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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.

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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.

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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.

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.

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.

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.

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.

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.

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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.

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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.

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.

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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.

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.

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.

Takai E, Yachida S. Genetic alterations in pancreatic cancer and their relevance to therapy. World J Gastroenterol. 2015 in press.

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.

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.

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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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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).

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

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.

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

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.

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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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.

Fujitomo T, Daigo Y, Matsuda K, Ueda K, Nakamura Y. Identification of a nuclear protein, LRRC42, involved in lung carcinogenesis. Int J Oncol 45 (2014) 147-156.

Fukatsu A, Ishiguro F, Tanaka I, Kudo T, Nakagawa K, Shinjo K, Kondo Y, Fujii M, Hasegawa Y, Tomizawa K, Mitsudomi T, Osada H, Hata Y, Sekido Y. RASSF3 downregulation increases malignant phenotypes of non-small cell lung cancer. Lung Cancer. 83: 23-9, 2014.

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Haferlach T, Nagata Y, Grossmann V, Okuno Y, Bacher U, Nagae G, Schnittger S, Sanada M, Kon A, Alpermann T, Yoshida K, Roller A, Nadarajah N, Shiraishi Y, Shiozawa Y, Chiba K, Tanaka H, Koeffler HP, Klein HU, Dugas M, Aburatani H, Kohlmann A, Miyano S, Haferlach C, Kern W, Ogawa S. Landscape of genetic lesions in 944 patients with myelodysplastic syndromes. Leukemia. 28(2):241-247, 2014. 10.1038/leu.2013.336

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Hascher A, Haase AK, Hebestreit K, Rohde C, Klein HU, Rius M, Jungen D, Witten A, Stoll M, Schulze I, Ogawa S, Wiewrodt R, Tickenbrock L, Berdel WE, Dugas M, Thoennissen NH, Muller-Tidow C. DNA Methyltransferase Inhibition Reverses Epigenetically Embedded Phenotypes in Lung Cancer Preferentially Affecting Polycomb Target Genes. Clin Cancer Res, 2014. 10.1158/1078-0432.CCR-13-1483

Hasegawa S, Imai K, Yoshida K, Okuno Y, Muramatsu H, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Kojima S, Ogawa S, Morio T, Mizutani S, Takagi M. Whole-exome sequence analysis of ataxia telangiectasia-like phenotype. J Neurol Sci, 2014. 10.1016/j.jns.2014.02.033

Hayashi A, Yamauchi N, Shibahara J, Kimura H, Morikawa T, Ishikawa S, Nagae G, Nishi A, Sakamoto Y, Kokudo N, Aburatani H, Fukayama M. Concurrent activation of acetylation and tri-methylation of H3K27 in a subset of hepatocellular carcinoma with aggressive behavior. PLoS One. 2014 Mar 10; 9(3): e91330. doi: 10.1371/journal.pone.0091330. eCollection 2014. PubMed PMID: 24614346

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Ibrahim R, Matsubara D, Osman W, Morikawa T, Goto A, Morita S, Ishikawa S, Aburatani H, Takai D, Nakajima J, Fukayama M, Niki T, Murakami Y. Expression of PRMT5 in lung adenocarcinoma and its significance in epithelial-mesenchymal transition. Hum Pathol. 2014 Jul;45(7):1397-405. doi:10.1016/j.humpath.2014.02.013. Epub 2014 Feb 28. PubMed PMID: 24775604.

Ito M, Mitsuhashi K, Igarashi H, Nosho K, Naito T, Yoshii S, Takahashi H, Fujita M, Sukawa Y, Yamamoto E, Takahashi T, Adachi Y, Nojima M, Sasaki Y, Tokino T, Baba Y, Maruyama R, Suzuki H, Imai K, Yamamoto H, Shinomura Y. MicroRNA-31 expression in relation to BRAF mutation, CpG island methylation and colorectal continuum in serrated lesions. Int J Cancer. 2014. doi: 10.1002/ijc.28920. [Epub ahead of print]

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Kakiuchi M, Nishizawa T, Ueda H, Gotoh K, Tanaka A, Hayashi A, Yamamoto S, Tatsuno K, Katoh H, Watanabe Y, Ichimura T, Ushiku T, Funahashi S, Tateishi K, Wada I, Shimizu N, Nomura S, Koike K, Sehamanato Y, Fukayama M, Aburatani H, Ishikawa S. Recurrent gain-of-function mutations of RHOA in diffuse-type gastric carcinoma. Nat Genet. 2014 Jun;46(6):583-7. doi: 10.1038/ng.2984. Epub 2014 May 11. PubMed PMID: 24816255.

