Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

Yamashita T, Peng Y, Knight C, Voth GA. Computationally Efficient Multiconfigurational Reactive Molecular Dynamics J Chem Theory Comput. 2012 Dec 11;8(12):4863-4875.

Insights into the mechanism of proton transport in cytochrome c oxidase

Yamashita T, Voth GA. Insights into the mechanism of proton transport in cytochrome c oxidase J Am Chem Soc. 2012 Jan 18;134(2):1147-52. doi: 10.1021/ja209176e. Epub 2012 Jan 6.

Host-protective effect of circulating pentraxin 3 (PTX3) and complex formation with neutrophil extracellular traps.

Daigo K, Hamakubo T. Host-protective effect of circulating pentraxin 3 (PTX3) and complex formation with neutrophil extracellular traps. Front Immunol. 2012 Dec 13;3:378. doi: 10.3389/fimmu.2012.00378. eCollection 2012.

Reciprocal contribution of pentraxin 3 and C-reactive protein to obesity and metabolic syndrome.

Yumura K, Ui M, Doi H, Hamakubo T, Kodama T, Tsumoto K, Sugiyama A. Reciprocal contribution of pentraxin 3 and C-reactive protein to obesity and metabolic syndrome. Protein Sci. 2013 Feb;22(2):213-21. doi: 10.1002/pro.2203. Epub 2013 Jan 4.

Mutations for decreasing the immunogenicity and maintaining the function of core streptavidin.

Yumura K, Ui M, Doi H, Hamakubo T, Kodama T, Tsumoto K, Sugiyama A. Mutations for decreasing the immunogenicity and maintaining the function of core streptavidin. Protein Sci. 2013 Feb;22(2):213-21. doi: 10.1002/pro.2203. Epub 2013 Jan 4.

Lola regulates glutamate receptor expression at the Drosophila neuromuscular junction.

Fukui A, Inaki M, Tonoe G, Hamatani H, Homma M, Morimoto T, Aburatani H, Nose A. Lola regulates glutamate receptor expression at the Drosophila neuromuscular junction. Biol Open. 2012 Apr 15;1(4):362-75. doi: 10.1242/bio.2012448. Epub 2012 Feb 16.

RNA-dependent RNA polymerase of hepatitis C virus binds to its coding region RNA stem-loop structure, 5BSL3.2, and its negative strand.

Mochizuki Y, Ohashi R, Kawamura T, Iwanari H, Kodama T, Naito M, Hamakubo T. RNA-dependent RNA polymerase of hepatitis C virus binds to its coding region RNA stem-loop structure, 5BSL3.2, and its negative strand. J Biol Chem. 2013 Jan 11;288(2):1009-21. doi: 10.1074/jbc.M112.395087. Epub 2012 Nov 27.

Phosphatidylinositol 3-phosphatase myotubularin-related protein 6 (MTMR6) is regulated by small GTPase Rab1B in the early secretory and autophagic pathways.

Mochizuki Y, Ohashi R, Kawamura T, Iwanari H, Kodama T, Naito M, Hamakubo T. Phosphatidylinositol 3-phosphatase myotubularin-related protein 6 (MTMR6) is regulated by small GTPase Rab1B in the early secretory and autophagic pathways. J Biol Chem. 2013 Jan 11;288(2):1009-21. doi: 10.1074/jbc.M112.395087. Epub 2012 Nov 27.

Lung cancer with loss of BRG1/BRM, shows epithelial mesenchymal transition phenotype and distinct histologic and genetic features.

Matsubara D, Kishaba Y, Ishikawa S, Sakatani T, Oguni S, Tamura T, Hoshino H, Sugiyama Y, Endo S, Murakami Y, Aburatani H, Fukayama M, Niki T. Lung cancer with loss of BRG1/BRM, shows epithelial mesenchymal transition phenotype and distinct histologic and genetic features. Cancer Sci. 2013 Feb;104(2):266-73. doi: 10.1111/cas.12065. Epub 2013 Jan 4.

