システムがん

システム的統合理解に基づくがんの先端的診断、治療、予防法の開発

文部科学省科学研究費補助金 新学術領域研究 (複合領域:4201)
研究期間:平成22年度~平成26年度
[English]

 

研究成果

研究代表者&分担者の表記

  • 代表者:下線付き太線
  • 分担者:下線付き

論文 2015

  1. 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. doi: 10.1093/bioinformatics/btu593. Epub 2014 Sep 4. 2015 Jan 1.
  2. Dobashi Y, Tsubochi H, Matsubara H, Inoue J, Inazawa J, Endo S, Ooi A. Diverse involvement of isoforms and gene aberrations of Akt in human lung carcinomas. Cancer Sci. 106(6):772-781, 2015. doi: 10.1111/cas.12669. Epub 2015 May 8. 2015 Jun.
  3. Dumitriu B, Feng X, Townsley DM, Ueda Y, Yoshizato T, Calado RT, Yang Y, Wakabayashi Y, Kajigaya S, Ogawa S, Zhu J, Young NS. Telomere attrition and candidate gene mutations preceding monosomy 7 in aplastic anemia. Blood. 125(4):706-709, 2015. doi: 10.1182/blood-2014-10-607572. Epub 2014 Nov 18. 2015 Jan 22.
  4. Fujimoto A, Furuta M, Shiraishi Y, Nguyen H, Shigemizu D, Gotoh K, Kawakami Y, Nakamura T, Ueno M, Ariizumi S, Shibata T, Abe T, Boroevich K, Nakano K, Sasaki A, Kitada R, Maejima K, Tanaka H, Shibuya T, Ojima H, Shimada K, Hayami S, Shigekawa Y, Aikata H, Arihiro K, Ohdan H, Marubashi S, Yamada T, Ishikawa O, Kubo M, Hirano S, 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. Nature Comm. 6:6120, 2015. doi: 10.1038/ncomms7120. 2015 Jan 30.
  5. Garg M, Okamoto R, Nagata Y, Kanojia D, Venkatesan S, M TA, Braunstein GD, Said JW, Doan NB, Ho Q, Akagi T, Gery S, Liu LZ, Tan KT, Chng WJ, Yang H, Ogawa S, Koeffler HP. Establishment and characterization of novel human primary and metastatic anaplastic thyroid cancer cell lines and their genomic evolution over a year as a primagraft. J Clin Endocrinol Metab. 100(2):725-735, 2015. doi: 10.1210/jc.2014-2359. Epub 2014 Nov 3. 2015 Feb.
  6. Hakimi AA, Tickoo SK, Jacobsen A, Sarungbam J, Sfakianos JP, Sato Y, Morikawa T, Kume H, Fukayama M, Homma Y, Chen YB, Sankin AI, Mano R, Coleman JA, Russo P, Ogawa S, Sander C, Hsieh JJ, Reuter VE. TCEB1-mutated renal cell carcinoma: a distinct genomic and morphological subtype. Mod Pathol. 28(6):845-853, 2015. doi:10.1038/modpathol.2015.6. Epub 2015 Feb 13. 2015 Jun.
  7. Hasegawa T, Mori T, Yamaguchi R, Shimamura T, Miyano S, Imoto S, Akutsu T. Genomic data assimilation using a higher filtering technique for restoration of gene regulatory. BMC Syst Biol. 9(1):14, 2015. doi: 10.1186/s12918-015-0154-2. 2015 March 13.
  8. 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. 2015 Jun 4.
  9. 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. 101:198-202, 2015. doi: 10.1007/s12185-014-1701-0. Epub 2014 Nov 22. 2015 Feb.
  10. Hosoda F, Arai Y, Okada N, Shimizu H, Miyamoto M, Kitagawa N, Katai H, Taniguchi H, Yanagihara K, Imoto I, Inazawa J, Ohki M, Shibata T. Integrated genomic and functional analyses reveal glyoxalase I as a novel metabolic oncogene in human gastric cancer. Oncogene. 34(9):1196-1206, 2015. doi: 10.1038/onc.2014.57. Epub 2014 Mar 24. 2015 Feb 26.
  11. Hosokawa H, Kato M, Tohyama H, Tamaki Y, Endo Y, Kimura MY, Tumes DJ, Motohashi S, Matsumoto M, Nakayama KI, Tanaka T, Nakayama T. Methylation of Gata3 at Arg261 regulates transactivation of the Il5 gene in T helper 2 cells. J Biol Chem. 290(21):13095-13103, 2015. doi: 10.1074/jbc.M114.621524. Epub 2015 Apr 10. 2015 May 22.
  12. Huang D, Nagata Y, Grossmann V, Radivoyevitch T, Okuno Y, Nagae G, Hosono N, Schnittger S, Sanada M, Przychodzen B, Kon A, Polprasert C, Shen W, Clemente MJ, Phillips JG, Alpermann T, Yoshida K, Nadarajah N, Sekeres MA, Oakley K, Nguyen N, Shiraishi Y, Shiozawa Y, Chiba K, Tanaka H, Koeffler HP, Klein HU, Dugas M, Aburatani H, Miyano S, Haferlach C, Kern W, Haferlach T, Du Y, Ogawa S, Makishima H. BRCC3 mutations in myeloid neoplasms. Haematologica. 100(8):1051-1057, 2015. doi: 10.3324/haematol.2014.111989. Epub 2015 May 22. 2015 Aug.
  13. Inoue T, Yachida S, Kashiwagi H, Otani T, Ishimura K, Kushida Y, Okano K, Usuki H, Wakabayashi H, Suzuki Y. A case of Barett’s esophageal adenocarcinoma associated with heterotopic pancreas. Esophagus. doi: 10.1007/s10388-014-0479-8. First online: 20 December 2014.
  14. Ishino K, Kato T, Kato M, Shibata T, Watanabe M, Wakabayashi K, Nakagama H, Totsuka Y. Comprehensive DNA adduct analysis reveals pulmonary inflammatory response contributes to genotoxic action of magnetite nanoparticles. Int J Mol Sci. 16(2):3474-92. doi: 10.3390/ijms16023474. 2015 Feb 4.
  15. Iwakawa R, Kohno T, Totoki Y, Shibata T, Tsuchihara K, Mimaki S, Tsuta K, Narita Y, Nishikawa R, Noguchi M, Harris CC, Robles AI, Yamaguchi R, Imoto S, Miyano S, Totsuka H, Yoshida T, Yokota J. Expression and clinical significance of genes frequently mutated in small cell lung cancers defined by whole exome/RNA sequencing. Carcinogenesis. 36(6):616-621, 2015. doi: 10.1093/carcin/bgv026. Epub 2015 Apr 11. 2015 Jun.
  16. Kanamori M, Higa T, Sonoda Y, Murakami S, Dodo M, Kitamura H, Taguchi K, Shibata T, Watanabe M, Suzuki H, Shibahara I, Saito R, Yamashita Y, Kumabe T, Yamamoto M, Motohashi H, Tominaga T. Activation of the NRF2 pathway and its impact on the prognosis of anaplastic glioma patients. Neuro Oncol. 17(4):555-565, 2015. doi: 10.1093/neuonc/nou282. Epub 2014 Oct 10. 2015 Apr.
  17. 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. 101:411-416, 2015. doi: 10.1007/s12185-014-1711-y. Epub 2014 Nov 28. 2015 Apr.
  18. Kishikawa T, Otsuka M, Tan PS, Ohno M, Sun X, Yoshikawa T, Shibata C, Takata A, Kojima K, Takehana K, Ohishi M, Ota S, Noyama T, Kondo Y, Sato M, Soga T, Hoshida Y, Koike K. Decreased miR122 in hepatocellular carcinoma leads to chemoresistance with increased arginine. Oncotarget. 6:8339-8352, 2015. Published online 2015 Mar 21. 2015 Apr 10.
  19. Kobayashi S, Sato M, Kasakoshi T, Tsutsui T, Sugimoto M, Osaki M, Okada F, Igarashi K, Hiratake J, Homma T, Conrad M, Fujii J, Soga T, Bannai S, Sato H. Cystathionine is a novel substrate of cystine/glutamate transporter: implications for immune function. J Biol Chem. 290:8778-8788, 2015. doi: 10.1074/jbc.M114.625053. Epub 2015 Feb 20. 2015 Apr 3.
  20. Konno M, Ishii H, Koseki J, Tanuma N, Nishida N, Kawamoto K, Nishimura T, Nakata A, Matsui H, Noguchi K, Ozaki M, Noguchi Y, Shima H, Gotoh N, Nagano H, Doki Y, Mori M. Pyruvate kinase M2, but not M1, allele maintains immature metabolic states of murine embryonic stem cells. Regenerative Therapy. 1:63-71, 2015. doi:10.1016/j.reth.2015.01.001. Available online 9 March 2015. June 2015.
  21. Koseki J, Colvin H, Fukusumi T, Nishida N, Konno M, Kawamoto K, Tsunekuni K, Matsui H, Doki Y, Mori M, Ishii H. Mathematical analysis predicts imbalanced IDH1/2 expression associates with 2-HG-inactivating β-oxygenation pathway in colorectal cancer. Int J Oncol. 46(3):1181-1191, 2015. doi: 10.3892/ijo.2015.2833. Epub 2015 Jan 12. 2015 Mar.
  22. 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. 29:126-136, 2015. doi: 10.1038/leu.2014.144. Epub 2014 Apr 30. 2015 Jan.
  23. Lo PH, Tanikawa C, Katagiri T, Nakamura Y, Matsuda K. Identification of novel epigenetically inactivated gene, PAMR1 in breast carcinoma. Oncol Rep. 33(1):267-73, 2015. doi: 10.3892/or.2014.3581. Epub 2014 Nov 3. 2015 Jan.
  24. 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. 2015 Jan 14.
  25. Matsuda Y, Ishiwata T, Yachida S, Suzuki A, Hamashima Y, Hamayasu H, Yoshimura H, Honma N, Aida J, Takubo K, Arai T. Clinicopathological features of 15 occult and 178 clinical pancreatic ductal adenocarcinomas in 8339 autopsied elderly patients. Pancreas. 2015 in press.
  26. Miya F, Kato M, Shiohama S, Okamoto N, Saitoh S, Yamasaki M, Shigemizu D, Abe T, Morizono T, Boroevich KA, Kosaki K, Kanemura Y, Tsunoda T. A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations. Sci Rep. 5:9331. doi: 10.1038/srep09331. 2015 Mar 19.
  27. Molenaar RJ, Thota S, Nagata Y, Patel B, Clemente M, Hirsh C, Viny AD, Hosano N, Bleeker FE, Meggendorfer M, Alpermann T, Shiraishi Y, Chiba K, Tanaka H, van Noorden CJ, Radivoyevitch T, Carraway H, 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. doi: 10.1038/leu.2015.91. [Epub ahead of print] 2015 Apr 3.
  28. Nakata A, Yoshida R, Yamaguchi R, Yamauchi M, Tamada Y, Fujita A, Shimamura T, Imoto S, Higuchi T, Nomura M, Kimura T, Nokihara H, Higashiyama M, Kondoh K, Nishihara H, Tojo A, Yano S, Miyano S, Gotoh N. Elevated β-catenin pathway as a novel target for patients with resistance to EGF receptor targeting drugs. Sci Rep. 5:13076, 2015. doi: 10.1038/srep13076. 2015 Aug 13.
  29. Nowak D, Liem NL, Mossner M, Klaumunzer M, Papa RA, Nowak V, Jann JC, Akagi T, Kawamata N, Okamoto R, Thoennissen NH, Kato M, Sanada M, Hofmann WK, Ogawa S, Marshall GM, Lock RB, Koeffler HP. Variegated clonality and rapid emergence of new molecular lesions in xenografts of acute lymphoblastic leukemia are associated with drug resistance. Exp Hematol. 43(1):32-43, e1-35, 2015. doi: 10.1016/j.exphem.2014.09.007. Epub 2014 Oct 29. 2015 Jan.
  30. 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. doi: 10.1089/cmb.2014.0197. Epub 2015 Jan 28. 2015 Feb.
  31. 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. Epub 2015 Apr 23. 2015 May 11.
  32. Saito M, Shimada Y, Shiraishi K, Sakamoto H, Tsuta K, Totsuka H, Chiku S, Ichikawa H, Kato M, Watanabe S, Yoshida T, Yokota J, Kohno T. Development of lung adenocarcinomas with exclusive dependence on oncogene fusions. Cancer Res. 75(11):2264-2271. doi: 10.1158/0008-5472.CAN-14-3282. Epub 2015 Apr 8. 2015 Jun 1.
  33. Saloura V, Cho HS, Kyiotani K, Alachkar H, Zuo Z, Nakakido M, Tsunoda T, Seiwert T, Lingen M, Licht J, Nakamura Y, Hamamoto R. WHSC1 promotes oncogenesis through regulation of NIMA-related kinase-7 in squamous cell carcinoma of the head and neck. Mol Cancer Res. 13(2):293-304, 2015. doi: 10.1158/1541-7786.MCR-14-0292-T. Epub 2014 Oct 3. 2015 Feb.
  34. 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. Nat Commun. 6:7557, 2015. doi: 10.1038/ncomms8557. 2015 Jul 3.
  35. Shibayama Y, Fujimori T, Nguyen G, Hirose Y, Totsune K, Ichihara A, Kitada K, Nakano D, Kobori H, Kohno M, Masaki T, Suzuki Y, Yachida S, Nishiyama A. (Pro)renin receptor is crucial for Wnt/ß-catenin-dependent genesis of pancreatic ductal adenocarcinoma. Sci Rep. 5:8854, 2015. doi: 10.1038/srep08854. 2015 Mar 9.
  36. 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. Epub 2015 Apr 21. 2015 Jul.
  37. 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. Nat Genet. 47(5):458-468, 2015. doi: 10.1038/ng.3273. Epub 2015 Apr 13. 2015 May.
  38. 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. Epub 2015 Jan 28. 2015 May.
  39. Takai E, Yachida S. Genetic alterations in pancreatic cancer and their relevance to therapy. World J Gastroenterol. 2015 in press.
  40. Takenaka M, Saito M, Iwakawa R, Yanaihara N, Saito M, Kato M, Ichikawa H, Shibata T, Yokota J, Okamoto A, Kohno T. Profiling of actionable gene alterations in ovarian cancer by targeted deep sequencing. Int J Oncol. 46(6):2389-2398, 2015. doi: 10.3892/ijo.2015.2951. Epub 2015 Apr 3. 2015 Jun.
  41. Tanaka I, Osada H, Fujii M, Fukatsu A, Hida T, Horio Y, Kondo Y, Sato A, Hasegawa Y, Tsujimura T, Sekido Y. LIM-domain protein AJUBA suppresses malignant mesothelioma cell proliferation via Hippo signaling cascade. Oncogene. 34(1):73-83, 2015. doi: 10.1038/onc.2013.528. Epub 2013 Dec 16. 2015 Jan 2.
  42. van Thuijl HF, Mazor T, Johnson BE, Fouse SD, Aihara K, Hong C, Malmström A, Hallbeck M, Heimans JJ, Kloezeman JJ, Stenmark-Askmalm M, Lamfers ML, Saito N, Aburatani H, Mukasa A, Berger MS, Söderkvist P, Taylor BS, Molinaro AM, Wesseling P, Reijneveld JC, Chang SM, Ylstra B, Costello JF. Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment. Acta Neuropathol. 129(4):597-607, 2015. doi: 10.1007/s00401-015-1403-6. Epub 2015 Feb 28. 2015 Apr.
  43. 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. pii: haematol.2015.127092. [Epub ahead of print] 2015 May 28.
  44. 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. Epub 2014 Nov 25. 2015 Mar.
  45. Yamaguchi K, Komura M, Yamaguchi R, Imoto S, Shimizu E, Kasuya S, Shibuya T, Hatakeyama S, Takahashi N, Ikenoue T, Hata K, Tsurita G, Shinozaki M, Suzuki Y, Sugano S, Miyano S, Furukawa Y. Detection of APC mosaicism by next-generation sequencing in an FAP patient. J Hum Genet. 60(5):227-231, 2015. doi: 10.1038/jhg.2015.14. Epub 2015 Feb 26. 2015 May.
  46. 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. [Epub ahead of print] 2015 Sep 2.
  47. 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. Epub 2015 Mar 7. 2015 Apr.
  48. Yanai A, Inoue N, Yagi T, Nishimukai A, Miyagawa Y, Murase K, Imamura M, Enomoto Y, Takatsuka Y, Watanabe T, Hirota S, Sasa M, Katagiri T, Miyoshi Y. Activation of mTOR/S6K But Not MAPK Pathways Might Be Associated With High Ki-67, ER+, and HER2- Breast Cancer. Clin Breast Cancer. 15(3):197-203, 2015. doi: 10.1016/j.clbc.2014.12.002. Epub 2014 Dec 24. 2015 Jun.
  49. 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. doi: 10.1056/NEJMoa1414799. 2015 Jul 2.

