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Methods for high-dimensonal analysis of cells dissociated from cyropreserved synovial tissue.

Donlin LT, Rao DA, Wei K, Slowikowski K, McGeachy MJ, Turner JD, Meednu N, Mizoguchi F, Gutierrez-Arcelus M, Lieb DJ, Keegan J, Muskat K, Hillman J, Rozo C, Ricker E, Eisenhaure TM, Li S, Browne EP, Chicoine A, Sutherby D, Noma A; Accelerating Medicines Partnership RA/SLE Network, Nusbaum C, Kelly S, Pernis AB, Ivashkiv LB, Goodman SM, Robinson WH, Utz PJ, Lederer JA, Gravallese EM, Boyce BF, Hacohen N, Pitzalis C, Gregersen PK, Firestein GS, Raychaudhuri S, Moreland LW, Holers VM, Bykerk VP, Filer A, Boyle DL, Brenner MB, Anolik JH.

Arthritis Res Ther. 2018 Jul 11;20(1):139. doi: 10.1186/s13075-018-1631-y.


A new myofilament contraction model with ATP consumption for ventricular cell model.

Muangkram Y, Noma A, Amano A.

J Physiol Sci. 2018 Sep;68(5):541-554. doi: 10.1007/s12576-017-0560-x. Epub 2017 Aug 2.


Regulation of the glucose supply from capillary to tissue examined by developing a capillary model.

Maeda A, Himeno Y, Ikebuchi M, Noma A, Amano A.

J Physiol Sci. 2018 Jul;68(4):355-367. doi: 10.1007/s12576-017-0538-8. Epub 2017 Apr 17.


Short- and long-term outcomes after pancreaticoduodenectomy following total gastorectomy: Report of case series and literature review.

Yokoyama S, Ueno K, Higashide Y, Noma A, Okishio Y, Masuda M, Miyamoto T, Kamimura R, Hosokawa S, Yonenaga Y, Ito D, Ichimiya M, Yamashita Y, Uyama S, Harb SE.

Int J Surg Case Rep. 2017;30:118-121. doi: 10.1016/j.ijscr.2016.11.022. Epub 2016 Nov 27.


Mechanisms underlying the volume regulation of interstitial fluid by capillaries: a simulation study.

Himeno Y, Ikebuchi M, Maeda A, Noma A, Amano A.

Integr Med Res. 2016 Mar;5(1):11-21. doi: 10.1016/j.imr.2015.12.006. Epub 2016 Jan 6.


A step from the physiology to the physiome.

Noma A, Youm JB.

Integr Med Res. 2016 Mar;5(1):1-2. doi: 10.1016/j.imr.2016.02.001. Epub 2016 Mar 4. No abstract available.


Modeling analysis of inositol 1,4,5-trisphosphate receptor-mediated Ca2+ mobilization under the control of glucagon-like peptide-1 in mouse pancreatic β-cells.

Takeda Y, Shimayoshi T, Holz GG, Noma A.

Am J Physiol Cell Physiol. 2016 Mar 1;310(5):C337-47. doi: 10.1152/ajpcell.00234.2015. Epub 2015 Nov 25.


A human ventricular myocyte model with a refined representation of excitation-contraction coupling.

Himeno Y, Asakura K, Cha CY, Memida H, Powell T, Amano A, Noma A.

Biophys J. 2015 Jul 21;109(2):415-27. doi: 10.1016/j.bpj.2015.06.017.


Location of α-tocopherol and α-tocotrienol to heterogeneous cell membranes and inhibition of production of peroxidized cholesterol in mouse fibroblasts.

Nakamura T, Noma A, Terao J.

Springerplus. 2014 Sep 23;3:550. doi: 10.1186/2193-1801-3-550. eCollection 2014.


EAD and DAD mechanisms analyzed by developing a new human ventricular cell model.

Asakura K, Cha CY, Yamaoka H, Horikawa Y, Memida H, Powell T, Amano A, Noma A.

Prog Biophys Mol Biol. 2014 Sep;116(1):11-24. doi: 10.1016/j.pbiomolbio.2014.08.008. Epub 2014 Sep 1.


