Improvement in Empirical Potential Functions for Increasing the Utility of Molecular Dynamics Simulations

Yamashita T. Improvement in Empirical Potential Functions for Increasing the Utility of Molecular Dynamics Simulations JPS Conf Proc. 2015, v. 5, p. 010003, DOI: http://dx.doi.org/10.7566/JPSCP.5.010003

90Y-Labeled Anti-ROBO1 Monoclonal Antibody Exhibits Antitumor Activity against Small Cell Lung Cancer Xenografts.

Kado Y, Mizohata E, Nagatoishi S, Iijima M, Shinoda K, Miyafusa T, Nakayama T, Yoshizumi T, Sugiyama A, Kawamura T, Lee YH, Matsumura H, Doi H, Fujitani H, Kodama T, Shibasaki Y, Tsumoto K, Inoue T. 90Y-Labeled Anti-ROBO1 Monoclonal Antibody Exhibits Antitumor Activity against Small Cell Lung Cancer Xenografts. J Biol Chem. 2016 Jan 29;291(5):2319-30. doi: 10.1074/jbc.M115.656009. Epub 2015 Dec 1.

Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES.

Kado Y, Mizohata E, Nagatoishi S, Iijima M, Shinoda K, Miyafusa T, Nakayama T, Yoshizumi T, Sugiyama A, Kawamura T, Lee YH, Matsumura H, Doi H, Fujitani H, Kodama T, Shibasaki Y, Tsumoto K, Inoue T. Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES. J Biol Chem. 2016 Jan 29;291(5):2319-30. doi: 10.1074/jbc.M115.656009. Epub 2015 Dec 1.

Lysophosphatidylcholine promotes SREBP-2 activation via rapid cholesterol efflux and SREBP-2-independent cytokine release in human endothelial cells.

Matsumura Y, Nakaki R, Inagaki T, Yoshida A, Kano Y, Kimura H, Tanaka T, Tsutsumi S, Nakao M, Doi T, Fukami K, Osborne TF, Kodama T, Aburatani H, Sakai J. Lysophosphatidylcholine promotes SREBP-2 activation via rapid cholesterol efflux and SREBP-2-independent cytokine release in human endothelial cells. Mol Cell. 2015 Nov 19;60(4):584-96. doi: 10.1016/j.molcel.2015.10.025.

H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte Differentiation.

Matsumura Y, Nakaki R, Inagaki T, Yoshida A, Kano Y, Kimura H, Tanaka T, Tsutsumi S, Nakao M, Doi T, Fukami K, Osborne TF, Kodama T, Aburatani H, Sakai J. H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte Differentiation. Mol Cell. 2015 Nov 19;60(4):584-96. doi: 10.1016/j.molcel.2015.10.025.

Folliculin-interacting proteins Fnip1 and Fnip2 play critical roles in kidney tumor suppression in cooperation with Flcn.

Takaba H, Morishita Y, Tomofuji Y, Danks L, Nitta T, Komatsu N, Kodama T, Takayanagi H. Folliculin-interacting proteins Fnip1 and Fnip2 play critical roles in kidney tumor suppression in cooperation with Flcn. Cell. 2015 Nov 5;163(4):975-87. doi: 10.1016/j.cell.2015.10.013.

Epigenomic Regulation of Smad1 Signaling During Cellular Senescence Induced by Ras Activation.

Kaneda A, Nonaka A, Fujita T, Yamanaka R, Fujimoto M, Miyazono K, Aburatani H. Epigenomic Regulation of Smad1 Signaling During Cellular Senescence Induced by Ras Activation. Methods Mol Biol. 2016;1344:341-53. doi: 10.1007/978-1-4939-2966-5_22.

Genetic and epigenetic aberrations occurring in colorectal tumors associated with serrated pathway.

Sakai E, Fukuyo M, Ohata K, Matsusaka K, Doi N, Mano Y, Takane K, Abe H, Yagi K, Matsuhashi N, Fukushima J, Fukayama M, Akagi K, Aburatani H, Nakajima A, Kaneda A. Genetic and epigenetic aberrations occurring in colorectal tumors associated with serrated pathway. Int J Cancer. 2016 Apr 1;138(7):1634-44. doi: 10.1002/ijc.29903. Epub 2015 Nov 12.

