Robotic crowd biology with Maholo LabDroids

Yachie N, Takahashi K, Katayama T, Sakurada T, Kanda GN, Takagi E, Hirose T, Katsura T, Moriya T, Kitano H, Tsujii J, Shiraki T, Kariyazaki H, Kamei M, Abe N, Fukuda T, Sawada Y, Hashiguchi Y, Matsukuma K, Murai S, Sasaki N, Ipposhi T, Urabe H, Kudo T, Umeno M, Ono S, Miyauchi K, Nakamura M, Kizaki T, Suyama T, Hatta T, Natsume T, Ohta T, Ozawa Y, Ihara S, Tamaki S, Antezana E, Garcia-Castro A, Perret JL, Ishiguro S, Mori H, Evans-Yamamoto D, Masuyama N, Tomita M, Katayama T, Matsumoto M, Nakayama H, Shirasawa A, Shimbo K, Yamada N, Nakayama KI, Shimizu T, Saya H, Yamashita S, Matsushima T, Asahara H, Eguchi H, Mikamori M, Mori M & Natsume T Robotic crowd biology with Maholo LabDroids Nature Biotechnology 35, 310-312

Epiregulin-blocking antibody inhibits epiregulin-dependent EGFR signaling.

Iijima M, Anai M, Kodama T, Shibasaki Y. Epiregulin-blocking antibody inhibits epiregulin-dependent EGFR signaling. Biochem Biophys Res Commun. 2017 Jul 15;489(1):83-88. doi: 10.1016/j.bbrc.2017.03.006. Epub 2017 Mar 6.

Generation and characterization of an antagonistic monoclonal antibody against an extracellular domain of mouse DP2 (CRTH2/GPR44) receptors for prostaglandin D2.

Nagata N, Iwanari H, Kumagai H, Kusano-Arai O, Ikeda Y, Aritake K, Hamakubo T, Urade Y. Generation and characterization of an antagonistic monoclonal antibody against an extracellular domain of mouse DP2 (CRTH2/GPR44) receptors for prostaglandin D2. PLoS One. 2017 Apr 10;12(4):e0175452. doi: 10.1371/journal.pone.0175452. eCollection 2017.

Differences in genetic and epigenetic alterations between von Hippel-Lindau disease-related and sporadic hemangioblastomas of the central nervous system.

Takayanagi S, Mukasa A, Tanaka S, Nomura M, Omata M, Yanagisawa S, Yamamoto S, Ichimura K, Nakatomi H, Ueki K, Aburatani H, Saito N. Differences in genetic and epigenetic alterations between von Hippel-Lindau disease-related and sporadic hemangioblastomas of the central nervous system. Neuro Oncol. 2017 Mar 30. doi: 10.1093/neuonc/nox034. [Epub ahead of print]

Visualization of ligand-induced Gi-protein activation in chemotaxing cells.

Masuda K, Kitakami JI, Kozasa T, Kodama T, Ihara S, Hamakubo T. Visualization of ligand-induced Gi-protein activation in chemotaxing cells. FASEB J. 2017 Mar;31(3):910-919. doi: 10.1096/fj.201601102R

Dynamically and epigenetically coordinated GATA/ETS/SOX transcription factor expression is indispensable for endothelial cell differentiation.

Kanki Y, Nakaki R, Shimamura T, Matsunaga T, Yamamizu K, Katayama S, Suehiro JI, Osawa T, Aburatani H, Kodama T, Wada Y, Yamashita JK, Minami T. Dynamically and epigenetically coordinated GATA/ETS/SOX transcription factor expression is indispensable for endothelial cell differentiation. Nucleic Acids Res. 2017 May 5;45(8):4344-4358. doi: 10.1093/nar/gkx159.

Genetic and epigenetic stability of oligodendrogliomas at recurrence.

Aihara K, Mukasa A, Nagae G, Nomura M, Yamamoto S, Ueda H, Tatsuno K, Shibahara J, Takahashi M, Momose T, Tanaka S, Takayanagi S, Yanagisawa S, Nejo T, Takahashi S, Omata M, Otani R, Saito K, Narita Y, Nagane M, Nishikawa R, Ueki K, et al. Genetic and epigenetic stability of oligodendrogliomas at recurrence. Acta Neuropathol Commun. 2017 Mar 7;5(1):18. doi: 10.1186/s40478-017-0422-z.