A single acetylation of 18 S rRNA is essential for biogenesis of the small ribosomal subunit in Saccharomyces cerevisiae.

Ito S, Akamatsu Y, Noma A, Kimura S, Miyauchi K, Ikeuchi Y, Suzuki T, Suzuki T.

J Biol Chem. 2014 Sep 19;289(38):26201-12. doi: 10.1074/jbc.M114.593996. Epub 2014 Aug 1.


Non-selective distribution of isomeric cholesterol hydroperoxides to microdomains in cell membranes and activation of matrix metalloproteinase activity in a model of dermal cells.

Nakamura T, Noma A, Shimada S, Ishii N, Bando N, Kawai Y, Terao J.

Chem Phys Lipids. 2013 Sep;174:17-23. doi: 10.1016/j.chemphyslip.2013.05.004. Epub 2013 Jun 7.


Torsin mediates primary envelopment of large ribonucleoprotein granules at the nuclear envelope.

Jokhi V, Ashley J, Nunnari J, Noma A, Ito N, Wakabayashi-Ito N, Moore MJ, Budnik V.

Cell Rep. 2013 Apr 25;3(4):988-95. doi: 10.1016/j.celrep.2013.03.015. Epub 2013 Apr 11.


Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine-tRNA.

Rodriguez V, Vasudevan S, Noma A, Carlson BA, Green JE, Suzuki T, Chandrasekharappa SC.

PLoS One. 2012;7(6):e39297. doi: 10.1371/journal.pone.0039297. Epub 2012 Jun 28.


Steady-state solutions of cell volume in a cardiac myocyte model elaborated for membrane excitation, ion homeostasis and Ca2+ dynamics.

Cha CY, Noma A.

J Theor Biol. 2012 Aug 21;307:70-81. doi: 10.1016/j.jtbi.2012.04.025. Epub 2012 May 11.


The nonlinear elastic and viscoelastic passive properties of left ventricular papillary muscle of a guinea pig heart.

Hassan MA, Hamdi M, Noma A.

J Mech Behav Biomed Mater. 2012 Jan;5(1):99-109. doi: 10.1016/j.jmbbm.2011.08.011. Epub 2011 Aug 27.


Analyzing electrical activities of pancreatic β cells using mathematical models.

Cha CY, Powell T, Noma A.

Prog Biophys Mol Biol. 2011 Nov;107(2):265-73. doi: 10.1016/j.pbiomolbio.2011.08.001. Epub 2011 Aug 7. Review.


Systems analysis of GLP-1 receptor signaling in pancreatic β-cells.

Takeda Y, Amano A, Noma A, Nakamura Y, Fujimoto S, Inagaki N.

Am J Physiol Cell Physiol. 2011 Oct;301(4):C792-803. doi: 10.1152/ajpcell.00057.2011. Epub 2011 Jul 6.


Time-dependent changes in membrane excitability during glucose-induced bursting activity in pancreatic β cells.

Cha CY, Santos E, Amano A, Shimayoshi T, Noma A.

J Gen Physiol. 2011 Jul;138(1):39-47. doi: 10.1085/jgp.201110612.


Ionic mechanisms and Ca2+ dynamics underlying the glucose response of pancreatic β cells: a simulation study.

Cha CY, Nakamura Y, Himeno Y, Wang J, Fujimoto S, Inagaki N, Earm YE, Noma A.

J Gen Physiol. 2011 Jul;138(1):21-37. doi: 10.1085/jgp.201110611.


Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae.

Noma A, Yi S, Katoh T, Takai Y, Suzuki T, Suzuki T.

RNA. 2011 Jun;17(6):1111-9. doi: 10.1261/rna.2653411. Epub 2011 Apr 25.


Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification.

Kato M, Araiso Y, Noma A, Nagao A, Suzuki T, Ishitani R, Nureki O.

Nucleic Acids Res. 2011 Mar;39(4):1576-85. doi: 10.1093/nar/gkq919. Epub 2010 Oct 23.