Kano Y, Konno M, Kawamoto K, Tamari K, Hayashi K, Fukusumi T, Satoh T, Tanaka S, Ogawa K, Mori M, Doki Y, Ishii H. Novel drug discovery system for cancer stem cells in human squamous cell carcinoma of the esophagus. Oncol. Rep. 31(3):1133-1138, 2014.

Kano Y, Ishii H, Konno M, Yamasaki M, Miyata H, Nishikawa S, Hamabe A, Ogawa H, Takahashi H, Ohta K, Hasegawa S, Tanaka K, Fukusumi T, Otsuka M, Kawamoto K, Haraguchi N, Fujimoto R, Isobe M, Tomita Y, Matsuura N, Takiguchi S, Mori M, Doki Y. Cells of origin of squamous epithelium, dysplasia and cancer in the head and neck region after bone marrow transplantation. Int. J. Oncol. 44(2):443-450,2014.

Kihara R, Nagata Y, Kiyoi H, Kato T, Yamamoto E, Suzuki K, Chen F, Asou N, Ohtake S, Miyawaki S, Miyazaki Y, Sakura T, Ozawa Y, Usui N, Kanamori H, Kiguchi T, Imai K, Uike N, Kimura F, Kitamura K, Nakaseko C, Onizuka M, Takeshita A, Ishida F, Suzushima H, Kato Y, Miwa H, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S, Naoe T. Comprehensive analysis of genetic alterations and their prognostic impacts in adult acute myeloid leukemia patients. Leukemia, 2014. 10.1038/leu.2014.55

Kikuchi S, Kaibe N, Morimoto K, Fukui H, Niwa H, Maeyama Y, Takemura M, Matsumoto M, Nakamori S, Miwa H, Hirota S, Sasako M. Overexpression of Ephrin A2 receptors in cancer stromal cells is a prognostic factor for the relapse of gastric cancer. Gastric Cancer. in press, 2014.

Kitagawa K, Shibata K, Matsumoto A, Matsumoto M, Ohhata T, Nakayama KI, Niida H, Kitagawa M. Fbw7 targets GATA3 through CDK2-dependent proteolysis and contributes to regulation of T-cell development. Mol Cell Biol. in press 2014.

Koga C., Kobayashi S, Nagano H, Tomimaru Y, Hama N, Wada H, Kawamoto K, Eguchi H, Konno M, Ishii H, Umeshita K, Doki Y, Mori M. Reprogramming Using microRNA-302 Improves Drug Sensitivity in Hepatocellular Carcinoma Cells. Ann. Surg. Oncol. 2014. (in press)

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Koyama-Nasu R, Haruta R, Nasu-Nishimura Y, Taniue K, Katou Y, Shirahige K, Todo T, Ino Y, Mukasa A, Saito N, Matsui M, Takahashi R, Hoshino-Okubo A, Sugano H, Manabe E, Funato K, Akiyama T. The pleiotrophin-ALK axis is required for tumorigenicity of glioblastoma stem cells. Oncogene 33(17):2236-44, 2014.