Identification of CCDC6-RET fusion in the human lung adenocarcinoma cell line, LC-2/ad.

Matsubara D, Kanai Y, Ishikawa S, Ohara S, Yoshimoto T, Sakatani T, Oguni S, Tamura T, Kataoka H, Endo S, Murakami Y, Aburatani H, Fukayama M, Niki T. Identification of CCDC6-RET fusion in the human lung adenocarcinoma cell line, LC-2/ad. J Thorac Oncol. 2012 Dec;7(12):1872-6. doi: 10.1097/JTO.0b013e3182721ed1.

CDX1 confers intestinal phenotype on gastric epithelial cells via induction of stemness-associated reprogramming factors SALL4 and KLF5.

Fujii Y, Yoshihashi K, Suzuki H, Tsutsumi S, Mutoh H, Maeda S, Yamagata Y, Seto Y, Aburatani H, Hatakeyama M. CDX1 confers intestinal phenotype on gastric epithelial cells via induction of stemness-associated reprogramming factors SALL4 and KLF5. Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20584-9. doi: 10.1073/pnas.1208651109. Epub 2012 Oct 29.

Class A scavenger receptor promotes osteoclast differentiation via the enhanced expression of receptor activator of NF-kappaB (RANK).

Papantonis A, Kohro T, Baboo S, Larkin JD, Deng B, Short P, Tsutsumi S, Taylor S, Kanki Y, Kobayashi M, Li G, Poh HM, Ruan X, Aburatani H, Ruan Y, Kodama T, Wada Y, Cook PR. Class A scavenger receptor promotes osteoclast differentiation via the enhanced expression of receptor activator of NF-kappaB (RANK). EMBO J. 2012 Nov 28;31(23):4404-14. doi: 10.1038/emboj.2012.288. Epub 2012 Oct 26.

Vascular endothelial growth factor activation of endothelial cells is mediated by early growth response-3.

Kusano-Arai O, Iwanari H, Mochizuki Y, Nakata H, Kodama T, Kitoh T, Hamakubo T. Vascular endothelial growth factor activation of endothelial cells is mediated by early growth response-3. Hybridoma (Larchmt). 2012 Oct;31(5):325-32. doi: 10.1089/hyb.2012.0014.

Evaluation of the asparagine synthetase level in leukemia cells by monoclonal antibodies.

Kusano-Arai O, Iwanari H, Mochizuki Y, Nakata H, Kodama T, Kitoh T, Hamakubo T. Evaluation of the asparagine synthetase level in leukemia cells by monoclonal antibodies. Hybridoma (Larchmt). 2012 Oct;31(5):325-32. doi: 10.1089/hyb.2012.0014.

Upregulation of CD200R1 in lineage-negative leukemic cells is characteristic of AML1-ETO-positive leukemia in mice.

Kagiyama Y, Kitaura J, Togami K, Uchida T, Inoue D, Matsukawa T, Izawa K, Kawabata KC, Komeno Y, Oki T, Nakahara F, Sato K, Aburatani H, Kitamura T. Upregulation of CD200R1 in lineage-negative leukemic cells is characteristic of AML1-ETO-positive leukemia in mice. Int J Hematol. 2012 Nov;96(5):638-48. doi: 10.1007/s12185-012-1207-6. Epub 2012 Oct 25.

Functional involvement of Tudor and dPRMT5 in the piRNA processing pathway in Drosophila germlines.

Suzuki T, Tsuzuku J, Hayashi A, Shiomi Y, Iwanari H, Mochizuki Y, Hamakubo T, Kodama T, Nishitani H, Masai H, Yamamoto T. Functional involvement of Tudor and dPRMT5 in the piRNA processing pathway in Drosophila germlines. J Biol Chem. 2012 Nov 23;287(48):40256-65. doi: 10.1074/jbc.M112.353805. Epub 2012 Oct 12.

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