Minor contribution of cytosolic Ca2+ transients to the pacemaker rhythm in guinea pig sinoatrial node cells.

Himeno Y, Toyoda F, Satoh H, Amano A, Cha CY, Matsuura H, Noma A.

Am J Physiol Heart Circ Physiol. 2011 Jan;300(1):H251-61. doi: 10.1152/ajpheart.00764.2010. Epub 2010 Oct 15.


Expanding role of the jumonji C domain as an RNA hydroxylase.

Noma A, Ishitani R, Kato M, Nagao A, Nureki O, Suzuki T.

J Biol Chem. 2010 Nov 5;285(45):34503-7. doi: 10.1074/jbc.M110.156398. Epub 2010 Aug 25.


Magnesium gating of cardiac gap junction channels.

Matsuda H, Kurata Y, Oka C, Matsuoka S, Noma A.

Prog Biophys Mol Biol. 2010 Sep;103(1):102-10. doi: 10.1016/j.pbiomolbio.2010.05.009. Epub 2010 May 27. Review.


Characterization of the cardiac Na+/K+ pump by development of a comprehensive and mechanistic model.

Oka C, Cha CY, Noma A.

J Theor Biol. 2010 Jul 7;265(1):68-77. doi: 10.1016/j.jtbi.2010.04.028. Epub 2010 May 6.


Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea.

de Crécy-Lagard V, Brochier-Armanet C, Urbonavicius J, Fernandez B, Phillips G, Lyons B, Noma A, Alvarez S, Droogmans L, Armengaud J, Grosjean H.

Mol Biol Evol. 2010 Sep;27(9):2062-77. doi: 10.1093/molbev/msq096. Epub 2010 Apr 9.


A novel method to quantify contribution of channels and transporters to membrane potential dynamics.

Cha CY, Himeno Y, Shimayoshi T, Amano A, Noma A.

Biophys J. 2009 Dec 16;97(12):3086-94. doi: 10.1016/j.bpj.2009.08.060.


A model of Na+/H+ exchanger and its central role in regulation of pH and Na+ in cardiac myocytes.

Cha CY, Oka C, Earm YE, Wakabayashi S, Noma A.

Biophys J. 2009 Nov 18;97(10):2674-83. doi: 10.1016/j.bpj.2009.08.053.


Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2.

Umitsu M, Nishimasu H, Noma A, Suzuki T, Ishitani R, Nureki O.

Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15616-21. doi: 10.1073/pnas.0905270106. Epub 2009 Aug 26.


Modeling the cardiac Na(+)/H (+) exchanger based on major experimental findings.

Cha CY, Noma A.

Mol Cells. 2009 Aug 31;28(2):81-5. doi: 10.1007/s10059-009-0115-y. Epub 2009 Aug 20. Review.


Role of Mg(2+) block of the inward rectifier K(+) current in cardiac repolarization reserve: A quantitative simulation.

Ishihara K, Sarai N, Asakura K, Noma A, Matsuoka S.

J Mol Cell Cardiol. 2009 Jul;47(1):76-84. doi: 10.1016/j.yjmcc.2009.03.008. Epub 2009 Mar 20.


Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.

Suzuki Y, Noma A, Suzuki T, Ishitani R, Nureki O.

Nucleic Acids Res. 2009 May;37(9):2910-25. doi: 10.1093/nar/gkp158. Epub 2009 Mar 14.


Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions.

Noma A, Sakaguchi Y, Suzuki T.

Nucleic Acids Res. 2009 Mar;37(4):1335-52. doi: 10.1093/nar/gkn1023. Epub 2009 Jan 16.


[Computer-based simulations of cardiac cell functions and its application].

Matsuda H, Noma A.

Nihon Yakurigaku Zasshi. 2008 Nov;132(5):313-5. Review. Japanese. No abstract available.


A simulation study on the activation of cardiac CaMKII delta-isoform and its regulation by phosphatases.

Chiba H, Schneider NS, Matsuoka S, Noma A.