Kurtovic-Kozaric A, Przychodzen B, Singh J, Konarska MM, Clemente MJ, Otrock ZK, Nakashima M, Hsi ED, Yoshida K, Ogawa S, Boultwood J, Maciejewski JP, Padgett RA, Makishima H. PRPF8 defects cause missplicing in myeloid malignancies. Leukemia, 2014. 10.1038/leu.2014.144

Lin DC, Hao JJ, Nagata Y, Xu L, Shang L, Meng X, Sato Y, Okuno Y, Varela AM, Ding LW, Garg M, Liu LZ, Yang H, Yin D, Shi ZZ, Jiang YY, Gu WY, Gong T, Zhang Y, Xu X, Kalid O, Shacham S, Ogawa S, Wang MR, Koeffler HP. Genomic and molecular characterization of esophageal squamous cell carcinoma. Nat Genet. 46(5):467-473, 2014. 10.1038/ng.2935

Lin DC, Meng X, Hazawa H, Nagata Y, Varela AM, Xu L, Sato Y, Liu LZ, Ding LW, Sharma A, Goh BC, Lee SC, Petersson BF, Yu FG, Macary P, Oo MZ, Ha SC, Yang H, Ogawa S, Loh K, Koeffler HP. The genomic landscape of nasopharyngeal carcinoma. Nature Genetics, in press

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Liu J, Edagawa M, Goshima H, Inoue M, Yagita H, Liu Z, Kitajima S. Role of ATF3 in synergistic cancer cell killing by a combination of HDAC inhibitors and agonistic 　anti-DR5 antibody through ER stress in human colon cancer cells. Biochem Biophys Res Commun. 445(2):320-6. 2014 doi: 10.1016/j.bbrc.2014.01.184.

Lovat F, Ishii, H, Schiappacassi M, Fassan M, Barbareschi M, Galligioni E, Gasparini P, Baldassarre G, Croce CM, Vecchione A. LZTS1 downregulation confers paclitaxel resistance and is associated with worse prognosis in breast cancer. Oncotarget. 28;5(4):970-977. 2014.

Matsunawa M, Yamamoto R, Sanada M, Sato-Otsubo A, Shiozawa Y, Otsu M, Isono K, Koseki H, Nakauchi H, Ogawa S. Haploinsufficiency of Sf3b1 leads to compromised stem cell function but not to myelodysplasia. Leukemia, 2014. 10.1038/leu.2014.73

Matsuo T, Komatsu M, Yoshimaru T, Kiyotani K, Miyoshi Y, Sasa M, Katagiri T. Involvement of B3GALNT2 overexpression in cell growth of breast cancer. Int J Oncol. 2014 Feb;44(2):427-34. doi: 10.3892/ijo.2013.2187. Epub 2013 Nov 27.

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Nakaya T, Ogawa S, Manabe I, Tanaka M, Sanada M, Sato T, Taketo MM, Nakao K, Clevers H, Fukayama M, Kuroda M, Nagai R. KLF5 regulates the integrity and oncogenicity of intestinal stem cells. Cancer Res, 2014. 10.1158/0008-5472.CAN-13-2574

Nishimura J, Yamamoto M, Hayashi S, Ohyashiki K, Ando K, Brodsky AL, Noji H, Kitamura K, Eto T, Takahashi T, Masuko M, Matsumoto T, Wano Y, Shichishima T, Shibayama H, Hase M, Li L, Johnson K, Lazarowski A, Tamburini P, Inazawa J, Kinoshita T, Kanakura Y. Genetic variants in C5 and poor response to eculizumab. N Engl J Med. 370:632-9. 2014

Obata F, Kuranaga E, Tomioka K, Ming M, Takeishi A, Chen C, Soga T, Miura M. Necrosis-driven systemic immune response alters SAM metabolism through the FOXO-GNMT axis. Cell Rep. 7, 821-833, 2014. DOI: 10.1016/j.celrep.2014.03.046

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Okamoto Y, Shinjo K, Shimizu Y, Sano T, Yamao K, Gao W, Fujii M, Osada H, Sekido Y, Murakami S, Tanaka Y, Joh T, Sato S, Takahashi S, Wakita T, Zhu J, Issa JP, Kondo Y. Hepatitis virus infection affects DNA methylation in mice with humanized livers. Gastroenterology. 146: 562-72, 2014.

Okano M, Konno M, Kano Y, Kim H, Kawamoto K, Ohkuma M, Haraguchi N, Yokobori T, Mimori K, Yamamoto H, Sekimoto M, Doki Y, Mori M, Ishii H. Human colorectal CD24+ cancer stem cells are susceptible to epithelial-mesenchymal transition. Int. J. Oncol. 45(2):575-580. 2014.