論文 2014

  1. Adam J, Yang M, Soga T, and Pollard PJ. Rare insights into cancer biology. Oncogene, 33(20), 2547-2556, 2014. doi: 10.1038/onc.2013.222
  2. Aihara K, Mukasa A, Gotoh K, Saito K, Nagae G, Tsuji S, Tatsuno K, Yamamoto S, Takayanagi S, Narita Y, Shibui S, Aburatani H, Saito N. H3F3A K27M mutations in thalamic gliomas from young adult patients. Neuro Oncol 16(1):140-6, 2014.
  3. Arai Y, Tototki Y, Hosoda F, Shirota T, Hama N, Nakamura H, Ojima H, Furuta K, Shimada K, Okusaka T, Kosuge T, Shibata T. FGFR2 tyrosine kinase fusions define a unique molecular subtype of cholangiocarcinoma. Hepatology, 59(4):1427-1434, 2014.
  4. Arima C, Kajino T, Tamada Y, Imoto S, ShimadaY, 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 (in press).
  5. Becker H, Yoshida K, Blagitko-Dorfs N, Claus R, Pantic M, Abdelkarim M, Niemoller C, Greil C, Hackanson B, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Dohner K, Schnittger S, Henneke P, Niemeyer CM, Flotho C, Pfeifer D, Ogawa S, Lubbert M. Tracing the development of acute myeloid leukemia in CBL syndrome. Blood, 2014. 10.1182/blood-2013-10-533844
  6. Chew SH, Okazaki Y, Nagai H, Misawa N, Akatsuka S, Yamashita K, Jiang L, Yamashita Y, Noguchi M, Hosoda K, Sekido Y, Takahashi T, Toyokuni S. Cancer-promoting role of adipocytes in asbestos-induced mesothelial carcinogenesis through dysregulated adipocytokine production. Carcinogenesis 35:164-172, 2014.
  7. Dobashi Y, Sato E, Oda Y, Inazawa J, Ooi A. Significance of Akt activation and AKT gene increases in soft tissue tumors. Hum Pathol. 45:127-36. 2014
  8. Echizen K, Nakada M, Hayashi T, Sabit H, Furuta T, Nakai M, Koyama-Nasu R, Nishimura Y, Taniue K, Morishita Y, Hirano S, Terai K, Todo T, Ino Y, Mukasa A, Takayanagi S, Ohtani R, Saito N, Akiyama T. PCDH10 is required for the tumorigenicity of glioblastoma cells. Biochem Biophys Res Commun 444(1):13-8, 2014.
  9. Edagawa M, J Kawauchi J, Hirata M, Goshima H, M Inoue M, Okamoto T, A Murakami A, Maehara Y, Kitajima S. Role of ATF3 for ER stress-induced sensitization of p53-deficient human colon cancer cells to TRAIL-mediated apoptosis through upregulation of DR5 by zerumbone and celecoxib. J Biol Chem. 2014 Jun 17. pii: jbc.M114.558890. [Epub ahead of print]
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  11. Fujinami D, Matsumoto M, Noguchi T, Sonomoto K, Kohda D. Structural elucidation of an asparagine-linked oligosaccharide from the hyperthermophilic archaeon, Pyrococcus furiosus. Carbohydr Res. 387: 30-36, 2014. doi: 10.1016/j.carres.2014.01.021.
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論文 2013