Extracellular Acidic pH Activates the Sterol Regulatory Element-Binding Protein 2 to Promote Tumor Progression.

Kondo A, Yamamoto S, Nakaki R, Shimamura T, Hamakubo T, Sakai J, Kodama T, Yoshida T, Aburatani H, Osawa T. Extracellular Acidic pH Activates the Sterol Regulatory Element-Binding Protein 2 to Promote Tumor Progression. Cell Rep. 2017 Feb 28;18(9):2228-2242. doi: 10.1016/j.celrep.2017.02.006.

Vitamin D Metabolite, 25-Hydroxyvitamin D, Regulates Lipid Metabolism by Inducing Degradation of SREBP/SCAP.

Asano L, Watanabe M, Ryoden Y, Usuda K, Yamaguchi T, Khambu B, Takashima M, Sato SI, Sakai J, Nagasawa K, Uesugi M. Vitamin D Metabolite, 25-Hydroxyvitamin D, Regulates Lipid Metabolism by Inducing Degradation of SREBP/SCAP. Cell Chem Biol. 2017 Feb 16;24(2):207-217. doi: 10.1016/j.chembiol.2016.12.017. Epub 2017 Jan 26.

Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories

Yamashita T. Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories Biomedical Sciences 2016, V. 2 (5), pp. 34-47 doi: 10.11648/j.bs.20160205.11

On the accurate molecular dynamics analysis of biological molecules

Yamashita T. On the accurate molecular dynamics analysis of biological molecules AIP Conf Proc. 2016, 1790, 020026; doi: http://dx.doi.org/10.1063/1.4968652

Molecular dynamics analysis to evaluate docking pose prediction.

Sakano T, Mahamood MI, Yamashita T, Fujitani H. Molecular dynamics analysis to evaluate docking pose prediction. Biophys Physicobiol. 2016 Jul 14;13:181-194. eCollection 2016.

Middle-Down and Chemical Proteomic Approaches to Reveal Histone H4 Modification Dynamics in Cell Cycle: Label-Free Semi-Quantification of Histone Tail Peptide Modifications Including Phosphorylation and Highly Sensitive Capture of Histone PTM Binding Proteins Using Photo-Reactive Crosslinkers.

Masuda K, Kitakami JI, Kozasa T, Kodama T, Ihara S, Hamakubo T. Middle-Down and Chemical Proteomic Approaches to Reveal Histone H4 Modification Dynamics in Cell Cycle: Label-Free Semi-Quantification of Histone Tail Peptide Modifications Including Phosphorylation and Highly Sensitive Capture of Histone PTM Binding Proteins Using Photo-Reactive Crosslinkers. FASEB J. 2017 Mar;31(3):910-919. doi: 10.1096/fj.201601102R. Epub 2016 Nov 23.

QRFP-Deficient Mice Are Hypophagic, Lean, Hypoactive and Exhibit Increased Anxiety-Like Behavior.

Okamoto K, Yamasaki M, Takao K, Soya S, Iwasaki M, Sasaki K, Magoori K, Sakakibara I, Miyakawa T, Mieda M, Watanabe M, Sakai J, Yanagisawa M, Sakurai T. QRFP-Deficient Mice Are Hypophagic, Lean, Hypoactive and Exhibit Increased Anxiety-Like Behavior. PLoS One. 2016 Nov 11;11(11):e0164716. doi: 10.1371/journal.pone.0164716. eCollection 2016.

CASTIN: a system for comprehensive analysis of cancer-stromal interactome.

Komura D, Isagawa T, Kishi K, Suzuki R, Sato R, Tanaka M, Katoh H, Yamamoto S, Tatsuno K, Fukayama M, Aburatani H, Ishikawa S. CASTIN: a system for comprehensive analysis of cancer-stromal interactome. BMC Genomics. 2016 Nov 9;17(1):899.

TET2 functions as a resistance factor against DNA methylation acquisition during Epstein-Barr virus infection.

Namba-Fukuyo H, Funata S, Matsusaka K, Fukuyo M, Rahmutulla B, Mano Y, Fukayama M, Aburatani H, Kaneda A. TET2 functions as a resistance factor against DNA methylation acquisition during Epstein-Barr virus infection. Oncotarget. 2016 Dec 6;7(49):81512-81526. doi: 10.18632/oncotarget.13130.