Okumura K, Saito M, Aoto Y, Hachiya T, Sakakibara Y, Katsuragi Y, Hirose S, Kominami R, Goitsuka R, Nakamura T, Wakabayashi Y. Meis1 regulates epidermal stem cells and is required for skin tumorigenesis. PLoS One, in press.

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Shigemizu D, Abe T, Morizono T, Johnson TA, Boroevich KA, Hirakawa Y, Ninomiya T, Kiyohara Y, Kubo M, Nakamura Y, Maeda S, Tsunoda T. The construction of risk prediction models using GWAS data and its application to a type 2 diabetes prospective cohort. PLoS One. 9(3):e92549, 2014. doi: 10.1371/journal.pone.0092549.

Shinjo K, Yamashita Y, Yamamoto E, Akatsuka S, Uno N, Kamiya A, Niimi K, Sakaguchi Y, Nagasaka T, Takahashi T, Shibata K, Kajiyama H, Kikkawa F, Toyokuni S. Expression of chromobox homolog 7 (CBX7) is associated with poor prognosis in ovarian clear cell adenocarcinoma via TRAIL-induced apoptotic pathway regulation. Int J Cancer. 135:308-318, 2014. DOI: 10.1002/ijc.28692.

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Takaoka M, Saito H, Takenaka K, Miki Y, Nakanishi A. BRCA2 phosphorylated by PLK1 moves to the midbody to regulate cytokinesis mediated by nonmuscle myosin IIC. Cancer Res. 2014 Mar 1;74(5):1518-28. doi: 10.1158/0008-5472.CAN-13-0504.

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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.

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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.

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

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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.

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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.

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.

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.

Fujita A, Kojima K, Patriota AG, Sato JR, Severino P, Miyano S. A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets. Bioinformatics. 26(18):2349-2351, 2010.

Fujita A, Nagasaki M, Imoto S, Saito A, Ikeda E, Shimamura T, Yamaguchi R, Hayashizaki Y, Miyano S. Comparison of gene expression profiles produced by CAGE, illumina microarray and Real Time RT-PCR. Genome Informatics. 24: 56-68, 2010.

Fujita A, Sato JR, Kojima K, Gomes LR, Sogayar MC, Miyano S. Identification of Granger causality between gene sets. J Bioinformatics and Computational Biology. 8(4): 679–701, 2010.

Fujita A, Severino P, Sato JR, Miyano S. Granger causality in systems biology: modeling gene networks in time series microarray data using vector autoregressive models. Lecture Notes in Bioinformatics. 6268: 13-24, 2010.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Koh CH, Nagasaki M, Saito A, Wong L, Miyano S. DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinformatics. 26(14):1794-1796, 2010.

Kojima K, Imoto S, Nagasaki M, Miyano S. Gene regulatory network clustering for graph layout based on microarray gene expression data. Genome Informatics. 24: 84-95, 2010.

Kojima K, Nagasaki M, Miyano S. An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. BMC Bioinformatics. 11:335, 2010.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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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.

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.

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.

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.

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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.

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.

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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.

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.

Shimamura T, Imoto S, Yamaguchi R, Nagasaki M, Miyano S. Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinformatics. 26(8):1064-1072, 2010.

Shimamura T, Imoto S, Nagasaki M, Yamauchi M, Yamaguchi R, Fujita A, Tamada Y, Gotoh N, Miyano S. Collocation-based sparse estimation for constructing dynamic gene networks. Genome Informatics. 24: 164-178, 2010.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Yanagisawa K, Konishi H, Arima C, Tomida S, Takeuchi T, Shimada Y, Yatabe Y, Mitsudomi T, Osada H, Takahashi T. Novel metastasis-related gene CIM functions in the regulation of multiple cellular stress response pathways. Cancer Res. 70:9949-9958, 2010.

Nakagami H, Sugiyama N, Ishihama Y and Shirasu K, Shotguns in the front line: phosphoproteomics in plants. Plant Cell Physiol. 53: 118-24, 2012.

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

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