  1. Adam J, Yang M, Bauerschmidt C, Kitagawa M, O’Flaherty L, Maheswaran P, O¨ zkan G, Sahgal N, Baban D, Kato K, Saito K, Iino K, Igarashi K, Stratford M, Pugh C, Tenant D, Ludwig C, Davies B, Ratcliffe PJ, El-Bahrawy M, Ashrafian H, Soga T, Pollard PJ. A Role for Cytosolic Fumarate Hydratase in Urea Cycle Metabolism and Renal Neoplasia. Cell Rep. 3(5), 1440-1448, 2013. DOI:10.1016/j.celrep.2013.04.006
  2. Afiahayati, Sato K, Sakakibara Y. An extended genovo metagenomic assembler by incorporating paired-end information. PeerJ, 1(20): e196, 2013. doi: 10.7717/peerj.196
  3. Arafat K, Iratni R, Takahashi T, Parekh K, Al Dhaheri Y, Adrian TE, Attoub S. Inhibitory effects of salinomycin on cell survival, colony growth, migration, and invasion of human non-small cell lung cancer A549 and LNM35: Involvement of NAG-1. PLoS ONE. 8:e66931, 2013. DOI: 10.1371/journal.pone.0066931
  4. Asanuma S, Yamagishi M, Kawanami K, Nakano K, Sato-Otsubo A, Muto S, Sanada M, Yamochi T, Kobayashi S, Utsunomiya A, Iwanaga M, Yamaguchi K, Uchimaru K, Ogawa S, Watanabe T. Adult T-cell leukemia cells are characterized by abnormalities of Helios expression that promote T cell growth. Cancer Sci. 104(8):1097-1106, 2013. 10.1111/cas.12181
  5. Attoub S, Sperandio O, Raza H, Arafat K, Al-Salam S, Al Sultan MA, Al Safi M, Takahashi T, Adem A. Thymoquinone as an anticancer agent: evidence from inhibition of cancer cells viability and invasion in vitro and tumor growth in vivo. Fundam Clin Pharmacol. 27: 557-569, 2013. DOI:10.1111/j.1472-8206.2012.01056.x
  6. Attoub S, Arafat K, Gelaude A, Sultan MAA, Bracke M, Collin, P, Takahashi T, Adrian, T, De Wever O. Frondoside A suppressive effects on lung cancer survival, tumor growth, angiogenesis, invasion, and metastasis. PLoS ONE 8:e53087, 2013. DOI: 10.1371/journal.pone.0053087.
  7. 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, Prebet T, Vey N, Legentil M, Duffourd Y, de Botton S, Preudhomme C, Birnbaum D, Bernard OA, Ogawa S, Fontenay M, Kosmider O. BCOR and BCORL1 mutations in myelodysplastic syndromes and related disorders. Blood. 122(18):3169-3177, 2013. 10.1182/blood-2012-11-469619
  8. Endo H, Muramatsu T, Furuta M, Uzawa N, Pimkhaokham A, Amagasa T, Inazawa J, Kozaki K. Potential of tumor-suppressive miR-596 targeting LGALS3BP as a therapeutic agent in oral cancer. Carcinogenesis. 34:560-9. 2013
  9. Fujiwara K, Ghosh S, Liang P, Morien E, Soma M, Nagase H. Genome-wide screening of aberrant DNA methylation which associated with gene expression in mouse skin cancers. Molecular Carcinogenesis 2013 Sep 24. doi: 10.1002/mc.22085. [Epub ahead of print] 
  10. 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:e60155. 2013
  11. Gomez-Segui 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. 10.1038/leu.2013.179
  12. Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N. Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods, 10(8):723-729, 2013.
  13. Han L, Pandian GN, Junetha S, Sato S, Anandhakumar C, Taniguchi J, Saha A, Bando T, Nagase H, Sugiyama H. A Synthetic Small Molecule Enforces Targeted Transcriptional Activation of Germ Cell Genes in a Human Somatic Cell. Angewandte Chemie 2013 9;52(50):13410-3. doi: 10.1002/anie.201306766. Epub 2013 Oct 18.
  14. Haraguchi N, Ishii H, Mimori K, Ohta K, Uemura M, Nishimura J, Hata T, Takemasa I, Mizushima T, Yamamoto H, Doki Y, Mori M. CD49f-positive cell population efficiently enriches colon cancer-initiating cells. Int J Oncol. 43(2):425-430, 2013.
  15. Harazono Y, Muramatsu T, Endo H, Uzawa N, Kawano T, Harada K, Inazawa J, Kozaki K. miR-655 is an EMT-suppressive microRNA targeting ZEB1 and TGFBR2. PLoS One. 8:e62757. 2013
  16. Hirano A, Yumimoto K, Tsunematsu R, Matsumoto M, Oyama M, Kozuka-Hata H, Nakagawa T, Lanjakornsiripan D, Nakayama KI, Fukada Y. FBXL21 regulates oscillation of the circadian clock through ubiquitination and stabilization of cryptochromes. Cell. 152(5): 1106-1118, 2013. doi: 10.1016/j.cell.2013.01.054.
  17. 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, 2013. 10.1182/blood-2013-06-507962
  18. Iguchi A, Fukuda N, Takahashi T, Watanabe T, Matsuda H, Nagase H, Bando T, Sugiyama H, Shimizu K. RNA binding properties of novel gene silencing pyrrole-imidazole polyamides. Biol Pharm Bull. 36(7):1152-8, 2013
  19. Ishiguro F, Murakami H, Mizuno T, Fujii M, Kondo Y, Usami N, Taniguchi T, Yokoi K, Osada H, Sekido Y. Membranous expression of activated leukocyte cell adhesion molecule contributes to poor prognosis and malignant phenotypes of non-small-cell lung cancer. J Surg Res. 179: 24-32, 2013.
  20. 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. 10.1038/ng.2731
  21. Kagawa Y, Matsumoto S, Kamioka, Y, Mimori, K, Naito, Y, Ishii T, Okuzaki D, Nishida N, Maeda S, Naito A, Kikuta J, Nishikawa K, Nishimura J, Haraguchi N, Takemasa I, Mizushima T, Ikeda M, Yamamoto H, Sekimoto M, Ishii H, Doki Y, Matsuda M, Kikuchi A, Mori M, Ishii M. Cell cycle-dependent Rho GTPase activity dynamically regulates cancer cell motility and invasion in vivo. PLoS One. 30;8(12):e83629. 2013.
  22. Kajita Y, Kato T Jr, Tamaki S, Furu M, Takahashi R, Nagayama S, Aoyama T, Nishiyama H, Nakamura E, Katagiri T, Nakamura Y, Ogawa O, Toguchida J. The transcription factor Sp3 regulates the expression of a metastasis-related marker of sarcoma, actin filament-associated protein 1-like 1 (AFAP1L1). PLoS One. 2013;8(1):e49709. doi: 10.1371/journal.pone.0049709. Epub 2013 Jan 9.
  23. Kalari S, Jung M, Kernstine KH, Takahashi T, *Pfeifer GP. The DNA methylation landscape of small cell lung cancer suggests a differentiation defect of neuroendocrine cells. Oncogene 32:3559-3568, 2013. doi: 10.1038/onc.2012.362.
  24. Kang D, Cho HS, Toyokawa G, Kogure M, Yamane Y, Iwai Y, Hayami S, Tsunoda T, Field HI, Matsuda K, Neal DE, Ponder BA, Maehara Y, Nakamura Y, Hamamoto R. The histone methyltransferase Wolf-Hirschhorn syndrome candidate 1-like 1 (WHSC1L1) is involved in human carcinogenesis. Genes Chromosomes Cancer, 52(2):126-139, 2013. doi: 10.1002/gcc.22012.
  25. Kano Y, Konno M, Ohta K, Haraguchi N, Nishikawa S, Kagawa Y, Hamabe A, Hasegawa, S, Ogawa H, Fukusumi T, Noguchi Y, Ozaki M, Kudo T, Sakai D, Satoh T, Ishii M, Mizohata E, Inoue T, Mori M, Doki Y, Ishii H., Jumonji/Arid1b (Jarid1b) protein modulates human esophageal cancer cell growth. Mol.Clin. Oncol. 1(4): 753-757,2013
  26. Kato M, Yasui N, Seki M, Kishimoto H, Sato-Otsubo A, Hasegawa D, Kiyokawa N, Hanada R, Ogawa S, Manabe A, Takita J, Koh K. Aggressive transformation of juvenile myelomonocytic leukemia associated with duplication of oncogenic KRAS due to acquired uniparental disomy. J Pediatr. 162(6):1285-1288, 1288 e1281, 2013. 10.1016/j.jpeds.2013.01.003
  27. Kawamata N, Moreilhon C, Saitoh T, Karasawa M, Bernstein BK, Sato-Otsubo A, Ogawa S, Raynaud S. Koeffler HP. Genetic differences between Asian and Caucasian chronic lymphocytic leukemia. International journal of oncology. 43(2):561-565, 2013. 10.3892/ijo.2013.1966
  28. Kawamoto K, Konno M, Nagano H, Nishikawa S, Tomimaru Y, Akita H, Hama N, Wada H, Kobayashi S, Eguchi H, Tanemura M, Ito T, Doki Y, Mori M, Ishii H. CD90- (Thy-1-) high selection enhances reprogramming capacity of murine adipose-derived mesenchymal stem cells. Dis. Markers. 35(5):573-579. 2013.
  29. Kawauchi J, Inoue M, Fukuda M, Yasukawa T, Conaway RC, Conaway JW, Aso T, Kitajima S. Transcriptional properties of mammalian Elongin A and its role in stress response. J Biol Chem. 288(34):24302-15. 2013 doi: 10.1074/jbc.M113.496703.
  30. 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. 10.1111/jth.12406
  31. Kogure M, Takawa M, Cho HS, Toyokawa G, Hayashi K, Tsunoda T, Kobayashi T, Daigo Y, Sugiyama M, Atomi Y, Nakamura Y, and Hamamoto R. Deregulation of the histone demethylase JMJD2A is involved in human carcinogenesis through regulation of the G1/S transition. Cancer Letters, 336(1):76-84, 2013. doi: 10.1016/j.canlet.2013.04.009.
  32. Kogure M, Takawa M, Saloura V, Sone K, Piao L, Ueda K, Ibrahim R, Tsunoda T, Sugiyama M, Atomi Y, Nakamura Y, and Hamamoto R. The Oncogenic Polycomb Histone Methyltransferase EZH2 Methylates Lysine 120 on Histone H2B and Competes Ubiquitination. Neoplasia, 15(11):1251-1261, 2013.
  33. 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. 2013 Oct;45(10):1232-7. doi: 10.1038/ng.2731. Epub 2013 Aug 18. PubMed PMID: 23955599
  34. Kon S, Minegishi N, Tanabe K, Watanabe T, Funaki T, Wong WF, Sakamoto D, Higuchi Y, Kiyonari H, Asano K, Iwakura Y, Fukumoto M, Osato M, Sanada M, Ogawa S, Nakamura T, Satake M. Smap1 deficiency perturbs receptor trafficking and predisposes mice to myelodysplasia. The Journal of clinical investigation. 123(3):1123-1137, 2013. 10.1172/JCI63711
  35. Konno M, Hamabe A, Hasegawa S, Ogawa H, Fukusumi T, Nishikawa S, Ohta K, Kano Y, Ozaki M, Noguchi Y, Sakai D, Kudoh T, Kawamoto K, Eguchi H, Satoh T, Tanemura M, Nagano H, Doki Y, Mori M, Ishii H. Adipose-derived mesenchymal stem cells and regenerative medicine. Dev. Growth Differ. 55(3):309-318, 2013.
  36. 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, Niimi G, Otsu M, Takahashi Y, Miyano S, Saito H, Kojima S, Ogawa S. ACTN1 Mutations Cause Congenital Macrothrombocytopenia. Am J Hum Genet. 92(3):431-438, 2013. 10.1016/j.ajhg.2013.01.015
  37. Kunishima S, Imai T, Kobayashi R, Kato M, Ogawa S, Saito H. Bernard-Soulier syndrome caused by a hemizygous GPIbbeta mutation and 22q11.2 deletion. Pediatr Int. 55(4):434-437, 2013. 10.1111/ped.12105
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  62. Ozaki T, Sugimoto H, Wu D, Nagase H, Nakagawara A. Runt-related transcription factor 2 (RUNX2) inhibits p53-dependent apoptosis through the collaboration with HDAC6 in response to DNA damage. Cell Death Dis., 4: e610, 2013 doi: 10.1038/cddis.2013.127
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  64. Roth FC, Mulder JE, Brien JF, Takahashi T, Massey TE. Cytotoxic interaction between amiodarone and desethylamiodarone in human peripheral lung epithelial cells. Chem Biol Interact. 204:135-139, 2013. DOI: 10.1016/j.cbi.2013.05.006
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  68. Shigemizu D, Fujimoto A, Akiyama S, Abe T, Nakano K, Boroevich KA, Yamamoto Y, Furuta M, Kubo M, Nakagawa H, and Tsunoda T. A practical method to detect SNVs and indels from whole genome and exome sequencing data. Scientific Reports, 3:2161, 2013. doi: 10.1038/srep02161.
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  72. Takada M, Higuchi T, Tozuka K, Takei H, Haruta M, Watanabe J, Kasai F, Inoue K, Kurosumi M, Miyazaki M, Sato-Otsubo A, Ogawa S, Kaneko Y. Alterations of the genes involved in the PI3K and estrogen-receptor pathways influence outcome in human epidermal growth factor receptor 2-positive and hormone receptor-positive breast cancer patients treated with trastuzumab-containing neoadjuvant chemotherapy. BMC cancer. 13:241, 2013. 10.1186/1471-2407-13-241
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論文 2012

