[[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 [2012/02/17 19:59] mlabadm [Papers] |
publications [2017/07/27 14:50] (現在) superregulator [Papers] |
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| ライン 2: | ライン 2: | ||
| ====== Papers ====== | ====== Papers ====== | ||
| + | ===== 2017 ===== | ||
| + | - 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 | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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]. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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]. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - 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] | ||
| + | - 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. | ||
| + | - 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. | ||
| + | - Kurashige J, Hasegawa T, Niida A, Sugimachi K, Deng N, Mima K, Uchi R, Sawada G, Takahashi Y, Eguchi H, Inomata M, Kitano S, Fukagawa T, Sasako M, Sasaki H, Sasaki S, Mori M, Yanagihara K, Baba H, Miyano S, Tan P, Mimori K. Integrated Molecular Profiling of Human Gastric Cancer Identifies DDR2 as a Potential Regulator of Peritoneal Dissemination. Sci Rep. 6:22371, 2016. doi: 10.1038/srep22371. | ||
| + | - 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. | ||
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| + | - 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. | ||
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| + | ===== 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 ===== | ===== 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. | + | - Fujimori S, Hino K, Saito A, Miyano S, Miyamoto-Sato E. PRD: A protein-RNA interaction database. Bioinformation. 8(15):729-730, 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. | + | - 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 ===== | ===== 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. | - 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. | ||
| ライン 15: | ライン 221: | ||
| - 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. | - 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, 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. | + | - 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] | - 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. | - 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), 53-70, 2011. [[http://ceur-ws.org/Vol-724/paper5.pdf|Link]] | + | - 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. | - 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. | - Matsuno H, Nagasaki M, Miyano S. Hybrid Petri net based modeling for biological pathway simulation. Natural Computing 10(3): 1099-1120, 2011. | ||
| ライン 25: | ライン 231: | ||
| - Osoda T, Miyano S. Noise-tolerant active learning algorithm. Proc. The 2011 International Conference on Data Mining. 10-14, 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. 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. | + | - 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, 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. | - 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. | ||
| ライン 39: | ライン 245: | ||
| - 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. | - 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 ===== | ===== 2010 ===== | ||
| - | - 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. | + | - 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. |
| - | - 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. | + | - 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. |
| - | - Fujimoto, A., Nakagawa, H., Hosono, N., Nakano, K., Abe, G., Boroevich, K.A., 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. In press. [[http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.691.html|Link]] | + | - 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., 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. | + | - 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., 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., 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. | + | - 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. |
| - | - 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. | + | - 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. |
| - | - 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. | + | - International Cancer Genome Consortium, Hudson TJ. et al. International network of cancer genome projects. Nature. 464(7291):993-998, 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. | + | - 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. |
| - | - International Cancer Genome Consortium, Hudson, T.J. et al. International network of cancer genome projects. Nature. 464(7291):993-998, 2010. [[http://www.nature.com/nature/journal/v464/n7291/full/nature08987.html|Link]] | + | - 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. |
| - | - Jeong, E., Nagasaki, M., Ueno, K., Miyano, S. Ontology-based instance data validation for high-quality curated biological pathways. BMC Bioinformatics. In press. | + | - 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. |
| - | - 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. | + | - 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., 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, 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. |
| - | - 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. | + | - 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. |
| - | - 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]] | + | - 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. |
| - | - 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, 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. |
| - | - 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]] | + | - 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. |
| - | - 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]] | + | - 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., 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. |
| - | - 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. In press.[[http://bioinformatics.oxfordjournals.org/content/early/2010/10/19/bioinformatics.btq592.abstract.html?|Link]] | + | - 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. |
| - | - 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., 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. |
| - | - 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. |
| - | - 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. | + | - 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. |
| - | - 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. In press. | + | - Yuji K, Matsumura T, Miyano S, Tsuchiya R, Kami M. Human papillomavirus vaccine coverage. Lancet. 376(9738):329-330, 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): 13-153, 2010. | + | |
| - | - Yuji, K., Matsumura, T., Miyano, S., Tsuchiya, R., Kami, M. Human papillomavirus vaccine coverage. Lancet. 376(9738):329-330, 2010. | + | |
| ===== 2009 ===== | ===== 2009 ===== | ||