Biophys J. 2008 Sep;95(5):2139-49. doi: 10.1529/biophysj.107.118505. Epub 2008 May 23.


Ionic mechanisms underlying the positive chronotropy induced by beta1-adrenergic stimulation in guinea pig sinoatrial node cells: a simulation study.

Himeno Y, Sarai N, Matsuoka S, Noma A.

J Physiol Sci. 2008 Feb;58(1):53-65. doi: 10.2170/physiolsci.RP015207. Epub 2008 Jan 19.


The cross-bridge dynamics during ventricular contraction predicted by coupling the cardiac cell model with a circulation model.

Shim EB, Amano A, Takahata T, Shimayoshi T, Noma A.

J Physiol Sci. 2007 Oct;57(5):275-85. Epub 2007 Oct 10.


A new integrated method for analyzing heart mechanics using a cell-hemodynamics-autonomic nerve control coupled model of the cardiovascular system.

Shim EB, Jun HM, Leem CH, Matusuoka S, Noma A.

Prog Biophys Mol Biol. 2008 Jan-Apr;96(1-3):44-59. Epub 2007 Aug 11. Review.


Wobble inosine tRNA modification is essential to cell cycle progression in G(1)/S and G(2)/M transitions in fission yeast.

Tsutsumi S, Sugiura R, Ma Y, Tokuoka H, Ohta K, Ohte R, Noma A, Suzuki T, Kuno T.

J Biol Chem. 2007 Nov 16;282(46):33459-65. Epub 2007 Sep 17.


Simulation analysis of intracellular Na+ and Cl- homeostasis during beta 1-adrenergic stimulation of cardiac myocyte.

Kuzumoto M, Takeuchi A, Nakai H, Oka C, Noma A, Matsuoka S.

Prog Biophys Mol Biol. 2008 Jan-Apr;96(1-3):171-86. Epub 2007 Aug 1.


Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA.

Suzuki Y, Noma A, Suzuki T, Senda M, Senda T, Ishitani R, Nureki O.

J Mol Biol. 2007 Oct 5;372(5):1204-14. Epub 2007 Jul 26.


Mass spectrometric identification and characterization of RNA-modifying enzymes.

Suzuki T, Ikeuchi Y, Noma A, Suzuki T, Sakaguchi Y.

Methods Enzymol. 2007;425:211-29. Review.


[Subcellular localization of RNA-modifying enzymes and maturation mechanism of RNA].

Noma A, Suzuki T.

Tanpakushitsu Kakusan Koso. 2006 Nov;51(14 Suppl):2226-31. Review. Japanese. No abstract available.


Role of Ca2+ transporters and channels in the cardiac cell volume regulation.

Takeuchi A, Tatsumi S, Sarai N, Terashima K, Matsuoka S, Noma A.

Ann N Y Acad Sci. 2007 Mar;1099:377-82.


Resistance of cardiac cells to NCX knockout: a model study.

Noble D, Sarai N, Noble PJ, Kobayashi T, Matsuoka S, Noma A.

Ann N Y Acad Sci. 2007 Mar;1099:306-9.


Strong Coupling System for the LV Motion Simulation in a Distributed Simulation Environment.

Amano A, Nishi T, Lu J, Schneider N, Matsuda T, Kotera H, Noma A.

Conf Proc IEEE Eng Med Biol Soc. 2005;5:5511-4.


Ribonucleome analysis identified enzyme genes responsible for wybutosine synthesis.

Noma A, Suzuki T.

Nucleic Acids Symp Ser (Oxf). 2006;(50):65-6.


Ionic mechanisms of cardiac cell swelling induced by blocking Na+/K+ pump as revealed by experiments and simulation.

Takeuchi A, Tatsumi S, Sarai N, Terashima K, Matsuoka S, Noma A.

J Gen Physiol. 2006 Nov;128(5):495-507.


A simulation study to rescue the Na+/Ca2+ exchanger knockout mice.

Sarai N, Kobayashi T, Matsuoka S, Noma A.

J Physiol Sci. 2006 Jun;56(3):211-7. Epub 2006 May 27.


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