  1. Abe H, Maeda D, Hino R, Otake Y, Isogai M, Ushiku AS, Matsusaka K, Kunita A, Ushiku T, Uozaki H, Tateishi Y, Hishima T, Iwasaki Y, Ishikawa S, Fukayama M. ARID1A expression loss in gastric cancer: pathway-dependent roles with and without Epstein-Barr virus infection and microsatellite instability. Virchows Arch. 461(4):367-377, 2012. doi: 10.1007/s00428-012-1303-2.
  2. Akamatsu S, Takahashi A, Takata R, Kubo M, Inoue T, Morizono T, Tsunoda T, Kamatani N, Haiman CA, Wan P, Chen GK, Le Marchand L, Kolonel LN, Henderson BE, Fujioka T, Habuchi T, Nakamura Y, Ogawa O, and Nakagawa H. Reproducibility, performance, and clinical utility of a genetic risk prediction model for prostate cancer in Japanese. PLoS One. 7(10):e46454, 2012. doi: 10.1371/journal.pone.0046454.
  3. Akamatsu S, Takata R, Haiman CA, Takahashi A, Inoue T, Kubo M, Furihata M, Kamatani N, Inazawa J, Chen GK, Le Marchand L, Kolonel LN, Katoh T, Yamano Y, Yamakado M, Takahashi H, Yamada H, Egawa S, Fujioka T, Henderson BE, Habuchi T, Ogawa O, Nakamura Y, Nakagawa H. Common variants at 11q12, 10q26 and 3p11.2 are associated with prostate cancer susceptibility in Japanese. Nat Genet. 44(4):426-429, 2012. doi: 10.1038/ng.1104.
  4. Akatsuka S, Yamashita Y, Ohara H, Liu Y-T, Izumiya M, Abe K, Ochiai M, Jiang L, Nagai H, Okazaki Y, Murakami H, Sekido Y, Arai E, Kanai Y, Hino O, Takahashi T, Nakagama H, Toyokuni S. Fenton reaction induced cancer in wild type rats recapitulates genomics alterations observed in human cancer. PLoS One. 7(8):e43403, 2012. doi: 10.1371/journal.pone.0043403.
  5. Arima Y, Hayashi H, Sasaki M, Hosonaga M, Goto TM, Chiyoda T, Kuninaka S, Shibata T, Ohata H, Nakagama H, Taya Y, Sata H. Induction of ZEB by inactivation of RB is a key determinant of the mesenchymal phenotype of breast cancer. J Bio Chem. 287:7896-7906, 2012. doi: 10.1074/jbc.M111.313759.
  6. Attoub S, Sperandio O, Raza H, Arafat K, Al-Salam S, Al Sultan MA, Al Safi M, Takahashi T, Adem A. Thymoquinone as an anticancer agent: evidence from inhibition of cancer cells viability and invasion in vitro and tumor growth in vivo. Fundam Clin Pharmacol. 2012. doi: 10.1111/j.1472-8206.2012.01056.x.
  7. Bai H, Inoue J, Kawano T, Inazawa J. A transcriptional variant of the LC3A gene is involved in autophagy and frequently inactivated in human cancers. Oncogene. 31:4397-4408, 2012.
  8. Cao K, Tanaka K, Komizu Y, Tamiya-Koizumi K, Murate T, Ueoka R, Kyogashima M, Usukura J, Takahashi T, Suzuki M. Hybrid liposomes affect cellular lipid constituents and caveolae structures. Bioorg Med Chem Lett. 22:1731-1733, 2012. doi: 10.1016/j.bmcl.2011.12.093.
  9. Chen LS, Saccone NL, Culverhouse RC, Bracci PM, Chen CH, Dueker N, Han Y, Huang H, Jin G, Kohno T, Ma JZ, Przybeck TR, Sanders AR, Smith JA, Sung YJ, Wenzlaff AS, Wu C, Yoon D, Chen YT, Cheng YC, Cho YS, David SP, Duan J, Eaton CB, Furberg H, Goate AM, Gu D, Hansen HM, Hartz S, Hu Z, Kim YJ, Kittner SJ, Levinson DF, Mosley TH, Payne TJ, Rao DC, Rice JP, Rice TK, Schwantes-An TH, Shete SS, Shi J, Spitz MR, Sun YV, Tsai FJ, Wang JC, Wrensch MR, Xian H, Gejman PV, He J, Hunt SC, Kardia SL, Li MD, Lin D, Mitchell BD, Park T, Schwartz AG, Shen H, Wiencke JK, Wu JY, Yokota J, Amos CI, Bierut LJ. Smoking and genetic risk variation across populations of European, Asian, and African American ancestry–a meta-analysis of chromosome 15q25. Genet Epidemiol. 36(4):340-351, 2012. doi: 10.1002/gepi.21627.
  10. Chiyoda T, Sugiyama N, Shimizu T, Naoe H, Kobayashi Y, Ishizawa J, Arima Y, Tsuda H, Ito M, Kaibuchi K, Aoki D, Ishihama Y, Saya H, Kuninaka S. LATS1/WARTS phosphorylates MYPT1 to counteract PLK1 and regulate mammalian mitotic progression. J Cell Biol. 197(5):625-641, 2012. doi: 10.1083/jcb.201110110.
  11. Cho HS, Toyokawa G, Daigo Y, Hayami S, Masuda K, Ikawa N, Yamane Y, Maejima K, Tsunoda T, Field HI, Kelly JD, Neal DE, Ponder BA, Maehara Y, Nakamura Y, and Hamamoto R. The JmjC domain-containing histone demethylase KDM3A is a positive regulator of the G(1)/S transition in cancer cells via transcriptional regulation of the HOXA1 gene. Int J Cancer. 131(3):E179-189, 2012. doi: 10.1002/ijc.26501.
  12. Dat LT, Matsuo T, Yoshimaru T, Kakiuchi S, Goto H, Hanibuchi M, Kuramoto T, Nshioka Y, Sone S, Katagiri T. Identification of genes potentially involved in bone-metastasis by genome-wide gene-expression profiling analysis of non-small cell lung cancer in mice. Int J Oncol. 40(5):1455-1469, 2012. doi: 10.3892/ijo.2012.1348.
  13. Dobashi Y, Kimura M, Matsubara H, Endo S, Inazawa J, Ooi A. Molecular alterations in AKT and its protein activation in human lung carcinomas. Hum Pathol. 43(12):2229-2240, 2012. doi: 10.1016/j.humpath.2012.03.015.
  14. Elgazzar S, Zembutsu H, Takahashi A, Kubo M, Aki F, Hirata K, Takatsuka Y, Okazaki M, Ohsumi S, Yamakawa T, Sasa M, Katagiri T, Miki Y, Nakamura Y. A genome-wide association study identifies a genetic variant in the SIAH2 locus associated with hormonal receptor-positive breast cancer in Japanese. J Hum Genet. 57(12):766-771, 2012. doi: 10.1038/jhg.2012.108.
  15. Elshazley M, Sato M, Hase T, Takeyama Y, Yamashita R, Yoshida K, Toyokuni S, Ishiguro F, Osada H, Sekido Y, Yokoi K, Usami N, Shames DS, Kondo M, Gazdar AF, Minna JD, Hasegawa Y. The circadian clock gene BMAL1 is a novel therapeutic target for malignant mesothelioma. Int J Cancer. 131(12):2820-2831, 2012. doi: 10.1002/ijc.27598.
  16. Endo M, Nakano M, Kadomatsu T, Fukuhara S, Kuroda H, Mikami S, Hato T, Aoi J, Horiguchi H, Miyata K, Odagiri H, Masuda T, Harada M, Horio H, Hishima T, Nomori H, Ito T Yamamoto Y, Minami T, Okada S, Takahashi T, Mochizuki N, Iwase H, Oike Y. A critical role for tumor cell-derived angiopoientin-like protein 2 in metastasis. Cancer Res. 72:1784-1794, 2012. doi: 10.1158/0008-5472.CAN-11-3878.
  17. Fujii M, Toyoda T, Nakanishi H, Yatabe Y, Sato A, Matsudaira Y, Ito H, Murakami H, Kondo Y, Kondo E, Hida T, Tsujimura T, Osada H, Sekido Y. TGF-β synergizes with defects in the Hippo pathway to stimulate human malignant mesothelioma growth. J Exp Med. 209:479-494, 2012. doi: 10.1084/jem.20111653.
  18. Fujimori S, Hirai N, Ohashi H, Masuoka K, Nishikimi A, Fukui Y, Washio T, Oshikubo T, Yamashita T, Miyamoto-Sato E. Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data. Sci Rep. 2:691, 2012. doi: 10.1038/srep00691.
  19. 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. doi: 10.1093/bioinformatics/bts289.
  20. Fujimori S, Hino K, Saito A, Miyano S, Miyamoto-Sato E. PRD: A protein-RNA interaction database. Bioinformation. 8(15):729-730, 2012. doi: 10.6026/97320630008729.
  21. Fujimoto A, Totoki Y, Abe T, Boroevich KA, Hosoda F, Nguyen HH, 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. Nat Genet. 44(7):760-764, 2012. doi: 10.1038/ng.2291.
  22. 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. doi: 10.1186/1752-0509-6-137.
  23. Fujiwara T, Hiramatsu M, Isagawa T, Ninomiya H, Inamura K, Ishikawa S, Ushijima M, Matsuura M, Jones MH, Shimane M, Nomura H, Ishikawa Y, Aburatani H. ASCL1-coexpression profiling but not single gene expression profiling defines lung adenocarcinomas of neuroendocrine nature with poor prognosis. Lung Cancer. 75(1):119-25, 2012. doi: 10.1016/j.lungcan.2011.05.028.
  24. Fukawa T, Ono M, Matsuo T, Uehara H, Miki T, Nakamura Y, Kanayama H, Katagiri T. DDX31 regulates the p53-HDM2 pathway and rRNA gene transcription through its interaction with NPM1 in renal cell carcinomas. Cancer Res. 72(22):5867-5877, 2012. doi: 10.1158/0008-5472.CAN-12-1645.
  25. Fukushima Y, Ota T, Mukasa A, Uozaki H, Kawai K, Saito N. Tumor-to-tumor metastasis: lung adenocarcinoma metastasizing to vestibular schwannoma suspected on preoperative [18F]-fluorodeoxyglucose positron emission tomography imaging. World Neurosurg. 78(5):553, 2012. doi: 10.1016/j.wneu.2011.10.031.
  26. Gaffney CJ, Oka T, Mazack V, Hilman D, Gat U, Muramatsu T, Inazawa J, Golden A, Carey DJ, Farooq A, Tromp G, Sudol M. Identification, basic characterization and evolutionary analysis of differentially spliced mRNA isoforms of human YAP1 gene. Gene. 509(2):215-22, 2012. doi: 10.1016/j.gene.2012.08.025.
  27. Helmy M, Sugiyama N, Tomita M, Ishihama Y. Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics. Genes Cells. 7(8):633-464, 2012. doi: 10.1111/j.1365-2443.2012.01615.x.
  28. Hirabayashi S, Flotho C, Moetter J, Heuser M, Hasle H, Gruhn B, Klingebiel T, Thol F, Schlegelberger B, Baumann I, Strahm B, Stary J, Locatelli F, Zecca M, Bergstraesser E, Dworzak M, van den Heuvel-Eibrink MM, De Moerloose B, Ogawa S, Niemeyer CM, Wlodarski MW. Spliceosomal gene aberrations are rare, coexist with oncogenic mutations, and are unlikely to exert a driver effect in childhood MDS and JMML. Blood. 119(11):e96-99, 2012. doi: 10.1182/blood-2011-12-395087.
  29. Honda S, Hayashi S, Nakane T, Imoto I, Kurosawa K, Mizuno S, Okamoto N, Kato M, Yoshihashi H, Kubota T, Nakagawa E, Goto Y, Inazawa J. The incidence of hypoplasia corpus callosum in patients with dup (X) (q28) involving MECP2 is associated with the location of distal breakpoints. Am J Med Genetics A. 158A:1292-303. 2012. doi: 10.1002/ajmg.a.35321.
  30. Hoshii T, Tadokoro Y, Naka K, Ooshio T, Muraguchi T, Sugiyama N, Soga T, Araki K, Yamamura K, Hirao A. mTORC1 is essential for leukemia propagation but not stem cell self-renewal. J Clin Invest. 122(6):2114-2129, 2012. doi: 10.1172/JCI62279.
  31. Hosokawa K, Katagiri T, Sugimori N, Ishiyama K, Sasaki Y, Seiki Y, Sato-Otsubo A, Sanada M, Ogawa S, Nakao S. Favorable outcome of patients who have 13q deletion: a suggestion for revision of the WHO 'MDS-U' designation. Haematologica. 97(12):1845-1849, 2012. doi: 10.3324/haematol.2011.061127.
  32. Hosono Y, Yamaguchi T, Mizutani E, Yanagisawa K, Arima C, Tomida S, Shimada Y, Hiraoka M, Kato S, Yokoi K, Suzuki M, Takahashi T. MYBPH, a transcriptional target of TTF-1, inhibits ROCK1, and reduces cell motility and metastasis. EMBO J. 31:481-493, 2012. doi: 10.1038/emboj.2011.416.
  33. Hosono Y, Usukura J, Yamaguchi T, Yanagisawa K, Suzuki M, Takahashi T. MYBPH inhibits NM IIA assembly via direct interaction with NMHC IIA and reduces cell motility. Biochem Biophys Res Commun. 428173-178, 2012. doi: 10.1016/j.bbrc.2012.10.036.
  34. 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.
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  110. Yamaguchi T, Yanagisawa K, Sugiyama R, Hosono Y, ShimadaY, Arima C, Kato S, Tomida S, Suzuki M, Osada H, Takahashi T. NKX2-1/TITF1/TTF-1-induced ROR1 is required to sustain EGFR survival signaling in lung adenocarcinoma. Cancer Cell. 21:348-361, 2012. doi: 10.1016/j.ccr.2012.02.008.
  111. Yamamoto S, Tsuda H, Honda K, Takano M, Tamai S, Imoto I, Inazawa J, Yamada T, Matsubara O. ACTN4 gene amplification and actinin-4 protein overexpression drive tumour development and histological progression in a high-grade subset of ovarian clear-cell adenocarcinomas. Histopathology. 60(7):1073-1083, 2012. doi: 10.1111/j.1365-2559.2011.04163.x.
  112. Yamamura T, Hikita J, Bleakley M, Hirosawa T, Sato-Otsubo A, Torikai H, Hamajima T, Nannya Y, Demachi-Okamura A, Maruya E, Saji H, Yamamoto Y, Takahashi T, Emi N, Morishima Y, Kodera Y, Kuzushima K, Riddell SR, Ogawa S, Akatsuka Y. HapMap SNP Scanner: an online program to mine SNPs responsible for cell phenotype. Tissue Antigens. 80(2):119-125, 2012. doi: 10.1111/j.1399-0039.2012.01883.x.
  113. 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. doi: 10.1371/journal.pone.0043923.
  114. 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. doi: 10.1186/1471-2105-13-279.
  115. Yasukawa T, Bhatt S, Takeuchi T, Kawauchi J, Takahashi H, Tsutsui A, Muraoka T, Inoue M, Tsuda M, Kitajima S, Conaway RC, Conaway JW, Trainor PA, Aso T. Transcriptional elongation factor elongin A regulates retinoic acid-induced gene expression during neuronal differentiation. Cell Rep. 2(5):1129-1136, 2012. doi: 10.1016/j.celrep.2012.09.031.
  116. Yoshida A, Ushiku T, Motoi T, Beppu Y, Fukayama M, Tsuda H, Shibata T. MDM2 and CDK4 immunohistochemical coexpression in high-grade osteosarcoma: correlation with a dedifferentiated subtype. Am J Surg Pathol. 36:423-431, 2012. doi: 10.1097/PAS.
  117. Yoshihara K, Tsunoda T, Shigemizu D, Fujiwara H, Hatae M, Fujiwara H, Masuzaki H, Katabuchi H, Kawakami Y, Okamoto A, Nogawa T, Matsumura N, Udagawa Y, Saito T, Itamochi H, Takano M, Miyagi E, Sudo T, Ushijima K, Iwase H, Seki H, Terao Y, Enomoto T, Mikami M, Akazawa K, Tsuda H, Moriya T, Tajima A, Inoue I, Tanaka K. Japanese Serous Ovarian Cancer Study Group. High-risk ovarian cancer based on 126-gene expression signature is uniquely characterized by down-regulation of antigen presentation pathway. Clin Cancer Res. 18(5):1374-1385, 2012. doi: 10.1158/1078-0432.CCR-11-2725.
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論文 2011

