html|]] | + | - Akutsu, T., Brusic, V., Miyano, S., Takagi, T., Kanehisa, M. (Eds.) Genome Informatics. 15(2), 2004. [[http://www.jsbi.org/modules/journal1/index.php/GI15_2.html|Link]] |
| - | - Mamitsuka, H., Smith, T.F., Holzhütter, H-G., Kanehisa, M., DeLisi, C., Heinrich, R, Miyano, S. (Eds.). Genome Informatics. 15(1), 2004. [[http://www.jsbi.org/modules/journal1/index.php/GI15_1.html|]] | + | - Mamitsuka, H., Smith, T.F., Holzhütter, H-G., Kanehisa, M., DeLisi, C., Heinrich, R, Miyano, S. (Eds.). Genome Informatics. 15(1), 2004. [[http://www.jsbi.org/modules/journal1/index.php/GI15_1.html|Link]] |
| - | - Gribskov, M., Kanehisa, M., Miyano, S., Takagi, T. (Eds.). Genome Informatics. 14, 2003. [[http://www.jsbi.org/modules/journal1/index.php/GI14.html|]] | + | - Gribskov, M., Kanehisa, M., Miyano, S., Takagi, T. (Eds.). Genome Informatics. 14, 2003. [[http://www.jsbi.org/modules/journal1/index.php/GI14.html|Link]] |
| - | - Lathrop, R., Nakai, K., Miyano, S., Takagi, T., Kanehisa, M. (Eds.). Genome Informatics. 13, 2002. [[http://www.jsbi.org/modules/journal1/index.php/GI13.html|]] | + | - Lathrop, R., Nakai, K., Miyano, S., Takagi, T., Kanehisa, M. (Eds.). Genome Informatics. 13, 2002. [[http://www.jsbi.org/modules/journal1/index.php/GI13.html|Link]] |
| - | - Matsuda, H., Miyano, S., Takagi, T., Wong, L. (Eds.) Genome Informatics. 12, 2001. [[http://www.jsbi.org/modules/journal1/index.php/GI12.html|]] | + | - Matsuda, H., Miyano, S., Takagi, T., Wong, L. (Eds.) Genome Informatics. 12, 2001. [[http://www.jsbi.org/modules/journal1/index.php/GI12.html|Link]] |
| - | - Dunker, A.K., Konagaya, A., Miyano, S., Takagi, T. (Eds.) Genome Informatics. 11, 2000. [[http://www.jsbi.org/modules/journal1/index.php/GI11.html|]] | + | - Dunker, A.K., Konagaya, A., Miyano, S., Takagi, T. (Eds.) Genome Informatics. 11, 2000. [[http://www.jsbi.org/modules/journal1/index.php/GI11.html|Link]] |
| - | - Asai, K., Miyano, S., Takagi, T. (Eds.) Genome Informatics. 10, 1999. [[http://www.jsbi.org/modules/journal1/index.php/GI10.html|]] | + | - Asai, K., Miyano, S., Takagi, T. (Eds.) Genome Informatics. 10, 1999. [[http://www.jsbi.org/modules/journal1/index.php/GI10.html|Link]] |
| - | - Miyano, S., Takagi, T. (Eds.) Genome Informatics. 9, 1998. [[http://www.jsbi.org/modules/journal1/index.php/GI09.html|]] | + | - Miyano, S., Takagi, T. (Eds.) Genome Informatics. 9, 1998. [[http://www.jsbi.org/modules/journal1/index.php/GI09.html|Link]] |
| - | - Miyano, S., Takagi, T. (Eds.) Genome Informatics. 8, 1997. [[http://www.jsbi.org/modules/journal1/index.php/GI08.html|]] | + | - Miyano, S., Takagi, T. (Eds.) Genome Informatics. 8, 1997. [[http://www.jsbi.org/modules/journal1/index.php/GI08.html|Link]] |
| - | - Akutsu, T., Asai, K., Hagiya, M., Kuhara, S., Miyano, S. and Nakai, K. (Eds.) Genome Informatics. 7, 1996. [[http://www.jsbi.org/modules/journal1/index.php/GI06.html|]] | + | - Akutsu, T., Asai, K., Hagiya, M., Kuhara, S., Miyano, S. and Nakai, K. (Eds.) Genome Informatics. 7, 1996. [[http://www.jsbi.org/modules/journal1/index.php/GI06.html|Link]] |
| - | - Asano, T., Igarashi, Y., Nagamochi, H., Miyano, S., Suri, S. Proc. 7th International Symposium on Algorithms and Computation (ISAAC '96), Lecture Notes in Computer Science. Vol. 1178, 1996. [[http://www.springer.com/computer/foundations/book/978-3-540-62048-8| ]] | + | - Asano, T., Igarashi, Y., Nagamochi, H., Miyano, S., Suri, S. Proc. 7th International Symposium on Algorithms and Computation (ISAAC '96), Lecture Notes in Computer Science. Vol. 1178, 1996. [[http://www.springer.com/computer/foundations/book/978-3-540-62048-8|Link]] |
| - | - Hagiya, M., Miyano, S., Nakai, K., Suyama, A., Yokomori, T., Takagi, T. (Eds.) Genome Informatics. 6, 1995. [[http://www.jsbi.org/modules/journal1/index.php/GI06.html|]] | + | - Hagiya, M., Miyano, S., Nakai, K., Suyama, A., Yokomori, T., Takagi, T. (Eds.) Genome Informatics. 6, 1995. [[http://www.jsbi.org/modules/journal1/index.php/GI06.html|Link]] |
| - | - Miyano, S., Akutsu, T., Imai, H., Gotoh, O., Takagi, T. (Eds.) Genome Informatics. 5, 1994. [[http://www.jsbi.org/modules/journal1/index.php/GI05.html|]] | + | - Miyano, S., Akutsu, T., Imai, H., Gotoh, O., Takagi, T. (Eds.) Genome Informatics. 5, 1994. [[http://www.jsbi.org/modules/journal1/index.php/GI05.html|Link]] |
| - | - Takagi, T., Imai, H., Miyano, S., Mitaku, S., Kanehisa, M. (Eds.) Genome Informatics. 4, 1993. [[http://www.jsbi.org/modules/journal1/index.php/GI04.html|]] | + | - Takagi, T., Imai, H., Miyano, S., Mitaku, S., Kanehisa, M. (Eds.) Genome Informatics. 4, 1993. [[http://www.jsbi.org/modules/journal1/index.php/GI04.html|Link]] |
| ====== 編集 ====== | ====== 編集 ====== | ||