Integrated molecular analysis of adult T cell leukemia/lymphoma.

Kataoka K, Nagata Y, Kitanaka A, Shiraishi Y, Shimamura T, Yasunaga J, Totoki Y, Chiba K, Sato-Otsubo A, Nagae G, Ishii R, Muto S, Kotani S, Watatani Y, Takeda J, Sanada M, Tanaka H, Suzuki H, Sato Y, Shiozawa Y, Yoshizato T, Yoshida K, et al. Integrated molecular analysis of adult T cell leukemia/lymphoma. Nat Genet. 2015 Nov;47(11):1304-15. doi: 10.1038/ng.3415. Epub 2015 Oct 5.

DNA methylation status as a biomarker of anti-epidermal growth factor receptor treatment for metastatic colorectal cancer.

Ouchi K, Takahashi S, Yamada Y, Tsuji S, Tatsuno K, Takahashi H, Takahashi N, Takahashi M, Shimodaira H, Aburatani H, Ishioka C. DNA methylation status as a biomarker of anti-epidermal growth factor receptor treatment for metastatic colorectal cancer. Cancer Sci. 2015 Dec;106(12):1722-9. doi: 10.1111/cas.12827. Epub 2015 Nov 12.

Transcriptome Analysis of K-877 (a Novel Selective PPARα Modulator (SPPARMα))-Regulated Genes in Primary Human Hepatocytes and the Mouse Liver.

Raza-Iqbal S, Tanaka T, Anai M, Inagaki T, Matsumura Y, Ikeda K, Taguchi A, Gonzalez FJ, Sakai J, Kodama T. Transcriptome Analysis of K-877 (a Novel Selective PPARα Modulator (SPPARMα))-Regulated Genes in Primary Human Hepatocytes and the Mouse Liver. J Atheroscler Thromb. 2015 Aug 26;22(8):754-72. doi: 10.5551/jat.28720. Epub 2015 Jun 4.

Design and synthesis of biotin analogues reversibly binding with streptavidin.

Tachibana K, Gotoh E, Kawamata N, Ishimoto K, Uchihara Y, Iwanari H, Sugiyama A, Kawamura T, Mochizuki Y, Tanaka T, Sakai J, Hamakubo T, Kodama T, Doi T. Design and synthesis of biotin analogues reversibly binding with streptavidin. Biochem Biophys Res Commun. 2015 Oct 2;465(4):725-31. doi: 10.1016/j.bbrc.2015.08.065. Epub 2015 Aug 18.

Analysis of the subcellular localization of the human histone methyltransferase SETDB1.

Tachibana K, Gotoh E, Kawamata N, Ishimoto K, Uchihara Y, Iwanari H, Sugiyama A, Kawamura T, Mochizuki Y, Tanaka T, Sakai J, Hamakubo T, Kodama T, Doi T. Analysis of the subcellular localization of the human histone methyltransferase SETDB1. Biochem Biophys Res Commun. 2015 Oct 2;465(4):725-31. doi: 10.1016/j.bbrc.2015.08.065. Epub 2015 Aug 18.

Structure-based design of a streptavidin mutant specific for an artificial biotin analogue.

Kato Y, Nakamura H, Tojo H, Nomura M, Nagao T, Kawamura T, Kodama T, Ohira T, Ikeda N, Fehniger T, Marko-Varga G, Nishimura T, Kato H. Structure-based design of a streptavidin mutant specific for an artificial biotin analogue. Clin Transl Med. 2015 Dec;4(1):64. doi: 10.1186/s40169-015-0064-3. Epub 2015 Jul 3.

Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma.

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, et al. Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma. Nat Commun. 2015 Jul 3;6:7557. doi: 10.1038/ncomms8557.

Age-Dependent Decrease of DNA Hydroxymethylation in Human T Cells.

Truong TP, Sakata-Yanagimoto M, Yamada M, Nagae G, Enami T, Nakamoto-Matsubara R, Aburatani H, Chiba S. Age-Dependent Decrease of DNA Hydroxymethylation in Human T Cells. J Clin Exp Hematop. 2015;55(1):1-6. doi: 10.3960/jslrt.55.1.