  1. Adam J, Hatipoglu E, O'Flaherty L, Ternette N, Sahgal N, Lockstone H, Baban D, Nye E, Stamp GW, Wolhuter K, Stevens M, Fischer R, Carmeliet P, Maxwell PH, Pugh CW, Frizzell N, Soga T, Kessler BM, El-Bahrawy M, Ratcliffe PJ, Pollard PJ. Renal cyst formation in Fh1-deficient mice is independent of the Hif/Phd pathway: roles for fumarate in KEAP1 succination and Nrf2 signaling. Cancer Cell. 20: 524-537, 2011.
  2. Arai E, Wakai-Ushijima S, Fujimoto H, Hosoda F, Shibata T, Kondo T, Yokoi S, Imoto I, Inazawa J, Hirohashi S, Kanai Y. Genome-wide DNA methylation profiles in renal tumors of various histological subtypes and non-tumorous renal tissues. Pathobiology. 78:1-9, 2011.
  3. Attoub S, Hassan AH, Vanhoecke B, Iratni R, Takahashi T, Gaben AM, Bracke M, Awad S, Kamalboor JA, Al Sultan MAH, Arafat K, Gespach C Petroianu G. Inhibition of cell survival, invasion, tumor growth and histone deacetylase activity by the dietary flavonoid luteolin in human epithelioid cancer cells. Eur J Pharmacol. 651: 18-25, 2011.
  4. 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):1545-56, 2011.
  5. Chung S, Nakagawa H, Uemura M, Piao L, Ashikawa K, Hosono N, Takata R, Akamatsu S, Kawaguchi T, Morizono T, Tsunoda T, Daigo Y, Matsuda K, Kamatani N, Nakamura Y, Kubo M. Association of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility. Cancer Sci. 102(1): 245-252, 2011.
  6. Cui R, Okada Y, Jang SG, Ku JL, Park JG, Kamatani Y, Hosono N, Tsunoda T, Kumar V, Tanikawa C, Kamatani N, Yamada R, Kubo M, Nakamura Y, Matsuda K. Common variant in 6q26-q27 is associated with distal colon cancer in an Asian population. Gut. 60(6): 799-805, 2011.
  7. Deng L, Shoji I, Ogawa W, Kaneda S, Soga T, Jiang DP, Ide YH, Hotta H. Hepatitis C virus infection promotes hepatic gluconeogenesis through an NS5A-mediated, FoxO1-dependent pathway. J Virol. 85: 8556-8568, 2011.
  8. 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.
  9. Furu M, Kajita Y, Nagayama S, Ishibe T, Shima Y, Uejima D, Aoyama T, Nakayama T, Nakamura T, Nakashima Y, Ikegawa M, Imoto S, Katagiri T, Nakamura Y, Toguchida J. Identification of AFAP1L1 as a prognostic marker for spindle cell sarcomas. Oncogene. 30: 4015-4025, 2011.
  10. Gotoh M, Arai E, Wakai-Ushijima S, Hiraoka N, Kosuge T, Hosoda F, Shibata T, Kondo T, Yokoi S, Imoto I, Inazawa J, Kanai Y. Diagnosis and prognostication of ductal adenocarcinomas of the pancreas based on genome-wide DNA methylation profiling by bacterial artificial chromosome array-based methylated CpG island amplification. J Biomed Biotechnol. 2011: 780836, 2011.
  11. Gurzov EN, Barthson J, Marhfour I, Ortis F, Naamane N, Estevel I, Gysemans C, Mathieu C, Kitajima S, Marchetti P, Orntoft T, Bakiri L, Wagner EF, Eiziril DL. Pancreatic b-cells activate a JunB/ATF3-dependent survival pathway during inflammation. Oncogene. 31:1723-32, 2011.
  12. Gustavsson C, Soga T, Wahlström E, Vesterlund M, Azimi A, Norstedt G, Tollet-Egnell P. Sex-dependent hepatic transcripts and metabolites in the development of glucose intolerance and insulin resistance in Zucker diabetic fatty rats. J Mol Endocrinol. 47(2):129-43, 2011.
  13. Hasebe T, Iwasaki M, Akashi-Tanaka S, Hojo T, Shibata T, Kinoshita T, Tsuda H. Important histologic outcome predictors for patients with invasive ductal carcinoma of the breast. Am J Surg Pathol. 35:1484-1497, 2011.
  14. Hasebe T, Iwasaki M, Akashi-Tanaka S, Hojo T, Shibata T, Sasajima Y, Kinoshita T, Tsuda H. Modified primary tumour/vessel tumour/nodal tumour classification for patients with invasive ductal carcinoma of the breast. Br J Cancer. 105:698-708, 2011.
  15. Hasebe T, Iwasaki M, Akashi-Tanaka S, Hojo T, Shibata T, Sasajima Y, Kinoshita T, Tsuda H. Prognostic significance of mitotic figures in metastatic mammary ductal carcinoma to the lymph nodes. Hum Pathol. 42:1823-1832, 2011.
  16. Hasebe T, Iwasaki M, Akashi-Tanaka S, Hojo T, Shimizu S, Andoh M, Shibata T, Sasajima Y, Kinoshita T, Tsuda H. Atypical tumor-stroma fibroblasts in the invasive ductal carcinomas of the breast. Am J Surg Pathol. 35:325-336, 2011.
  17. Hasebe T, Iwasaki M, Akashi-Tanaka S, Hojo T, Shimizu S, Andoh M, Fujiwara Y, Shibata T, Sasajima Y, Kinoshita T, Tsuda H. Atypical tumor-stromal fibroblasts in invasive ductal carcinomas of the breast treated with neoadjuvant therapy. Human Pathol. 42:998-1006, 2011.
  18. Hasegawa T, Yamaguchi R, Nagasaki M, Imoto S, Miyano S. Comprehensive pharmacogenomic pathway screening by data assimilation. Lecture Notes in Computer Science. 6674: 160-171, 2011.
  19. Hashimoto Y, Ochi H, Abe H, Hayashida Y, Tsuge M, Mitsui F, Hiraga N, Imamura M, Takahashi S, Nelson Hayes C, Ohishi W, Kubo M, Tsunoda T, Kamatani N, Nakamura Y, Chayama K. Prediction of response to peginterferon-alfa-2b plus ribavirin therapy in Japanese patients infected with hepatitis C virus genotype 1b. J Med Virol. 83(6): 981-988, 2011.
  20. Hayami S, Kelly JD, Cho HS, Yoshimatsu M, Unoki M, Tsunoda T, Field HI, Neal DE, Yamaue H, Ponder BA, Nakamura Y, Hamamoto R. Overexpression of LSD1 contributes to human carcinogenesis through chromatin regulation in various cancers. Int J Cancer. 128(3): 574-586, 2011.
  21. Hayashi K, Sasamura H, Hishiki T, Suematsu M, Ikeda S, Soga T, Itoh H. Use of serum and urine metabolome analysis for the detection of metabolic changes in patients with stage 1-2 chronic kidney disease. Nephro-Urol Mon. 3:164-171, 2011.
  22. Hew HC, Liu H, Miki Y, Yoshida K. PKCδ regulates Mdm2 independently of p53 in the apoptotic response to DNA damage. Mol Carcinog. 50:719-731, 2011.
  23. 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.
  24. Isagawa T, Nagae G, Shiraki N, Fujita T, Sato N, Ishikawa S, Kume S, Aburatani H. DNA methylation profiling of embryonic stem cell differentiation into the three germ layers. PLoS One. 6(10):e26052, 2011.
  25. Ishihara T, Inoue J, Kozaki K, Imoto I, Inazawa J. The HECT-type ubiquitin ligase ITCH targets lysosomal-associated protein multispanning transmembrane 5 (LAPTM5) and prevents LAPTM5-mediated cell death. J Biol Chem. 286:44086-94. 2011.
  26. Ito Y, Nagasaki K, Miki Y, Iwase T, Akiyama F, Matsuura M, Horii R, Makita M, Tokudome N, Ushijima M, Yoshimoto M, Takahashi S, Noda T, Hatake K. Prospective randomized phase II study determines the clinical usefulness of genetic biomarkers for sensitivity to primary chemotherapy with paclitaxel in breast cancer. Cancer Sci. 102:130-136, 2011.
  27. Ishihara T, Inoue J, Kozaki K, Imoto I, Inazawa J. The HECT-type ubiquitin ligase ITCH targets lysosomal-associated protein multispanning transmembrane 5 (LAPTM5) and prevents LAPTM5-mediated cell death. J Biol Chem. 286:44086-94. 2011.
  28. Iwakawa R, Kohno T, Kato M, Shiraishi K, Tsuta K, Noguchi M, Ogawa S, Yokota J. MYC amplification as a prognostic marker of early stage lung adenocarcinoma identified by whole genome copy number analysis. Clin Cancer Research. 17: 1481-1489, 2011.
  29. 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.
  30. 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.
  31. Johnson TA, Niimura Y, Tanaka H, Nakamura Y, Tsunoda T. hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets. Genome Biol. 12(3):R21, 2011.
  32. Kao HW, Sanada M, Liang DC, Lai CL, Lee EH, Kuo MC, Lin TL, Shih YS, Wu JH, Huang CF, Ogawa S, Shih LY. A high occurrence of acquisition and/or expansion of C-CBL mutant clones in the progression of high-risk myelodysplastic syndrome to acute myeloid leukemia. Neoplasia. 13:1035-1042, 2011.
  33. Katagiri T, Sato-Otsubo A, Kashiwase K, Morishima S, Sato Y, Mori Y, Kato M, Sanada M, Morishima Y, Hosokawa K, Sasaki Y, Ohtake S, Ogawa S, Nakao S. Frequent loss of HLA alleles associated with copy number-neutral 6pLOH in acquired aplastic anemia. Blood. 118(25):6601-6609, 2011
  34. Kato T, Niizuma S, Inuzuka Y, Kawashima T, Okuda J, Kawamoto A, Tamaki Y, Iwanaga Y, Soga T, Kita T, Kimura T, Shioi T. Analysis of liver metabolism in a rat model of heart failure. Int J Cardiol. 2011 Aug 10. [Epub ahead of print] doi:10.1016/j.ijcard.2011.07.056.
  35. Kato M, Yoon S, Hosono N, Leotta A, Sebat J, Tsunoda T, Zhang MQ. Inferring haplotypes of copy number variations from high-throughput data with uncertainty. G3: Genes, Genomes, Genetics. 1(1): 35–42, 2011.
  36. Kawai T, Caaveiro JM, Abe R, Katagiri T, Tsumoto K. Catalytic activity of MsbA reconstituted in nanodisc particles is modulated by remote interactions with the bilayer. FEBS Lett. 585: 3533-3537, 2011.
  37. Kawaoka T, Hayes CN, Ohishi W, Ochi H, Maekawa T, Abe H, Tsuge M, Mitsui F, Hiraga N, Imamura M, Takahashi S, Kubo M, Tsunoda T, Nakamura Y, Kumada H, Chayama K. Predictive value of the IL28B polymorphism on the effect of interferon therapy in chronic hepatitis C patients with genotypes 2a and 2b. J Hepatol. 54(3):408-14, 2011.
  38. Kimura T, Takabatake Y, Takahashi A, Kaimori J, Matsui I, Namba T, Kitamura H, Niimura F, Matsusaka T, Soga T, Rakugi H, Isaka Y. Autophagy protects the proximal tubule from degeneration and acute ischemic injury. J Am Soc Nephrol. 22:902-913, 2011.
  39. Kitagawa D, Gouda M, Kirii Y, Sugiyama N, Ishihama Y, Fujii I, Narumi Y, Akita K and Yokota K. Characterization of kinase inhibitors using different phosphorylation states of colony stimulating factor-1 receptor tyrosine kinase. J Biochem. 151: 47-55, 2011.
  40. 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.
  41. 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 Research. 71(20):6320-6326, 2011. Erratum in: Cancer Research. 72(4):1039, 2012.
  42. Koren-Michowitz M, Sato-Otsubo A, Nagler A, Haferlach T, Ogawa S, Koeffler HP. Older patients with normal karyotype acute myeloid leukemia have a higher rate of genomic changes compared to young patients as determined by SNP array analysis. Leuk Res. 36(4):467-473, 2011.
  43. Kubota D, Orita H, Yoshida A, Gotoh M, Kanda T, Tsuda H, Hasegawa T, Katai H, Shimada Y, Kaneko K, Kawai A, Suehara Y, Kikuta K, Sato K, Tochigi N, Seki K, Shibata T, Toyama Y, Beppu Y, Kondo T. Pfetin as a prognostic biomarker for gastrointestinal stromal tumor: Validation study in multiple clinical facilities. Jpn J Clin Oncol. 41:1194-1202, 2011.
  44. Kumar V, Matsuo K, Takahashi A, Hosono N, Tsunoda T, Kamatani N, Kong SY, Nakagawa H, Cui R, Tanikawa C, Seto M, Morishima Y, Kubo M, Nakamura Y, Matsuda K. Common variants on 14q32 and 13q12 are associated with DLBCL susceptibility. J Hum Genetics. 56: 436-439, 2011.
  45. Kurasawa Y, Kozaki K, Pimkhaokham A, Muramatsu T, Ono H, Ishihara T, Uzawa N, Imoto I, Amagasa T, Inazawa J. Stabilization of phenotypic plasticity through mesenchymal-specific DNA hypermethylation in cancer cells. Oncogene. 31(15):1963-74, 2011.
  46. Li M, Mukasa A, Inda MM, Zhang J, Chin L, Cavenee WK, Furnari F. Guanylate binding protein-1 is a novel effector of EGFR-driven invasion in glioblastoma. J Exp Med. 208:2657-73, 2011.
  47. Maeda D, Shibahara J, Sakuma T, Isobe M, Teshima S, Mori M, Oda K, Nakagawa S, Taketani Y, Ishikawa S, Fukayama M. β-catenin (CTNNB1) S33C mutation in ovarian microcystic stromal tumors. Am J Surg Pathol. 35(10):1429-40, 2011.
  48. Maeda K, Fukano Y, Yamamichi S, Nitta D, Kurata H. An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks. Bioprocess Biosyst Eng. 34(4):433-446, 2011.
  49. Masuda T, Sugiyama N, Tomita M and Ishihama Y. Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines. Anal Chem. 83: 7698-703, 2011.
  50. Matsui T, Miyamoto K, Kubo A, Kawasaki H, Ebihara T, Hata K, Tanahashi S, Ichinose S, Imoto I, Inazawa J, Kudoh J, Amagai M. SASPase regulates stratum corneum hydration through profilaggrin-to-filaggrin processing. EMBO Mol Med. 3(6):320-333, 2011.
  51. Matsuno H, Nagasaki M, Miyano S. Hybrid Petri net based modeling for biological pathway simulation. Natural Computing. 10(3):1099-1120, 2011.
  52. Matsuyama Y, Suzuki M, Arima C, Huang QM, Tomida S, Takeuchi T, Sugiyama R, Itoh Y, Yatabe Y, Goto H, Takahashi T. Proteasomal non-catalytic subunit PSMD2 as a potential therapeutic target in association with various clinicopathologic features in lung adenocarcinomas. Mol Carcinogenesis. 50: 301-309, 2011.
  53. Miki D, Ochi H, Hayes CN, Abe H, Yoshima T, Aikata H, Ikeda K, Kumada H, Toyota J, Morizono T, Tsunoda T, Kubo M, Nakamura Y, Kamatani N, Chayama K. Variation in the DEPDC5 locus is associated with progression to hepatocellular carcinoma in chronic hepatitis C virus carriers. Nature Genetics. 43:797-800, 2011.
  54. Miyamoto M, Ojima H, Iwasaki M, Shimizu H, Kokubu A, Hiraoka N, Kosuge T, Yoshikawa D, Kono T, Furukawa H, Shibata T. Prognostic significance of overexpression of c-Met oncoprotein in cholangiocarcinoma. Br J Cancer. 105:131-138, 2011.
  55. Mulder JE, Brien JF, Racz WJ, Takahashi T, Massey T. Mechanisms of amiodarone and desethylamiodarone cytotoxicity in non-transformed human peripheral lung epithelial cells. J Pharmacol Exp Ther. 336:551-559, 2011.
  56. Muramatsu T, Imoto I, Matsui T, Kzsaki K, Haruki S, Sudol M, Shimada Y, Tsuda H, Kawano T, Inazawa J. YAP is a candidate oncogene for esophageal squamous-cell carcinoma. Carcinogenesis. 32:389-398, 2011.
  57. Nagae G, Isagawa T, Shiraki N, Fujita T, Yamamoto S, Tsutsumi S, Nonaka A, Yoshiba S, Matsusaka K, Midorikawa Y, Ishikawa S, Soejima H, Fukayama M, Suemori H, Nakatsuji N, Kume S, Aburatani H. Tissue-specific demethylation in CpG-poor promoters during cellular differentiation. Hum Mol Genetics. 20(14):2710-2721, 2011.
  58. 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.
  59. Nishikawa E, Osada H, Okazaki Y, Arima C, Tomida S, Tatematsu Y, Taguchi A, Shimada Y, Yanagisawa K, Yatabe Y, Toyokuni S, Sekido Y, Takahashi T. miR-375 is activated by ASH1 and inhibits YAP1 in a lineage-dependent manner in lung cancer. Cancer Research. 71:6165-6173, 2011.
  60. Nishiyama N, Arai E, Nagashio R, Fujimoto H, Hosoda F, Shibata T, Tsukamoto T, Yokoi S, Imoto I, Inazawa J, Kanai Y. Copy number alterations in urothelial carcinomas: Their clinicopathological significance and correlation with DNA methylation alterations. Carcinogenesis. 32:462-469, 2011.
  61. Ochi H, Maekawa T, Abe H, Hayashida Y, Nakano R, Imamura M, Hiraga N, Kawakami Y, Aimitsu S, Kao JH, Kubo M, Tsunoda T, Kumada H, Nakamura Y, Hayes CN, Chayama K. IL-28B predicts response to chronic hepatitis C therapy – fine-mapping and replication study in Asian populations. J General Virology. 92(Pt 5):1071-1081, 2011.
  62. Ochiai D, Goda N, Hishiki T, Kanai M, Senoo-Matsuda N, Soga T, Johnson RS, Yoshimura Y, Suematsu M. Disruption of HIF-1α in hepatocytes impairs glucose metabolism in diet-induced obesity mice. Biochem Biophys Res Commun. 415(3):445-9, 2011.
  63. Ogawa S, Takita J, Sanada M, Hayashi Y. Oncogenic mutations of ALK in neuroblastoma. Cancer Sci. 102:302-308, 2011.
  64. Ogawa Y, Koike N, Kurisawa G, Soga T, Tomita M, Tei H. Positive autoregulation delays the expression phase of mammalian clock gene Per2. PLoS One. 6(4): e18663, 2011.
  65. Ogawa S, Takita J, Sanada M, Hayashi Y. Oncogenic mutations of ALK in neuroblastoma. Cancer Sci. 102:302-308, 2011.
  66. Okamoto N, Yasukawa M, Nguyen C, Kasim V, Maida Y, Possemato R, Shibata T, Ligon K, Fukami K, Hahn W, Masutomi K. Maintenance of tumor initiating cells of defined genetic composition by a complex composed of nucleostemin, hTERT and BRG1. Proc Natl Acad Sci USA. 108:20388-20393, 2011.
  67. Oki K, Takita J, Hiwatari M, Nishimura R, Sanada M, Okubo J, Adachi M, Sotomatsu M, Kikuchi A, Igarashi T, Hayashi Y, Ogawa S. IDH1 and IDH2 mutations are rare in pediatric myeloid malignancies. Leukemia. 25:382-384, 2011.
  68. Osada H, Takahashi T. let-7 and miR-17-92: Small-sized major players in lung cancer development. Cancer Sci. 102:9-17, 2011.
  69. Ozeki C, Sawai Y, Shibata T, Kohno T, Okamoto K, Yokota J, Tashiro F, Tanuma S, Sakai R, Kawase T, Kitabayashi I, Taya Y, Ohki R. Cancer susceptibility polymorphism of p53 at codon 72 affects phopshorylation and degradation of p53 protein. J Bio Chem. 286:18251-18260, 2011.
  70. Park J, Katagiri T, Chung S, Kijima K, Nakamura Y. Polypeptide N-acetylgalactosaminyltransferase 6 (GALNT6) disrupts mammary acinar morphogenesis through O-glycosylation of fibronectin. Neoplasia. 13: 320-326, 2011.
  71. Saito M, Schetter AJ, Mollerup S, Kohno T, Skaug V, Bowman ED, Mathe E, Takenoshita S, Yokota J, Haugen A, Harris CC. The association of microRNA expression with prognosis and progression in early stage, non-small cell lung adenocarcinoma: a retrospective analysis of three cohorts. Clin Cancer Research. 17: 1875-1882, 2011.
  72. Sakata-Yanagimoto M, Sakai T, Miyake Y, Saito TI, Maruyama H, Morishita Y, Nakagami-Yamaguchi E, Kumano K, Yagita H, Fukayama M, Ogawa S, Kurokawa M, Yasutomo K, Chiba S. Notch2 signaling is required for proper mast cell distribution and mucosal immunity in the intestine. Blood. 117:128-134, 2011.
  73. Seo S, Nakamoto T, Takeshita M, Lu J, Sato T, Suzuki T, Kamikubo Y, Ichikawa M, Noda M, Ogawa S, Honda H, Oda H, Kurokawa M. Cas-L regulates myeloid cell motility and suppresses progression of leukemia induced by p210Bcr/Abl. Cancer Sci. 102(12):2109-2117, 2011.
  74. 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. doi:10.1049/el.2011.0526
  75. Shiba N, Park MJ, Taki T, Takita J, Hiwatari M, Kanazawa T, Sotomatsu M, Ishii E, Arakawa H, Ogawa S, Hayashi Y. CBL mutations in infant acute lymphoblastic leukaemia. Br J Haematol. 156(5):672-674, 2011.
  76. Shibata T, Kokubu A, Miyamoto M, Sasajima Y, Yamazaki Y. Mutant IDH1 confers an in vivo growth in a melanoma cell line with BRAF mutation. Am J Pathol. 178:1395-1402, 2011.
  77. Shibata T, Kokubu A, Saito S, Narisawa-Saito N, Sasaki H, Aoyagi K, Yoshimatsu Y, Tachimori Y, Kushima R, Kiyono T, Yamamoto M. NRF2 mutation confers malignant potential and resistance to chemoradiation therapy in advanced esophageal squamous cancer. Neoplasia. 13:864-873, 2011.
  78. Sides M, Klingsberg RC, Shan B, Gordon KA, Nguyen HT, Lin Z, Takahashi T, Flemington EK, Lasky JA. The Epstein-Barr virus LMP 1 and TGF-1 synergistically induce EMT in lung epithelial cells. Am J Resp Cell Mol Biol. 44(6):852-862, 2011.
  79. 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.
  80. Shiraishi Y, Okada-Hatakeyama M, Miyano S. A rank-based statistical test for measuring synergistic effects between two gene sets. Bioinformatics. 27 (17): 2399-2405, 2011.
  81. Shirakihara T, Horiguchi K, Miyazawa K, Ehata S, Shibata T, Morita I, Miyazono K, Saitoh M. TGF- regulates isoform switching of FGF receptors and epithelial-mesenchymal transition. EMBO J. 30:783-795, 2011.
  82. Soga T, Sugimoto M, Honma M, Mori M, Igarashi K, Kashikura K, Ikeda S, Hirayama A, Yamamoto T, Yoshida H, Otsuka M, Tsuji S, Yatomi Y, Sakuragawa T, Watanabe H, Nihei K, Saito T, Kawata S, Suzuki H, Tomita M, Suematsu M. Serum metabolomics reveals γ-glutamyl dipeptides as biomarkers for differentiation among different forms of liver disease. J Hepatol. 55: 896-905, 2011.
  83. Suzuki T, Toyohara T, Akiyama Y, Takeuchi Y, Mishima E, Suzuki C, Ito S, Soga T, Abe T. Transcriptional regulation of organic anion transporting polypeptide SLCO4C1 as a new therapeutic modality to prevent chronic kidney disease. J Pharm Sci. 100: 3696-3707, 2011.
  84. 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.
  85. Takahashi K, Oka A, Mizuguchi M, Saitoh M, Takita J, Sato A, Mimaki M, Kato M, Ogawa S, Igarashi T. Interstitial deletion of 13q14.13-q32.3 presenting with Arima syndrome and bilateral retinoblastoma. Brain Dev. 33(4): 353-356, 2011.
  86. Takita J, Chen Y, Okubo J, Sanada M, Adachi M, Ohki K, Nishimura R, Hanada R, Igarashi T, Hayashi Y, Ogawa S. Aberrations of NEGR1 on 1p31 and MYEOV on 11q13 in neuroblastoma. Cancer Sci. 102(9):1645-1650, 2011.
  87. 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.
  88. Tamada Y, Imoto S, Miyano S. Parallel algorithm for learning optimal Bayesian network structure. J Machine Learning Research. 12: 2437-2459, 2011.
  89. 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.
  90. 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.
  91. Tanaka M, Shibahara J, Fukushima N, Shinozaki A, Umeda M, Ishikawa S, Kokudo N, Fukayama M. Claudin-18 is an early-stage marker of pancreatic carcinogenesis. J Histochem Cytochem. 59(10):942-952, 2011.
  92. Tanaka Y, Nakamura A, Suimye Morioka M, Inoue S, Adachi M, Yamada K, Taketani K, Kawauchi J, Tanaka H, Kitajima S. Systems analysis of ATF3 in stress response and cancer reveals opposing effects on pro-apoptotic genes in p53 pathway. PLoS One. 6(10):e26848, 2011.
  93. Tateno C, Kataoka M, Utoh R, Tachibana A, Itamoto T, Asahara T, Miya F, Tsunoda T, Yoshizato K. Growth hormone-dependent pathogenesis of human hepatic steatosis in a novel mouse model bearing a human hepatocyte-repopulated liver. Endocrinology. 152(4):1479-1491, 2011.
  94. Thoennissen NH, Lasho T, Thoennissen GB, Ogawa S, Tefferi A, Koeffler HP. Novel CUX1 missense mutation in association with 7q- at leukemic transformation of MPN. Am J Hematol. 86:703-705, 2011.
  95. Totoki Y, Tatsuno K, Yamamoto S, Arai Y, Hosoda F, Ishikawa S, Tsutsumi S, Sonoda K, Totsuka H, Shirakihara T, Sakamoto H, Wang L, Ojima H, Shimada K, Kosuge T, Okusaka T, Kato K, Kusuda J, Yoshida T, Aburatani H, _Shibata T_. High-resolution characterization of a hepatocellular carcinoma genome. Nature Genetics. 43(5):464-469, 2011.
  96. Toyokawa G, Cho HS, Iwai Y, Yoshimatsu M, Takawa M, Hayami S, Maejima K, Shimizu N, Tanaka H, Tsunoda T, Field HI, Kelly JD, Neal DE, Ponder BA, Maehara Y, Nakamura Y, Hamamoto R. The histone demethylase JMJD2B plays an essential role in human carcinogenesis through positive regulation of cyclin-dependent kinase 6. Cancer Prevention Research. 4: 2051-61, 2011.
  97. Toyokawa G, Cho HS, Masuda K, Yamane Y, Yoshimatsu M, Hayami S, Takawa M, Iwai Y, Daigo Y, Tsuchiya E, Tsunoda T, Field HI, Kelly JD, Neal DE, Maehara Y, Ponder BA, Nakamura Y, Hamamoto R. Histone lysine methyltransferase Wolf-Hirschhorn syndrome candidate 1 is involved in human carcinogenesis through regulation of the Wnt pathway. Neoplasia. 13: 887-98, 2011.
  98. Travis WD, Brambilla E, Noguchi M, Nicholson AG, Geisinger KR, Yatabe Y, Beer DG, Powell CA, Eiely GJ, Van Schil PE, Garg, K, Austin JHM, Asamura H, Rusch, VW, Hirsch FR, Scagliotti G, MisudomiT, Huber RM, Ishikawa Y, Jett, J, Sanchez-Cespedes, M, Sculier, JP, Takahashi T, Tsuboi, M, Vansteenkiste J, Wistuba I, Yang, P-C, Aberle D, Brambilla C, Flieder D, Franklin W, Johnson B, Johnson D, Kerr K, Kuriyama K, Lee JS, Miller VA, pertersen I, Roggli V, Rosell R, Saijo N, Thunnissen E, Tsao M, Yankelewitz D. International Association for the Study of Lung Cancer/Amerian Thoracic Society/European Respiratory Society International Multidisciplinary Classification of lung adenocarcinoma. J Thorac Oncol. 6: 244-285, 2011.
  99. Tsuda H, Seki K, Hasebe T, Sasajima Y, Shibata T, Iwamoto E, Kinoshita T. A histopathological study for evaluation of therapeutic effects of radiofrequency ablation in patients with breast cancer. Breast Cancer. 18:24-32, 2011.
  100. Tsuruta T, Kozaki K, Uesugi A, Furuta M, Hirasawa A, Imoto I, Susumu N, Aoki D, Inazawa J. miR-152 is a tumor suppressor microRNA that is silenced by DNA hypermethylation in endometrial cancer. Cancer Research. 71:6450-62. 2011.
  101. Uesugi A, Kozaki K, Tsuruta T, Furuta M, Morita K, Imoto I, Omura K, Inazawa J. The tumor suppressive microRNA miR-218 targets the mTOR component Rictor and inhibits AKT phosphorylation in oral cancer. Cancer Research. 71:5765-78. 2011.
  102. Wang HF, Takenaka K, Nakanishi A, Miki Y. BRCA2 and nucleophosmin coregulate centrosome amplification and form a complex with the Rho effector kinase ROCK2. Cancer Research. 71: 68-77, 2011.
  103. Watanabe T, Chuma S, Yamamoto Y, Kuramochi-Miyagawa S, Totoki Y, Toyoda A, Hoki Y, Fujiyama A, Shibata T, Sado T, Noce T, Nakatsuji N, Lin H, Sasaki H. MotoPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline. Dev Cell. 20:364-375, 2011.
  104. Watanabe A, Ogiwara H, Ehata S, Mukasa A, Ishikawa S, Maeda D, Ueki K, Ino Y, Todo T, Yamada Y, Fukayama M, Saito N, Miyazono K, Aburatani H. Homozygously deleted gene DACH1 regulates tumor-initiating activity of glioma cells. Proc Natl Acad Sci U S A. 108(30):12384-12389, 2011.
  105. Watanabe T, Tomizawa S, Mitsuya K, Totoki Y, Yamamoto Y, Kuramochi-Miyagawa S, Iida N, Hoki Y, Murphy PJ, Toyoda A, Gotoh K, Hiura H, Arima T, Fujiyama A, Sado T, Shibata T, Nakano T, Lin H, Ichiyanagi K, Soloway PD, Sasaki H. Role for piRNAs and a novel non-coding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus. Science. 332:848-852, 2011.
  106. 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.
  107. Yamauchi M, Yoshino I, Yamaguchi R, Shimamura T, Nagasaki M, Imoto S, Niida A, Koizumi F, Kohno T, Yokota J, Miyano S, Goto N. N-cadherin expression is a potential survival mechanism of gefitinib-resistant lung cancer cells. Am J Cancer Research. 1: 823-833, 2011.
  108. 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. 478:64-69, 2011.
  109. Yoshida K, Sanada M, Kato M, Kawahata R, Matsubara A, Takita J, Shih LY, Mori H, Koeffler HP, Ogawa S. A nonsense mutation of IDH1 in myelodysplastic syndromes and related disorders. Leukemia. 25:184-186, 2011.
  110. Yoshida A, Tsuta K, Nakamura H, Kohno T, Takahashi F, Asamura H, Sekine I, Fukayama M, Shibata T, Furuta K, Tsuda H. Comprehensive histological analysis of ALK-rearranged lung carcinomas. Am J Surg Pathol. 35:1226-1234, 2011
  111. Yoshida A, Tsuta K, Nitta H, Hatanaka Y, Asamura H, Sekine I, Grogan TM, Fukayama M, Shibata T, Furuta K, Kohno T, Tsuda H. Bright-field dual-color chromogenic in situ hybridization for diagnosing echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase-positive lung adenocarcinomas. J Thoracic Oncology. 6:1677-1686, 2011.
  112. Yoshimatsu M, Toyokawa G, Hayami S, Unoki M, Tsunoda T, Field HI, Kelly JD, Neal DE, Maehara Y, Ponder BA, Nakamura Y, Hamamoto R. Dysregulation of PRMT1 and PRMT6, Type I arginine methyltransferases, is involved in various types of human cancers. Int J Cancer. 128(3):562-573, 2011.

論文 2010

  1. Alifano M, Souaze F, Dupouy S, Camilleri-Broet S, Takahashi T, Ahmed-Zaid S, Cancellieri A, Damiani S, Boaron M, Broet P, Miller LD, Gespach G, Regnard JF, Forgez P. Neurotensin receptor 1 determines the outcome of non-small cell lung cancer. Clin Cancer Res. 16: 4401-4410, 2010.
  2. An B, Kondo Y, Okamoto Y, Shinjo K, Kanemitsu Y, Komori K, Hirai T, Sawaki A, Tajika M, Nakamura T, Yamao K, Yatabe Y, Fujii M, Murakami H, Osada H, Tani T, Matsuo K, Shen L, Issa JP, Sekido Y. Characteristic methylation profile in CpG island methylator phenotype-negative distal colorectal cancers. Int J Cancer. 127:2095-2105, 2010.
  3. Asaoka Y, Tada M, Ikenoue T, Seto M, Imai M, Miyabayashi K, Yamamoto K, Yamamoto S, Kudo Y, Mohri D, Isomura Y, Ijichi H, Tateishi K, Kanai F, Ogawa S, Omata M, Koike K. Gastric cancer cell line Hs746T harbors a splice site mutation of c-Met causing juxtamembrane domain deletion. Biochem Biophys Res Commun. 394:1042-1046, 2010.
  4. Bryant CM, Albertus DL, Kim S, Guedj M, Travis WD, Yatabe Y, Takahashi T, Brambilla E, Beer DG. Clinically relevant characterization of lung adenocarcinoma subtypes based on cellular pathways. PLoS One. 5:e11712, 2010.
  5. Fujimoto A, Nakagawa H, Hosono N, Nakano K, Abe T, Boroevich KA, Nagasaki M, Yamaguchi R, Shibuya T, Kubo M, Miyano S, Nakamura Y, Tsunoda T. Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet. 42(11):931-936, 2010.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Furuta M, Kzsaki K, Tanaka S, Arii S, Imoto I, Inazawa J. miR-124 and miR-203 are epigenetically silenced tumor-suppressive microRNAs in hepatocellular carcinoma. Carcinogenesis. 31:766-776, 2010.
  11. Haruki S, Imoto I, Kzsaki K, Matsui T, Kawachi H, Komatsu S, Muramatsu T, Shimada Y, Kawano T, Inazawa J. Frequent silencing of protocadherin 17, a candidate tumour suppressor for esophageal squamous-cell carcinoma. Carcinogenesis. 31:1027-1036, 2010.
  12. Heishi T, Hosaka T, Suzuki H, Suzuki Y, Miyashita H, Oike Y, Takahashi T, Nakamura T, Arioka S, Mitsuda Y, Takakura T, Hojo K, Matsumoto M, Yamauchi C, Ohta H, Sonoda H, Sato Y. Endogenous angiogenesis inhibitor vasohibin1 exhibits a broad-spectrum anti-lymphangiogenic activity and suppresses lymph node metastasis. Am J Pathol. 176:1950-1958, 2010.
  13. Higashigaki T, Kojima K, Yamaguchi R, Inoue M, Imoto S, Miyano S. Identifying hidden confounders in gene networks by Bayesian networks. Proc. 10th IEEE International Symposium on Bioinformatics and Bioengineering. IEEE Computer Society Press. 168-173, 2010.
  14. Horio Y, Osada H, Shimizu J, Ogawa S, Hida T, Sekido Y. Relationship of mRNA expressions of RanBP2 and topoisomerase II isoforms to cytotoxicity of amrubicin in human lung cancer cell lines. Cancer Chemother Pharmacol. 66:237-243, 2010.
  15. Hu Q, Akatsuka S, Yamashita Y, Ohara H, Nagai H, Okazaki Y, Takahashi T, Toyokuni S. Homozygous deletion of CDKN2A/2B is a hallmark of iron-induced high-grade rat mesothelioma. Lab Invest. 90:360-373, 2010.
  16. Huang QA, Akashi T, Matsuda Y, Kamiya K, Takahashi T, Suzuki M. Roles of POLD4, smallest subunit of DNA polymerase δ, in nuclear structures and genomic stability of human cells. Biochem Biophys Res Comm. 391:542-546, 2010.
  17. Huang QA, Tomida S, Masuda Y, Arima C, Cao K, Kisahara T, Osada H, Yatabe Y, Kamiya K, Takahashi T, Suzuki M. Regulation of DNA polymerase POLD4 influences genomic instability in lung cancer. Cancer Res. 70:8407-8416, 2010.
  18. 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. 10th IEEE International Symposium on Bioinformatics and Bioengineering. IEEE Computer Society Press. 253-258, 2010.
  19. Kiyotani K, Mushiroda T, Hosono N, Tsunoda T, Kubo M, Aki F, Okazaki Y, Hirata K, Takatsuka Y, Okazaki M, Ohsumi S, Yamakawa T, Sasa M, Nakamura Y, Zembutsu H. Lessons for pharmacogenomics studies: association study between CYP2D6 genotype and tamoxifen response. Pharmacogenet Genomics. 20(9):565-568, 2010.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. Lilljebjorn H, Soneson C, Andersson A, Heldrup J, Behrendtz M, Kawamata N, Ogawa S, Koeffler HP, Mitelman F, Johansson B, Fontes M, Fioretos T. The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias. Hum Mol Genet. 19:3150-3158, 2010.
  25. Miki D, Kubo M, Takahashi A, Yoon K-A, Kim J, Lee GK, Zo JI, Lee JS, Hosono N, Morizono T, Tsunoda T, Kamatani N, Chayama K, Takahashi T, Inazawa J, Nakamura Y, Daigo Y. Variation in TP63 is associated with lung adenocarcinoma susceptibility in Japanese and Korean populations. Nat Genet. 42:893-896, 2010.
  26. Miwa Y, Li C, Ge QW, 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.
  27. Miwa Y, Murakami Y, Ge QW, 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.
  28. Morishima S, Ogawa S, Matsubara A, Kawase T, Nannya Y, Kashiwase K, Satake M, Saji H, Inoko H, Kato S, Kodera Y, Sasazuki T, Morishima Y. Impact of highly conserved HLA haplotype on acute graft-versus-host disease. Blood. 115:4664-4670, 2010.
  29. 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.
  30. Nakahara F, Sakata-Yanagimoto M, Komeno Y, Kato N, Uchida T, Haraguchi K, Kumano K, Harada Y, Harada H, Kitaura J, Ogawa S, Kurokawa M, Kitamura T, Chiba S. Hes1 immortalizes committed progenitors and plays a role in blast crisis transition in chronic myelogenous leukemia. Blood. 115:2872-2881, 2010.
  31. 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.
  32. 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.
  33. Nishiyama N, Arai E, Chihara Y, Fujimoto H, Hosoda F, Shibata T, Kondo T, Tsukamoto T, Yokoi S, Imoto I, Inazawa J, Hirohashi S, Kanai Y. Genome-wide DNA methylation profiles in urothelial carcinomas and urothelia at the precancerous stage. Cancer Sci. 101:231-240, 2010.
  34. Nowak D, Ogawa S, Muschen M, Kato M, Kawamata N, Meixel A, Nowak V, Kim HS, Kang S, Paquette R, Chang MS, Thoenissen NH, Mossner M, Hofmann WK, Kohlmann A, Weiss T, Haferlach T, Haferlach C, Koeffler HP. SNP array analysis of tyrosine kinase inhibitor-resistant chronic myeloid leukemia identifies heterogeneous secondary genomic alterations. Blood. 115:1049-1053, 2010.
  35. Ochi H, Maekawa T, Abe H, Hayashida Y, Nakano R, Kubo M, Tsunoda T, Hayes CN, Kumada H, Nakamura Y, Chayama K. ITPA polymorphism affects ribavirin-induced anemia and outcomes of therapy–a genome-wide study of Japanese HCV virus patients. Gastroenterology. 139(4):1190-1197, 2010.
  36. Ogawa S, Sanada M, Shih LY, Suzuki T, Otsu M, Nakauchi H, Koeffler HP. Gain-of-function c-CBL mutations associated with uniparental disomy of 11q in myeloid neoplasms. Cell Cycle. 9(6):1051-1056, 2010.
  37. Ogawa S, Shih LY, Suzuki T, Otsu M, Nakauchi H, Koeffler HP, Sanada M. Deregulated Intracellular Signaling by Mutated c-CBL in Myeloid Neoplasms. Clin Cancer Res. 16:3825-3831, 2010.
  38. Okamoto R, Ogawa S, Nowak D, Kawamata N, Akagi T, Kato M, Sanada M, Weiss T, Haferlach C, Dugas M, Ruckert C, Haferlach T, Koeffler HP. Genomic profiling of adult acute lymphoblastic leukemia by single nucleotide polymorphism oligonucleotide microarray and comparison to pediatric acute lymphoblastic leukemia. Haematologica. 95:1481-1488, 2010.
  39. Prapinjumrune C, Morita KI, Kuribayashi Y, Hanabata Y, Shi Q, Nakajima Y, Inazawa J, Omura K. DNA amplification and expression of FADD in oral squamous cell carcinoma. J Oral Pathol Med. 39:525-532, 2010.
  40. Sadej R, Romanska H, Kavanagh D, Baldwin G, Takahashi T, Kalia N, Berditchevski F. Tetraspanin CD151 regulates TGF-beta signalling: implication in tumour metastasis. Cancer Res. 70:6059-6070, 2010.
  41. Saitoh Y, Martinez Bruyn VJ, Uota S, Hasegawa A, Yamamoto N, Imoto I, Inazawa J, Yamaoka S. Overexpression of NF-kappaB inducing kinase underlies constitutive NF-kappaB activation in lung cancer cells. Lung Cancer. 70:263-270, 2010.
  42. Sherborne AL, Hosking FJ, Prasad RB, Kumar R, Koehler R, Vijayakrishnan J, Papaemmanuil E, Bartram CR, Stanulla M, Schrappe M, Gast A, Dobbins SE, Ma Y, Sheridan E, Taylor M, Kinsey SE, Lightfoot T, Roman E, Irving JA, Allan JM, Moorman AV, Harrison CJ, Tomlinson IP, Richards S, Zimmermann M, Szalai C, Semsei AF, Erdelyi DJ, Krajinovic M, Sinnett D, Healy J, Neira AG, Kawamata N, Ogawa S, Koeffler HP, Hemminki K, Greaves M, Houlston RS. Variation in CDKN2A at 9p21.3 influences childhood acute lymphoblastic leukemia risk. Nat Genet. 42:492-494, 2010.
  43. Shiba N, Kato M, Park MJ, Sanada M, Ito E, Fukushima K, Sako M, Arakawa H, Ogawa S, Hayashi Y. CBL mutations in juvenile myelomonocytic leukemia and pediatric myelodysplastic syndrome. Leukemia. 24:1090-1092, 2010.
  44. Shibata T, Kokubu A, Miyamoto M, Hosoda F, Gotoh M, Tsuta K, Asamura H, Matsuno Y, Kondo T, Imoto I, Inazawa J, Hirohashi S. DEK oncoprotein regulates transcriptional modifiers and sustains tumor initiation activity in high-grade neuroendocrine carcinoma of the lung. Oncogene. 29:4671-4681, 2010.
  45. 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.
  46. 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.
  47. Shimizu T, Ishikawa T, Sugihara E, Kuninaka S, Miyamoto T, Mabuchi Y, Matsuzaki Y, Tsunoda T, Miya F, Morioka H, Nakayama R, Kobayashi E, Toyama Y, Kawai A, Ichikawa H, Hasegawa T, Okada S, Ito T, Ikeda Y, Suda T, Saya H. c-MYC overexpression with loss of Ink4a/Arf transforms bone marrow stromal cells into osteosarcoma accompanied by loss of adipogenesis. Oncogene. 29(42):5687-5699, 2010.
  48. Suda K, Murakami I, Katayama T, Tomizawa K, Osada H, Sekido Y, Maehara Y, Yatabe Y, Mitsudomi T. Reciprocal and complementary role of MET amplification and EGFR T790M mutation in acquired resistance to kinase inhibitors in lung cancer. Clin Cancer Res. 16:5489-98, 2010.
  49. Tada M, Kanai F, Tanaka Y, Sanada M, Nannya Y, Tateishi K, Ohta M, Asaoka Y, Seto M, Imazeki F, Yoshida H, Ogawa S, Yokosuka O, Omata M. Prognostic significance of genetic alterations detected by high-density single nucleotide polymorphism array in gastric cancer. Cancer Sci. 101:1261-1269, 2010.
  50. Tagi T, Matsui T, Kikuchi S, Hoshi S, Ochiai T, Kokuba Y, Kinoshita-Ida Y, Kisumi-Hayashi F, Morimoto K, Imai T, Imoto I, Inazawa J, Otsuji E. Dermokine as a novel biomarker for early-stage colorectal cancer. J Gastroenterol. 45:1201-1211. 2010.
  51. Takata R, Akamatsu S, Kubo M, Takahashi A, Hosono N, Kawaguchi T, Tsunoda T, Inazawa J, Kamatani N, Ogawa O, Fujioka T, Nakamura Y, Nakagawa H. Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population. Nat Genet. 42(9):751-754, 2010.
  52. Tanaka S, Cao K, Niimi A, Limsirichaikul S, Huang Q, Nakamura N, Murate T, Hasegawa Y, Takahashi T, Suzuki M. Functions of base selection step in human DNA polymerase alpha. DNA Repair. 9:534-541, 2010.
  53. Tanaka S, Mogushi K, Yasen M, Noguchi N, Kudo A, Nakamura N, Ito K, Miki Y, Inazawa J, Tanaka H, Arii S. Gene-expression phenotypes for vascular invasiveness of hepatocellular carcinomas. Surgery. 147:405-414, 2010.
  54. 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.
  55. Thoennissen NH, Krug UO, Lee DH, Kawamata N, Iwanski GB, Lasho T, Weiss T, Nowak D, Koren-Michowitz M, Kato M, Sanada M, Shih LY, Nagler A, Raynaud SD, Muller-Tidow C, Mesa R, Haferlach T, Gilliland DG, Tefferi A, Ogawa S, Koeffler HP. Prevalence and prognostic impact of allelic imbalances associated with leukemic transformation of Philadelphia chromosome-negative myeloproliferative neoplasms. Blood. 115:2882-2890, 2010.
  56. Villalobos IB, Takahashi Y, Akatsuka Y, Muramatsu H, Nishio N, Hama A, Yagasaki H, Saji H, Kato M, Ogawa S, Kojima S. Relapse of leukemia with loss of mismatched HLA resulting from uniparental disomy after haploidentical hematopoietic stem cell transplantation. Blood. 115:3158-3161, 2010.
  57. Warren EH, Fujii N, Akatsuka Y, Chaney CN, Mito JK, Loeb KR, Gooley TA, Brown ML, Koo KK, Rosinski KV, Ogawa S, Matsubara A, Appelbaum FR, Riddell SR. Therapy of relapsed leukemia after allogeneic hematopoietic cell transplantation with T cells specific for minor histocompatibility antigens. Blood. 115:3869-3878, 2010.
  58. Yamaguchi-Kabata Y, Tsunoda T, Takahashi A, Hosono N, Kubo M, Nakamura Y, Kamatani N. Making a haplotype catalog with estimated frequencies based on SNP homozygotes. J Hum Gen. 55(8):500-506, 2010.
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英文総説 2010~2012

  1. Nakagami H, Sugiyama N, Ishihama Y and Shirasu K, Shotguns in the front line: phosphoproteomics in plants. Plant Cell Physiol. 53: 118-24, 2012.
  2. Imoto S, Tamada Y, Araki H, Miyano S. Computational Drug Target Pathway Discovery: A Bayesian Network Approach. Lu H, Schokop B, Zhao H (Eds.) Handbook of Computational Statistics: Statistical Bioinformatics. Springer. 501-532, 2011

和文総説 2010~2012

  1. 若林真樹, 杉山直幸, 石濱 泰. リン酸化プロテオミクスを用いた分子標的薬プロファイリング. 「遺伝子医学MOOK20号」. メディカル ドウ. 102-108, 2012.
  2. 石川俊平, 吉本倫子, 馬場洋介. 臨床病理検査におけるゲノミクス.「病理と臨床増刊 病理診断に役立つ分子生物学」. 文光堂. 492-507, 2011.
  3. 石川俊平. 癌のデジタルトランスクリプトーム解析.「医学のあゆみ 特集」. 医歯薬出版. 236 (6): 593-598, 2011.
  4. 曽我朋義. 新規酸化ストレスマーカーγ-グルタミルジペプチドによる肝疾患スクリーニング. 「酸化ストレスと肝疾患第7巻」. メディカルトリビューン. 115-123, 2011. 
  5. 平山明由, 曽我朋義. CE-MSメタボローム測定法. 「Diabetes Frontier」. メディカルレビュー社. 22(6): 673-678, 2011. 
  6. 曽我朋義. CE-MS法によるメタボローム解析と医薬への応用. 「遺伝子医学MOOK19号」. メディカル ドウ. 66-70, 2011.
  7. 平山明由, 曽我朋義. CE-MSメタボロミクス.「Hormone Frontier in Glynecology」. メディカルビュー社. 18(1): 19-25, 2011.
  8. 平山明由, 曽我朋義. メタボローム解析による癌代謝特性の包括的解明.「細胞工学」. 学研メディカル秀潤社. 30(1): 25-29, 2011.
  9. 曽我朋義. CE-MSメタボロミクスの最新動向. 「ぶんせき」. 日本分析化学会. 461(11): 585-590, 2010.
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